diff --git a/PROJECT-MANAGEMENT.md b/PROJECT-MANAGEMENT.md index 161684b7..272f83b1 100644 --- a/PROJECT-MANAGEMENT.md +++ b/PROJECT-MANAGEMENT.md @@ -1,13 +1,13 @@ # OCR-v2 Project Management Log -> **Branch:** `feat/figure-pipeline-vnext` | **Last Updated:** 2026-07-03 -> **Active work:** Figure pipeline vnext cutover completed in worktree. Wrapper now points to vnext by default. 346 tests pass. Next: merge branch back to `master`. +> **Branch:** `feat/ocr-pairing-framework` | **Last Updated:** 2026-07-03 +> **Active work:** Generic OCR pairing framework extracted; figure and table now both run on the shared pairing core in worktree. Targeted merge-unblock verification passed: 357 tests green, touched-file `ruff check`/`ruff format --check` green, 6 runnable real-paper table fixtures validated. Next: merge branch back to `master`. --- ## 0. Executive Summary -**Current state:** Figure pipeline vnext is now fully implemented (11 passes incl. accounting), cutover corpus reviewed on 5 papers with 0 consumed-asset regressions, and the public wrapper has been switched to vnext on this branch. 346 tests pass (`59` vnext + `258` figure + `29` render). Next: merge `feat/figure-pipeline-vnext` back to `master`. +**Current state:** The OCR pairing framework branch is merge-ready. Figure and table pipelines now share `ocr_pairing_types.py` / `ocr_pairing_state.py` / `ocr_pairing_framework.py`, while domain-specific logic stays in `ocr_figure_domain.py` and `ocr_table_domain.py`. The last merge blockers were cleared by (1) moving figure-only rotation enrichment out of generic state into a figure-domain hook, (2) hardening table semantic parity validation across all runnable real-paper fixtures including `37LK5T97`, and (3) cleaning touched-file lint/format issues. Verification: 357 targeted tests passed. Next: merge `feat/ocr-pairing-framework` back to `master`. --- ## 1. Architecture @@ -46,31 +46,25 @@ raw observations → structural signatures → stable anchors/families → zone ## 2. Current Status -### 2.1 Test Suite +### 2.1 Test / Verification Status
| Suite | Result | |-------|--------| -| Figure stack (figures + reader + containment + backmatter boundary) | **286 passed** ✅ | -| Document + roles + render + gate + rebuild + state machine + trace | **330 passed, 0 failed** ✅ | -| Author bio detection (ocr_bio) | **37 passed** ✅ | -| Spec contracts | All passed ✅ | -| Real-paper regressions | All passed ✅ | -| **Total OCR tests** | **1018 passed, 275 skipped (fixture unavailable), 0 failed** ✅ | +| Pairing framework cutover suites (`test_ocr_figures` + `test_ocr_rebuild` + `test_ocr_tables` + `test_ocr_pairing_framework` + `test_ocr_table_pairing_framework`) | **357 passed, 0 failed** ✅ | +| Real-paper table parity fixtures | **6 runnable fixtures checked** ✅ | +| Touched-file lint (`ruff check`) | **OK** ✅ | +| Touched-file format (`ruff format --check`) | **OK** ✅ |
+| Component | Status | +|-----------|--------| | Structural gate | Installed | | Role assignment (seed only) | ✅ | | Zone inference + fallback | ✅ | -| Figure inventory | Global distance clustering — correct | -| Backmatter boundary | ✅ Ref-anchored partition committed | -| Pre-ref tail zone | ✅ Fixed | -| Abstract detection | ✅ Fixed | -| Frontmatter heading normalization | ✅ Fixed — no text matching | -| non_body_insert clustering | ✅ Fixed — page-1 guard threshold | -| Render (backmatter headings) | ✅ Correct heading rendering | -| State machine | ✅ Accepts done_degraded as terminal | -| Rebuild (span backfill skip) | ✅ Version match check fixed | -| Author bio detection (Passes B+C) | ✅ P0: post-ref text-only bios as backmatter_body. P1: figure-residual portrait assets as author_bio_asset + figure_caption support | -| Figure pipeline vnext | ✅ Default wrapper switched; 11-pass pipeline active; cutover corpus reviewed (5 papers, 0 regressions) | +| Figure pipeline vnext | ✅ Shared pairing core + figure-only pre-enricher hook | +| Table pipeline vnext | ✅ Shared pairing core + semantic parity validation | +| Pairing framework core | ✅ `ocr_pairing_*` modules active for both figure and table | +| Rebuild/orchestrator seam | ✅ Public wrappers unchanged; callers still use `build_figure_inventory(...)` / `build_table_inventory(...)` | +| Cross-domain figure/table conflict resolution | ✅ Still external to pairing core | ### 2.3 Fix Status @@ -95,48 +89,40 @@ raw observations → structural signatures → stable anchors/families → zone | 18 | — | **Issue 2**: Demoted-caption figure inner-text leakage | Container bbox regions | Validated `_container_bbox` regions in `tag_figure_contained_text` via 3 helpers + containment-only integration | `0e4ecbc` | | 19 | — | **Issue 5**: Cross-column page_assets groups falsely accepted | Column-homogeneity gate | `_column_band_id` + rejection in `_is_safe_page_assets_group` | `4ab227e` | | 20 | — | **Issue 6**: Same asset consumed by figure AND table | Post-hoc arbitration | `resolve_media_asset_conflicts` resolves asymmetric cases; weak/weak stays in `ownership_conflicts` | `4ab227e` | +| 21 | — | Pairing framework extraction + figure migration | Refactor | Extracted shared `ocr_pairing_*` core from figure vnext; preserved public seams and figure behavior | `6229f6c`, `7cfbb5f`, `32541cf` | +| 22 | — | Table vnext on pairing framework + public cutover | Refactor/feature | Added `ocr_table_domain.py` + `ocr_table_passes.py`, preserved resolver-consumed fields, switched `build_table_inventory(...)` to vnext | `db01518`, `ea6a1f0`, `a9e68ac`, `a2e5788` | +| 23 | 37LK5T97 + cutover corpus | Merge-unblock hardening | Moved figure-only rotation enrichment out of generic state, validated 6 runnable real-paper table fixtures semantically, fixed touched-file lint/format issues | working tree (pre-merge session) | #### P2#1a — Previous-page legend locator bridge (✅ Fixed `3f61f4a`) WV2FF4NV Fig 10: locator "See legend on previous page" on p16 not bridged to full legend (in rejected_legends, misclassified as body_paragraph) -#### Remaining P2 +#### Remaining P2 / P3 -1. **Figure containment gaps** — `cluster_bbox` containment only runs on matched figures; composite figures with demoted caption upstream never enter containment. Inner-text detection misses `vision_footnote`/`paragraph_title` raw_labels. -2. **Short "Table N" caption matching** — bare `"Table 1."` labels miss table_asset in ownership pipeline. Existing code partially handles it; residual cases remain. -3. **Page-1 body paragraph OCR text extraction failure** (was: width check) — W33NLVJ2 right col Introduction block: OCR detected text region (raw_label=text) but extracted empty string. Pipeline previously mis-signaled as `unknown_structural`. Fixed: now `ocr_text_missing`. -4. **Body text backfill overlap** — `backfill_missing_text_from_pdf` uses `get_text("words", clip=expanded)` returning words beyond block's bbox; can cause text duplication at render level. -5. **2HEUD5P9 reference ordering** — ✅ Fixed by F12 (raw_label=reference_content signal) -6. **Mixed-column tail page zone absorption** — ✅ Fixed: tighten year-period regex - -### P3 (Boundary / Edge Cases) - -1. **DW biography page mismatch** — pages 32-34 vs expectations 33-34. -2. **AJR side-caption recovery** — deliberately deferred; not part of generic inventory refactor. -3. **Chinese Windows encoding** — non-ASCII PDF filenames garbled via GBK codepage. Glob fallback added; residual `meta.json` corruption from earlier runs. -4. **`backfill_missing_text_from_pdf` bbox-exact filtering** — need decision on render-level dedup vs backfill-level bbox clamp. -5. **Multi-caption page column collapse** — `page_assets` group on multi-column pages merges separate figures in different columns. -6. **Figure/table shared-consumption registry** — no shared consumed registry for ambiguous image-like blocks. -7. **Short papers (<3 pages) health falsely red** — no headings/abstract in Letter/Editor formats. +1. **Compatibility naming debt** — `figure_no`, `legend`, and `FigurePipelineState` remain backwards-compat names inside the shared pairing core. They are intentionally deferred cleanup, not release blockers. +2. **37LK5T97 legacy consumption bug** — legacy table inventory drops caption `block_id=0` from `consumed_block_ids` because `if bid` treats `0` as falsy; vnext keeps `'0'`. Validation now treats this as a known legacy bug, not a vnext regression. +3. **Figure containment gaps** — `cluster_bbox` containment only runs on matched figures; composite figures with demoted caption upstream still do not enter containment. +4. **Short "Table N" caption matching** — bare `"Table 1."` labels still have residual weak cases outside the validated fixture set. +5. **Chinese Windows encoding** — non-ASCII PDF filenames can still surface GBK path issues in older artifacts. +6. **Shared consumed registry for ambiguous image-like blocks** — figure/table post-hoc arbitration exists, but there is still no first-class shared consumed registry for unresolved image-like assets. ## 4. Active Queue -1. ✅ P1 backmatter boundary (ref-anchored partition) -2. ✅ Pre-ref tail zone fix (4KCHGV2Z) -3. ✅ Gate 5 frontmatter fix series (24YKLTHQ) -4. ✅ Stale trace-vs-expectation fixtures cleared (10 assertion updates) -5. ✅ All stale test expectations reconciled (non_body_insert, caffard, legend_like, structural gate, render, state machine, rebuild, truth docs) -6. ✅ P0 author bio detection (post_ref_bio_cleanup for reference_item) -7. ✅ P1 author bio detection (residual_author_bio_pass + figure_caption support + tag_figure_contained_text protection) -8. **NEXT: Merge `feat/figure-pipeline-vnext` → `master`** +1. ✅ Pairing framework extraction complete +2. ✅ Figure migration onto shared pairing core complete +3. ✅ Table migration onto shared pairing core complete +4. ✅ Generic-state impurity removed (`_match_pre_enricher` hook at figure boundary) +5. ✅ Real-paper table semantic parity validation hardened (6 runnable fixtures) +6. ✅ Touched-file lint / format cleanup complete +7. **NEXT: Merge `feat/ocr-pairing-framework` → `master`** ### 4.1 Immediate Next Steps -- [x] Phase 0-4 vnext implementation complete -- [x] Phase 5 cutover evaluation complete -- [x] Cutover corpus: 5 papers, all 9 spec categories covered -- [x] Cutover diff review: improvement=2, equivalent=2, parity=1, regression=0 -- [x] Wrapper switched to vnext in branch -- [x] Full verification: 346 passed -- [ ] Merge `feat/figure-pipeline-vnext` into `master` +- [x] Shared `ocr_pairing_*` core active for figure + table +- [x] Public wrappers preserved +- [x] Table parity checks upgraded from smoke shape to semantic comparison +- [x] `37LK5T97` made runnable under `tests/fixtures/ocr_vnext_real_papers/` +- [x] Generic state made domain-neutral for match enrichment +- [x] Targeted verification: 357 passed +- [ ] Merge `feat/ocr-pairing-framework` into `master` --- @@ -236,6 +222,9 @@ WV2FF4NV Fig 10: locator "See legend on previous page" on p16 not bridged to ful | 2026-07-01 | Broaden recovery gate to handle normal prematch unknown figures | Synthetic-figure gate (`bbox_only_asset` flag) excluded `figure_unknown_NNN` from normal rotated prematch path. Gate now allows figure_unknown figures without synthetic flags. | | 2026-07-03 | Cutover uses evidence gates, not code confidence | VNext matched or improved on the full cutover corpus with identical consumed asset sets; wrapper switch became a release decision only after diff review + gate verification. | | 2026-07-03 | Legacy schema tests must be upgraded before wrapper switch | Real-paper behavior was cutover-ready earlier, but `test_ocr_figures.py` still asserted legacy-only inventory keys. Updating the test contract was required to make wrapper switch honest. | +| 2026-07-03 | Generic state uses a domain hook for figure rotation enrichment | Figure rotation metadata had to stay behaviorally intact without polluting the shared pairing state used by table passes. A pre-match enricher hook keeps the core generic and the figure path exact. | +| 2026-07-03 | Table parity comparison normalizes benign storage drift only | int/str block IDs, ordering differences, and `None` vs empty unmatched asset IDs are storage-level drift already tolerated downstream. Validation now compares semantic fields rather than raw serialization artifacts. | +| 2026-07-03 | Legacy `block_id=0` drop is treated as a legacy bug, not a parity target | `37LK5T97` showed legacy dropping consumed caption id `0` via falsy filtering. The branch keeps vnext truth and documents the legacy defect instead of reproducing it. | --- @@ -327,6 +316,7 @@ python -m ruff check paperforge/worker/ocr_*.py | 2026-07-02 | Round 2 truth audit + 3 targeted bug fixes for 37LK5T97 | Batch-audited 10 fresh papers (5 GREEN / 4 YELLOW / 1 RED). 37LK5T97 found with Figure 1 broken (sidecar caption demoted) + 6 unmatched rotated tables. Fixes: (1) `_is_sidecar_candidate` guard in candidate_resolution, (2) `adjacent_x`+`y_overlap` in score_table_match for rotated captions, (3) rotated table render bbox+270° correction. Also: rotated figure crop quality fix (4x zoom + coordinate normalization in `_crop_asset_from_pdf`). Commits: `59cd01a`, `bd3f3b6`, `86e0d14`. 428 regression tests pass. | §9.20 | | 2026-07-02 | Zone/role robustness completion — Figure caption prefix recovery + inline table fix + table matching audit | Figure caption prefix recovery from PDF text layer (`_recover_figure_heading_prefix`): 5S7UI34M 4→9 matched figures, 33→1 unmatched. Inline `` HTML role fix: 650 blocks now `table_html` after rebuild (priority bug: raw_label=table fired before `
` check). Table matching audit: 620 remaining `media_asset` pending full rebuild. 585 figure/table/role tests pass. | §9.21 | | 2026-07-03 | Figure pipeline vnext cutover completed | Implemented all remaining vnext passes (composite parent, group/classic sequential, unresolved consolidation, accounting), expanded compare harness, curated 5-paper cutover corpus covering all 9 spec categories, generated diff review (improvement=2 / equivalent=2 / parity=1 / regression=0), updated legacy figure tests for vnext contract, and switched `build_figure_inventory(...)` wrapper to vnext on branch `feat/figure-pipeline-vnext`. Verification: 346 tests passed. | §9.22 | +| 2026-07-03 | OCR pairing framework merge-unblock pass | Cleared the remaining merge blockers on `feat/ocr-pairing-framework`: moved figure-only rotation enrichment out of generic state, upgraded table cutover validation to semantic parity across 6 runnable real-paper fixtures including `37LK5T97`, and cleaned touched-file lint/format issues. Verification: 357 targeted tests passed; merge-ready. | §9.23 | ## 9. Historical Detail Archive @@ -596,3 +586,43 @@ Full-day debugging session across 8 gold papers. 98 bug annotations, 8 pipeline - `paperforge/worker/ocr_roles.py` — inline `
` before raw_label=table - `paperforge/worker/ocr_document.py` — removed `table_html_candidate` dead path - `paperforge/worker/ocr_structural_gate.py` — `table_html` verifier + +### 9.22 Plan A: OCR Pairing Framework Extraction (2026-07-03) + +**Goal:** Extract generic OCR pairing mechanics from figure vnext and migrate figure onto the framework with no behavior change. Table vnext deferred to Plan B. + +**Architecture (Option B):** +- Generic framework: `ocr_pairing_types.py`, `ocr_pairing_state.py`, `ocr_pairing_framework.py` +- Figure domain: `ocr_figure_domain.py` (FigureCorpus, FigureCandidateIndex), 8 pass files (import paths only) +- Compatibility shims: `ocr_figure_vnext_types.py`, `ocr_figure_vnext_state.py`, `ocr_figure_vnext_corpus.py` each re-export from framework/domain +- `ocr_figures.py`: orchestration loop replaced with `run_pairing_passes(state, pass_classes)` from framework + +**Key decisions:** +- Keep `figure_no` and `FigurePipelineState` names in Plan A (rename deferred until migration stable) +- Plan A extracts pass orchestration only, not full framework-owned arbitration +- Table vnext deferred — no table file changes + +**Commits (branch `feat/ocr-pairing-framework`, 6 commits over master):** +| # | Commit | Description | +|---|--------|-------------| +| 1 | `0f94123` | docs: add Plan A implementation document | +| 2 | `96a5ddd` | fix(tests): update stale span_backfill_version constants | +| 3 | `1cc44b5` | test(ocr): lock figure vnext extraction baseline | +| 4 | `6229f6c` | refactor(ocr): extract generic pairing types and state | +| 5 | `7cfbb5f` | refactor(ocr): add pairing pass runner and figure domain module | +| 6 | `32541cf` | test(ocr): prove rebuild compatibility with pairing framework | + +**Files changed:** 21 files, +1546 -364 + +**Tests:** 288 pass in figure + rebuild + pairing suites (0 failed). Pre-existing `paperforge.resources` ModuleNotFoundError in test_ocr_document.py unrelated. + +**Verification gates:** +- Pre-existing rebuild test fixed (stale version constant) +- `build_figure_inventory` → `build_figure_inventory_vnext` delegation test passes +- Shim identity tests prove re-exports are the same class (not copies) +- Rebuild compatibility test calls `run_derived_rebuild_for_keys()` for real and asserts `build_figure_inventory` is invoked +- No table file changes in diff + +**Spec:** `docs/superpowers/specs/2026-07-03-ocr-pairing-framework-design.md` +**Plan:** `docs/superpowers/plans/2026-07-03-ocr-pairing-framework-plan-a.md` +**Branch:** `feat/ocr-pairing-framework` (in worktree `.worktrees/feat-ocr-pairing-framework/`) diff --git a/docs/superpowers/plans/2026-07-03-ocr-pairing-framework-plan-a.md b/docs/superpowers/plans/2026-07-03-ocr-pairing-framework-plan-a.md new file mode 100644 index 00000000..99c019b8 --- /dev/null +++ b/docs/superpowers/plans/2026-07-03-ocr-pairing-framework-plan-a.md @@ -0,0 +1,903 @@ +# OCR Pairing Framework Plan A Implementation Plan + +> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking. + +**Goal:** Extract a generic OCR pairing framework from the current figure vnext implementation and migrate figure pairing onto it with no intended behavior change. + +**Architecture:** Keep the external seam unchanged: `build_figure_inventory(...)` continues to return the same inventory contract and `ocr_rebuild.py` / OCR post-processing continue calling it the same way. Extract only the generic pairing mechanics into `ocr_pairing_*` modules, keep figure facts/hypotheses/assembly in figure-domain modules, and do not implement table vnext in this plan. + +**Tech Stack:** Python 3.x, pytest, OCR worker modules under `paperforge/worker/` + +## Global Constraints + +- This plan is **Plan A only**. +- Do **not** implement table vnext in this plan. +- Do **not** change table heuristics in this plan. +- Do **not** redesign OCR roles, layout, zones, or document structure. +- Treat figure migration as a **no-behavior-change refactor**. +- Preserve the external contract of `build_figure_inventory(...)` and `build_figure_inventory_vnext(...)`. +- Preserve current pass order inside figure vnext. +- In Plan A, extract **pass orchestration only** into `ocr_pairing_framework.py`; do **not** claim this plan centralizes proposal arbitration. +- Keep passes using existing `OwnershipLedger` and state accept methods where they already do; do **not** introduce new direct ownership bypasses in Plan A. +- If compatibility shims are needed for old `ocr_figure_vnext_types.py` / `ocr_figure_vnext_state.py`, make them explicit and temporary. + +--- + +## File Map + +- `paperforge/worker/ocr_figures.py` — figure entrypoints and vnext orchestration +- `paperforge/worker/ocr_figure_vnext_types.py` — current generic pairing types to extract +- `paperforge/worker/ocr_figure_vnext_state.py` — current ledger/state to extract +- `paperforge/worker/ocr_figure_vnext_corpus.py` — current figure corpus/index, target of domain migration +- `paperforge/worker/ocr_figure_vnext_passes.py` — primary figure passes +- `paperforge/worker/ocr_figure_vnext_sidecar_pass.py` — figure sidecar pass +- `paperforge/worker/ocr_figure_vnext_locator_pass.py` — figure locator pass +- `paperforge/worker/ocr_figure_vnext_group_seq_pass.py` — figure group-sequential pass +- `paperforge/worker/ocr_figure_vnext_composite_pass.py` — figure composite pass +- `paperforge/worker/ocr_figure_vnext_classic_seq_pass.py` — figure classic sequential / unresolved-cluster passes +- `paperforge/worker/ocr_figure_vnext_bundle_pass.py` — figure legend bundle pass +- `paperforge/worker/ocr_figure_vnext_accounting_pass.py` — final figure accounting pass +- `paperforge/worker/ocr_rebuild.py` — rebuild caller that must remain contract-compatible +- `tests/test_ocr_figures.py` — main figure regression and unit coverage +- `tests/test_ocr_rebuild.py` — rebuild smoke coverage if needed for compatibility proof + +Target new files: + +- `paperforge/worker/ocr_pairing_types.py` +- `paperforge/worker/ocr_pairing_state.py` +- `paperforge/worker/ocr_pairing_framework.py` +- `paperforge/worker/ocr_figure_domain.py` +- `tests/test_ocr_pairing_framework.py` + +--- + +### Task 1: Establish the no-behavior-change baseline + +**Files:** +- Modify: `tests/test_ocr_figures.py` +- Create: `tests/test_ocr_pairing_framework.py` +- Optional Create: `scripts/dev/compare_figure_inventory_vnext_baseline.py` + +**Interfaces:** +- Consumes: `build_figure_inventory(structured_blocks, page_width=1200, page_pdf_lines_by_page=None) -> dict[str, Any]` +- Produces: + - `test_build_figure_inventory_delegates_to_vnext()` + - `test_vnext_types_module_is_currently_generic_surface()` + - `test_vnext_state_module_is_currently_generic_surface()` + - optional baseline helper: `compare_vnext_inventory_baseline(...) -> int` + +- [ ] **Step 1: Write the failing baseline tests** + +Add to `tests/test_ocr_figures.py`: + +```python +def test_build_figure_inventory_delegates_to_vnext(monkeypatch): + from paperforge.worker import ocr_figures + + called = {} + + def fake_vnext(structured_blocks, page_width=1200, page_pdf_lines_by_page=None): + called["args"] = (structured_blocks, page_width, page_pdf_lines_by_page) + return {"pipeline_mode": "vnext", "matched_figures": []} + + monkeypatch.setattr(ocr_figures, "build_figure_inventory_vnext", fake_vnext) + + blocks = [{"block_id": "b1", "page": 1, "role": "body_text", "text": "x"}] + result = ocr_figures.build_figure_inventory(blocks, page_width=777, page_pdf_lines_by_page={1: []}) + + assert result["pipeline_mode"] == "vnext" + assert called["args"] == (blocks, 777, {1: []}) +``` + +Add to `tests/test_ocr_pairing_framework.py`: + +```python +def test_vnext_types_module_is_currently_generic_surface(): + from paperforge.worker.ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef + + assert ResourceRef.__name__ == "ResourceRef" + assert ClaimProposal.__name__ == "ClaimProposal" + assert PassReport.__name__ == "PassReport" + + +def test_vnext_state_module_is_currently_generic_surface(): + from paperforge.worker.ocr_figure_vnext_state import FigurePipelineState, OwnershipLedger + + state = FigurePipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + + assert state.matches == [] + assert state.reservations == [] + assert state.unresolved == [] +``` + +- [ ] **Step 2: Run tests to verify the baseline is real** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_figures.py::test_build_figure_inventory_delegates_to_vnext \ + tests/test_ocr_pairing_framework.py::test_vnext_types_module_is_currently_generic_surface \ + tests/test_ocr_pairing_framework.py::test_vnext_state_module_is_currently_generic_surface -q +``` + +Expected: PASS. If any test fails, stop and fix the baseline before extraction. + +- [ ] **Step 3: Add a representative output-baseline smoke helper** + +Create `scripts/dev/compare_figure_inventory_vnext_baseline.py`: + +```python +from __future__ import annotations + +import json +from pathlib import Path + +from paperforge.worker.ocr_figures import build_figure_inventory + + +def compare_vnext_inventory_baseline(fixture_root: Path) -> dict[str, object]: + structured_path = fixture_root / "structure" / "blocks.structured.jsonl" + blocks = [json.loads(line) for line in structured_path.read_text(encoding="utf-8").splitlines() if line.strip()] + inventory = build_figure_inventory(blocks) + return { + "pipeline_mode": inventory.get("pipeline_mode"), + "matched_ids": [m.get("figure_id") for m in inventory.get("matched_figures", [])], + "match_count": len(inventory.get("matched_figures", [])), + } +``` + +Do not overbuild this script. It exists only to capture a pre-extraction baseline on representative fixtures. + +- [ ] **Step 4: Run the baseline helper on one representative real-paper fixture** + +Run: + +```bash +python -c "from pathlib import Path; from scripts.dev.compare_figure_inventory_vnext_baseline import compare_vnext_inventory_baseline; print(compare_vnext_inventory_baseline(Path('tests/fixtures/ocr_real_papers/6QNRHRKX')))" +``` + +Expected: a small dict showing `pipeline_mode='vnext'` and stable figure IDs / count. + +- [ ] **Step 5: Commit** + +```bash +git add \ + tests/test_ocr_figures.py \ + tests/test_ocr_pairing_framework.py \ + scripts/dev/compare_figure_inventory_vnext_baseline.py +git commit -m "test(ocr): lock figure vnext extraction baseline" +``` + +--- + +### Task 2: Extract generic pairing types into `ocr_pairing_types.py` + +**Files:** +- Create: `paperforge/worker/ocr_pairing_types.py` +- Modify: `paperforge/worker/ocr_figure_vnext_types.py` +- Modify: `tests/test_ocr_pairing_framework.py` + +**Interfaces:** +- Consumes: current `ResourceRef`, `OwnershipConflict`, `ClaimProposal`, `PassReport` +- Produces: + - `paperforge.worker.ocr_pairing_types.ResourceRef` + - `paperforge.worker.ocr_pairing_types.OwnershipConflict` + - `paperforge.worker.ocr_pairing_types.ClaimProposal` + - `paperforge.worker.ocr_pairing_types.PassReport` + - compatibility shim behavior in `ocr_figure_vnext_types.py` + +- [ ] **Step 1: Write the failing extraction tests** + +Add to `tests/test_ocr_pairing_framework.py`: + +```python +def test_pairing_types_module_exports_generic_types(): + from paperforge.worker.ocr_pairing_types import ClaimProposal, PassReport, ResourceRef + + ref = ResourceRef(kind="legend", page=1, block_id="b1") + proposal = ClaimProposal( + pass_name="p", + figure_no=1, + claim_type="match", + legends=[ref], + assets=[], + groups=[], + confidence=0.9, + evidence_rank=1, + reason="test", + ) + report = PassReport(pass_name="p") + + assert proposal.pass_name == "p" + assert report.pass_name == "p" + assert ref.page == 1 + + +def test_figure_vnext_types_module_reexports_framework_types(): + from paperforge.worker.ocr_pairing_types import ResourceRef as FrameworkResourceRef + from paperforge.worker.ocr_figure_vnext_types import ResourceRef as FigureModuleResourceRef + + assert FigureModuleResourceRef is FrameworkResourceRef + + +def test_resource_ref_rejects_page_agnostic_asset(): + import pytest + + from paperforge.worker.ocr_pairing_types import ResourceRef + + with pytest.raises(ValueError): + ResourceRef(kind="asset", page=None, block_id="a1") + + +def test_resource_ref_normalizes_block_id_type(): + from paperforge.worker.ocr_pairing_types import ResourceRef + + assert ResourceRef(kind="asset", page=1, block_id=1) == ResourceRef(kind="asset", page=1, block_id="1") + + +def test_resource_ref_rejects_group_without_group_id(): + import pytest + + from paperforge.worker.ocr_pairing_types import ResourceRef + + with pytest.raises(ValueError): + ResourceRef(kind="group", page=1, block_id=None) + +- [ ] **Step 2: Run tests to verify they fail** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py::test_pairing_types_module_exports_generic_types \ + tests/test_ocr_pairing_framework.py::test_figure_vnext_types_module_reexports_framework_types \ + tests/test_ocr_pairing_framework.py::test_resource_ref_rejects_page_agnostic_asset \ + tests/test_ocr_pairing_framework.py::test_resource_ref_normalizes_block_id_type \ + tests/test_ocr_pairing_framework.py::test_resource_ref_rejects_group_without_group_id -q +``` + +Expected: FAIL because `ocr_pairing_types.py` does not exist yet. + +- [ ] **Step 3: Write the minimal extraction** + +Create `paperforge/worker/ocr_pairing_types.py` with the current dataclasses moved verbatim first: + +```python +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import Any, Literal + + +@dataclass(frozen=True) +class ResourceRef: + kind: Literal["legend", "asset", "group"] + page: int | None + block_id: str | None + group_id: str | None = None + figure_no: int | None = field(default=None, compare=False) + origin: str | None = field(default=None, compare=False) + + def __post_init__(self) -> None: + if self.page is not None: + object.__setattr__(self, "page", int(self.page)) + if self.block_id is not None: + object.__setattr__(self, "block_id", str(self.block_id)) + if self.group_id is not None: + object.__setattr__(self, "group_id", str(self.group_id)) + + if self.kind == "asset" and (self.page is None or self.block_id is None): + raise ValueError("asset ResourceRef requires page + block_id") + if self.kind == "legend" and (self.page is None or self.block_id is None): + raise ValueError("legend ResourceRef requires page + block_id") + if self.kind == "group" and (self.page is None or self.group_id is None): + raise ValueError("group ResourceRef requires page + group_id") + + +@dataclass(frozen=True) +class OwnershipConflict: + resource: ResourceRef + current_owner: ResourceRef | None + attempted_owner: ResourceRef | None + reason: str + + +@dataclass +class ClaimProposal: + pass_name: str + figure_no: int | None + claim_type: Literal["match", "reserve", "block", "unresolved_cluster", "composite_parent"] + legends: list[ResourceRef] + assets: list[ResourceRef] + groups: list[ResourceRef] + confidence: float + evidence_rank: int + reason: str + diagnostics: dict[str, Any] = field(default_factory=dict) + + +@dataclass +class PassReport: + pass_name: str + proposals: list[ClaimProposal] = field(default_factory=list) + accepted: list[ClaimProposal] = field(default_factory=list) + rejected: list[ClaimProposal] = field(default_factory=list) + conflicts: list[OwnershipConflict] = field(default_factory=list) + invariant_errors: list[str] = field(default_factory=list) +``` + +Then replace `paperforge/worker/ocr_figure_vnext_types.py` with a compatibility shim: + +```python +from .ocr_pairing_types import ClaimProposal, OwnershipConflict, PassReport, ResourceRef + +__all__ = ["ResourceRef", "OwnershipConflict", "ClaimProposal", "PassReport"] +``` + +Do not rename `figure_no` to `entity_no` in Plan A. That belongs to a later compatibility-tightening task only after figure migration is stable. + +- [ ] **Step 4: Run tests to verify they pass** + +Run the command from Step 2. + +Expected: PASS. + +- [ ] **Step 5: Commit** + +```bash +git add \ + paperforge/worker/ocr_pairing_types.py \ + paperforge/worker/ocr_figure_vnext_types.py \ + tests/test_ocr_pairing_framework.py +git commit -m "refactor(ocr): extract generic pairing types" +``` + +--- + +### Task 3: Extract generic state and ledger into `ocr_pairing_state.py` + +**Files:** +- Create: `paperforge/worker/ocr_pairing_state.py` +- Modify: `paperforge/worker/ocr_figure_vnext_state.py` +- Modify: `tests/test_ocr_pairing_framework.py` + +**Interfaces:** +- Consumes: `ResourceRef`, `ClaimProposal`, `OwnershipConflict` +- Produces: + - `paperforge.worker.ocr_pairing_state.OwnershipLedger` + - `paperforge.worker.ocr_pairing_state.FigurePipelineState` (keep existing class name in Plan A for compatibility) + - compatibility shim behavior in `ocr_figure_vnext_state.py` + +- [ ] **Step 1: Write the failing ledger / reexport tests** + +Add to `tests/test_ocr_pairing_framework.py`: + +```python +def test_pairing_state_module_exports_ownership_ledger(): + from paperforge.worker.ocr_pairing_state import OwnershipLedger + from paperforge.worker.ocr_pairing_types import ResourceRef + + ledger = OwnershipLedger() + owner = ResourceRef(kind="legend", page=1, block_id="cap") + asset = ResourceRef(kind="asset", page=1, block_id="asset") + + assert ledger.try_claim_assets([asset], owner=owner, reason="test") is None + assert ledger.owner_of_asset(page=1, block_id="asset") == owner + + +def test_figure_vnext_state_module_reexports_framework_ledger(): + from paperforge.worker.ocr_pairing_state import OwnershipLedger as FrameworkLedger + from paperforge.worker.ocr_figure_vnext_state import OwnershipLedger as FigureModuleLedger + + assert FigureModuleLedger is FrameworkLedger +``` + +- [ ] **Step 2: Run tests to verify they fail** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py::test_pairing_state_module_exports_ownership_ledger \ + tests/test_ocr_pairing_framework.py::test_figure_vnext_state_module_reexports_framework_ledger -q +``` + +Expected: FAIL because `ocr_pairing_state.py` does not exist yet. + +- [ ] **Step 3: Write the minimal extraction** + +Create `paperforge/worker/ocr_pairing_state.py` by moving the current `OwnershipLedger` and `FigurePipelineState` verbatim first, only changing imports: + +```python +from __future__ import annotations + +from dataclasses import dataclass, field + +from .ocr_pairing_types import ClaimProposal, OwnershipConflict, ResourceRef + + +class OwnershipLedger: + ... + + +@dataclass +class FigurePipelineState: + corpus: object | None + candidate_index: object | None + ledger: OwnershipLedger + matches: list[dict] = field(default_factory=list) + unresolved: list[dict] = field(default_factory=list) + hypotheses: list[dict] = field(default_factory=list) + diagnostics: list[dict] = field(default_factory=list) + reservations: list[dict] = field(default_factory=list) + completeness: dict = field(default_factory=dict) + + def accept_match(self, proposal: ClaimProposal, match_record: dict) -> None: + ... + + def accept_reservation(self, proposal: ClaimProposal) -> None: + ... +``` + +Then replace `paperforge/worker/ocr_figure_vnext_state.py` with a compatibility shim: + +```python +from .ocr_pairing_state import FigurePipelineState, OwnershipLedger + +__all__ = ["OwnershipLedger", "FigurePipelineState"] +``` + +Do not rename `FigurePipelineState` yet. That compatibility cleanup belongs after the framework extraction is proven stable. + +- [ ] **Step 4: Run tests to verify they pass** + +Run the command from Step 2. + +Expected: PASS. + +- [ ] **Step 5: Commit** + +```bash +git add \ + paperforge/worker/ocr_pairing_state.py \ + paperforge/worker/ocr_figure_vnext_state.py \ + tests/test_ocr_pairing_framework.py +git commit -m "refactor(ocr): extract generic pairing state and ledger" +``` + +--- + +### Task 4: Add `ocr_pairing_framework.py` and migrate figure orchestration imports + +**Files:** +- Create: `paperforge/worker/ocr_pairing_framework.py` +- Modify: `paperforge/worker/ocr_figures.py` +- Modify: all figure pass files under `paperforge/worker/ocr_figure_vnext_*.py` +- Modify: `tests/test_ocr_figures.py` +- Modify: `tests/test_ocr_pairing_framework.py` + +**Interfaces:** +- Consumes: `FigurePipelineState`, `PassReport`, existing figure pass classes +- Produces: + - `run_pairing_passes(state, pass_classes) -> list[PassReport]` + - figure pass imports now sourced from `ocr_pairing_types` / `ocr_pairing_state` + - no change to per-pass arbitration behavior in Plan A +- [ ] **Step 1: Write the failing runner test** + +Add to `tests/test_ocr_pairing_framework.py`: + +```python +def test_run_pairing_passes_executes_in_declared_order(): + from paperforge.worker.ocr_pairing_framework import run_pairing_passes + from paperforge.worker.ocr_pairing_state import FigurePipelineState, OwnershipLedger + from paperforge.worker.ocr_pairing_types import PassReport + + seen = [] + + class FirstPass: + name = "first" + def run(self, state): + seen.append(self.name) + return PassReport(pass_name=self.name) + + class SecondPass: + name = "second" + def run(self, state): + seen.append(self.name) + return PassReport(pass_name=self.name) + + state = FigurePipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + reports = run_pairing_passes(state, [FirstPass, SecondPass]) + + assert seen == ["first", "second"] + assert [r.pass_name for r in reports] == ["first", "second"] +``` + +- [ ] **Step 2: Run test to verify it fails** + +Run: + +```bash +python -m pytest tests/test_ocr_pairing_framework.py::test_run_pairing_passes_executes_in_declared_order -q +``` + +Expected: FAIL because `ocr_pairing_framework.py` does not exist yet. + +- [ ] **Step 3: Write the minimal framework runner and migrate imports** + +Create `paperforge/worker/ocr_pairing_framework.py`: + +```python +from __future__ import annotations + +from collections.abc import Sequence + + +def run_pairing_passes(state, pass_classes: Sequence[type]) -> list: + reports = [] + for pass_cls in pass_classes: + reports.append(pass_cls().run(state)) + return reports +``` + +In `paperforge/worker/ocr_figures.py`, replace the local orchestration loop inside `build_figure_inventory_vnext(...)`: + +```python +reports = [] +for pass_cls in ( + PrimarySamePagePass, + CompositeParentPass, + SidecarPass, + LocatorBridgePass, + CrossPageReservationPass, + CrossPageSettlementPass, + LegendBundlePass, + GroupSequentialPass, + ClassicSequentialPass, + UnresolvedClusterConsolidation, + FinalAccountingPass, +): + reports.append(pass_cls().run(state)) +``` + +with: + +```python +from .ocr_pairing_framework import run_pairing_passes + +reports = run_pairing_passes( + state, + [ + PrimarySamePagePass, + CompositeParentPass, + SidecarPass, + LocatorBridgePass, + CrossPageReservationPass, + CrossPageSettlementPass, + LegendBundlePass, + GroupSequentialPass, + ClassicSequentialPass, + UnresolvedClusterConsolidation, + FinalAccountingPass, + ], +) +``` + +Then update all figure pass files to import from the extracted modules, for example: + +```python +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_state import FigurePipelineState +``` + +Keep pass logic unchanged in Plan A. This task only extracts **orchestration**, not framework-owned arbitration. Do not refactor passes to centralize proposal commit logic in this plan. + +- [ ] **Step 4: Run focused tests to verify the runner is wired correctly** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py::test_run_pairing_passes_executes_in_declared_order \ + tests/test_ocr_figures.py::test_build_figure_inventory_delegates_to_vnext -q +``` + +Expected: PASS. + +- [ ] **Step 5: Commit** + +```bash +git add \ + paperforge/worker/ocr_pairing_framework.py \ + paperforge/worker/ocr_figures.py \ + paperforge/worker/ocr_figure_vnext_*.py \ + tests/test_ocr_pairing_framework.py \ + tests/test_ocr_figures.py +git commit -m "refactor(ocr): add pairing pass runner for figure vnext" +``` + +--- + +### Task 5: Move figure facts and hypotheses into `ocr_figure_domain.py` + +**Files:** +- Create: `paperforge/worker/ocr_figure_domain.py` +- Modify: `paperforge/worker/ocr_figure_vnext_corpus.py` +- Modify: `paperforge/worker/ocr_figures.py` +- Modify: `tests/test_ocr_pairing_framework.py` +- Modify: `tests/test_ocr_figures.py` + +**Interfaces:** +- Consumes: current `FigureCorpus`, `FigureCandidateIndex` +- Produces: + - `paperforge.worker.ocr_figure_domain.FigureCorpus` + - `paperforge.worker.ocr_figure_domain.FigureCandidateIndex` + - compatibility shim behavior in `ocr_figure_vnext_corpus.py` + +- [ ] **Step 1: Write the failing domain-module reexport tests** + +Add to `tests/test_ocr_pairing_framework.py`: + +```python +def test_figure_domain_module_exports_corpus_and_candidate_index(): + from paperforge.worker.ocr_figure_domain import FigureCandidateIndex, FigureCorpus + + assert FigureCorpus.__name__ == "FigureCorpus" + assert FigureCandidateIndex.__name__ == "FigureCandidateIndex" + + +def test_legacy_vnext_corpus_module_reexports_figure_domain_types(): + from paperforge.worker.ocr_figure_domain import FigureCorpus as DomainFigureCorpus + from paperforge.worker.ocr_figure_vnext_corpus import FigureCorpus as LegacyModuleFigureCorpus + + assert LegacyModuleFigureCorpus is DomainFigureCorpus +``` + +- [ ] **Step 2: Run tests to verify they fail** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py::test_figure_domain_module_exports_corpus_and_candidate_index \ + tests/test_ocr_pairing_framework.py::test_legacy_vnext_corpus_module_reexports_figure_domain_types -q +``` + +Expected: FAIL because `ocr_figure_domain.py` does not exist yet. + +- [ ] **Step 3: Write the minimal domain extraction** + +Create `paperforge/worker/ocr_figure_domain.py` by moving `FigureCorpus` and `FigureCandidateIndex` from `ocr_figure_vnext_corpus.py` first. + +If the moved code needs helpers from `ocr_figures.py`, keep those imports lazy inside methods or classmethods. Preferred pattern: + +```python +class FigureCandidateIndex: + @classmethod + def from_corpus(cls, corpus): + from . import ocr_figures + ... +``` + +Do **not** add a new top-level import cycle between `ocr_figures.py` and `ocr_figure_domain.py`. + +Then replace `paperforge/worker/ocr_figure_vnext_corpus.py` with: + +```python +from .ocr_figure_domain import FigureCandidateIndex, FigureCorpus + +__all__ = ["FigureCorpus", "FigureCandidateIndex"] +``` + +In `paperforge/worker/ocr_figures.py`, change: + +```python +from .ocr_figure_vnext_corpus import FigureCandidateIndex, FigureCorpus +``` + +to: + +```python +from .ocr_figure_domain import FigureCandidateIndex, FigureCorpus +``` + +Do not edit corpus/index behavior in this task beyond lazy-import adjustments needed to avoid circular imports. + +- [ ] **Step 4: Run focused tests and one representative figure regression** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py::test_figure_domain_module_exports_corpus_and_candidate_index \ + tests/test_ocr_pairing_framework.py::test_legacy_vnext_corpus_module_reexports_figure_domain_types \ + tests/test_ocr_figures.py -q +``` + +Expected: PASS. + +- [ ] **Step 5: Commit** + +```bash +git add \ + paperforge/worker/ocr_figure_domain.py \ + paperforge/worker/ocr_figure_vnext_corpus.py \ + paperforge/worker/ocr_figures.py \ + tests/test_ocr_pairing_framework.py \ + tests/test_ocr_figures.py +git commit -m "refactor(ocr): move figure corpus and candidate index into domain module" +``` + +--- + +### Task 6: Prove rebuild compatibility and close Plan A + +**Files:** +- Modify: `tests/test_ocr_rebuild.py` +- Modify: `tests/test_ocr_pairing_framework.py` +- Optional Modify: `paperforge/worker/ocr_rebuild.py` only if imports need compatibility cleanup + +**Interfaces:** +- Consumes: extracted framework modules, unchanged `build_figure_inventory(...)` +- Produces: + - rebuild-level compatibility test + - final baseline comparison results proving no intended figure behavior change + +- [ ] **Step 1: Write the rebuild compatibility test against the real rebuild path** + +Add to `tests/test_ocr_rebuild.py`: + +```python +def test_run_derived_rebuild_for_keys_still_uses_public_build_figure_inventory(tmp_path: Path, monkeypatch) -> None: + import json + + from paperforge.worker.ocr_rebuild import run_derived_rebuild_for_keys + + key = "TESTKEY1" + paper_root = tmp_path / "System" / "PaperForge" / "ocr" / key + (paper_root / "canonical").mkdir(parents=True) + (paper_root / "raw").mkdir(parents=True) + (paper_root / "structure").mkdir(parents=True) + + (paper_root / "canonical" / "blocks.raw.jsonl").write_text( + json.dumps( + { + "paper_id": key, + "page": 1, + "block_id": "p1_b1", + "raw_label": "text", + "raw_order": 0, + "text": "Example text", + "bbox": [10, 10, 100, 40], + "page_width": 600, + "page_height": 800, + } + ) + + "\\n", + encoding="utf-8", + ) + (paper_root / "raw" / "source_metadata.json").write_text( + json.dumps({"title": "Example Title"}), + encoding="utf-8", + ) + (paper_root / "meta.json").write_text(json.dumps({"source_pdf": ""}), encoding="utf-8") + + called = {"count": 0} + + def fake_build_figure_inventory(structured_blocks, page_width=1200, page_pdf_lines_by_page=None): + called["count"] += 1 + return { + "pipeline_mode": "vnext", + "matched_figures": [], + "ambiguous_figures": [], + "unmatched_legends": [], + "unmatched_assets": [], + "unresolved_clusters": [], + "held_figures": [], + "rejected_legends": [], + "page_ledger": {}, + "residual_ledger": {}, + "local_pairing_hypotheses": [], + "pass_reports": [], + "completeness": {"total_numbered_legends": 0, "accounted_for": 0, "details": []}, + } + + monkeypatch.setattr("paperforge.worker.ocr_figures.build_figure_inventory", fake_build_figure_inventory) + monkeypatch.setattr("paperforge.worker.ocr_blocks.write_structured_blocks_jsonl", lambda *args, **kwargs: None) + monkeypatch.setattr( + "paperforge.worker.ocr_metadata.extract_frontmatter_candidates_from_blocks", + lambda structured: {"title": "Example Title", "authors_text": None, "doi_candidates": []}, + ) + + result = run_derived_rebuild_for_keys(tmp_path, [key]) + + assert result["rebuild_count"] == 1 + assert called["count"] > 0 +``` + +This test must call `run_derived_rebuild_for_keys(...)` for real. Do not replace it with a hand-call to the fake function. + +- [ ] **Step 2: Run the focused rebuild and framework tests** + +Run: + +```bash +python -m pytest \ + tests/test_ocr_pairing_framework.py \ + tests/test_ocr_rebuild.py::test_run_derived_rebuild_for_keys_still_uses_public_build_figure_inventory -q +``` + +Expected: PASS. + +- [ ] **Step 3: Run representative figure regression proof** + +Run: + +```bash +python -m pytest tests/test_ocr_figures.py -q +python -c "from pathlib import Path; from scripts.dev.compare_figure_inventory_vnext_baseline import compare_vnext_inventory_baseline; print(compare_vnext_inventory_baseline(Path('tests/fixtures/ocr_real_papers/6QNRHRKX')))" +``` + +Expected: + +- all figure tests PASS +- baseline helper output remains unchanged from Task 1 + +- [ ] **Step 4: Remove any accidental table changes from the diff** + +Run: + +```bash +git diff --name-only -- paperforge/worker/ocr_tables.py tests/test_ocr_tables.py +``` + +Expected: no output. If there is output, revert it before committing. + +- [ ] **Step 5: Commit** + +```bash +git add \ + tests/test_ocr_rebuild.py \ + tests/test_ocr_pairing_framework.py \ + scripts/dev/compare_figure_inventory_vnext_baseline.py \ + paperforge/worker/ocr_pairing_types.py \ + paperforge/worker/ocr_pairing_state.py \ + paperforge/worker/ocr_pairing_framework.py \ + paperforge/worker/ocr_figure_domain.py \ + paperforge/worker/ocr_figure_vnext_types.py \ + paperforge/worker/ocr_figure_vnext_state.py \ + paperforge/worker/ocr_figure_vnext_corpus.py \ + paperforge/worker/ocr_figure_vnext_*.py \ + paperforge/worker/ocr_figures.py +git commit -m "refactor(ocr): migrate figure vnext onto pairing framework" +``` + +--- + +## Self-Review Checklist + +- Spec coverage: + - Preflight baseline gate -> Task 1 + - Framework type extraction -> Task 2 + - Framework state/ledger extraction -> Task 3 + - Framework runner / arbitration seam -> Task 4 + - Figure-domain migration -> Task 5 + - Rebuild compatibility and no-behavior proof -> Task 6 + - Table vnext intentionally excluded -> enforced in Global Constraints and Task 6 Step 4 +- Placeholder scan: + - No `TODO` / `TBD` / “similar to Task N” placeholders remain. + - One note in Task 6 explicitly tells the implementer to reuse existing rebuild fixture helpers in-file instead of inventing new infrastructure; this is intentional scoping guidance, not a missing design detail. +- Type consistency: + - Plan A keeps `figure_no` and `FigurePipelineState` names for compatibility. + - Framework extraction is import-path-first; neutral renames like `entity_no` and `anchor` are deferred until after migration stability is proven. + +## Execution Handoff + +**Plan complete and saved to `docs/superpowers/plans/2026-07-03-ocr-pairing-framework-plan-a.md`. Two execution options:** + +**1. Subagent-Driven (recommended)** - I dispatch a fresh subagent per task, review between tasks, fast iteration + +**2. Inline Execution** - Execute tasks in this session using executing-plans, batch execution with checkpoints + +**Which approach?** diff --git a/paperforge/worker/ocr_figure_domain.py b/paperforge/worker/ocr_figure_domain.py new file mode 100644 index 00000000..bb31ed6a --- /dev/null +++ b/paperforge/worker/ocr_figure_domain.py @@ -0,0 +1,128 @@ +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import Any + + +@dataclass +class FigureCorpus: + """Immutable facts extracted from structured blocks. + + This dataclass stores raw, unfiltered data plus computed layout profiles. + No derived hypotheses or candidate logic lives here. + """ + + blocks: list[dict] + page_width: float + raw_legends: list[dict] = field(default_factory=list) + raw_assets: list[dict] = field(default_factory=list) + locator_candidates: list[dict] = field(default_factory=list) + page_layouts: dict[int, Any] = field(default_factory=dict) + + @classmethod + def from_blocks(cls, blocks: list[dict], page_width: float = 1200) -> FigureCorpus: + from paperforge.worker.ocr_document import _build_page_layout_profiles + + from . import ocr_figures + + raw_legends = [ + b for b in blocks if b.get("role") in {"figure_caption", "figure_caption_candidate"} + ] + raw_assets = [ + b for b in blocks if b.get("role") in {"figure_asset", "media_asset"} + ] + locator_candidates = [ + b for b in raw_legends if ocr_figures._is_previous_page_legend_locator(b) + ] + return cls( + blocks=list(blocks), + page_width=page_width, + raw_legends=raw_legends, + raw_assets=raw_assets, + locator_candidates=locator_candidates, + page_layouts=_build_page_layout_profiles(blocks), + ) + + +@dataclass +class FigureCandidateIndex: + """Derived hypotheses and candidates built from a FigureCorpus. + + These are derived interpretations — lists of formal legends, deduped legends + (currently same as formal_legends — dedup over groups may be added later), + rejected legends that didn't meet criteria for formal status, candidate + groups built from assets, and per-page maps for sidecar/competition detection. + """ + + formal_legends: list[dict] + held_legends: list[dict] + rejected_legends: list[dict] + deduped_legends: list[dict] + candidate_groups: list[dict] + competing_caption_pages: set[int] + sidecar_candidates: dict[int, list[dict]] + bundle_source_legend_ids: set[str] + locator_candidates: list[dict] + composite_parent_candidates: list[dict] = field(default_factory=list) + + @classmethod + def from_corpus(cls, corpus: FigureCorpus) -> FigureCandidateIndex: + from . import ocr_figures + + formal_legends = [ + b + for b in corpus.raw_legends + if ocr_figures._is_formal_legend( + str(b.get("text", "")), b, corpus.page_width + ) + ] + rejected_legends = [b for b in corpus.raw_legends if b not in formal_legends] + candidate_groups = ocr_figures._build_candidate_figure_groups_from_assets( + corpus.raw_assets, + corpus.blocks, + formal_legends, + page_width=corpus.page_width, + ) + competing_caption_pages = { + int(leg.get("page")) + for leg in formal_legends + if leg.get("page") is not None + and ocr_figures._extract_figure_number(str(leg.get("text", ""))) + is not None + } + # Populate sidecar_candidates: pages with >=2 aligned narrow captions. + sidecar_candidates: dict[int, list[dict]] = {} + _legends_by_page: dict[int, list[dict]] = {} + for leg in formal_legends: + _legends_by_page.setdefault(int(leg.get("page", 0) or 0), []).append(leg) + for sp, spl in _legends_by_page.items(): + narrow_set = ocr_figures._same_page_narrow_caption_column(spl, corpus.page_width) + if len(narrow_set) >= 2: + sidecar_candidates[sp] = narrow_set + + # Populate bundle_source_legend_ids: legends on pages with >=3 numbered legends + # and zero assets on that page. + bundle_source_legend_ids = ocr_figures._identify_bundle_source_legend_ids( + formal_legends, corpus.raw_assets + ) + + # Populate composite_parent_candidates: same-page atomic groups with + # horizontal alignment + vertical adjacency (2x2 grid, columnar stacks). + composite_parent_candidates = ocr_figures._build_composite_parent_figure_groups_visual_only( + candidate_groups, + corpus.raw_assets, + corpus.blocks, + corpus.page_width, + ) + return cls( + formal_legends=formal_legends, + held_legends=[], + rejected_legends=rejected_legends, + deduped_legends=formal_legends, + candidate_groups=candidate_groups, + competing_caption_pages=competing_caption_pages, + sidecar_candidates=sidecar_candidates, + bundle_source_legend_ids=bundle_source_legend_ids, + locator_candidates=corpus.locator_candidates, + composite_parent_candidates=composite_parent_candidates, + ) diff --git a/paperforge/worker/ocr_figure_vnext_accounting_pass.py b/paperforge/worker/ocr_figure_vnext_accounting_pass.py index c8b7ab89..2a90b930 100644 --- a/paperforge/worker/ocr_figure_vnext_accounting_pass.py +++ b/paperforge/worker/ocr_figure_vnext_accounting_pass.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import PassReport, ResourceRef +from .ocr_pairing_types import PassReport, ResourceRef class FinalAccountingPass: diff --git a/paperforge/worker/ocr_figure_vnext_bundle_pass.py b/paperforge/worker/ocr_figure_vnext_bundle_pass.py index 5f706b6e..2498ff6f 100644 --- a/paperforge/worker/ocr_figure_vnext_bundle_pass.py +++ b/paperforge/worker/ocr_figure_vnext_bundle_pass.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef _NON_PURE_ROLES = frozenset({ "body_paragraph", diff --git a/paperforge/worker/ocr_figure_vnext_classic_seq_pass.py b/paperforge/worker/ocr_figure_vnext_classic_seq_pass.py index 4c776b69..0253bc2a 100644 --- a/paperforge/worker/ocr_figure_vnext_classic_seq_pass.py +++ b/paperforge/worker/ocr_figure_vnext_classic_seq_pass.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_composite_pass.py b/paperforge/worker/ocr_figure_vnext_composite_pass.py index a2a183c6..7533b831 100644 --- a/paperforge/worker/ocr_figure_vnext_composite_pass.py +++ b/paperforge/worker/ocr_figure_vnext_composite_pass.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_corpus.py b/paperforge/worker/ocr_figure_vnext_corpus.py index 801bfab9..99e36e29 100644 --- a/paperforge/worker/ocr_figure_vnext_corpus.py +++ b/paperforge/worker/ocr_figure_vnext_corpus.py @@ -1,127 +1,3 @@ -from __future__ import annotations +from .ocr_figure_domain import FigureCandidateIndex, FigureCorpus -from dataclasses import dataclass, field -from typing import Any - - -@dataclass -class FigureCorpus: - """Immutable facts extracted from structured blocks. - - This dataclass stores raw, unfiltered data plus computed layout profiles. - No derived hypotheses or candidate logic lives here. - """ - - blocks: list[dict] - page_width: float - raw_legends: list[dict] = field(default_factory=list) - raw_assets: list[dict] = field(default_factory=list) - locator_candidates: list[dict] = field(default_factory=list) - page_layouts: dict[int, Any] = field(default_factory=dict) - - @classmethod - def from_blocks(cls, blocks: list[dict], page_width: float = 1200) -> FigureCorpus: - from paperforge.worker.ocr_document import _build_page_layout_profiles - - from . import ocr_figures - - raw_legends = [ - b for b in blocks if b.get("role") in {"figure_caption", "figure_caption_candidate"} - ] - raw_assets = [ - b for b in blocks if b.get("role") in {"figure_asset", "media_asset"} - ] - locator_candidates = [ - b for b in raw_legends if ocr_figures._is_previous_page_legend_locator(b) - ] - return cls( - blocks=list(blocks), - page_width=page_width, - raw_legends=raw_legends, - raw_assets=raw_assets, - locator_candidates=locator_candidates, - page_layouts=_build_page_layout_profiles(blocks), - ) - - -@dataclass -class FigureCandidateIndex: - """Derived hypotheses and candidates built from a FigureCorpus. - - Every field here is a computed / filtered view of the raw corpus facts. - No raw data is duplicated — references point back into the corpus. - """ - - formal_legends: list[dict] - held_legends: list[dict] - rejected_legends: list[dict] - deduped_legends: list[dict] - candidate_groups: list[dict] - competing_caption_pages: set[int] - sidecar_candidates: dict[int, list[dict]] - bundle_source_legend_ids: set[str] - locator_candidates: list[dict] - composite_parent_candidates: list[dict] = field(default_factory=list) - - @classmethod - def from_corpus(cls, corpus: FigureCorpus) -> FigureCandidateIndex: - from . import ocr_figures - - formal_legends = [ - b - for b in corpus.raw_legends - if ocr_figures._is_formal_legend( - str(b.get("text", "")), b, corpus.page_width - ) - ] - rejected_legends = [b for b in corpus.raw_legends if b not in formal_legends] - candidate_groups = ocr_figures._build_candidate_figure_groups_from_assets( - corpus.raw_assets, - corpus.blocks, - formal_legends, - page_width=corpus.page_width, - ) - competing_caption_pages = { - int(leg.get("page")) - for leg in formal_legends - if leg.get("page") is not None - and ocr_figures._extract_figure_number(str(leg.get("text", ""))) - is not None - } - # Populate sidecar_candidates: pages with ≥2 aligned narrow captions. - sidecar_candidates: dict[int, list[dict]] = {} - _legends_by_page: dict[int, list[dict]] = {} - for leg in formal_legends: - _legends_by_page.setdefault(int(leg.get("page", 0) or 0), []).append(leg) - for sp, spl in _legends_by_page.items(): - narrow_set = ocr_figures._same_page_narrow_caption_column(spl, corpus.page_width) - if len(narrow_set) >= 2: - sidecar_candidates[sp] = narrow_set - - # Populate bundle_source_legend_ids: legends on pages with ≥3 numbered legends - # and zero assets on that page. - bundle_source_legend_ids = ocr_figures._identify_bundle_source_legend_ids( - formal_legends, corpus.raw_assets - ) - - - # Populate composite_parent_candidates: same-page atomic groups with - # horizontal alignment + vertical adjacency (2x2 grid, columnar stacks). - composite_parent_candidates = ocr_figures._build_composite_parent_figure_groups_visual_only( - candidate_groups, - corpus.raw_assets, - corpus.blocks, - corpus.page_width, - ) - return cls( - formal_legends=formal_legends, - held_legends=[], - rejected_legends=rejected_legends, - deduped_legends=formal_legends, - candidate_groups=candidate_groups, - competing_caption_pages=competing_caption_pages, - sidecar_candidates=sidecar_candidates, - bundle_source_legend_ids=bundle_source_legend_ids, - locator_candidates=corpus.locator_candidates, - composite_parent_candidates=composite_parent_candidates, - ) +__all__ = ["FigureCorpus", "FigureCandidateIndex"] diff --git a/paperforge/worker/ocr_figure_vnext_group_seq_pass.py b/paperforge/worker/ocr_figure_vnext_group_seq_pass.py index 47a21f81..c7a00d1b 100644 --- a/paperforge/worker/ocr_figure_vnext_group_seq_pass.py +++ b/paperforge/worker/ocr_figure_vnext_group_seq_pass.py @@ -8,7 +8,7 @@ next-page, then previous-page (with guard) order. from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_locator_pass.py b/paperforge/worker/ocr_figure_vnext_locator_pass.py index a7236d17..878d68ba 100644 --- a/paperforge/worker/ocr_figure_vnext_locator_pass.py +++ b/paperforge/worker/ocr_figure_vnext_locator_pass.py @@ -11,7 +11,7 @@ Run AFTER PrimarySamePagePass and cross-page passes but BEFORE generic fallback. from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_passes.py b/paperforge/worker/ocr_figure_vnext_passes.py index 4e92fbcd..e3b2a85a 100644 --- a/paperforge/worker/ocr_figure_vnext_passes.py +++ b/paperforge/worker/ocr_figure_vnext_passes.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_sidecar_pass.py b/paperforge/worker/ocr_figure_vnext_sidecar_pass.py index e47cb365..258357ec 100644 --- a/paperforge/worker/ocr_figure_vnext_sidecar_pass.py +++ b/paperforge/worker/ocr_figure_vnext_sidecar_pass.py @@ -1,6 +1,6 @@ from __future__ import annotations -from .ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef def _resource_page(block: dict) -> int | None: diff --git a/paperforge/worker/ocr_figure_vnext_state.py b/paperforge/worker/ocr_figure_vnext_state.py index cc57229e..64ad7c9b 100644 --- a/paperforge/worker/ocr_figure_vnext_state.py +++ b/paperforge/worker/ocr_figure_vnext_state.py @@ -1,145 +1,3 @@ -from __future__ import annotations +from .ocr_pairing_state import FigurePipelineState, OwnershipLedger -from dataclasses import dataclass, field - -from .ocr_figure_vnext_types import ClaimProposal, OwnershipConflict, ResourceRef - - -class OwnershipLedger: - def __init__(self) -> None: - self._reserved_groups: set[ResourceRef] = set() - self._owners: dict[ResourceRef, ResourceRef] = {} - self._journal: list[dict[str, object]] = [] - - def claim_assets(self, assets: list[ResourceRef], *, owner: ResourceRef, reason: str) -> None: - conflict = self.try_claim_assets(assets, owner=owner, reason=reason) - if conflict is not None: - raise ValueError(f"asset already owned: {conflict.resource}") - - def try_claim_assets( - self, assets: list[ResourceRef], *, owner: ResourceRef, reason: str - ) -> OwnershipConflict | None: - for asset in assets: - current = self._owners.get(asset) - if current is not None and current != owner: - conflict = OwnershipConflict( - resource=asset, - current_owner=current, - attempted_owner=owner, - reason=reason, - ) - self._journal.append({ - "action": "conflict", - "resource": asset, - "current_owner": current, - "attempted_owner": owner, - "reason": reason, - }) - return conflict - for asset in assets: - self._owners[asset] = owner - self._journal.append({"action": "claim", "resource": asset, "owner": owner, "reason": reason}) - return None - - def owner_of(self, resource: ResourceRef) -> ResourceRef | None: - return self._owners.get(resource) - - def owner_of_asset(self, *, page: int, block_id: int | str) -> ResourceRef | None: - return self.owner_of(ResourceRef(kind="asset", page=page, block_id=block_id)) - - def reserve_group(self, group: ResourceRef, *, reason: str) -> None: - self._reserved_groups.add(group) - self._journal.append({"action": "reserve_group", "resource": group, "reason": reason}) - - def can_claim_group(self, group: ResourceRef) -> bool: - return group not in self._reserved_groups - - def transition_reserved_group_to_claimed( - self, group: ResourceRef, *, owner: ResourceRef, reason: str - ) -> None: - self._reserved_groups.discard(group) - self._journal.append({ - "action": "transition_to_claimed", - "resource": group, - "owner": owner, - "reason": reason, - }) - - def snapshot(self) -> list[dict[str, object]]: - return list(self._journal) - - -@dataclass -class FigurePipelineState: - corpus: object | None - candidate_index: object | None - ledger: OwnershipLedger - matches: list[dict] = field(default_factory=list) - unresolved: list[dict] = field(default_factory=list) - hypotheses: list[dict] = field(default_factory=list) - diagnostics: list[dict] = field(default_factory=list) - reservations: list[dict] = field(default_factory=list) - completeness: dict = field(default_factory=dict) - - def accept_match(self, proposal: ClaimProposal, match_record: dict) -> None: - # Enrich match_record with rotation metadata if the legend has rotated text. - self._enrich_rotation(proposal, match_record) - self.matches.append(match_record) - self.diagnostics.append({ - "event": "match_accepted", - "pass_name": proposal.pass_name, - "figure_no": proposal.figure_no, - "reason": proposal.reason, - "resources": { - "legends": proposal.legends, - "assets": proposal.assets, - "groups": proposal.groups, - }, - }) - - def _enrich_rotation(self, proposal: ClaimProposal, match_record: dict) -> None: - """Detect rotated caption and add rotation_correction_deg + cluster_bbox.""" - from .ocr_figures import _caption_has_rotated_text, _prepare_rotated_caption_normalization - - if not self.corpus or not proposal.legends: - return - legend_ref = proposal.legends[0] - # Find the legend block in the corpus - legend_block = None - for b in self.corpus.blocks: - if str(b.get("block_id", "")) == str(legend_ref.block_id) and b.get("page") == legend_ref.page: - legend_block = b - break - if legend_block is None or not _caption_has_rotated_text(legend_block): - return - # Find the first asset block from the proposal - if not proposal.assets or not self.corpus.raw_assets: - return - asset_ref = proposal.assets[0] - asset_block = None - for a in self.corpus.raw_assets: - if str(a.get("block_id", "")) == str(asset_ref.block_id) and a.get("page") == asset_ref.page: - asset_block = a - break - if asset_block is None: - return - normalized = _prepare_rotated_caption_normalization(legend_block, asset_block) - if normalized is not None: - match_record["rotation_correction_deg"] = normalized["rotation_correction_deg"] - match_record["cluster_bbox"] = normalized["rotation_union_bbox"] - - def accept_reservation(self, proposal: ClaimProposal) -> None: - self.reservations.append({ - "pass_name": proposal.pass_name, - "figure_no": proposal.figure_no, - "reason": proposal.reason, - "legends": list(proposal.legends), - "groups": list(proposal.groups), - }) - self.diagnostics.append({ - "event": "reservation_accepted", - "pass_name": proposal.pass_name, - "figure_no": proposal.figure_no, - "reason": proposal.reason, - "resources": {"groups": proposal.groups}, - }) +__all__ = ["OwnershipLedger", "FigurePipelineState"] diff --git a/paperforge/worker/ocr_figure_vnext_types.py b/paperforge/worker/ocr_figure_vnext_types.py index ebf2bcaf..49d43085 100644 --- a/paperforge/worker/ocr_figure_vnext_types.py +++ b/paperforge/worker/ocr_figure_vnext_types.py @@ -1,61 +1,3 @@ -from __future__ import annotations +from .ocr_pairing_types import ClaimProposal, OwnershipConflict, PassReport, ResourceRef -from dataclasses import dataclass, field -from typing import Any, Literal - - -@dataclass(frozen=True) -class ResourceRef: - kind: Literal["legend", "asset", "group"] - page: int | None - block_id: str | None - group_id: str | None = None - figure_no: int | None = field(default=None, compare=False) - origin: str | None = field(default=None, compare=False) - - def __post_init__(self) -> None: - if self.page is not None: - object.__setattr__(self, "page", int(self.page)) - if self.block_id is not None: - object.__setattr__(self, "block_id", str(self.block_id)) - if self.group_id is not None: - object.__setattr__(self, "group_id", str(self.group_id)) - - if self.kind == "asset" and (self.page is None or self.block_id is None): - raise ValueError("asset ResourceRef requires page + block_id") - if self.kind == "legend" and (self.page is None or self.block_id is None): - raise ValueError("legend ResourceRef requires page + block_id") - if self.kind == "group" and (self.page is None or self.group_id is None): - raise ValueError("group ResourceRef requires page + group_id") - - -@dataclass(frozen=True) -class OwnershipConflict: - resource: ResourceRef - current_owner: ResourceRef | None - attempted_owner: ResourceRef | None - reason: str - - -@dataclass -class ClaimProposal: - pass_name: str - figure_no: int | None - claim_type: Literal["match", "reserve", "block", "unresolved_cluster", "composite_parent"] - legends: list[ResourceRef] - assets: list[ResourceRef] - groups: list[ResourceRef] - confidence: float - evidence_rank: int - reason: str - diagnostics: dict[str, Any] = field(default_factory=dict) - - -@dataclass -class PassReport: - pass_name: str - proposals: list[ClaimProposal] = field(default_factory=list) - accepted: list[ClaimProposal] = field(default_factory=list) - rejected: list[ClaimProposal] = field(default_factory=list) - conflicts: list[OwnershipConflict] = field(default_factory=list) - invariant_errors: list[str] = field(default_factory=list) +__all__ = ["ResourceRef", "OwnershipConflict", "ClaimProposal", "PassReport"] diff --git a/paperforge/worker/ocr_figures.py b/paperforge/worker/ocr_figures.py index 5aa9eae2..5c03f345 100644 --- a/paperforge/worker/ocr_figures.py +++ b/paperforge/worker/ocr_figures.py @@ -34,10 +34,7 @@ def _has_frontmatter_visual_veto(text: str) -> bool: lower = " ".join(text.lower().split()) if re.search(r"\btoc\b", lower): return True - return any( - phrase in lower - for phrase in _FRONTMATTER_VISUAL_VETO - ) + return any(phrase in lower for phrase in _FRONTMATTER_VISUAL_VETO) _BODY_MENTION_VERBS = ( @@ -194,7 +191,7 @@ def _validate_page_local_caption_grammar( m = _GRAMMAR_PREFIX_PATTERN.search(text) if not m: return "" - prefix_start = text[:m.start(1)] + prefix_start = text[: m.start(1)] return prefix_start.strip().lower().replace(".", "").replace(":", "").replace(" ", "") legend_by_id: dict[str, dict] = {} @@ -319,12 +316,14 @@ def _is_safe_page_assets_group( # 6. Compact geometry: media_blocks must form ONE semantic cluster semantic_clusters = _cluster_semantic_page_assets( - media_blocks, page_blocks, page_width, page_height, + media_blocks, + page_blocks, + page_width, + page_height, ) group_block_ids = {str(b.get("block_id")) for b in media_blocks if b.get("block_id")} cluster_member_ids = [ - {str(b.get("block_id")) for b in cluster if b.get("block_id")} - for cluster in semantic_clusters + {str(b.get("block_id")) for b in cluster if b.get("block_id")} for cluster in semantic_clusters ] if group_block_ids not in cluster_member_ids: return False, ["media_not_compact"] @@ -350,10 +349,7 @@ def _is_safe_page_assets_group( cw = cluster_bbox[2] - cluster_bbox[0] full_width_group = cw >= page_width * 0.65 and page_numbered_legend_count == 1 if not full_width_group: - bands = { - _column_band_id(mb.get("bbox") or [0, 0, 0, 0], page_width) - for mb in media_blocks - } + bands = {_column_band_id(mb.get("bbox") or [0, 0, 0, 0], page_width) for mb in media_blocks} bands.discard(None) if len(bands) > 1: return False, ["cross_column_media"] @@ -397,9 +393,7 @@ def _looks_like_figure_narrative_prose(text: str) -> bool: prose_markers = ["we ", "our ", "this study ", "here we ", "in this "] if any(m in text.lower() for m in prose_markers): return True - if re.search(r"\$?\^\{[^}]+\}\$?", text): - return True - return False + return bool(re.search(r"\$?\^\{[^}]+\}\$?", text)) def _is_body_mention(block: dict) -> bool: @@ -413,9 +407,7 @@ def _is_body_mention(block: dict) -> bool: if raw_role == "figure_caption_candidate": text = block.get("text", "") if text and _FIGURE_NUMBER_PATTERN.search(text): - if _looks_like_inline_figure_mention(text, block): - return True - return False + return _looks_like_inline_figure_mention(text, block) if text and _looks_like_figure_narrative_prose(text): return True if block.get("block_label", "") == "text": @@ -484,10 +476,7 @@ def _is_insufficient_legend_evidence(block: dict) -> bool: return False if style_family != "legend_like": return False - if not _TRUNCATED_LEGEND_ONLY_PATTERN.fullmatch(text): - return False - - return True + return bool(_TRUNCATED_LEGEND_ONLY_PATTERN.fullmatch(text)) def _has_strong_explicit_caption_text(block: dict) -> bool: @@ -541,6 +530,7 @@ def _is_tight_asset_cluster(assets: list[dict], below_top: float) -> bool: # and horizontal spread is within page width limits. return spread_y < (below_top - union_top) * 0.9 and spread_x < 1500 + def _is_formal_legend(text: str, block: dict | None = None, page_width: float = 1200) -> bool: if not text: return False @@ -966,9 +956,7 @@ def _build_semantic_figure_groups_from_assets( g["page_group_count"] = page_group_count g["page_distance_cluster_count"] = page_distance_cluster_count g["safe_auto_match"] = ( - page_group_count == 1 - and g["group_type"] == "distance_cluster" - and len(g.get("media_blocks", [])) >= 2 + page_group_count == 1 and g["group_type"] == "distance_cluster" and len(g.get("media_blocks", [])) >= 2 ) groups.extend(page_groups) @@ -1041,7 +1029,7 @@ def _build_candidate_figure_groups_from_assets( for page, page_groups in groups_by_page.items(): page_blocks = [b for b in all_blocks if int(b.get("page", 0) or 0) == page] page_height = _estimate_page_height(page_blocks) - page_legends = [l for l in legends if l.get("page") == page] + page_legends = [leg for leg in legends if leg.get("page") == page] band_assist = _build_caption_band_group_assist( page_groups, page_legends, @@ -1050,13 +1038,16 @@ def _build_candidate_figure_groups_from_assets( ) for group in page_groups: group["page_legend_count"] = len(page_legends) - group["assist"] = band_assist.get(str(group.get("group_id", "")), { - "caption_band_ids": [], - "best_caption_band_id": None, - "overlap_ratio": 0.0, - "band_overlap": {}, - "evidence": [], - }) + group["assist"] = band_assist.get( + str(group.get("group_id", "")), + { + "caption_band_ids": [], + "best_caption_band_id": None, + "overlap_ratio": 0.0, + "band_overlap": {}, + "evidence": [], + }, + ) return groups @@ -1112,8 +1103,12 @@ def _score_legend_to_group( "evidence": ["page_assets_missing_page_context"], } safe, gate_evidence = _is_safe_page_assets_group( - group, legend, page_blocks, page_numbered_legend_count, - page_width=page_width, page_height=page_height, + group, + legend, + page_blocks, + page_numbered_legend_count, + page_width=page_width, + page_height=page_height, ) if not safe: return { @@ -1191,7 +1186,9 @@ def _make_local_pairing_hypothesis( else: group_page = group.get("page", 0) asset_ids = [ - aid for block_id in group.get("asset_block_ids", []) if (aid := _asset_page_id(group_page, block_id)) is not None + aid + for block_id in group.get("asset_block_ids", []) + if (aid := _asset_page_id(group_page, block_id)) is not None ] return { "legend_block_id": str(legend.get("block_id", "")), @@ -1450,14 +1447,18 @@ def _fallback_can_consume( grouped_asset_page_ids: set[tuple[int, str]] | None = None, allow_grouped: bool = False, ) -> bool: - normalized = [aid for aid in (_asset_page_id(page, block_id) for page, block_id in asset_page_ids) if aid is not None] - return len(_fallback_eligible_asset_page_ids( - normalized, - used_asset_page_ids=used_asset_page_ids, - blocked_asset_page_ids=blocked_asset_page_ids, - grouped_asset_page_ids=grouped_asset_page_ids, - allow_grouped=allow_grouped, - )) == len(normalized) + normalized = [ + aid for aid in (_asset_page_id(page, block_id) for page, block_id in asset_page_ids) if aid is not None + ] + return len( + _fallback_eligible_asset_page_ids( + normalized, + used_asset_page_ids=used_asset_page_ids, + blocked_asset_page_ids=blocked_asset_page_ids, + grouped_asset_page_ids=grouped_asset_page_ids, + allow_grouped=allow_grouped, + ) + ) == len(normalized) def _fallback_eligible_groups( @@ -1477,10 +1478,7 @@ def _fallback_eligible_groups( continue asset_ids = [ aid - for aid in ( - _asset_page_id(group.get("page", 0), bid) - for bid in group.get("asset_block_ids", []) - ) + for aid in (_asset_page_id(group.get("page", 0), bid) for bid in group.get("asset_block_ids", [])) if aid is not None ] if not _fallback_can_consume( @@ -1548,7 +1546,9 @@ def _expand_matched_assets_locally( if touches_stack and wide_enough_overlap: current.append(asset) - ownership.mark_assets_owned([(ap, aid)], owner_id=str(legend.get("block_id", "")), owner_family="figure") + ownership.mark_assets_owned( + [(ap, aid)], owner_id=str(legend.get("block_id", "")), owner_family="figure" + ) changed = True current.sort(key=lambda a: ((a.get("bbox") or [0, 0, 0, 0])[1], (a.get("bbox") or [0, 0, 0, 0])[0])) @@ -1790,7 +1790,9 @@ def _normalized_caption_body(text: str) -> str: return body -def _legend_dedup_priority(legend: dict, *, bundle_source_legend_ids: set[str], assets: list[dict]) -> tuple[int, int, int, int, int]: +def _legend_dedup_priority( + legend: dict, *, bundle_source_legend_ids: set[str], assets: list[dict] +) -> tuple[int, int, int, int, int]: legend_id = str(legend.get("block_id", "")) role = str(legend.get("role") or "") return ( @@ -1857,13 +1859,13 @@ def _build_composite_parent_figure_groups_visual_only( # Union-Find for connected components parent = list(range(n)) - def find(i: int) -> int: + def find(i: int, parent=parent) -> int: while parent[i] != i: parent[i] = parent[parent[i]] i = parent[i] return i - def union(i: int, j: int) -> None: + def union(i: int, j: int, parent=parent) -> None: ri, rj = find(i), find(j) if ri != rj: parent[ri] = rj @@ -1886,7 +1888,7 @@ def _build_composite_parent_figure_groups_visual_only( root = find(i) components.setdefault(root, []).append(i) - for root, indices in components.items(): + for _root, indices in components.items(): if len(indices) < 2: continue child_groups = [page_groups[i] for i in indices] @@ -1894,10 +1896,7 @@ def _build_composite_parent_figure_groups_visual_only( all_assets = [] for g in child_groups: all_assets.extend(g.get("asset_block_ids", [])) - all_bboxes = [ - b for g in child_groups - if (b := g.get("cluster_bbox")) and len(b) >= 4 - ] + all_bboxes = [b for g in child_groups if (b := g.get("cluster_bbox")) and len(b) >= 4] cluster_bbox = _cluster_bbox(all_bboxes) if all_bboxes else [0, 0, 0, 0] # Confidence scoring @@ -1927,21 +1926,23 @@ def _build_composite_parent_figure_groups_visual_only( confidence += 0.05 confidence = min(0.75, confidence) - results.append({ - "group_id": f"composite_parent_{page:04d}_{len(results):03d}", - "group_type": "composite_parent", - "page": page, - "child_group_ids": child_ids, - "asset_block_ids": list(dict.fromkeys(all_assets)), - "cluster_bbox": cluster_bbox, - "parent_evidence": [ - "same_page", - "horizontal_alignment", - f"{len(child_groups)}_child_groups", - ], - "parent_confidence": confidence, - "ownership_enabled": False, - }) + results.append( + { + "group_id": f"composite_parent_{page:04d}_{len(results):03d}", + "group_type": "composite_parent", + "page": page, + "child_group_ids": child_ids, + "asset_block_ids": list(dict.fromkeys(all_assets)), + "cluster_bbox": cluster_bbox, + "parent_evidence": [ + "same_page", + "horizontal_alignment", + f"{len(child_groups)}_child_groups", + ], + "parent_confidence": confidence, + "ownership_enabled": False, + } + ) return results @@ -1949,11 +1950,7 @@ def _build_composite_parent_figure_groups_visual_only( def _compute_grid_score(envelopes: list[dict]) -> float: if len(envelopes) < 2: return 0.0 - bboxes = [ - cb - for env in envelopes - if (cb := env.get("cluster_bbox") or env.get("bbox")) and len(cb) >= 4 - ] + bboxes = [cb for env in envelopes if (cb := env.get("cluster_bbox") or env.get("bbox")) and len(cb) >= 4] if len(bboxes) < 2: return 0.0 y_centers = [(b[1] + b[3]) / 2 for b in bboxes] @@ -2026,48 +2023,46 @@ def _build_dense_composite_parent_candidates( cluster_bbox = _cluster_bbox([e["cluster_bbox"] for e in envelopes]) page_area = page_width * 1600.0 envelope_area = ( - (cluster_bbox[2] - cluster_bbox[0]) * (cluster_bbox[3] - cluster_bbox[1]) - if len(cluster_bbox) >= 4 - else 0.0 + (cluster_bbox[2] - cluster_bbox[0]) * (cluster_bbox[3] - cluster_bbox[1]) if len(cluster_bbox) >= 4 else 0.0 ) compactness = min(1.0, envelope_area / max(1.0, page_area)) grid_score = _compute_grid_score(envelopes) child_group_ids = [str(g.get("group_id", "")) for g in page_groups if g.get("group_id")] - unresolved_cluster_ids = [ - str(uc.get("cluster_id", "")) for uc in page_ucs if uc.get("cluster_id") - ] - all_asset_ids: list[str] = list(dict.fromkeys( - bid for g in page_groups for bid in g.get("asset_block_ids", []) if bid is not None - )) + unresolved_cluster_ids = [str(uc.get("cluster_id", "")) for uc in page_ucs if uc.get("cluster_id")] + all_asset_ids: list[str] = list( + dict.fromkeys(bid for g in page_groups for bid in g.get("asset_block_ids", []) if bid is not None) + ) reason = ["dense_fragment_page", f"{fragment_count}_visual_fragments"] if page_ucs: reason.append(f"{len(page_ucs)}_unresolved_clusters") - results.append({ - "group_id": f"dense_composite_parent_{page:04d}_{len(results):03d}", - "group_type": "composite_parent", - "parent_subtype": "dense_composite", - "page": page, - "child_group_ids": child_group_ids, - "unresolved_cluster_ids": unresolved_cluster_ids, - "asset_block_ids": all_asset_ids, - "embedded_text_block_ids": [], - "cluster_bbox": cluster_bbox, - "parent_evidence": reason, - "parent_confidence": round(grid_score, 4), - "fragment_count": fragment_count, - "atomic_child_count": len(page_groups), - "unresolved_child_count": len(page_ucs), - "visual_mass": float(len(all_asset_ids)), - "compactness": round(compactness, 4), - "grid_score": round(grid_score, 4), - "construction_reason": reason, - "crosses_caption_boundary": False, - "ownership_enabled": False, - }) + results.append( + { + "group_id": f"dense_composite_parent_{page:04d}_{len(results):03d}", + "group_type": "composite_parent", + "parent_subtype": "dense_composite", + "page": page, + "child_group_ids": child_group_ids, + "unresolved_cluster_ids": unresolved_cluster_ids, + "asset_block_ids": all_asset_ids, + "embedded_text_block_ids": [], + "cluster_bbox": cluster_bbox, + "parent_evidence": reason, + "parent_confidence": round(grid_score, 4), + "fragment_count": fragment_count, + "atomic_child_count": len(page_groups), + "unresolved_child_count": len(page_ucs), + "visual_mass": float(len(all_asset_ids)), + "compactness": round(compactness, 4), + "grid_score": round(grid_score, 4), + "construction_reason": reason, + "crosses_caption_boundary": False, + "ownership_enabled": False, + } + ) return results @@ -2128,11 +2123,7 @@ def _should_suppress_panel_title_candidate( return False block_width = bbox[2] - bbox[0] block_page = int(block.get("page", 0) or 0) - page_envelopes = [ - env - for env in visual_envelopes - if int(env.get("page", 0) or 0) == block_page - ] + page_envelopes = [env for env in visual_envelopes if int(env.get("page", 0) or 0) == block_page] inside_envelope = False for env in page_envelopes: eb = env.get("cluster_bbox") or env.get("bbox") or [0, 0, 0, 0] @@ -2147,9 +2138,7 @@ def _should_suppress_panel_title_candidate( break if not inside_envelope: return False - if block_width > page_width * 0.7: - return False - return True + return not (block_width > page_width * 0.7) def _asset_vertical_side(legend: dict, group: dict) -> str: @@ -2225,7 +2214,7 @@ def _partition_assets_by_caption_bands( captions_precede_assets = bool(asset_centers) and min(caption_tops) <= min(asset_centers) boundaries: list[float] = [0.0] - for upper, lower in zip(ordered, ordered[1:]): + for upper, lower in zip(ordered, ordered[1:], strict=False): ub = upper.get("bbox") or [0, 0, 0, 0] lb = lower.get("bbox") or [0, 0, 0, 0] boundaries.append(((ub[1] + ub[3]) / 2 + (lb[1] + lb[3]) / 2) / 2) @@ -2297,9 +2286,7 @@ def _is_structurally_matchable_group(group: dict, *, competing_caption_pages: se cb = group.get("cluster_bbox") if not cb or len(cb) < 4: return False - if group.get("group_type") == "page_assets" and group.get("page") in competing_caption_pages: - return False - return True + return not (group.get("group_type") == "page_assets" and group.get("page") in competing_caption_pages) def _is_unowned_matchable_group( @@ -2314,10 +2301,7 @@ def _is_unowned_matchable_group( if str(group.get("group_id", "")) in used_group_ids: return False g_page = group.get("page", 0) - for bid in group.get("asset_block_ids", []): - if bid and (g_page, bid) in used_asset_page_ids: - return False - return True + return all(not (bid and (g_page, bid) in used_asset_page_ids) for bid in group.get("asset_block_ids", [])) def _build_page_ledger(legends: list[dict], candidate_groups: list[dict]) -> dict[int, dict]: @@ -2484,8 +2468,8 @@ def _reserve_cross_page_objects( if k <= 0: continue page_legends = sorted( - [l for l in legends_by_page.get(page, []) if _is_strong_numbered_legend(l)], - key=lambda l: (l.get("bbox") or [0, 0, 0, 0])[1], + [leg for leg in legends_by_page.get(page, []) if _is_strong_numbered_legend(leg)], + key=lambda leg: (leg.get("bbox") or [0, 0, 0, 0])[1], ) for leg in page_legends[:k]: reserved_legend_ids.add((int(leg.get("page", 0) or 0), str(leg.get("block_id", "")))) @@ -2558,10 +2542,7 @@ def _settle_cross_page_reserved_objects( competing_caption_pages: set[int], page_width: float = 1200, ) -> None: - legends_by_id = { - (int(leg.get("page", 0) or 0), str(leg.get("block_id", ""))): leg - for leg in legends - } + legends_by_id = {(int(leg.get("page", 0) or 0), str(leg.get("block_id", ""))): leg for leg in legends} groups_by_id = {str(g.get("group_id", "")): g for g in candidate_groups} failed_legend_ids: set[tuple[int, str]] = set() @@ -2590,7 +2571,6 @@ def _settle_cross_page_reserved_objects( if not target_groups: continue best_group = target_groups[0] - came_from_reserved = str(best_group.get("group_id", "")) in reserved_group_ids legend_text = str(legend.get("text") or "") fn = _extract_figure_number(legend_text) @@ -2635,8 +2615,7 @@ def _settle_cross_page_reserved_objects( } ) unmatched_legends[:] = [ - u for u in unmatched_legends - if (int(u.get("page", 0) or 0), str(u.get("block_id", ""))) != lid + u for u in unmatched_legends if (int(u.get("page", 0) or 0), str(u.get("block_id", ""))) != lid ] break else: @@ -2660,14 +2639,14 @@ def _settle_cross_page_reserved_objects( continue candidate_legends = sorted( [ - l - for l in legends - if str(l.get("block_id", "")) not in _used_legend_ids - and (int(l.get("page", 0) or 0), str(l.get("block_id", ""))) not in failed_legend_ids - and int(l.get("page", 0) or 0) == np - and _is_strong_numbered_legend(l) + leg + for leg in legends + if str(leg.get("block_id", "")) not in _used_legend_ids + and (int(leg.get("page", 0) or 0), str(leg.get("block_id", ""))) not in failed_legend_ids + and int(leg.get("page", 0) or 0) == np + and _is_strong_numbered_legend(leg) ], - key=lambda l: (l.get("bbox") or [0, 0, 0, 0])[1], + key=lambda leg: (leg.get("bbox") or [0, 0, 0, 0])[1], ) if not candidate_legends: continue @@ -2824,8 +2803,13 @@ def _infer_missing_main_figure_numbers( if not isinstance(asset_block_ids, list) or not asset_block_ids: continue settlement_type = item.get("settlement_type", "") - if settlement_type not in {"same_page", "group_sequential", "cross_page_forward", - "cross_page_backward", "composite_parent"}: + if settlement_type not in { + "same_page", + "group_sequential", + "cross_page_forward", + "cross_page_backward", + "composite_parent", + }: continue item_text = str(item.get("text", "")) legend_text = "" @@ -2978,15 +2962,20 @@ def _infer_missing_main_figure_numbers( return inventory -def build_figure_inventory(structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None) -> dict[str, Any]: +def build_figure_inventory( + structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None +) -> dict[str, Any]: return build_figure_inventory_vnext(structured_blocks, page_width, page_pdf_lines_by_page) -def build_figure_inventory_vnext(structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None) -> dict[str, Any]: + +def build_figure_inventory_vnext( + structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None +) -> dict[str, Any]: + from .ocr_figure_domain import FigureCandidateIndex, FigureCorpus from .ocr_figure_vnext_accounting_pass import FinalAccountingPass from .ocr_figure_vnext_bundle_pass import LegendBundlePass from .ocr_figure_vnext_classic_seq_pass import ClassicSequentialPass, UnresolvedClusterConsolidation from .ocr_figure_vnext_composite_pass import CompositeParentPass - from .ocr_figure_vnext_corpus import FigureCandidateIndex, FigureCorpus from .ocr_figure_vnext_group_seq_pass import GroupSequentialPass from .ocr_figure_vnext_locator_pass import LocatorBridgePass from .ocr_figure_vnext_passes import ( @@ -3005,6 +2994,7 @@ def build_figure_inventory_vnext(structured_blocks: list[dict], page_width: floa if role in {"figure_caption", "figure_caption_candidate"}: text = str(block.get("text", "") or "") from .ocr_figures import _extract_figure_number, _recover_figure_heading_prefix + if _extract_figure_number(text) is None: recovered = _recover_figure_heading_prefix(block, page_pdf_lines_by_page) if recovered: @@ -3013,32 +3003,41 @@ def build_figure_inventory_vnext(structured_blocks: list[dict], page_width: floa corpus = FigureCorpus.from_blocks(structured_blocks, page_width=page_width) candidate_index = FigureCandidateIndex.from_corpus(corpus) state = FigurePipelineState(corpus=corpus, candidate_index=candidate_index, ledger=OwnershipLedger()) - reports = [] - for pass_cls in ( - PrimarySamePagePass, - CompositeParentPass, - SidecarPass, - LocatorBridgePass, - CrossPageReservationPass, - CrossPageSettlementPass, - LegendBundlePass, - GroupSequentialPass, - ClassicSequentialPass, - UnresolvedClusterConsolidation, - FinalAccountingPass, - ): - reports.append(pass_cls().run(state)) + state._match_pre_enricher = _enrich_figure_match_rotation + from .ocr_pairing_framework import run_pairing_passes + + reports = run_pairing_passes( + state, + [ + PrimarySamePagePass, + CompositeParentPass, + SidecarPass, + LocatorBridgePass, + CrossPageReservationPass, + CrossPageSettlementPass, + LegendBundlePass, + GroupSequentialPass, + ClassicSequentialPass, + UnresolvedClusterConsolidation, + FinalAccountingPass, + ], + ) matched_ids = {str(m.get("legend_block_id", "")) for m in state.matches} result = { "pipeline_mode": "vnext", "matched_figures": state.matches, "ambiguous_figures": [], - "unmatched_legends": [b for b in candidate_index.deduped_legends if str(b.get("block_id", "")) not in matched_ids], + "unmatched_legends": [ + b for b in candidate_index.deduped_legends if str(b.get("block_id", "")) not in matched_ids + ], "unmatched_assets": [ - a for a in corpus.raw_assets - if (_resource_page(a) is not None - and state.ledger.owner_of_asset(page=_resource_page(a), block_id=a.get("block_id")) is None) + a + for a in corpus.raw_assets + if ( + _resource_page(a) is not None + and state.ledger.owner_of_asset(page=_resource_page(a), block_id=a.get("block_id")) is None + ) ], "unresolved_clusters": list(state.unresolved), "held_figures": list(candidate_index.held_legends), @@ -3047,7 +3046,8 @@ def build_figure_inventory_vnext(structured_blocks: list[dict], page_width: floa "residual_ledger": {}, "local_pairing_hypotheses": [], "pass_reports": [asdict(r) for r in reports], - "completeness": state.completeness or { + "completeness": state.completeness + or { "total_numbered_legends": len(candidate_index.deduped_legends), "accounted_for": len(state.matches), "details": [], @@ -3057,11 +3057,15 @@ def build_figure_inventory_vnext(structured_blocks: list[dict], page_width: floa # Recover figure numbers from PDF lines inside figure assets if page_pdf_lines_by_page: from .ocr_figures import _recover_missing_figure_numbers_from_assets + _recover_missing_figure_numbers_from_assets(result, page_pdf_lines_by_page) return result -def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None) -> dict[str, Any]: + +def build_figure_inventory_legacy( + structured_blocks: list[dict], page_width: float = 1200, page_pdf_lines_by_page: dict[int, list[dict]] | None = None +) -> dict[str, Any]: """[DEPRECATED] Legacy figure inventory builder — use build_figure_inventory_vnext instead. Retained for comparison tooling (scripts/dev/compare_figure_inventory_legacy_vs_vnext.py). @@ -3110,7 +3114,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo # Re-activating it via geometry/style signals causes body text to leak # into legend matching (e.g. YGH7VEX6 Figure 11). if role == "body_paragraph" and str(block.get("seed_role") or "") in { - "figure_caption_candidate", "figure_caption" + "figure_caption_candidate", + "figure_caption", }: block["_rejected_legend"] = { "reason": "demoted_body_paragraph", @@ -3138,8 +3143,10 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo and _looks_like_figure_description_opening(text) ) if role == "figure_caption_candidate" and ( - (str(block.get("zone") or "") == "body_zone" - and _extract_figure_number(block.get("text", "")) is None) # skips recovery-rescued captions + ( + str(block.get("zone") or "") == "body_zone" + and _extract_figure_number(block.get("text", "")) is None + ) # skips recovery-rescued captions or ( str(block.get("zone") or "") != "display_zone" and str(block.get("style_family") or "") != "legend_like" @@ -3257,9 +3264,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo and not new_is_bundle ): _dedup_map[key] = winner - _same_number_distinct_keys.add( - (ns, fn, int(loser.get("page", 0) or 0), str(loser.get("block_id", ""))) - ) + _same_number_distinct_keys.add((ns, fn, int(loser.get("page", 0) or 0), str(loser.get("block_id", "")))) else: _dedup_map[key] = winner @@ -3355,11 +3360,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo _numbered_pages_early, page_width, ) - _parent_dict = { - str(p.get("group_id", "")): p - for p in composite_parent_candidates - if str(p.get("group_id", "")) - } + _parent_dict = {str(p.get("group_id", "")): p for p in composite_parent_candidates if str(p.get("group_id", ""))} for p in _early_dense_parents: pid = str(p.get("group_id", "")) if pid: @@ -3396,7 +3397,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo remaining_legends.append(leg) legends = remaining_legends ordered_legends = [ - leg for leg in ordered_legends + leg + for leg in ordered_legends if not _should_suppress_panel_title_candidate( leg, page_has_numbered_legend=int(leg.get("page", 0) or 0) in _numbered_pages, @@ -3421,9 +3423,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if not (g.get("group_type") == "page_assets" and g.get("page") in _competing_caption_pages) ] _candidate_groups_by_id = { - str(group.get("group_id", "")): group - for group in candidate_groups - if str(group.get("group_id", "")) + str(group.get("group_id", "")): group for group in candidate_groups if str(group.get("group_id", "")) } # --- Stage 1: page ledger, reservation --- @@ -3455,9 +3455,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo _page_height_by_page: dict[int, float] = {} for page, page_blocks_on_page in _page_blocks_by_page.items(): - explicit = max( - (float(b.get("page_height") or 0)) for b in page_blocks_on_page - ) + explicit = max((float(b.get("page_height") or 0)) for b in page_blocks_on_page) _page_height_by_page[page] = explicit if explicit > 0 else _estimate_page_height(page_blocks_on_page) _numbered_legend_count_by_page: dict[int, int] = {} @@ -3479,10 +3477,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if fig_num is None: ms = legend.get("marker_signature") or {} if ms.get("type") == "figure_number": - try: + with contextlib.suppress(ValueError, TypeError): fig_num = int(float(ms.get("number", 0) or 0)) - except (ValueError, TypeError): - pass is_validation_first_candidate = _is_validation_first_legend_candidate(legend) is_weak_truncated = _is_insufficient_legend_evidence(legend) @@ -3501,7 +3497,6 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if caption_score.get("decision") == "rejected": caption_score["decision"] = "candidate" - candidates = [] anchor_supported = _has_anchor_supported_legend_context(legend) caption_text_supported = _has_strong_explicit_caption_text(legend) @@ -3518,7 +3513,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if fig_num is not None: _page_parents = [ - cp for cp in composite_parent_candidates + cp + for cp in composite_parent_candidates if cp.get("page") == legend_page and not cp.get("ownership_consumed", False) and not ( @@ -3542,9 +3538,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo for child_gid in _best_parent.get("child_group_ids", []) if child_gid in _candidate_groups_by_id and str( - ( - _candidate_groups_by_id[child_gid].get("assist", {}) or {} - ).get("best_caption_band_id") or "" + (_candidate_groups_by_id[child_gid].get("assist", {}) or {}).get("best_caption_band_id") or "" ) == legend_id ] @@ -3557,18 +3551,17 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo # For dense parents with a single caption, consume all child groups. # With competing captions, keep caption-band scoping. _effective_child_groups = ( - _all_child_groups if (_is_dense and not _has_competing_caption) + _all_child_groups + if (_is_dense and not _has_competing_caption) else (_matching_child_groups or _all_child_groups) ) _effective_child_group_ids = [ - str(group.get("group_id", "")) for group in _effective_child_groups if str(group.get("group_id", "")) + str(group.get("group_id", "")) + for group in _effective_child_groups + if str(group.get("group_id", "")) ] _effective_asset_ids = list( - dict.fromkeys( - bid - for group in _effective_child_groups - for bid in group.get("asset_block_ids", []) - ) + dict.fromkeys(bid for group in _effective_child_groups for bid in group.get("asset_block_ids", [])) ) _band_scoped_parent = len(_matching_child_groups) >= 2 _dense_parent_unresolved_count = int(_best_parent.get("unresolved_child_count", 0) or 0) @@ -3628,7 +3621,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo "settlement_type": "composite_parent", } ) - unmatched_legends = [l for l in unmatched_legends if l.get("block_id") != legend.get("block_id")] + unmatched_legends = [leg for leg in unmatched_legends if leg.get("block_id") != legend.get("block_id")] continue # skip normal same-page candidate scan for this legend # --- end P1B composite parent arbitration --- @@ -3657,7 +3650,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if _group_asset_ids: _hint_map = {str(a.get("block_id", "")): a for a in assets} _table_like_count = sum( - 1 for bid in _group_asset_ids + 1 + for bid in _group_asset_ids if _hint_map.get(str(bid), {}).get("asset_family_hint") == "table_like" and float(_hint_map.get(str(bid), {}).get("asset_family_confidence", 0) or 0) >= 0.70 ) @@ -3775,7 +3769,9 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo else: matched_assets = best_group.get("media_blocks", []) g_page = best_group.get("page", 0) - ownership.match_group(best_group, owner_id=str(legend.get("block_id", "")), owner_family="figure") + ownership.match_group( + best_group, owner_id=str(legend.get("block_id", "")), owner_family="figure" + ) matched_assets = _expand_matched_assets_locally( legend, matched_assets, @@ -3831,7 +3827,9 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo else: matched_assets = best_group.get("media_blocks", []) g_page = best_group.get("page", 0) - ownership.match_group(best_group, owner_id=str(legend.get("block_id", "")), owner_family="figure") + ownership.match_group( + best_group, owner_id=str(legend.get("block_id", "")), owner_family="figure" + ) matched_assets = _expand_matched_assets_locally( legend, matched_assets, @@ -3983,7 +3981,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo "page": legend_page, "text": legend_text, "figure_number": fig_num, - "matched_assets": [_project_asset_record(a) for a in matched_assets], + "matched_assets": [_project_asset_record(a) for a in matched_assets], "group_type": region_match.get("group_type", "") if region_match is not None else "", "group_evidence": region_match.get("group_evidence", []) if region_match is not None else [], "confidence": match_score["score"], @@ -3992,7 +3990,9 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo "caption_score": caption_score, "legend_page": legend_page, "asset_pages": sorted({int(a.get("page", 0) or 0) for a in matched_assets}) or [legend_page], - "settlement_type": "same_page_rotated" if region_match and region_match.get("rotation_correction_deg") else "same_page", + "settlement_type": "same_page_rotated" + if region_match and region_match.get("rotation_correction_deg") + else "same_page", } if region_match and region_match.get("rotation_correction_deg"): entry["rotation_correction_deg"] = region_match["rotation_correction_deg"] @@ -4099,7 +4099,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo # when the normal spatial matching violates vertical ordering (top # caption should own top assets, bottom caption bottom assets). nid_set = {str(cap.get("block_id", "")) for cap in narrow_set} - page_unmatched = any(str(l.get("block_id", "")) in nid_set for l in unmatched_legends) + page_unmatched = any(str(leg.get("block_id", "")) in nid_set for leg in unmatched_legends) page_ambiguous = any(str(af.get("legend_block_id", "")) in nid_set for af in ambiguous_figures) def _median_y(items: list[dict]) -> float: @@ -4108,9 +4108,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo page_narrow_matched = [mf for mf in matched_figures if str(mf.get("legend_block_id", "")) in nid_set] page_unresolved_legend_ids = { - str(item.get("block_id", "")) - for item in unmatched_legends - if str(item.get("block_id", "")) in nid_set + str(item.get("block_id", "")) for item in unmatched_legends if str(item.get("block_id", "")) in nid_set } | { str(item.get("legend_block_id", "")) for item in ambiguous_figures @@ -4132,8 +4130,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo (int(a.get("page", mf.get("page", sidecar_page)) or 0), str(a.get("block_id", ""))) for mf in page_narrow_matched for a in mf.get("matched_assets", []) - if a.get("block_id") not in (None, "") - and str(mf.get("legend_block_id", "")) not in protected_by_legend_id + if a.get("block_id") not in (None, "") and str(mf.get("legend_block_id", "")) not in protected_by_legend_id } violation = len(page_narrow_matched) != len(narrow_set) if not violation and len(page_narrow_matched) > 1: @@ -4164,9 +4161,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo sidecar_promoted: list[dict] = [] sidecar_consumed_ids: set[tuple] = set() page_narrow_matched_by_legend = { - str(mf.get("legend_block_id", "")): mf - for mf in page_narrow_matched - if str(mf.get("legend_block_id", "")) + str(mf.get("legend_block_id", "")): mf for mf in page_narrow_matched if str(mf.get("legend_block_id", "")) } for cap in narrow_set: lid = str(cap.get("block_id", "")) @@ -4174,7 +4169,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo fig_num = _extract_figure_number(cap_text) cap_ns = _extract_figure_namespace(cap_text) current_match = page_narrow_matched_by_legend.get(lid) - cap_is_unresolved = any(str(l.get("block_id", "")) == lid for l in unmatched_legends) or any( + cap_is_unresolved = any(str(leg.get("block_id", "")) == lid for leg in unmatched_legends) or any( str(af.get("legend_block_id", "")) == lid for af in ambiguous_figures ) if lid in protected_by_legend_id: @@ -4185,7 +4180,8 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo asset for asset in band_map.get(lid, []) if (int(asset.get("page", 0) or 0), str(asset.get("block_id", ""))) not in protected_asset_page_ids - and (int(asset.get("page", 0) or 0), str(asset.get("block_id", ""))) not in hypothesis_protected_asset_page_ids + and (int(asset.get("page", 0) or 0), str(asset.get("block_id", ""))) + not in hypothesis_protected_asset_page_ids ] # In sidecar mode _partition_assets_by_caption_bands is the # ownership unit. Row-coupled geometry is too strict for @@ -4298,7 +4294,9 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo ul for ul in unmatched_legends if str(ul.get("block_id", "")) != str(legend.get("block_id", "")) ] matched_figures.extend(sidecar_promoted) - ownership.mark_assets_owned(list(sidecar_consumed_ids), owner_id=f"sidecar_page_{sidecar_page}", owner_family="figure") + ownership.mark_assets_owned( + list(sidecar_consumed_ids), owner_id=f"sidecar_page_{sidecar_page}", owner_family="figure" + ) # Preproof legend-bundling: when a page packs 3+ figure captions # with zero same-page assets, match them 1:1 by page order to @@ -4320,10 +4318,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if _extract_figure_number(str(leg.get("text", ""))) is not None: page_captions.setdefault(cp, []).append(leg) for cp, caps in sorted(page_captions.items()): - has_bundle_source = any( - str(cap.get("block_id", "")) in bundle_source_legend_ids - for cap in caps - ) + has_bundle_source = any(str(cap.get("block_id", "")) in bundle_source_legend_ids for cap in caps) if len(caps) < 3 and not has_bundle_source: continue page_has_assets = any(a.get("page", 0) == cp for a in unmatched_assets) @@ -4392,9 +4387,11 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo for ast in page_assets: bid = ast.get("block_id", "") if bid: - ownership.mark_assets_owned([(ap, bid)], owner_id=str(cap.get("block_id", "")), owner_family="figure") + ownership.mark_assets_owned( + [(ap, bid)], owner_id=str(cap.get("block_id", "")), owner_family="figure" + ) consumed.append(_project_asset_record(ast)) - unmatched_legends = [l for l in unmatched_legends if l.get("block_id") != cap.get("block_id")] + unmatched_legends = [leg for leg in unmatched_legends if leg.get("block_id") != cap.get("block_id")] cp_page = int(cap.get("page", 0) or 0) matched_figures.append( { @@ -4423,7 +4420,6 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo } ambiguous_figures[:] = [a for a in ambiguous_figures if a.get("legend_block_id") not in bundle_legend_ids] - # === Previous-page legend locator bridge === # Some papers use a short locator caption like "Fig. 10 (See legend on previous page.)" # on the figure's page instead of a full legend. The full legend lives on the preceding @@ -4490,7 +4486,6 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if full_legend is None: continue - # Find visual group on locator's page: # 1) Priority: candidate_groups (distance_cluster, composite_parent) # 2) Fallback: only if there's one tight cluster above locator @@ -4509,18 +4504,13 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo if len(g_bbox) < 4 or g_bbox[3] > locator_top: continue g_asset_ids = g.get("asset_block_ids", []) - g_unowned = [ - bid for bid in g_asset_ids - if (locator_page, str(bid)) not in used_asset_page_ids - ] + g_unowned = [bid for bid in g_asset_ids if (locator_page, str(bid)) not in used_asset_page_ids] if not g_unowned: continue g_type = g.get("group_type", "") g_dist = abs(g_bbox[3] - locator_top) score = ( - 0 if g_type == "composite_parent" else - 1 if g_type == "distance_cluster" else - 2, + 0 if g_type == "composite_parent" else 1 if g_type == "distance_cluster" else 2, -len(g_unowned), g_dist, ) @@ -4532,18 +4522,19 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo best = scored_groups[0] g_unowned = best[2] best_group_assets = [ - a for a in _filter_figure_assets(assets) - if int(a.get("page", 0) or 0) == locator_page - and str(a.get("block_id", "")) in g_unowned + a + for a in _filter_figure_assets(assets) + if int(a.get("page", 0) or 0) == locator_page and str(a.get("block_id", "")) in g_unowned ] # Fallback: no candidate group, but one tight asset cluster above locator if not best_group_assets: page_assets = [ - a for a in _unowned_by_page.get(locator_page, []) + a + for a in _unowned_by_page.get(locator_page, []) if (locator_page, str(a.get("block_id", ""))) not in used_asset_page_ids ] - above = [a for a in page_assets if (a.get("bbox") or [0,0,0,0])[3] <= locator_top] + above = [a for a in page_assets if (a.get("bbox") or [0, 0, 0, 0])[3] <= locator_top] if above and _is_tight_asset_cluster(above, locator_top): best_group_assets = above @@ -4554,10 +4545,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo fig_id = _format_figure_id(ns, fn) consumed = [_project_asset_record(a) for a in best_group_assets] # Compute cluster_bbox from consumed asset bboxes - asset_bboxes = [ - a.get("bbox") or a.get("block_bbox") or [0, 0, 0, 0] - for a in best_group_assets - ] + asset_bboxes = [a.get("bbox") or a.get("block_bbox") or [0, 0, 0, 0] for a in best_group_assets] valid_bboxes = [b for b in asset_bboxes if len(b) >= 4 and b[2] > b[0] and b[3] > b[1]] cluster_bbox = _cluster_bbox(valid_bboxes) if valid_bboxes else [0, 0, 0, 0] @@ -4575,49 +4563,59 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo str(full_legend.get("block_id", "")), ) unmatched_legends = [ - l for l in unmatched_legends - if (int(l.get("page", 0) or 0), str(l.get("block_id", ""))) != full_key + leg + for leg in unmatched_legends + if (int(leg.get("page", 0) or 0), str(leg.get("block_id", ""))) != full_key ] # Remove consumed assets from unmatched_assets consumed_ids = {(locator_page, str(a.get("block_id", ""))) for a in best_group_assets} unmatched_assets = [ - a for a in unmatched_assets + a + for a in unmatched_assets if (int(a.get("page", 0) or 0), str(a.get("block_id", ""))) not in consumed_ids ] - matched_figures.append({ - "figure_id": fig_id, - "figure_namespace": ns, - "legend_block_id": full_legend.get("block_id", ""), - "legend_page": prev_page, - "text": str(full_legend.get("text", "")), - "figure_number": fn, - "matched_assets": consumed, - "asset_block_ids": [c["block_id"] for c in consumed], - "cluster_bbox": cluster_bbox, - "group_type": "previous_page_locator_bridge", - "group_evidence": ["explicit_previous_page_locator", "previous_page_full_legend", "same_page_visual_group"], - "bridge_block_ids": [str(locator.get("block_id", ""))], - "caption_score": score_figure_caption( - full_legend, nearby_media=True, caption_style_match=False, body_prose_likelihood=False - ), - "match_score": {"score": 0.5, "decision": "matched", "evidence": ["previous_page_locator_bridge"]}, - "confidence": 0.5, - "flags": ["previous_page_locator_match"], - "page": locator_page, - "locator_block_id": locator.get("block_id", ""), - "locator_page": locator_page, - "asset_pages": [locator_page], - "settlement_type": "previous_page_legend_locator", - }) + matched_figures.append( + { + "figure_id": fig_id, + "figure_namespace": ns, + "legend_block_id": full_legend.get("block_id", ""), + "legend_page": prev_page, + "text": str(full_legend.get("text", "")), + "figure_number": fn, + "matched_assets": consumed, + "asset_block_ids": [c["block_id"] for c in consumed], + "cluster_bbox": cluster_bbox, + "group_type": "previous_page_locator_bridge", + "group_evidence": [ + "explicit_previous_page_locator", + "previous_page_full_legend", + "same_page_visual_group", + ], + "bridge_block_ids": [str(locator.get("block_id", ""))], + "caption_score": score_figure_caption( + full_legend, nearby_media=True, caption_style_match=False, body_prose_likelihood=False + ), + "match_score": {"score": 0.5, "decision": "matched", "evidence": ["previous_page_locator_bridge"]}, + "confidence": 0.5, + "flags": ["previous_page_locator_match"], + "page": locator_page, + "locator_block_id": locator.get("block_id", ""), + "locator_page": locator_page, + "asset_pages": [locator_page], + "settlement_type": "previous_page_legend_locator", + } + ) # Clean up ambiguous_figures that referenced the locator (page-aware) locator_key = (locator_page, str(locator.get("block_id", ""))) ambiguous_figures[:] = [ - af for af in ambiguous_figures + af + for af in ambiguous_figures if ( int(af.get("page", 0) or 0), str(af.get("legend_block_id", "")), - ) != locator_key + ) + != locator_key ] # === Group-aware sequential fallback === @@ -4710,7 +4708,9 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo asset = local_asset_by_page_id.get((group_page, str(bid))) if asset: group_assets.append(asset) - ownership.mark_assets_owned([(group_page, str(bid))], owner_id=str(legend.get("block_id", "")), owner_family="figure") + ownership.mark_assets_owned( + [(group_page, str(bid))], owner_id=str(legend.get("block_id", "")), owner_family="figure" + ) if not group_assets: continue @@ -4723,7 +4723,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo "page": group_page, "text": cap_text, "figure_number": fn, - "matched_assets": [_project_asset_record(a) for a in group_assets], + "matched_assets": [_project_asset_record(a) for a in group_assets], "asset_block_ids": [str(a.get("block_id", "")) for a in group_assets], "bridge_block_ids": [], "group_type": best_group.get("group_type", ""), @@ -4782,8 +4782,6 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo cap_ns = _extract_figure_namespace(cap_text) cp = cap.get("page", 0) or 0 - cap_bbox = cap.get("bbox") or [0, 0, 0, 0] - cap_top = cap_bbox[1] if len(cap_bbox) >= 4 else 0 previous_page_asset = None future_page_asset = None scan_index = ai @@ -4854,9 +4852,11 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo } ) if asset_bid: - ownership.mark_assets_owned([(asset_page, asset_bid)], owner_id=str(cap.get("block_id", "")), owner_family="figure") + ownership.mark_assets_owned( + [(asset_page, asset_bid)], owner_id=str(cap.get("block_id", "")), owner_family="figure" + ) for cap, asset in seq_matched: - unmatched_legends[:] = [l for l in unmatched_legends if l is not cap] + unmatched_legends[:] = [leg for leg in unmatched_legends if leg is not cap] if int(asset.get("page", 0) or 0) < int(cap.get("page", 0) or 0): ambiguous_figures[:] = [ af for af in ambiguous_figures if str(af.get("legend_block_id", "")) != str(cap.get("block_id", "")) @@ -4885,13 +4885,10 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo ) if unresolved_clusters: consumed = { - (int(uc.get("page", 0) or 0), str(bid)) - for uc in unresolved_clusters - for bid in uc["media_block_ids"] + (int(uc.get("page", 0) or 0), str(bid)) for uc in unresolved_clusters for bid in uc["media_block_ids"] } unmatched_assets = [ - a for a in unmatched_assets - if (int(a.get("page", 0) or 0), str(a.get("block_id", ""))) not in consumed + a for a in unmatched_assets if (int(a.get("page", 0) or 0), str(a.get("block_id", ""))) not in consumed ] unmatched_assets = _recompute_final_unmatched_assets(assets, used_asset_page_ids, unresolved_clusters) @@ -4918,9 +4915,7 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo # parent candidate exists, leftover unmatched assets are grouped into # unresolved clusters --- _dense_parent_pages = { - int(p.get("page", 0) or 0) - for p in composite_parent_candidates - if p.get("parent_subtype") == "dense_composite" + int(p.get("page", 0) or 0) for p in composite_parent_candidates if p.get("parent_subtype") == "dense_composite" } if unmatched_assets and _dense_parent_pages: for cluster in _media_clusters(unmatched_assets, page_width): @@ -4942,19 +4937,16 @@ def build_figure_inventory_legacy(structured_blocks: list[dict], page_width: flo ) if unresolved_clusters: consumed_dense = { - (int(uc.get("page", 0) or 0), str(bid)) - for uc in unresolved_clusters - for bid in uc["media_block_ids"] + (int(uc.get("page", 0) or 0), str(bid)) for uc in unresolved_clusters for bid in uc["media_block_ids"] } unmatched_assets = [ - a for a in unmatched_assets + a + for a in unmatched_assets if (int(a.get("page", 0) or 0), str(a.get("block_id", ""))) not in consumed_dense ] # --- P2: page-local caption grammar validation --- - local_pairing_hypotheses = _validate_page_local_caption_grammar( - local_pairing_hypotheses, ordered_legends - ) + local_pairing_hypotheses = _validate_page_local_caption_grammar(local_pairing_hypotheses, ordered_legends) # --- Remove blocks already matched to figures from unresolved clusters # (clusters are built before matching completes; dedup afterward) --- @@ -5252,7 +5244,6 @@ def _promote_sequence_matches(figure_inventory: dict, blocks: list[dict]) -> dic return figure_inventory - def _collect_matched_figure_asset_ids_from_list(matched_figures: list[dict]) -> set[tuple[int, str]]: consumed: set[tuple[int, str]] = set() for fig in matched_figures: @@ -5288,7 +5279,8 @@ def _dedup_unmatched_assets_against_matched_figures(inventory: dict) -> None: if not consumed: return inventory["unmatched_assets"] = [ - a for a in inventory.get("unmatched_assets", []) or [] + a + for a in inventory.get("unmatched_assets", []) or [] if (int(a.get("page", 0) or 0), str(a.get("block_id", "") or "")) not in consumed ] @@ -5300,8 +5292,7 @@ def _dedup_unresolved_clusters_against_matched_figures(inventory: dict) -> None: cleaned = [] for cluster in inventory.get("unresolved_clusters", []) or []: page = int(cluster.get("page", 0) or 0) - kept = [str(bid) for bid in (cluster.get("media_block_ids", []) or []) - if (page, str(bid)) not in consumed] + kept = [str(bid) for bid in (cluster.get("media_block_ids", []) or []) if (page, str(bid)) not in consumed] if not kept: continue cluster = dict(cluster) @@ -5309,6 +5300,7 @@ def _dedup_unresolved_clusters_against_matched_figures(inventory: dict) -> None: cleaned.append(cluster) inventory["unresolved_clusters"] = cleaned + def _collect_figure_owned_asset_ids(figure_inventory: dict) -> set[tuple[int, str]]: return _collect_matched_figure_asset_ids(figure_inventory) @@ -5323,6 +5315,7 @@ def _collect_table_owned_asset_ids(table_inventory: dict) -> set[tuple[int, str] owned.add(asset_id) return owned + def _table_ownership_strength(table: dict) -> tuple[int, int]: explicit = 1 if str(table.get("caption_text") or "").lower().startswith("table") else 0 strong = 1 if str(table.get("match_status") or "") == "matched" else 0 @@ -5353,9 +5346,7 @@ def resolve_media_asset_conflicts(figure_inventory: dict, table_inventory: dict) kept_figures = [] for fig in figure_inventory.get("matched_figures", []): asset_ids = [ - (int(fig.get("page", 0) or 0), str(bid)) - for bid in fig.get("asset_block_ids", []) - if bid is not None + (int(fig.get("page", 0) or 0), str(bid)) for bid in fig.get("asset_block_ids", []) if bid is not None ] conflict_id = next((aid for aid in asset_ids if aid in tables_by_asset), None) if conflict_id is None: @@ -5383,7 +5374,6 @@ def resolve_media_asset_conflicts(figure_inventory: dict, table_inventory: dict) return resolutions - def _build_ownership_conflicts(figure_inventory: dict, table_inventory: dict) -> list[dict]: figure_owned = _collect_figure_owned_asset_ids(figure_inventory) table_owned = _collect_table_owned_asset_ids(table_inventory) @@ -5421,10 +5411,17 @@ def write_back_figure_roles(inventory: dict, structured_blocks: list[dict]) -> N _LEAK_ROLES = { - "body_paragraph", "section_heading", "subsection_heading", - "sub_subsection_heading", "backmatter_heading", "backmatter_body", - "tail_candidate_body", "footnote", "structured_insert", - "non_body_insert", "frontmatter_noise", + "body_paragraph", + "section_heading", + "subsection_heading", + "sub_subsection_heading", + "backmatter_heading", + "backmatter_body", + "tail_candidate_body", + "footnote", + "structured_insert", + "non_body_insert", + "frontmatter_noise", } @@ -5438,9 +5435,7 @@ def _container_area_ok(container_bbox: list[float], page_width: float, page_heig container_area = max(1.0, cw * ch) if container_area >= page_area * 0.65: return False - if cw >= page_width * 0.98 and ch >= page_height * 0.45: - return False - return True + return not (cw >= page_width * 0.98 and ch >= page_height * 0.45) def _container_has_media_asset(container_bbox: list[float], page_blocks: list[dict]) -> bool: @@ -5502,16 +5497,14 @@ def _cluster_bboxes_by_proximity( ax1, ay1, ax2, ay2 = bboxes[i] for j in range(i + 1, n): bx1, by1, bx2, by2 = bboxes[j] - if (max(ax1, bx1) - margin < min(ax2, bx2) + margin - and max(ay1, by1) - margin < min(ay2, by2) + margin): + if max(ax1, bx1) - margin < min(ax2, bx2) + margin and max(ay1, by1) - margin < min(ay2, by2) + margin: _union(i, j) clusters: dict[int, list[list[float]]] = {} for i in range(n): clusters.setdefault(_find(i), []).append(bboxes[i]) return [ - [min(b[0] for b in g), min(b[1] for b in g), - max(b[2] for b in g), max(b[3] for b in g)] + [min(b[0] for b in g), min(b[1] for b in g), max(b[2] for b in g), max(b[3] for b in g)] for g in clusters.values() ] @@ -5609,7 +5602,8 @@ def tag_figure_contained_text( if not _highly_overlaps_any_matched_region(cr, figure_regions): figure_regions.append(("container", cr)) fallback_assets = [ - b for b in page_blocks + b + for b in page_blocks if (int(b.get("page", 0) or 0), str(b.get("block_id", ""))) not in covered_asset_keys and b.get("role") in {"figure_asset", "media_asset"} and b.get("role") not in {"table_html", "table_asset"} @@ -5630,10 +5624,17 @@ def tag_figure_contained_text( if block.get("_object_owner_family") == "author_bio" or block.get("_excluded_from_figure_inventory"): continue role = str(block.get("role") or "") - if role in {"figure_asset", "media_asset", "noise", "author_bio_asset", - "figure_caption", "figure_caption_candidate", - "table_html", "table_asset", - "figure_inner_text"}: + if role in { + "figure_asset", + "media_asset", + "noise", + "author_bio_asset", + "figure_caption", + "figure_caption_candidate", + "table_html", + "table_asset", + "figure_inner_text", + }: continue bbox = block.get("bbox") if not bbox or len(bbox) < 4: @@ -5649,10 +5650,11 @@ def tag_figure_contained_text( def write_figure_inventory(dst: Path, inventory: dict[str, Any]) -> None: write_json(dst, inventory) + def _is_synthetic_vector_caption_candidate(caption: dict) -> bool: text = str(caption.get("text") or "") - return bool(_FIGURE_DESCRIPTION_OPENING.match(text.strip())) \ - or bool(_extract_figure_number(text) is not None) + return bool(_FIGURE_DESCRIPTION_OPENING.match(text.strip())) or bool(_extract_figure_number(text) is not None) + def _caption_has_rotated_text(caption: dict) -> bool: span = caption.get("span_metadata") or [] @@ -5684,10 +5686,7 @@ def _rotate_rect_within_union(rect: list[float], union: list[float], *, clockwis (rx2 - ux1, ry2 - uy1), (rx1 - ux1, ry2 - uy1), ] - if clockwise: - rotated = [(height - y, x) for x, y in pts] - else: - rotated = [(y, width - x) for x, y in pts] + rotated = [(height - y, x) for x, y in pts] if clockwise else [(y, width - x) for x, y in pts] xs = [p[0] for p in rotated] ys = [p[1] for p in rotated] return [min(xs), min(ys), max(xs), max(ys)] @@ -5723,6 +5722,41 @@ def _prepare_rotated_caption_normalization(legend: dict, asset: dict) -> dict | } +def _enrich_figure_match_rotation(proposal, match_record, state) -> None: + """Detect rotated caption and add rotation_correction_deg + cluster_bbox. + + Standalone enrichment intended to be wired as ``state._match_pre_enricher`` + in the figure pipeline so the generic pairing state stays domain-neutral. + + This is the extracted body of the old ``FigurePipelineState._enrich_rotation``, + now living in the figure domain where it belongs. + """ + if not state.corpus or not proposal.legends: + return + legend_ref = proposal.legends[0] + legend_block = None + for b in state.corpus.blocks: + if str(b.get("block_id", "")) == str(legend_ref.block_id) and b.get("page") == legend_ref.page: + legend_block = b + break + if legend_block is None or not _caption_has_rotated_text(legend_block): + return + if not proposal.assets or not state.corpus.raw_assets: + return + asset_ref = proposal.assets[0] + asset_block = None + for a in state.corpus.raw_assets: + if str(a.get("block_id", "")) == str(asset_ref.block_id) and a.get("page") == asset_ref.page: + asset_block = a + break + if asset_block is None: + return + normalized = _prepare_rotated_caption_normalization(legend_block, asset_block) + if normalized is not None: + match_record["rotation_correction_deg"] = normalized["rotation_correction_deg"] + match_record["cluster_bbox"] = normalized["rotation_union_bbox"] + + def _score_legend_to_asset_with_orientation( legend: dict, asset: dict, @@ -5764,7 +5798,6 @@ def _score_legend_to_asset_with_orientation( ) - def _score_caption_to_unmatched_asset_for_synthetic(caption: dict, asset: dict) -> float: cb = caption.get("bbox") or caption.get("block_bbox") or [0, 0, 0, 0] ab = asset.get("bbox") or asset.get("block_bbox") or [0, 0, 0, 0] @@ -5824,11 +5857,14 @@ def _build_bbox_only_synthetic_figure(caption, asset, *, index, score): fig_id = _format_figure_id(ns, fn) if fn is not None else f"synthetic_figure_p{page}_{asset.get('block_id', index)}" normalized = _prepare_rotated_caption_normalization(caption, asset) entry = { - "figure_id": fig_id, "figure_namespace": ns, + "figure_id": fig_id, + "figure_namespace": ns, "legend_block_id": caption.get("block_id", ""), - "page": page, "legend_page": int(caption.get("page", 0) or 0), + "page": page, + "legend_page": int(caption.get("page", 0) or 0), "asset_pages": [page] if page else [], - "text": text, "figure_number": fn, + "text": text, + "figure_number": fn, "matched_assets": [asset_record], "asset_block_ids": [asset_record.get("block_id", "")], "cluster_bbox": ( @@ -5842,8 +5878,7 @@ def _build_bbox_only_synthetic_figure(caption, asset, *, index, score): caption_style_match=False, body_prose_likelihood=False, ), - "match_score": {"score": score, "decision": "matched", - "evidence": ["bbox_only_synthetic_vector_fallback"]}, + "match_score": {"score": score, "decision": "matched", "evidence": ["bbox_only_synthetic_vector_fallback"]}, "confidence": min(0.55, score), "flags": ["synthetic_vector_asset", "bbox_only_asset"], "truth_source": "vector_bbox", @@ -5859,12 +5894,18 @@ def _build_bbox_only_synthetic_figure(caption, asset, *, index, score): def _apply_bbox_only_synthetic_vector_fallback( - *, matched_figures, unmatched_legends, rejected_legends, unmatched_assets, ownership, + *, + matched_figures, + unmatched_legends, + rejected_legends, + unmatched_assets, + ownership, ) -> None: if not unmatched_assets: return - candidates = [c for c in list(unmatched_legends) + list(rejected_legends) - if _is_synthetic_vector_caption_candidate(c)] + candidates = [ + c for c in list(unmatched_legends) + list(rejected_legends) if _is_synthetic_vector_caption_candidate(c) + ] if not candidates: return @@ -5890,11 +5931,14 @@ def _apply_bbox_only_synthetic_vector_fallback( continue page_assets = [ - a for a in unmatched_assets + a + for a in unmatched_assets if int(a.get("page", 0) or 0) == cap_page and str(a.get("role") or "") in {"media_asset", "figure_asset"} - and (a.get("asset_family_hint") == "figure_like" - or str(a.get("raw_label") or "") in {"image", "chart", "figure"}) + and ( + a.get("asset_family_hint") == "figure_like" + or str(a.get("raw_label") or "") in {"image", "chart", "figure"} + ) ] scored = [] for asset in page_assets: @@ -5932,14 +5976,20 @@ def _apply_bbox_only_synthetic_vector_fallback( # Clean up consumed legends and assets if used_caption_ids: - unmatched_legends[:] = [c for c in unmatched_legends if str(c.get("block_id", "") or "") not in used_caption_ids] + unmatched_legends[:] = [ + c for c in unmatched_legends if str(c.get("block_id", "") or "") not in used_caption_ids + ] rejected_legends[:] = [c for c in rejected_legends if str(c.get("block_id", "") or "") not in used_caption_ids] if used_asset_ids: - unmatched_assets[:] = [a for a in unmatched_assets if (int(a.get("page", 0) or 0), str(a.get("block_id", "") or "")) not in used_asset_ids] + unmatched_assets[:] = [ + a + for a in unmatched_assets + if (int(a.get("page", 0) or 0), str(a.get("block_id", "") or "")) not in used_asset_ids + ] + + # === Asset-internal figure number recovery === -_FIGURE_DESCRIPTION_OPENING = re.compile( - r"^(this|the)\s+figure\b", re.IGNORECASE -) +_FIGURE_DESCRIPTION_OPENING = re.compile(r"^(this|the)\s+figure\b", re.IGNORECASE) _INTERNAL_FIGURE_LABEL_PATTERN = re.compile( r"^(?:Figure|Fig\.?)\s+(\d+(?:\.\d+)?)(?:[A-Za-z])?" @@ -5956,9 +6006,7 @@ def _looks_like_internal_figure_label(text: str) -> bool: if not _INTERNAL_FIGURE_LABEL_PATTERN.match(stripped): return False lower = stripped.lower() - if re.match(r"^(?:figure|fig\.?)\s+\d+\s+(?:shows|showed|demonstrates|illustrates|indicates)\b", lower): - return False - return True + return not re.match(r"^(?:figure|fig\.?)\s+\d+\s+(?:shows|showed|demonstrates|illustrates|indicates)\b", lower) def _needs_asset_internal_figure_number_recovery(fig: dict) -> bool: @@ -6023,8 +6071,7 @@ def _asset_edge_band_score(line_bbox, asset_bbox) -> float: right_dist = abs(cx - ax2) top_dist = abs(cy - ay1) bottom_dist = abs(cy - ay2) - edge_dist = min(left_dist / asset_w, right_dist / asset_w, - top_dist / asset_h, bottom_dist / asset_h) + edge_dist = min(left_dist / asset_w, right_dist / asset_w, top_dist / asset_h, bottom_dist / asset_h) if edge_dist <= 0.08: return 1.0 if edge_dist <= 0.15: @@ -6041,7 +6088,9 @@ def _iter_matched_figure_assets(fig: dict) -> list[dict]: def _recover_asset_internal_figure_number( - pdf_lines: list[dict], asset: dict, existing_numbers: set, + pdf_lines: list[dict], + asset: dict, + existing_numbers: set, ) -> dict | None: """Scan pdf_lines for a figure label inside asset bbox. Returns recovery dict with figure_number, text, bbox, figure_namespace, or None. @@ -6065,13 +6114,15 @@ def _recover_asset_internal_figure_number( number = int(m.group(1)) edge_score = _asset_edge_band_score(lb, ab) if edge_score > 0: - candidates.append({ - "figure_namespace": "figure", - "figure_number": number, - "text": text, - "bbox": lb, - "edge_score": edge_score, - }) + candidates.append( + { + "figure_namespace": "figure", + "figure_number": number, + "text": text, + "bbox": lb, + "edge_score": edge_score, + } + ) if not candidates: return None # Multiple different figure numbers -> conflict, don't recover @@ -6130,9 +6181,14 @@ def _recover_missing_figure_numbers_from_assets( fig["recovered_label_text"] = recovered["text"] fig["recovered_label_bbox"] = recovered["bbox"] fig["figure_number_source"] = "asset_internal_pdf_line" - fig["flags"] = list(dict.fromkeys((fig.get("flags") or []) + [ - "figure_number_recovered_from_asset_text", - ])) + fig["flags"] = list( + dict.fromkeys( + (fig.get("flags") or []) + + [ + "figure_number_recovered_from_asset_text", + ] + ) + ) def _recover_figure_heading_prefix( @@ -6162,7 +6218,7 @@ def _recover_figure_heading_prefix( # Sort PDF lines top-to-bottom by y-center sorted_lines = sorted( pdf_lines, - key=lambda l: (l.get("bbox") or [0, 0, 0, 0])[1], + key=lambda leg: (leg.get("bbox") or [0, 0, 0, 0])[1], ) for i, line in enumerate(sorted_lines): @@ -6183,7 +6239,7 @@ def _recover_figure_heading_prefix( # Common-prefix match: at least 15 chars case-insensitive common = 0 - for a, b in zip(next_text.lower(), block_text.lower()): + for a, b in zip(next_text.lower(), block_text.lower(), strict=False): if a == b: common += 1 else: diff --git a/paperforge/worker/ocr_pairing_framework.py b/paperforge/worker/ocr_pairing_framework.py new file mode 100644 index 00000000..a06caab3 --- /dev/null +++ b/paperforge/worker/ocr_pairing_framework.py @@ -0,0 +1,10 @@ +from __future__ import annotations + +from collections.abc import Sequence + + +def run_pairing_passes(state, pass_classes: Sequence[type]) -> list: + reports = [] + for pass_cls in pass_classes: + reports.append(pass_cls().run(state)) + return reports diff --git a/paperforge/worker/ocr_pairing_state.py b/paperforge/worker/ocr_pairing_state.py new file mode 100644 index 00000000..9c6fb180 --- /dev/null +++ b/paperforge/worker/ocr_pairing_state.py @@ -0,0 +1,146 @@ +from __future__ import annotations + +from collections.abc import Callable +from dataclasses import dataclass, field + +from .ocr_pairing_types import ClaimProposal, OwnershipConflict, ResourceRef + + +class OwnershipLedger: + def __init__(self) -> None: + self._reserved_groups: set[ResourceRef] = set() + self._owners: dict[ResourceRef, ResourceRef] = {} + self._journal: list[dict[str, object]] = [] + + def claim_assets(self, assets: list[ResourceRef], *, owner: ResourceRef, reason: str) -> None: + conflict = self.try_claim_assets(assets, owner=owner, reason=reason) + if conflict is not None: + raise ValueError(f"asset already owned: {conflict.resource}") + + def try_claim_assets( + self, assets: list[ResourceRef], *, owner: ResourceRef, reason: str + ) -> OwnershipConflict | None: + for asset in assets: + current = self._owners.get(asset) + if current is not None and current != owner: + conflict = OwnershipConflict( + resource=asset, + current_owner=current, + attempted_owner=owner, + reason=reason, + ) + self._journal.append( + { + "action": "conflict", + "resource": asset, + "current_owner": current, + "attempted_owner": owner, + "reason": reason, + } + ) + return conflict + for asset in assets: + self._owners[asset] = owner + self._journal.append({"action": "claim", "resource": asset, "owner": owner, "reason": reason}) + return None + + def owner_of(self, resource: ResourceRef) -> ResourceRef | None: + return self._owners.get(resource) + + def owner_of_asset(self, *, page: int, block_id: int | str) -> ResourceRef | None: + return self.owner_of(ResourceRef(kind="asset", page=page, block_id=block_id)) + + def reserve_group(self, group: ResourceRef, *, reason: str) -> None: + self._reserved_groups.add(group) + self._journal.append({"action": "reserve_group", "resource": group, "reason": reason}) + + def can_claim_group(self, group: ResourceRef) -> bool: + return group not in self._reserved_groups + + def transition_reserved_group_to_claimed(self, group: ResourceRef, *, owner: ResourceRef, reason: str) -> None: + self._reserved_groups.discard(group) + self._journal.append( + { + "action": "transition_to_claimed", + "resource": group, + "owner": owner, + "reason": reason, + } + ) + + def snapshot(self) -> list[dict[str, object]]: + return list(self._journal) + + def journal_text_attachment(self, texts: list[ResourceRef], *, owner: ResourceRef, reason: str) -> None: + for text in texts: + self._journal.append( + { + "action": "attach_text", + "resource": text, + "owner": owner, + "reason": reason, + } + ) + + def text_attachments_for(self, owner: ResourceRef) -> list[ResourceRef]: + return [ + entry["resource"] + for entry in self._journal + if entry.get("action") == "attach_text" and entry.get("owner") == owner + ] + + +@dataclass +class FigurePipelineState: + corpus: object | None + candidate_index: object | None + ledger: OwnershipLedger + matches: list[dict] = field(default_factory=list) + unresolved: list[dict] = field(default_factory=list) + hypotheses: list[dict] = field(default_factory=list) + diagnostics: list[dict] = field(default_factory=list) + reservations: list[dict] = field(default_factory=list) + completeness: dict = field(default_factory=dict) + # Hook set by domain code (e.g., figures) to enrich match_records before storing. + _match_pre_enricher: Callable | None = None + + def accept_match(self, proposal: ClaimProposal, match_record: dict) -> None: + if self._match_pre_enricher is not None: + self._match_pre_enricher(proposal, match_record, self) + self.matches.append(match_record) + self.diagnostics.append( + { + "event": "match_accepted", + "pass_name": proposal.pass_name, + "figure_no": proposal.figure_no, + "reason": proposal.reason, + "resources": { + "legends": proposal.legends, + "assets": proposal.assets, + "groups": proposal.groups, + }, + } + ) + + def accept_reservation(self, proposal: ClaimProposal) -> None: + self.reservations.append( + { + "pass_name": proposal.pass_name, + "figure_no": proposal.figure_no, + "reason": proposal.reason, + "legends": list(proposal.legends), + "groups": list(proposal.groups), + } + ) + self.diagnostics.append( + { + "event": "reservation_accepted", + "pass_name": proposal.pass_name, + "figure_no": proposal.figure_no, + "reason": proposal.reason, + "resources": {"groups": proposal.groups}, + } + ) + + +PipelineState = FigurePipelineState diff --git a/paperforge/worker/ocr_pairing_types.py b/paperforge/worker/ocr_pairing_types.py new file mode 100644 index 00000000..7caa1b00 --- /dev/null +++ b/paperforge/worker/ocr_pairing_types.py @@ -0,0 +1,71 @@ +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import Any, Literal + + +@dataclass(frozen=True) +class ResourceRef: + kind: Literal["legend", "asset", "group", "text"] + page: int | None + block_id: str | None + group_id: str | None = None + figure_no: int | None = field(default=None, compare=False) + origin: str | None = field(default=None, compare=False) + role: str | None = field(default=None, compare=False) + @property + def entity_no(self) -> int | None: + return self.figure_no + + def __post_init__(self) -> None: + if self.page is not None: + object.__setattr__(self, "page", int(self.page)) + if self.block_id is not None: + object.__setattr__(self, "block_id", str(self.block_id)) + if self.group_id is not None: + object.__setattr__(self, "group_id", str(self.group_id)) + + if self.kind == "asset" and (self.page is None or self.block_id is None): + raise ValueError("asset ResourceRef requires page + block_id") + if self.kind == "legend" and (self.page is None or self.block_id is None): + raise ValueError("legend ResourceRef requires page + block_id") + if self.kind == "group" and (self.page is None or self.group_id is None): + raise ValueError("group ResourceRef requires page + group_id") + if self.kind == "text" and (self.page is None or self.block_id is None): + raise ValueError("text ResourceRef requires page + block_id") + + +@dataclass(frozen=True) +class OwnershipConflict: + resource: ResourceRef + current_owner: ResourceRef | None + attempted_owner: ResourceRef | None + reason: str + + +@dataclass +class ClaimProposal: + pass_name: str + figure_no: int | None + claim_type: Literal["match", "reserve", "block", "unresolved_cluster", "composite_parent", "attach_text"] + legends: list[ResourceRef] + assets: list[ResourceRef] + groups: list[ResourceRef] + confidence: float + evidence_rank: int + reason: str + diagnostics: dict[str, Any] = field(default_factory=dict) + texts: list[ResourceRef] = field(default_factory=list) + + @property + def entity_no(self) -> int | None: + return self.figure_no + +@dataclass +class PassReport: + pass_name: str + proposals: list[ClaimProposal] = field(default_factory=list) + accepted: list[ClaimProposal] = field(default_factory=list) + rejected: list[ClaimProposal] = field(default_factory=list) + conflicts: list[OwnershipConflict] = field(default_factory=list) + invariant_errors: list[str] = field(default_factory=list) diff --git a/paperforge/worker/ocr_table_domain.py b/paperforge/worker/ocr_table_domain.py new file mode 100644 index 00000000..fb2c4fb6 --- /dev/null +++ b/paperforge/worker/ocr_table_domain.py @@ -0,0 +1,177 @@ +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import Any + + +@dataclass +class TableCorpus: + blocks: list[dict] + raw_captions: list[dict] = field(default_factory=list) + raw_assets: list[dict] = field(default_factory=list) + page_footnote_prior: dict[int, float] = field(default_factory=dict) + page_max_y: dict[int, float] = field(default_factory=dict) + + @classmethod + def from_blocks(cls, blocks: list[dict]) -> TableCorpus: + from . import ocr_tables + + raw_captions = [ + b + for b in blocks + if b.get("role") in {"table_caption", "table_caption_candidate"} + or ocr_tables._is_validation_first_table_candidate(b) + ] + raw_assets = [] + for block in blocks: + role = block.get("role", "") + raw_label = str(block.get("raw_label", "") or "").strip() + if role not in ("table_asset", "table_html", "media_asset", "figure_asset"): + continue + if role == "figure_asset" and raw_label != "table": + continue + raw_assets.append(block) + + page_footnote_prior = ocr_tables._collect_page_footnote_prior(blocks) + page_max_y: dict[int, float] = {} + for block in blocks: + bbox = block.get("bbox") or [0, 0, 0, 0] + if len(bbox) >= 4: + page = int(block.get("page", 0) or 0) + page_max_y[page] = max(page_max_y.get(page, 0.0), float(bbox[3])) + + return cls( + blocks=blocks, + raw_captions=raw_captions, + raw_assets=raw_assets, + page_footnote_prior=page_footnote_prior, + page_max_y=page_max_y, + ) + + +@dataclass +class TableCandidateIndex: + caption_records: list[dict] + assets_by_page: dict[int, list[tuple[int, dict]]] + + @classmethod + def from_corpus(cls, corpus: TableCorpus) -> TableCandidateIndex: + from . import ocr_tables + + captions = sorted( + corpus.raw_captions, + key=lambda block: ( + int(block.get("page", 0) or 0), + str(block.get("block_id", "")), + ), + ) + caption_records = [] + for caption in captions: + text = str(caption.get("text", "") or "") + caption_records.append( + { + "caption": caption, + "caption_block_id": str(caption.get("block_id", "")), + "caption_text": text, + "table_number": ocr_tables._extract_table_number(text), + "formal_table_number": ocr_tables._extract_base_table_number(text), + "is_continuation": ocr_tables._is_continuation_caption(text), + "is_validation_first_candidate": ocr_tables._is_validation_first_table_candidate( + caption + ), + "is_weak_truncated": ocr_tables._is_insufficient_table_caption_evidence( + caption + ), + "is_weak_explicit_caption": ocr_tables._is_weak_explicit_table_caption( + caption + ), + "continuation_ids": [], + "status": "pending", + "candidate_assets": [], + } + ) + + assets_by_page: dict[int, list[tuple[int, dict]]] = {} + for idx, asset in enumerate(corpus.raw_assets): + page = int(asset.get("page", 0) or 0) + assets_by_page.setdefault(page, []).append((idx, asset)) + + return cls(caption_records=caption_records, assets_by_page=assets_by_page) + + +def assemble_table_inventory( + state, candidate_index: TableCandidateIndex +) -> dict[str, Any]: + matched_caption_ids = { + t.get("caption_block_id", "") + for t in state.matches + if t.get("has_asset") + } + used_asset_ids = { + str(t.get("asset_block_id", "")) + for t in state.matches + if t.get("has_asset") and t.get("asset_block_id") + } + held_tables = [ + record["held_table"] + for record in candidate_index.caption_records + if record.get("status") == "held" and "held_table" in record + ] + unmatched_captions = [ + record["caption"] + for record in candidate_index.caption_records + if record["caption_block_id"] not in matched_caption_ids + and record.get("status") != "held" + ] + # Create has_asset=False table entries for unmatched captions (legacy-compat) + unmatched_table_entries: list[dict] = [] + for record in candidate_index.caption_records: + if record["caption_block_id"] in matched_caption_ids or record.get("status") == "held": + continue + caption = record["caption"] + unmatched_table_entries.append( + { + "caption_block_id": record["caption_block_id"], + "page": caption.get("page", 0), + "caption_text": record["caption_text"], + "table_number": record["table_number"], + "formal_table_number": record["formal_table_number"], + "asset_block_id": None, + "asset_bbox": [], + "assistive_text": "", + "truth_source": "image", + "has_asset": False, + "segments": [], + "note_block_ids": [], + "note_texts": [], + "note_bboxes": [], + "note_band_bbox": [], + "note_match_reason": "", + "note_confidence": 0.0, + "bridge_block_ids": [], + "consumed_block_ids": [], + "is_continuation": record["is_continuation"], + "continuation_of": None, + "match_score": {"decision": "unmatched", "evidence": [], "matched_asset_id": "", "score": 0.0}, + "match_status": record.get("status", "unmatched_caption"), + "candidate_assets": record["candidate_assets"], + "render_bbox": None, + "render_rotation_deg": 0, + } + ) + + unmatched_assets = [ + asset + for page_assets in candidate_index.assets_by_page.values() + for _, asset in page_assets + if str(asset.get("block_id", "")) not in used_asset_ids + ] + return { + "tables": list(state.matches) + unmatched_table_entries, + "held_tables": held_tables, + "unmatched_captions": unmatched_captions, + "unmatched_assets": unmatched_assets, + "official_table_count": len( + [t for t in state.matches if t.get("has_asset") and not t.get("is_continuation")] + ), + } diff --git a/paperforge/worker/ocr_table_passes.py b/paperforge/worker/ocr_table_passes.py new file mode 100644 index 00000000..d44dbb41 --- /dev/null +++ b/paperforge/worker/ocr_table_passes.py @@ -0,0 +1,387 @@ +from __future__ import annotations + +from .ocr_pairing_types import ClaimProposal, PassReport, ResourceRef + + +class TableWeakCaptionRecoveryPass: + name = "table_weak_caption_recovery" + + def run(self, state): + from . import ocr_tables + + report = PassReport(pass_name=self.name) + for record in state.candidate_index.caption_records: + if not record["is_weak_truncated"]: + continue + caption = record["caption"] + continuation = ocr_tables._find_table_caption_continuation(caption, state.corpus.blocks) + materialized, continuation_ids = ocr_tables._materialize_table_caption(caption, continuation) + record["caption"] = materialized + record["caption_text"] = str(materialized.get("text", "") or "") + record["continuation_ids"] = continuation_ids + if record["is_validation_first_candidate"]: + same_page_assets = state.candidate_index.assets_by_page.get(int(caption.get("page", 0) or 0), []) + if not same_page_assets: + record["status"] = "held" + record["held_table"] = { + "table_id": f"held_table_{len([r for r in state.candidate_index.caption_records if r.get('status') == 'held']) + 1:03d}", + "caption_block_id": record["caption_block_id"], + "page": caption.get("page", 0), + "caption_text": record["caption_text"], + "table_number": record["table_number"], + "formal_table_number": record["formal_table_number"], + "hold_reason": "insufficient_caption_evidence", + "zone": caption.get("zone", ""), + "style_family": caption.get("style_family", ""), + "marker_signature": caption.get("marker_signature", {}), + } + return report + + +class TableSamePagePass: + name = "table_same_page" + + def run(self, state): + from . import ocr_tables + + report = PassReport(pass_name=self.name) + for record in state.candidate_index.caption_records: + if record.get("status") != "pending": + continue + caption = record["caption"] + caption_page = int(caption.get("page", 0) or 0) + page_assets = [ + (idx, asset) + for idx, asset in state.candidate_index.assets_by_page.get(caption_page, []) + if state.ledger.owner_of_asset(page=caption_page, block_id=asset.get("block_id")) is None + ] + scored = ocr_tables._score_candidate_assets(page_assets, caption, is_continuation=record["is_continuation"]) + scored.sort(key=lambda item: item[2].get("score", 0.0), reverse=True) + record["candidate_assets"] = [ + {"asset_block_id": asset.get("block_id", ""), "match_score": score} + for _, asset, score in scored[:3] + ] + if not scored: + continue + top_idx, top_asset, top_score = scored[0] + second_score = scored[1][2].get("score", 0.0) if len(scored) > 1 else -1.0 + top_score_val = top_score.get("score", 0.0) + if top_score_val < 0.4: + continue + if top_score_val - second_score < 0.15: + record["status"] = "ambiguous" + continue + owner = ResourceRef(kind="legend", page=caption_page, block_id=record["caption_block_id"], figure_no=record["formal_table_number"]) + asset_ref = ResourceRef(kind="asset", page=int(top_asset.get("page", 0) or 0), block_id=top_asset.get("block_id")) + conflict = state.ledger.try_claim_assets([asset_ref], owner=owner, reason=self.name) + if conflict is not None: + report.conflicts.append(conflict) + continue + match_status = "matched" if top_score.get("score", 0.0) >= 0.6 else "matched_low_confidence" + state.accept_match( + ClaimProposal( + pass_name=self.name, + figure_no=record["formal_table_number"], + claim_type="match", + legends=[owner], + assets=[asset_ref], + groups=[], + texts=[], + confidence=float(top_score.get("score", 0.0)), + evidence_rank=0, + reason=self.name, + ), + { + "caption_block_id": record["caption_block_id"], + "page": caption_page, + "caption_text": record["caption_text"], + "table_number": record["table_number"], + "formal_table_number": record["formal_table_number"], + "asset_block_id": top_asset.get("block_id", ""), + "asset_bbox": top_asset.get("bbox", [0, 0, 0, 0]), + "assistive_text": str(top_asset.get("text", "") or ""), + "truth_source": "image", + "has_asset": True, + "segments": [ + { + "page": top_asset.get("page", 0), + "asset_block_id": top_asset.get("block_id", ""), + "asset_bbox": top_asset.get("bbox", [0, 0, 0, 0]), + "is_continuation": record["is_continuation"], + } + ], + "note_block_ids": [], + "note_texts": [], + "note_bboxes": [], + "note_band_bbox": [], + "note_match_reason": "", + "note_confidence": 0.0, + "bridge_block_ids": [], + "consumed_block_ids": [record["caption_block_id"], top_asset.get("block_id", ""), *record.get("continuation_ids", [])], + "is_continuation": record["is_continuation"], + "continuation_of": None, + "match_status": match_status, + "candidate_assets": record["candidate_assets"], + "match_score": top_score, + "render_bbox": None, + "render_rotation_deg": 0, + "asset_family_hint": top_asset.get("asset_family_hint"), + "asset_family_confidence": top_asset.get("asset_family_confidence"), + "asset_family_evidence": top_asset.get("asset_family_evidence"), + }, + ) + record["status"] = "matched" + return report + + +class TableAdjacentPagePass: + name = "table_adjacent_page" + + def run(self, state): + from . import ocr_tables + + report = PassReport(pass_name=self.name) + for record in state.candidate_index.caption_records: + if record.get("status") != "pending": + continue + caption = record["caption"] + caption_page = int(caption.get("page", 0) or 0) + candidate_pages = [caption_page - 1, caption_page, caption_page + 1] + all_candidates = [] + for page in candidate_pages: + if page < 1: + continue + page_assets = [ + (idx, asset) + for idx, asset in state.candidate_index.assets_by_page.get(page, []) + if state.ledger.owner_of_asset(page=page, block_id=asset.get("block_id")) is None + ] + all_candidates.extend(ocr_tables._score_candidate_assets(page_assets, caption, is_continuation=record["is_continuation"])) + + for _, asset, score_dict in all_candidates: + a_page = int(asset.get("page", 0) or 0) + if a_page == caption_page - 1: + ab = asset.get("bbox") or [0, 0, 0, 0] + cb = caption.get("bbox") or [0, 0, 0, 0] + if len(ab) >= 4 and len(cb) >= 4: + x_ratio = (min(cb[2], ab[2]) - max(cb[0], ab[0])) / max(1.0, min(cb[2] - cb[0], ab[2] - ab[0])) + page_h = max(state.corpus.page_max_y.values()) if state.corpus.page_max_y else 1.0 + if x_ratio >= 0.5 and float(ab[3]) >= page_h * 0.85 and float(cb[1]) <= page_h * 0.15: + score_dict["score"] = min(score_dict.get("score", 0.0) + 0.15, 1.0) + score_dict.setdefault("evidence", []).append("continuation_geometry_elevation") + + all_candidates.sort(key=lambda item: item[2].get("score", 0.0), reverse=True) + record["candidate_assets"] = [ + {"asset_block_id": asset.get("block_id", ""), "match_score": score} + for _, asset, score in all_candidates[:3] + ] + if not all_candidates: + record["status"] = "unmatched_caption" + continue + top_idx, top_asset, top_score = all_candidates[0] + second_score = all_candidates[1][2].get("score", 0.0) if len(all_candidates) > 1 else -1.0 + if top_score.get("score", 0.0) < 0.4: + record["status"] = "unmatched_caption" + continue + if top_score.get("score", 0.0) - second_score < 0.15: + record["status"] = "ambiguous" + continue + owner = ResourceRef(kind="legend", page=caption_page, block_id=record["caption_block_id"], figure_no=record["formal_table_number"]) + asset_ref = ResourceRef(kind="asset", page=int(top_asset.get("page", 0) or 0), block_id=top_asset.get("block_id")) + conflict = state.ledger.try_claim_assets([asset_ref], owner=owner, reason=self.name) + if conflict is not None: + report.conflicts.append(conflict) + continue + match_status = "matched" if top_score.get("score", 0.0) >= 0.6 else "matched_low_confidence" + continuation_of = None + if record["is_continuation"] and record["formal_table_number"] is not None: + for existing in state.matches: + if existing.get("formal_table_number") == record["formal_table_number"] and not existing.get("is_continuation"): + continuation_of = record["formal_table_number"] + break + state.accept_match( + ClaimProposal( + pass_name=self.name, + figure_no=record["formal_table_number"], + claim_type="match", + legends=[owner], + assets=[asset_ref], + groups=[], + texts=[], + confidence=float(top_score.get("score", 0.0)), + evidence_rank=1, + reason=self.name, + ), + { + "caption_block_id": record["caption_block_id"], + "page": caption_page, + "caption_text": record["caption_text"], + "table_number": record["table_number"], + "formal_table_number": record["formal_table_number"], + "asset_block_id": top_asset.get("block_id", ""), + "asset_bbox": top_asset.get("bbox", [0, 0, 0, 0]), + "assistive_text": str(top_asset.get("text", "") or ""), + "truth_source": "image", + "has_asset": True, + "segments": [ + { + "page": top_asset.get("page", 0), + "asset_block_id": top_asset.get("block_id", ""), + "asset_bbox": top_asset.get("bbox", [0, 0, 0, 0]), + "is_continuation": record["is_continuation"], + } + ], + "note_block_ids": [], + "note_texts": [], + "note_bboxes": [], + "note_band_bbox": [], + "note_match_reason": "", + "note_confidence": 0.0, + "bridge_block_ids": [], + "consumed_block_ids": [record["caption_block_id"], top_asset.get("block_id", ""), *record.get("continuation_ids", [])], + "is_continuation": record["is_continuation"], + "continuation_of": continuation_of, + "match_status": match_status, + "candidate_assets": record["candidate_assets"], + "match_score": top_score, + "render_bbox": None, + "render_rotation_deg": 0, + "asset_family_hint": top_asset.get("asset_family_hint"), + "asset_family_confidence": top_asset.get("asset_family_confidence"), + "asset_family_evidence": top_asset.get("asset_family_evidence"), + }, + ) + record["status"] = "matched" + return report + + +class TableNotesAttachmentPass: + name = "table_notes_attachment" + + def run(self, state): + from . import ocr_tables + + report = PassReport(pass_name=self.name) + for table in state.matches: + if not table.get("has_asset"): + table.setdefault("note_block_ids", []) + table.setdefault("note_texts", []) + table.setdefault("note_bboxes", []) + table.setdefault("note_band_bbox", []) + table.setdefault("note_match_reason", "") + table.setdefault("note_confidence", 0.0) + table.setdefault("bridge_block_ids", []) + continue + + asset_page = int(table.get("page", 0) or 0) + asset_bbox = table.get("asset_bbox", [0, 0, 0, 0]) + asset_bottom = asset_bbox[3] if len(asset_bbox) >= 4 else 0 + + candidates = [] + note_match_reason = "" + for block in state.corpus.blocks: + if int(block.get("page", 0) or 0) != asset_page: + continue + brole = str(block.get("role", "") or "") + braw_label = str(block.get("raw_label", "") or "").strip() + btext = str(block.get("text", "") or "").strip() + is_note = ( + brole == "footnote" + or braw_label == "vision_footnote" + or ( + 0 < len(btext) < 120 + and brole not in { + "noise", "page_footer", "page_header", "frontmatter_noise", + "table_caption", "table_caption_candidate", + "table_asset", "media_asset", "figure_caption", + "section_heading", "subsection_heading", "reference_heading", + } + ) + ) + if not is_note: + continue + bbbox = block.get("bbox") or [0, 0, 0, 0] + if len(bbbox) < 4: + note_match_reason = "invalid_bbox" + continue + if bbbox[1] < asset_bottom or bbbox[1] > asset_bottom + 100: + note_match_reason = "outside_vertical_range" + continue + if ocr_tables._table_note_falls_into_page_footnote_prior(bbbox, asset_page, state.corpus.page_footnote_prior): + note_match_reason = "page_footnote_prior_rejected" + continue + if ocr_tables._looks_like_body_text_below_table(block, asset_bbox): + note_match_reason = "body_text_like_excluded" + continue + candidates.append(block) + + if candidates: + candidates.sort(key=lambda b: (b.get("bbox") or [0, 0, 0, 0])[1]) + table["note_block_ids"] = [str(b.get("block_id", "")) for b in candidates if b.get("block_id")] + table["note_texts"] = [str(b.get("text", "") or "").strip() for b in candidates if str(b.get("text", "") or "").strip()] + table["note_bboxes"] = [b.get("bbox", [0, 0, 0, 0]) for b in candidates] + table["note_band_bbox"] = [ + min(bb[0] for bb in table["note_bboxes"]), + min(bb[1] for bb in table["note_bboxes"]), + max(bb[2] for bb in table["note_bboxes"]), + max(bb[3] for bb in table["note_bboxes"]), + ] + table["note_match_reason"] = "note_band_geometry_match" + table["note_confidence"] = 0.85 + else: + table.setdefault("note_block_ids", []) + table.setdefault("note_texts", []) + table.setdefault("note_bboxes", []) + table.setdefault("note_band_bbox", []) + table["note_match_reason"] = note_match_reason or "no_footnote_role" + table.setdefault("note_confidence", 0.0) + + asset_block = next( + (a for a in state.corpus.raw_assets if str(a.get("block_id", "")) == str(table.get("asset_block_id", "")) and int(a.get("page", 0) or 0) == asset_page), + None, + ) + if asset_block is not None: + rot = ocr_tables._table_has_rotated_content(asset_block) + if rot: + ab = table.get("asset_bbox", []) + caption = next( + (r["caption"] for r in state.candidate_index.caption_records if r["caption_block_id"] == table.get("caption_block_id")), + None, + ) + cb = (caption.get("bbox") or caption.get("block_bbox") or []) if caption else [] + if len(ab) >= 4 and len(cb) >= 4: + table["render_bbox"] = [min(cb[0], ab[0]), min(cb[1], ab[1]), max(cb[2], ab[2]), max(cb[3], ab[3])] + table["render_rotation_deg"] = rot + + # Bridge block detection + table["bridge_block_ids"] = [ + str(block.get("block_id") or "") + for block in state.corpus.blocks + if int(block.get("page", 0) or 0) == asset_page + and block.get("bridge_eligible") + and str(block.get("layout_region") or "") == "display_zone" + and block.get("block_id") + ] + + # Consumed block IDs include notes + existing_ids = set(table.get("consumed_block_ids") or []) + for bid in table.get("note_block_ids", []): + if bid not in existing_ids: + table.setdefault("consumed_block_ids", []).append(bid) + return report + + +class TableFinalAccountingPass: + name = "table_final_accounting" + + def run(self, state): + report = PassReport(pass_name=self.name) + state.completeness = { + "total_numbered_tables": len([r for r in state.candidate_index.caption_records if r.get("formal_table_number") is not None]), + "accounted_for": len([r for r in state.candidate_index.caption_records if r.get("status") in {"matched", "held"}]), + "details": [ + {"caption_block_id": r["caption_block_id"], "status": r.get("status", "pending")} + for r in state.candidate_index.caption_records + ], + } + return report diff --git a/paperforge/worker/ocr_tables.py b/paperforge/worker/ocr_tables.py index 7495152b..8fbacf57 100644 --- a/paperforge/worker/ocr_tables.py +++ b/paperforge/worker/ocr_tables.py @@ -1,6 +1,7 @@ from __future__ import annotations import re +from dataclasses import asdict from pathlib import Path from typing import Any @@ -114,7 +115,6 @@ def _is_weak_explicit_table_caption(block: dict) -> bool: def _find_table_caption_continuation(caption: dict, structured_blocks: list[dict]) -> dict | None: """Find the block immediately after a weak-truncated table caption that looks like a continuation (stolen as figure_caption or similar).""" - caption_page = caption.get("page", 0) caption_bbox = caption.get("bbox") or [0, 0, 0, 0] next_idx = None for i, block in enumerate(structured_blocks): @@ -233,7 +233,7 @@ def _table_note_falls_into_page_footnote_prior( return float(note_bbox[1]) >= float(prior_by_page[page]) def build_table_inventory(structured_blocks: list[dict]) -> dict[str, Any]: - return build_table_inventory_legacy(structured_blocks) + return build_table_inventory_vnext(structured_blocks) def build_table_inventory_legacy(structured_blocks: list[dict]) -> dict[str, Any]: @@ -637,3 +637,33 @@ def write_back_table_roles(inventory: dict, structured_blocks: list[dict]) -> No def write_table_inventory(dst: Path, inventory: dict[str, Any]) -> None: write_json(dst, inventory) + + +def build_table_inventory_vnext(structured_blocks: list[dict]) -> dict[str, Any]: + from .ocr_pairing_framework import run_pairing_passes + from .ocr_pairing_state import OwnershipLedger, PipelineState + from .ocr_table_domain import TableCandidateIndex, TableCorpus, assemble_table_inventory + from .ocr_table_passes import ( + TableAdjacentPagePass, + TableFinalAccountingPass, + TableNotesAttachmentPass, + TableSamePagePass, + TableWeakCaptionRecoveryPass, + ) + + corpus = TableCorpus.from_blocks(structured_blocks) + candidate_index = TableCandidateIndex.from_corpus(corpus) + state = PipelineState(corpus=corpus, candidate_index=candidate_index, ledger=OwnershipLedger()) + reports = run_pairing_passes( + state, + [ + TableWeakCaptionRecoveryPass, + TableSamePagePass, + TableAdjacentPagePass, + TableNotesAttachmentPass, + TableFinalAccountingPass, + ], + ) + inventory = assemble_table_inventory(state, candidate_index) + inventory["pass_reports"] = [asdict(r) for r in reports] + return inventory diff --git a/project/current/ocr-v2-active-queue.md b/project/current/ocr-v2-active-queue.md index e6eaa1e6..f64903e6 100644 --- a/project/current/ocr-v2-active-queue.md +++ b/project/current/ocr-v2-active-queue.md @@ -1,27 +1,30 @@ # OCR-v2 Active Queue -> Status: ACTIVE QUEUE — Round 2 truth audit + 3 targeted bug fixes. 428 regression tests pass. -> Last updated: 2026-07-02 -> Scope: post-audit cleanup +> Status: ACTIVE QUEUE — OCR pairing framework branch is merge-ready after merge-unblock verification. 357 targeted tests pass. +> Last updated: 2026-07-03 +> Scope: pairing framework integration / post-merge follow-up ## Current Priorities -1. **Monitor production OCR** after rotated-figure prematch, asset-internal recovery, sidecar/table fixes -2. **Archive stale `project/current/` files** -3. **Group-first figure inventory refactor** (deferred) +1. **Merge `feat/ocr-pairing-framework`** back to `master` +2. **Monitor production OCR** after pairing-core unification (figure + table on shared framework) +3. **Archive stale `project/current/` files** +4. **Compatibility naming cleanup** (`figure_no` / `legend` / `FigurePipelineState`) — deferred ## Completed This Session (cumulative) -- **Round 2 truth audit**: 10 new papers batch-audited via ocr_truth_audit.py (high-risk mode) - - 5 GREEN / 4 YELLOW / 1 RED (37LK5T97 — Figure 1 broken, tables unmatched) - - 2 vision agents dispatched for RED papers - - Findings: `docs/superpowers/specs/2026-07-02-ocr-truth-audit-round2-findings.md` -- **37LK5T97 Figure 1 sidecar fix** (ocr_document.py) - - Add `_is_sidecar_candidate` guard in candidate_resolution demotion - - Sidecar caption in adjacent column no longer demoted as narrative prose - - Figure 1 matched: `figure_001`, asset=block_id=9 -- **37LK5T97 rotated table matching fix** (ocr_scores.py) - - Add `adjacent_x` + `y_overlap_with_asset` checks in score_table_match for rotated captions - - All 6 tables matched with has_asset=true -- **37LK5T97 rotated table render fix** (ocr_tables.py, ocr_objects.py) - - `_table_has_rotated_content` detects dir=[0,-1], computes union render_bbox + rotation_deg=270 - - Tables 1-5 rendered at correct orientation (1908×2858 → 2858×1908) - - Same approach as rotated figure rendering -- Git: commits `16f9403` (recovery), `59cd01a` (figure quality), `bd3f3b6` (sidecar+table match), `86e0d14` (table render) +- **Pairing framework extraction**: + - Shared `ocr_pairing_types.py`, `ocr_pairing_state.py`, `ocr_pairing_framework.py` + - Figure pipeline migrated onto shared core without changing public seam +- **Table pipeline migration**: + - Added `ocr_table_domain.py` + ordered `ocr_table_passes.py` + - `build_table_inventory(...)` now routes to table vnext on shared core +- **Merge-unblock hardening**: + - Generic-state figure rotation enrichment moved behind figure-only `_match_pre_enricher` + - Table semantic parity validation upgraded across 6 runnable real-paper fixtures + - Added runnable `tests/fixtures/ocr_vnext_real_papers/37LK5T97/blocks.structured.jsonl` + - Touched-file `ruff check` / `ruff format --check` green +- **Verification**: + - `tests/test_ocr_figures.py` + - `tests/test_ocr_rebuild.py` + - `tests/test_ocr_tables.py` + - `tests/test_ocr_pairing_framework.py` + - `tests/test_ocr_table_pairing_framework.py` + - Result: **357 passed, 0 failed** diff --git a/scripts/dev/compare_figure_inventory_vnext_baseline.py b/scripts/dev/compare_figure_inventory_vnext_baseline.py new file mode 100644 index 00000000..efc54924 --- /dev/null +++ b/scripts/dev/compare_figure_inventory_vnext_baseline.py @@ -0,0 +1,17 @@ +from __future__ import annotations + +import json +from pathlib import Path + +from paperforge.worker.ocr_figures import build_figure_inventory + + +def compare_vnext_inventory_baseline(fixture_root: Path) -> dict[str, object]: + structured_path = fixture_root / "structure" / "blocks.structured.jsonl" + blocks = [json.loads(line) for line in structured_path.read_text(encoding="utf-8").splitlines() if line.strip()] + inventory = build_figure_inventory(blocks) + return { + "pipeline_mode": inventory.get("pipeline_mode"), + "matched_ids": [m.get("figure_id") for m in inventory.get("matched_figures", [])], + "match_count": len(inventory.get("matched_figures", [])), + } diff --git a/scripts/dev/compare_table_inventory_legacy_vs_vnext.py b/scripts/dev/compare_table_inventory_legacy_vs_vnext.py new file mode 100644 index 00000000..74a53e6e --- /dev/null +++ b/scripts/dev/compare_table_inventory_legacy_vs_vnext.py @@ -0,0 +1,74 @@ +from __future__ import annotations + +import copy +import json +from pathlib import Path + +from paperforge.worker.ocr_tables import build_table_inventory_legacy, build_table_inventory_vnext + + +def _load_blocks(fixture_root: Path) -> list[dict]: + # Check both fixture_root/structure/blocks.structured.jsonl and fixture_root/blocks.structured.jsonl + candidate = fixture_root / "structure" / "blocks.structured.jsonl" + if not candidate.exists(): + candidate = fixture_root / "blocks.structured.jsonl" + return [json.loads(line) for line in candidate.read_text(encoding="utf-8").splitlines() if line.strip()] + + +def _str_id(val: object) -> str | None: + """Normalize a block ID to str, or None if empty/missing.""" + if val is None or val == "": + return None + return str(val) + + +def _str_ids_sorted(vals: list) -> list[str]: + """Normalize block ID list to sorted strings, dropping None/empty entries.""" + return sorted(str(v) for v in (vals or []) if v is not None and v != "") + + +def _normalize_table(table: dict) -> dict[str, object]: + """Normalize a table inventory entry so legacy and vnext results are comparable. + + Benign drift handled: + - block IDs stored as int vs str -> normalized to str + - ``asset_block_id`` stored as ``""`` (legacy) vs ``None`` (vnext) -> both become None + - ordering of list fields -> sorted + """ + asset_id = _str_id(table.get("asset_block_id")) + return { + "caption_block_id": _str_id(table.get("caption_block_id")), + "page": table.get("page"), + "formal_table_number": table.get("formal_table_number"), + "asset_block_id": asset_id, # None if empty in either pipeline + "match_status": table.get("match_status"), + "note_block_ids": _str_ids_sorted(table.get("note_block_ids", [])), + "bridge_block_ids": _str_ids_sorted(table.get("bridge_block_ids", [])), + "consumed_block_ids": _str_ids_sorted(table.get("consumed_block_ids", [])), + "render_rotation_deg": table.get("render_rotation_deg", 0), + } + + +def _table_sort_key(t: dict) -> tuple: + return (t.get("page") or 0, t.get("formal_table_number") or 0) + + +def compare_table_inventory_legacy_vs_vnext(fixture_root: Path) -> dict[str, object]: + blocks = _load_blocks(fixture_root) + legacy = build_table_inventory_legacy(copy.deepcopy(blocks)) + vnext = build_table_inventory_vnext(copy.deepcopy(blocks)) + legacy_norm = [_normalize_table(t) for t in legacy.get("tables", [])] + vnext_norm = [_normalize_table(t) for t in vnext.get("tables", [])] + # Sort deterministically so ordering drift does not cause false diffs. + legacy_norm.sort(key=_table_sort_key) + vnext_norm.sort(key=_table_sort_key) + return { + "legacy_raw": legacy, + "vnext_raw": vnext, + "legacy": legacy_norm, + "vnext": vnext_norm, + "diff": { + "legacy_only": [item for item in legacy_norm if item not in vnext_norm], + "vnext_only": [item for item in vnext_norm if item not in legacy_norm], + }, + } diff --git a/tests/fixtures/ocr_vnext_real_papers/37LK5T97/blocks.structured.jsonl b/tests/fixtures/ocr_vnext_real_papers/37LK5T97/blocks.structured.jsonl new file mode 100644 index 00000000..ba88665b --- /dev/null +++ b/tests/fixtures/ocr_vnext_real_papers/37LK5T97/blocks.structured.jsonl @@ -0,0 +1,292 @@ +{"paper_id": "37LK5T97", "page": 1, "block_id": 0, "raw_label": "header", "raw_order": null, "bbox": [114, 66, 352, 142], "text": "TISSUE ENGINEERING: Part B\nVolume 21, Number 3, 2015\n© Mary Ann Liebert, Inc.\nDOI: 10.1089/ten.teb.2014.0419", "page_width": 1224, "page_height": 1584, "role": "noise", "role_confidence": 0.9, "evidence": ["header label"], "seed_role": "noise", "seed_confidence": 0.9, "seed_evidence": ["header label"], "span_metadata": [{"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvPSSym", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 7.970200061798096, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 0, "page": 1, "raw_label": "header", "text": "TISSUE ENGINEERING: Part B\nVolume 21, Number 3, 2015\n© Mary Ann Liebert, Inc.\nDOI: 10.1089/ten.teb.2014.0419", "bbox": [114, 66, 352, 142], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "TISSUE ENGINEERING: Part B\nVolume 21, Number 3, 2015\n© Mary Ann Liebert, Inc.\nDOI: 10.1089/ten.teb.2014.0419"}, "layout_signature": {"width": 238, "width_bucket": 250, "height": 76, "left": 114, "top": 66, "right": 352, "bottom": 142, "x_center": 233.0, "x_center_bucket": 225, "y_center": 104.0, "x_ratio": 0.1904, "y_ratio": 0.0657, "width_ratio": 0.1944, "height_ratio": 0.048, "line_count": 1}, "span_signature": {"font_size": 7.97, "font_size_median": 7.97, "font_size_bucket": 8.0, "font_family_norm": "AdvP6EC0", "bold": false, "italic": true, "span_count": 28}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": false, "index_default": false, "zone": "frontmatter_main_zone", "style_family": "support_like", "style_family_authority": "zone_context", "insert_score": {"score": 0.15, "decision": "body", 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Connor Dennis, BS, $ ^{1,2} $ Cory J. Berkland, PhD, $ ^{1-3} $ Lynda F. Bonewald, PhD, $ ^{4} $ and Michael S. Detamore, PhD $ ^{1,2} $", "bbox": [334, 382, 883, 436], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "S. Connor Dennis, BS, $ ^{1,2} $ Cory J. Berkland, PhD, $ ^{1-3} $ Lynda F. Bonewald, PhD, $ ^{4} $ and Michael S. 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Consequently, many marginally successful bone tissue engineering strategies have focused on mimicking portions of ABG's \"ideal\" osteoconductive, osteoinductive, and osteogenic composition resembling the late reparative stage extracellular matrix (ECM) in bone fracture repair, also known as the \"hard\" or \"bony\" callus. An alternative, less common approach that has emerged in the last decade harnesses endochondral (EC) ossification through developmental engineering principles, which acknowledges that the molecular and cellular mechanisms involved in developmental skeletogenesis, specifically EC ossification, are closely paralleled during native bone healing. EC ossification naturally occurs during the majority of bone fractures and, thus, can potentially be utilized to enhance bone regeneration for nearly any orthopedic indication, especially in avascular critical-sized defects where hypoxic conditions favor initial chondrogenesis instead of direct intramembranous ossification. The body's native EC ossification response, however, is not capable of regenerating critical-sized defects without intervention. We propose that an underexplored potential exists to regenerate bone through the native EC ossification response by utilizing strategies which mimic the initial inflammatory or fibrocartilaginous ECM (i.e., \"pro-\" or \"soft\" callus) observed in the early reparative stage of bone fracture repair. To date, the majority of strategies utilizing this approach rely on clinically burdensome in vitro cell expansion protocols. This review will focus on the confluence of two evolving areas, (1) native ECM biomaterials and (2) developmental engineering, which will attempt to overcome the technical, business, and regulatory challenges that persist in the area of bone regeneration. Significant attention will be given to native \"raw\" materials and ECM-based designs that provide necessary osteo- and chondro-conductive and inductive features for enhancing EC ossification. In addition, critical perspectives on existing stem cell-based therapeutic strategies will be discussed with a focus on their use as an extension of the acellular ECM-based designs for specific clinical indications. 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Consequently, many marginally successful bone tissue engineering strategies have focused on mimicking portions of ABG's \"ideal\" osteoconductive, osteoinductive, and osteogenic composition resembling the late reparative stage extracellular matrix (ECM) in bone fracture repair, also known as the \"hard\" or \"bony\" callus. An alternative, less common approach that has emerged in the last decade harnesses endochondral (EC) ossification through developmental engineering principles, which acknowledges that the molecular and cellular mechanisms involved in developmental skeletogenesis, specifically EC ossification, are closely paralleled during native bone healing. EC ossification naturally occurs during the majority of bone fractures and, thus, can potentially be utilized to enhance bone regeneration for nearly any orthopedic indication, especially in avascular critical-sized defects where hypoxic conditions favor initial chondrogenesis instead of direct intramembranous ossification. The body's native EC ossification response, however, is not capable of regenerating critical-sized defects without intervention. We propose that an underexplored potential exists to regenerate bone through the native EC ossification response by utilizing strategies which mimic the initial inflammatory or fibrocartilaginous ECM (i.e., \"pro-\" or \"soft\" callus) observed in the early reparative stage of bone fracture repair. To date, the majority of strategies utilizing this approach rely on clinically burdensome in vitro cell expansion protocols. This review will focus on the confluence of two evolving areas, (1) native ECM biomaterials and (2) developmental engineering, which will attempt to overcome the technical, business, and regulatory challenges that persist in the area of bone regeneration. Significant attention will be given to native \"raw\" materials and ECM-based designs that provide necessary osteo- and chondro-conductive and inductive features for enhancing EC ossification. In addition, critical perspectives on existing stem cell-based therapeutic strategies will be discussed with a focus on their use as an extension of the acellular ECM-based designs for specific clinical indications. Within this framework, a novel realm of unexplored design strategies for bone tissue engineering will be introduced into the collective consciousness of the regenerative medicine field.", "bbox": [112, 515, 1106, 1072], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Autologous bone grafting (ABG) remains entrenched as the gold standard of treatment in bone regenerative surgery. Consequently, many marginally successful bone tissue engineering strategies have focused on mimicking portions of ABG's \"ideal\" osteoconductive, osteoinductive, and osteogenic composition resembling the late reparative stage extracellular matrix (ECM) in bone fracture repair, also known as the \"hard\" or \"bony\" callus. An alternative, less common approach that has emerged in the last decade harnesses endochondral (EC) ossification through developmental engineering principles, which acknowledges that the molecular and cellular mechanisms involved in developmental skeletogenesis, specifically EC ossification, are closely paralleled during native bone healing. EC ossification naturally occurs during the majority of bone fractures and, thus, can potentially be utilized to enhance bone regeneration for nearly any orthopedic indication, especially in avascular critical-sized defects where hypoxic conditions favor initial chondrogenesis instead of direct intramembranous ossification. The body's native EC ossification response, however, is not capable of regenerating critical-sized defects without intervention. We propose that an underexplored potential exists to regenerate bone through the native EC ossification response by utilizing strategies which mimic the initial inflammatory or fibrocartilaginous ECM (i.e., \"pro-\" or \"soft\" callus) observed in the early reparative stage of bone fracture repair. To date, the majority of strategies utilizing this approach rely on clinically burdensome in vitro cell expansion protocols. This review will focus on the confluence of two evolving areas, (1) native ECM biomaterials and (2) developmental engineering, which will attempt to overcome the technical, business, and regulatory challenges that persist in the area of bone regeneration. Significant attention will be given to native \"raw\" materials and ECM-based designs that provide necessary osteo- and chondro-conductive and inductive features for enhancing EC ossification. In addition, critical perspectives on existing stem cell-based therapeutic strategies will be discussed with a focus on their use as an extension of the acellular ECM-based designs for specific clinical indications. Within this framework, a novel realm of unexplored design strategies for bone tissue engineering will be introduced into the collective consciousness of the regenerative medicine field."}, "layout_signature": {"width": 994, "width_bucket": 1000, "height": 557, "left": 112, "top": 515, "right": 1106, "bottom": 1072, "x_center": 609.0, "x_center_bucket": 600, "y_center": 793.5, "x_ratio": 0.4975, "y_ratio": 0.5009, "width_ratio": 0.8121, "height_ratio": 0.3516, "line_count": 1}, "span_signature": {"font_size": 10.94, "font_size_median": 10.94, "font_size_bucket": 11.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 343}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "frontmatter_main_zone", "style_family": "support_like", "style_family_authority": "zone_context", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.0, "decision": "body", "evidence": []}, "role_verification_status": "ACCEPT", "role_source": "abstract_span_missing_fallback", "role_evidence": ["abstract body accepted from seed (no span to verify)"]} +{"paper_id": "37LK5T97", "page": 1, "block_id": 4, "raw_label": "paragraph_title", "raw_order": 4, "bbox": [114, 1123, 229, 1145], "text": "Introduction", "page_width": 1224, "page_height": 1584, "role": "section_heading", "role_confidence": 0.9, "evidence": ["explicit scholarly heading: Introduction"], "seed_role": "section_heading", "seed_confidence": 0.9, "seed_evidence": ["explicit scholarly heading: Introduction"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC5", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 4, "page": 1, "raw_label": "paragraph_title", "text": "Introduction", "bbox": [114, 1123, 229, 1145], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "canonical_section_name", "raw_marker": "Introduction", "number": null, "kind": "heading", "normalized_text": "Introduction"}, "layout_signature": {"width": 115, "width_bucket": 125, "height": 22, "left": 114, "top": 1123, "right": 229, "bottom": 1145, "x_center": 171.5, "x_center_bucket": 175, "y_center": 1134.0, "x_ratio": 0.1401, "y_ratio": 0.7159, "width_ratio": 0.094, "height_ratio": 0.0139, "line_count": 1}, "span_signature": {"font_size": 8.97, "font_size_median": 8.97, "font_size_bucket": 9.0, "font_family_norm": "AdvP6EC5", "bold": false, "italic": true, "span_count": 1}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "heading_like", "style_family_authority": "heading_marker", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "accepted_heading", "role_evidence": ["heading verified by heading artifact"]} +{"paper_id": "37LK5T97", "page": 1, "block_id": 5, "raw_label": "text", "raw_order": 5, "bbox": [111, 1166, 601, 1367], "text": "THE HUMAN BODY HAS AN EXTENSIVE capacity to regenerate bone tissue after trauma. Disruption of the surrounding vasculature and bone marrow resulting from a bone fracture initially facilitates a cascade of coagulation and inflammatory events within the fracture space (Fig. 1). $ ^{1-8} $ The subsequent bone-healing process overlaps with this inflammatory phase spatiotemporally via both bone developmental pathways: intramembranous (IM) and endochondral (EC) ossification. $ ^{1-8} $ Large defects above a “critical-size,” however, cannot be restored without intervention and often lead to nonunion. $ ^{9,10} $ Although current surgical intervention strategies, most notably autologous bone grafting (ABG), have yielded favorable bone healing outcomes in these situations, it is clear from the past decade’s surge in clinically available tissue-engineered bone implants, some coupled with stem cell-based therapeutics (SCBTs), that alternative bone regenerative strategies have gained a significant market share. $ ^{11} $", "page_width": 1224, "page_height": 1584, "role": 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Disruption of the surrounding vasculature and bone marrow resulting from a bone fracture initially facilitates a cascade of coagulation and inflammatory events within the fracture space (Fig. 1). $ ^{1-8} $ The subsequent bone-healing process overlaps with this inflammatory phase spatiotemporally via both bone developmental pathways: intramembranous (IM) and endochondral (EC) ossification. $ ^{1-8} $ Large defects above a “critical-size,” however, cannot be restored without intervention and often lead to nonunion. $ ^{9,10} $ Although current surgical intervention strategies, most notably autologous bone grafting (ABG), have yielded favorable bone healing outcomes in these situations, it is clear from the past decade’s surge in clinically available tissue-engineered bone implants, some coupled with stem cell-based therapeutics (SCBTs), that alternative bone regenerative strategies have gained a significant market share. $ ^{11} $", "bbox": [111, 1166, 601, 1367], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "THE HUMAN BODY HAS AN EXTENSIVE capacity to regenerate bone tissue after trauma. 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Both IM and EC ossification occurs during the bone-healing process in three overlapping regeneration phases. Critical-sized bone defects favor EC ossification over direct IM ossification, primarily due to the large, avascular nature of these defects. Four ECM-based biomaterial strategies (boxes) are highlighted with regard to bone regeneration. The intermediate fibrocartilaginous ECM remains underexplored (**) as a strategy to potentially enhance quality and extent of EC ossification and overall bone regeneration. ABG, autologous bone grafting; EC, endochondral; ECM, extracellular matrix; IM, intramembranous. Color images available online at www.liebertpub.com/teb", "bbox": [118, 135, 364, 640], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "figure_number", "raw_marker": "FIG. 1", "number": 1, "kind": "figure", "normalized_text": "FIG. 1. Both IM and EC ossification occurs during the bone-healing process in three overlapping regeneration phases. Critical-sized bone defects favor EC ossification over direct IM ossification, primarily due to the large, avascular nature of these defects. Four ECM-based biomaterial strategies (boxes) are highlighted with regard to bone regeneration. The intermediate fibrocartilaginous ECM remains underexplored (**) as a strategy to potentially enhance quality and extent of EC ossification and overall bone regeneration. ABG, autologous bone grafting; EC, endochondral; ECM, extracellular matrix; IM, intramembranous. 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Initial progenitor cells likely fail to survive early inflammatory phase. IM and EC ossification begin with BMSCs recruited from periosteum and marrow. Fibrous and cartilage tissue dominate bulk of fracture space. Revascularization initiating along periphery of the fracture. Procallus ECM breakdown and mineralization initiates fracture angiogenesis, which proceeds ossification. Woven bony callus spans bulk of fracture tissue, and may support mechanical load.", "page_width": 1224, "page_height": 1584, "role": "non_body_insert", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": null, "raw_observation": {"block_id": 4, "page": 2, "raw_label": "text", "text": "Damaged vasculature and marrow facilitate hematoma formation along with influx of inflammatory cells and BMSCs. Initial progenitor cells likely fail to survive early inflammatory phase. IM and EC ossification begin with BMSCs recruited from periosteum and marrow. Fibrous and cartilage tissue dominate bulk of fracture space. Revascularization initiating along periphery of the fracture. Procallus ECM breakdown and mineralization initiates fracture angiogenesis, which proceeds ossification. Woven bony callus spans bulk of fracture tissue, and may support mechanical load.", "bbox": [394, 186, 553, 292], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Damaged vasculature and marrow facilitate hematoma formation along with influx of inflammatory cells and BMSCs. Initial progenitor cells likely fail to survive early inflammatory phase. IM and EC ossification begin with BMSCs recruited from periosteum and marrow. Fibrous and cartilage tissue dominate bulk of fracture space. Revascularization initiating along periphery of the fracture. Procallus ECM breakdown and mineralization initiates fracture angiogenesis, which proceeds ossification. 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Dictated often by external mechanical load conditions and results in restoring healthy bone architecture.", "page_width": 1224, "page_height": 1584, "role": "non_body_insert", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": null, "raw_observation": {"block_id": 8, "page": 2, "raw_label": "text", "text": "Resorption of excess callus and replacement of woven bone with stronger lamellar bone. Dictated often by external mechanical load conditions and results in restoring healthy bone architecture.", "bbox": [931, 185, 1089, 305], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Resorption of excess callus and replacement of woven bone with stronger lamellar bone. 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As a result, many bone regeneration strategies have focused on mimicking portions of the complex composition and bioactive signals present in ABG, such as demineralized bone matrix (DBM), which resembles the late reparative stage extracellular matrix (ECM) in bone fracture repair (i.e., “hard” or “bony” callus). $ ^{1-8} $ These efforts have yielded dozens of clinical products, including synthetic scaffolds, allografts, and xenografts $ ^{15,16} $; however, the majority of orthopedic procedures continue to utilize ABG. $ ^{6,12-14} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", 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limitations, including donor site morbidity and pain, increased risk of infection, limited handling capacity, graft resorption problems, and restricted tissue availability. $ ^{6,12-14} $ Nearly three decades of bone tissue engineering research have been aimed at overcoming these limitations by finding performance competitive alternatives to ABG. As a result, many bone regeneration strategies have focused on mimicking portions of the complex composition and bioactive signals present in ABG, such as demineralized bone matrix (DBM), which resembles the late reparative stage extracellular matrix (ECM) in bone fracture repair (i.e., “hard” or “bony” callus). $ ^{1-8} $ These efforts have yielded dozens of clinical products, including synthetic scaffolds, allografts, and xenografts $ ^{15,16} $; however, the majority of orthopedic procedures continue to utilize ABG. $ ^{6,12-14} $", "bbox": [118, 706, 606, 1060], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "and thus osteogenic capabilities. $ ^{6,12-14} $ Despite these advantages, ABG has key clinical limitations, including donor site morbidity and pain, increased risk of infection, limited handling capacity, graft resorption problems, and restricted tissue availability. $ ^{6,12-14} $ Nearly three decades of bone tissue engineering research have been aimed at overcoming these limitations by finding performance competitive alternatives to ABG. As a result, many bone regeneration strategies have focused on mimicking portions of the complex composition and bioactive signals present in ABG, such as demineralized bone matrix (DBM), which resembles the late reparative stage extracellular matrix (ECM) in bone fracture repair (i.e., “hard” or “bony” callus). $ ^{1-8} $ These efforts have yielded dozens of clinical products, including synthetic scaffolds, allografts, and xenografts $ ^{15,16} $; however, the majority of orthopedic procedures continue to utilize ABG. $ ^{6,12-14} $"}, "layout_signature": {"width": 488, "width_bucket": 500, "height": 354, "left": 118, "top": 706, "right": 606, "bottom": 1060, "x_center": 362.0, "x_center_bucket": 350, "y_center": 883.0, "x_ratio": 0.2958, "y_ratio": 0.5574, "width_ratio": 0.3987, "height_ratio": 0.2235, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 228}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 2, "block_id": 11, "raw_label": "text", "raw_order": 9, "bbox": [117, 1060, 606, 1388], "text": "To date, acellular biomaterial-based products have dominated the alternative bone implant market at the commercial level. $ ^{11,15,16} $ A major characteristic of these products is the ability to mimic the biological ECM environment that is specific for bone regeneration. These materials possess both conductive scaffold moieties and inductive signaling molecules that have been difficult to match with synthetic designs. $ ^{17-21} $ Within the realm of bone biomimetics, native ECM-based biomaterials (e.g., DBM) have been a key protagonist. $ ^{15} $ However, there may be underexplored potential to enhance the bone regenerative response with native ECM biomaterials that instead mimic the initial inflammatory or fibrocartilaginous ECM (i.e., “pro-” or “soft” callus) observed in the early reparative stage of the native bone fracture healing process.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 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Critical-sized bone defects often require surgical intervention within hours as opposed to weeks, because delayed bone healing leads to a higher risk of nonunion. $ ^{9} $ Therefore, traditional cell expansion procedures represent a nonfeasible clinical option in most critical-sized defect indications. 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Critical-sized bone defects often require surgical intervention within hours as opposed to weeks, because delayed bone healing leads to a higher risk of nonunion. $ ^{9} $ Therefore, traditional cell expansion procedures represent a nonfeasible clinical option in most critical-sized defect indications. Advances in intraoperative SCBT strategies offer innovative solutions to overcome this challenge by combining cell harvest, isolation, and implantation in one surgical setting without compromising progenitor cell and signal efficacy, thus eliminating the prolonged cell expansion phase. $ ^{25} $ Although SCBT strategies could revolutionize the orthopedic market, basic biomaterial designs incorporating the appropriate native ECM components to accompany these SCBTs will be crucial in the advancement of bone regenerative medicine.", "bbox": [111, 117, 602, 446], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "in vitro cell expansion. Critical-sized bone defects often require surgical intervention within hours as opposed to weeks, because delayed bone healing leads to a higher risk of nonunion. $ ^{9} $ Therefore, traditional cell expansion procedures represent a nonfeasible clinical option in most critical-sized defect indications. Advances in intraoperative SCBT strategies offer innovative solutions to overcome this challenge by combining cell harvest, isolation, and implantation in one surgical setting without compromising progenitor cell and signal efficacy, thus eliminating the prolonged cell expansion phase. $ ^{25} $ Although SCBT strategies could revolutionize the orthopedic market, basic biomaterial designs incorporating the appropriate native ECM components to accompany these SCBTs will be crucial in the advancement of bone regenerative medicine."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 329, "left": 111, "top": 117, "right": 602, "bottom": 446, "x_center": 356.5, "x_center_bucket": 350, "y_center": 281.5, "x_ratio": 0.2913, "y_ratio": 0.1777, "width_ratio": 0.4011, "height_ratio": 0.2077, "line_count": 1}, "span_signature": {"font_size": 9.81, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimItalLieb", "bold": false, "italic": true, "span_count": 159}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 3, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [111, 447, 602, 752], "text": "An alternative strategy to reduce or remove the cell expansion step may reside in extending developmental engineering principles to in vivo designs (i.e., within the graft or implant), thus removing in vitro chondrogenic priming requirements altogether. Inspiration for in vivo developmental designs already exists with native ECM biomaterials, specifically acellular DBM grafts, which have already been shown to elicit some EC ossification in addition to the IM pathway. $ ^{26-32} $ However, as previously mentioned, DBM composition reflects the physicochemical properties of the late bone reparative stage ECM (Fig. 1) $ ^{6,9,33,34} $ and suggests that designs aimed at mimicking the composition of bone ECM may insufficiently elicit an EC ossification response inside healing fractures.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", 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Inspiration for in vivo developmental designs already exists with native ECM biomaterials, specifically acellular DBM grafts, which have already been shown to elicit some EC ossification in addition to the IM pathway. $ ^{26-32} $ However, as previously mentioned, DBM composition reflects the physicochemical properties of the late bone reparative stage ECM (Fig. 1) $ ^{6,9,33,34} $ and suggests that designs aimed at mimicking the composition of bone ECM may insufficiently elicit an EC ossification response inside healing fractures.", "bbox": [111, 447, 602, 752], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "An alternative strategy to reduce or remove the cell expansion step may reside in extending developmental engineering principles to in vivo designs (i.e., within the graft or implant), thus removing in vitro chondrogenic priming requirements altogether. Inspiration for in vivo developmental designs already exists with native ECM biomaterials, specifically acellular DBM grafts, which have already been shown to elicit some EC ossification in addition to the IM pathway. $ ^{26-32} $ However, as previously mentioned, DBM composition reflects the physicochemical properties of the late bone reparative stage ECM (Fig. 1) $ ^{6,9,33,34} $ and suggests that designs aimed at mimicking the composition of bone ECM may insufficiently elicit an EC ossification response inside healing fractures."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 305, "left": 111, "top": 447, "right": 602, "bottom": 752, "x_center": 356.5, "x_center_bucket": 350, "y_center": 599.5, "x_ratio": 0.2913, "y_ratio": 0.3785, "width_ratio": 0.4011, "height_ratio": 0.1926, "line_count": 1}, "span_signature": {"font_size": 9.81, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 172}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 3, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [112, 753, 602, 843], "text": "This review will highlight essential design criteria involved in the underexplored regenerative area of developmentally engineering bone in vivo (Fig. 2). Traditional strategies have approached tissue-engineered construction through a combination of factors described in the tissue engineering triad: cells, signals, and scaffolds. However, the use of “raw” ECM biomaterials may serve to bridge the gap between the latter two components of this triad by recognizing their integrated contribution to the local ECM, $ ^{20} $ potentially obviating the need for additional incorporation of cells and signaling molecules. Crucial to developmentally engineering the process of EC ossification inside an implant will not only be the selection of native biomaterials that mimic the relevant tissue’s ECM composition but also materials which serve to modulate the developmental process. The primary focus will be on acellular ECM strategies, where the physicochemical cues that native ECM biomaterials possess may sufficiently elicit a bone regenerative response. 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Current landscape of EC ossification strategies (blue boxes) along with underexplored design space (dashed outlines) highlighted in this review. Some combined cell and material strategies are not shown explicitly (dashed arrows). This includes several in vitro priming studies that utilized cell and material approaches (**) and are further explored elsewhere (Tables 2–4). All strategies will be critically evaluated with regard to technical, regulatory, and commercial challenges. ABG, autologous bone grafting; ADSCs, adipose-derived stem cells; BMA, bone marrow aspirate; DBM, demineralized bone matrix; DCC, decellularized cartilage; GMP, good manufacturing practice. Color images available online at www.liebertpub.com/teb", "bbox": [113, 1354, 1105, 1478], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "figure_number", "raw_marker": "FIG. 2", "number": 2, "kind": "figure", "normalized_text": "FIG. 2. Current landscape of EC ossification strategies (blue boxes) along with underexplored design space (dashed outlines) highlighted in this review. Some combined cell and material strategies are not shown explicitly (dashed arrows). This includes several in vitro priming studies that utilized cell and material approaches (**) and are further explored elsewhere (Tables 2–4). All strategies will be critically evaluated with regard to technical, regulatory, and commercial challenges. ABG, autologous bone grafting; ADSCs, adipose-derived stem cells; BMA, bone marrow aspirate; DBM, demineralized bone matrix; DCC, decellularized cartilage; GMP, good manufacturing practice. 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"style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_075", "display_cluster_candidate_id": "", "layout_region": "body_flow", "boundary_before": "none", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 4, "block_id": 2, "raw_label": "text", "raw_order": 1, "bbox": [117, 114, 606, 621], "text": "and bioactive signals. $ ^{1-9} $ Initially, disrupted vasculature and bone marrow during the inflammatory phase facilitates a coagulation cascade along with an influx of progenitor cells, including bone mesenchymal stem cells (BMSCs), into the fracture space forming a hematoma. Without permanent vasculature, however, the fracture space becomes hypoxic, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to play an active role in subsequent tissue regeneration. $ ^{1-9} $ Established bioactive signaling from the inflammatory phase ECM subsequently recruits progenitor cells from both the exposed periosteum and bone marrow that migrate into the fracture space, initiating both bone developmental pathways: IM and EC ossification. $ ^{1-8} $ Primary differences in these pathways reside in precursor requirements. 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bone marrow during the inflammatory phase facilitates a coagulation cascade along with an influx of progenitor cells, including bone mesenchymal stem cells (BMSCs), into the fracture space forming a hematoma. Without permanent vasculature, however, the fracture space becomes hypoxic, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to play an active role in subsequent tissue regeneration. $ ^{1-9} $ Established bioactive signaling from the inflammatory phase ECM subsequently recruits progenitor cells from both the exposed periosteum and bone marrow that migrate into the fracture space, initiating both bone developmental pathways: IM and EC ossification. $ ^{1-8} $ Primary differences in these pathways reside in precursor requirements. While IM requires condensation and proliferation of progenitor BMSCs for ossification, EC requires cartilage and fibrous intermediate tissue formation before ossification. $ ^{1-9} $ EC ossification, therefore, can further be divided into three generalized steps: (1) chondrogenesis, (2) cartilage hypertrophy, and (3) ossification. $ ^{1-9} $ Regardless of the pathway, however, neo-vascularization and angiogenesis are necessary before ossification can proceed. $ ^{5,6,35-38} $", "bbox": [117, 114, 606, 621], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "and bioactive signals. $ ^{1-9} $ Initially, disrupted vasculature and bone marrow during the inflammatory phase facilitates a coagulation cascade along with an influx of progenitor cells, including bone mesenchymal stem cells (BMSCs), into the fracture space forming a hematoma. Without permanent vasculature, however, the fracture space becomes hypoxic, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to play an active role in subsequent tissue regeneration. $ ^{1-9} $ Established bioactive signaling from the inflammatory phase ECM subsequently recruits progenitor cells from both the exposed periosteum and bone marrow that migrate into the fracture space, initiating both bone developmental pathways: IM and EC ossification. $ ^{1-8} $ Primary differences in these pathways reside in precursor requirements. While IM requires condensation and proliferation of progenitor BMSCs for ossification, EC requires cartilage and fibrous intermediate tissue formation before ossification. $ ^{1-9} $ EC ossification, therefore, can further be divided into three generalized steps: (1) chondrogenesis, (2) cartilage hypertrophy, and (3) ossification. $ ^{1-9} $ Regardless of the pathway, however, neo-vascularization and angiogenesis are necessary before ossification can proceed. $ ^{5,6,35-38} $"}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 507, "left": 117, "top": 114, "right": 606, "bottom": 621, "x_center": 361.5, "x_center_bucket": 350, "y_center": 367.5, "x_ratio": 0.2953, "y_ratio": 0.232, "width_ratio": 0.3995, "height_ratio": 0.3201, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 271}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 4, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [117, 621, 606, 950], "text": "In contrast, chondrogenesis predominantly occurs in avascular environments where oxygen tension is low. $ ^{39-43} $ The main consequence of this difference is that IM and EC ossification is manifested in physiologically distinct regions of the fracture space, where the former primarily occurs adjacent to the fracture ends and the latter occurs primarily in the avascular bulk of the fracture space. $ ^{2,5,6} $ Collectively, this early reparative stage climaxes in the formation of a spanning fibrocartilaginous callus (i.e., “pro-” or “soft” callus) in the majority of the fracture space developing from EC ossification. The procallus serves both a chemical and mechanical function and acts as a primed template for subsequent osteoblast infiltration, woven bone ossification (i.e., “hard” or “bony” callus), and, finally, bone remodeling to restore healthy lamellar bone architecture. $ ^{1-9} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, 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is low. $ ^{39-43} $ The main consequence of this difference is that IM and EC ossification is manifested in physiologically distinct regions of the fracture space, where the former primarily occurs adjacent to the fracture ends and the latter occurs primarily in the avascular bulk of the fracture space. $ ^{2,5,6} $ Collectively, this early reparative stage climaxes in the formation of a spanning fibrocartilaginous callus (i.e., “pro-” or “soft” callus) in the majority of the fracture space developing from EC ossification. The procallus serves both a chemical and mechanical function and acts as a primed template for subsequent osteoblast infiltration, woven bone ossification (i.e., “hard” or “bony” callus), and, finally, bone remodeling to restore healthy lamellar bone architecture. $ ^{1-9} $", "bbox": [117, 621, 606, 950], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "In contrast, chondrogenesis predominantly occurs in avascular environments where oxygen tension is low. $ ^{39-43} $ The main consequence of this difference is that IM and EC ossification is manifested in physiologically distinct regions of the fracture space, where the former primarily occurs adjacent to the fracture ends and the latter occurs primarily in the avascular bulk of the fracture space. $ ^{2,5,6} $ Collectively, this early reparative stage climaxes in the formation of a spanning fibrocartilaginous callus (i.e., “pro-” or “soft” callus) in the majority of the fracture space developing from EC ossification. The procallus serves both a chemical and mechanical function and acts as a primed template for subsequent osteoblast infiltration, woven bone ossification (i.e., “hard” or “bony” callus), and, finally, bone remodeling to restore healthy lamellar bone architecture. $ ^{1-9} $"}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 329, "left": 117, "top": 621, "right": 606, "bottom": 950, "x_center": 361.5, "x_center_bucket": 350, "y_center": 785.5, "x_ratio": 0.2953, "y_ratio": 0.4959, "width_ratio": 0.3995, "height_ratio": 0.2077, "line_count": 1}, "span_signature": {"font_size": 9.8, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 188}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 4, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [117, 950, 606, 1239], "text": "While the process mentioned earlier describes successful bone regeneration within the body, it is well understood that large defects above a “critical-size” are incapable of completely restoring native bone structure without intervention and often lead to nonunion. $ ^{9,10} $ It is important to note that critical-sized defects are inherently large, avascular spaces that present favorable conditions for EC ossification as opposed to IM. This review will outline several studies (Tables 1–3) that have leveraged EC ossification and developmental engineering strategies within critical-sized defects in various animal models. Collectively, this evidence suggests that enhancing EC ossification may be a viable, underexplored strategy for improving bone regeneration.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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Inspiration for in vivo developmental designs already exists in the form of native ECM biomaterials. There is significant evidence that EC ossification occurs in acellular DBM grafts, $ ^{26-29} $ which inherently resemble the composition of late reparative stage bone-healing ECM. $ ^{1-8,15} $ In a critical-sized rat femoral defect model, Oakes et al. $ ^{26} $ observed histological evidence of increased EC ossification foci in human DBM implants suspended in a hyaluronic acid carrier fluid compared with similar DBM implants suspended in a glycerol solution. However, radiographic scoring at 16 weeks postimplantation revealed no significant difference in their mineral content. $ ^{26} $ Although the authors did not further pursue developmental differences between groups, this evidence suggests that both EC and IM pathways were utilized within DBM implants. This could have been due to differences in carrier fluid. Hyaluronic acid is known to be a major component of cartilage ECM $ ^{4} $ and, therefore, could play a regulatory role in both chondrogenesis and EC ossification. $ ^{8} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 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Inspiration for in vivo developmental designs already exists in the form of native ECM biomaterials. There is significant evidence that EC ossification occurs in acellular DBM grafts, $ ^{26-29} $ which inherently resemble the composition of late reparative stage bone-healing ECM. $ ^{1-8,15} $ In a critical-sized rat femoral defect model, Oakes et al. $ ^{26} $ observed histological evidence of increased EC ossification foci in human DBM implants suspended in a hyaluronic acid carrier fluid compared with similar DBM implants suspended in a glycerol solution. However, radiographic scoring at 16 weeks postimplantation revealed no significant difference in their mineral content. $ ^{26} $ Although the authors did not further pursue developmental differences between groups, this evidence suggests that both EC and IM pathways were utilized within DBM implants. This could have been due to differences in carrier fluid. Hyaluronic acid is known to be a major component of cartilage ECM $ ^{4} $ and, therefore, could play a regulatory role in both chondrogenesis and EC ossification. $ ^{8} $", "bbox": [618, 773, 1110, 1213], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Characterizing the influence of DBM on ossification pathway. Inspiration for in vivo developmental designs already exists in the form of native ECM biomaterials. There is significant evidence that EC ossification occurs in acellular DBM grafts, $ ^{26-29} $ which inherently resemble the composition of late reparative stage bone-healing ECM. $ ^{1-8,15} $ In a critical-sized rat femoral defect model, Oakes et al. $ ^{26} $ observed histological evidence of increased EC ossification foci in human DBM implants suspended in a hyaluronic acid carrier fluid compared with similar DBM implants suspended in a glycerol solution. However, radiographic scoring at 16 weeks postimplantation revealed no significant difference in their mineral content. $ ^{26} $ Although the authors did not further pursue developmental differences between groups, this evidence suggests that both EC and IM pathways were utilized within DBM implants. This could have been due to differences in carrier fluid. Hyaluronic acid is known to be a major component of cartilage ECM $ ^{4} $ and, therefore, could play a regulatory role in both chondrogenesis and EC ossification. $ ^{8} $"}, "layout_signature": {"width": 492, "width_bucket": 500, "height": 440, "left": 618, "top": 773, "right": 1110, "bottom": 1213, "x_center": 864.0, "x_center_bucket": 875, "y_center": 993.0, "x_ratio": 0.7059, "y_ratio": 0.6269, "width_ratio": 0.402, "height_ratio": 0.2778, "line_count": 1}, "span_signature": {"font_size": 9.74, "font_size_median": 9.84, "font_size_bucket": 9.5, "font_family_norm": "AdvP6EC0", "bold": false, "italic": true, "span_count": 291}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_073", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 4, "block_id": 16, "raw_label": "text", "raw_order": 15, "bbox": [618, 1213, 1110, 1480], "text": "Regardless of this, the DBM composition containing conductive and inductive biological agents likely influences developmental pathways during bone healing. $ ^{26-29} $ DBM composition, however, is not uniform throughout the body. There exist compositional differences in bone ECM originating from IM sources during fetal development (e.g., cranium) and EC sources (e.g., femur). $ ^{44} $ Furthermore, DBM originating from IM and EC bone have been shown in a series of studies by Rabie et al. $ ^{28,30-32} $ to elicit different healing pathways during regeneration of parietal bone defects in New Zealand White Rabbits. The parietal bone is formed by IM ossification during fetal development, $ ^{44} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": 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healing. $ ^{26-29} $ DBM composition, however, is not uniform throughout the body. There exist compositional differences in bone ECM originating from IM sources during fetal development (e.g., cranium) and EC sources (e.g., femur). $ ^{44} $ Furthermore, DBM originating from IM and EC bone have been shown in a series of studies by Rabie et al. $ ^{28,30-32} $ to elicit different healing pathways during regeneration of parietal bone defects in New Zealand White Rabbits. The parietal bone is formed by IM ossification during fetal development, $ ^{44} $", "bbox": [618, 1213, 1110, 1480], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Regardless of this, the DBM composition containing conductive and inductive biological agents likely influences developmental pathways during bone healing. $ ^{26-29} $ DBM composition, however, is not uniform throughout the body. There exist compositional differences in bone ECM originating from IM sources during fetal development (e.g., cranium) and EC sources (e.g., femur). $ ^{44} $ Furthermore, DBM originating from IM and EC bone have been shown in a series of studies by Rabie et al. $ ^{28,30-32} $ to elicit different healing pathways during regeneration of parietal bone defects in New Zealand White Rabbits. 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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Yamada et al.1042003BMSCsFibrin and beta-TCPIsolated rat BMSCs were chondrogenically primed on beta-TCP blocks and implanted with fibrin glue.Implanted subcutaneously in nude mice.EC ossification was only seen in primed rBMSC constructs. Noncellular and unprimed rBMSC scaffolds did not produce EC ossification.
Simmons et al.1052004BMSCsAlginate Matrix (RGD conjugation)Isolated rat BMSCs were chondrogenically primed and implanted with dual growth factor encapsulation (BMP-2 and TGF- $ \\beta $).Implanted subcutaneously in nude mice.Significantly higher amount of EC ossification was seen in scaffolds with dual GF compared with single GF and nonloaded controls.
Peltari et al.722006BMSCsFibrin MatrixIsolated human BMSCs were primed in chondrogenic medium for 4 to 7 weeks. Human ACs were isolated for implantation, and a portion of hACs were expanded in chondrogenic medium.Implanted subcutaneously in nude mice.hBMSCs exhibited extensive EC ossification, while hACs remained stable cartilage. Chondrogenically expanded hACs did not undergo EC ossification, suggesting that they are locked into a stable cartilage phase.
Farrell et al.642009BMSCsCollagen and GAGIsolated human BMSCs were cultured for 21 days in chondrogenic medium. Three groups were cultured for 14 extra days in (a) the same medium, (b) mineralizing chondrogenic medium, or (c) osteogenic medium. Unprimed control medium was also used.Implanted subcutaneously in nude mice.Chondrogenic priming led to collagen II and X production along with vessel ingrowth in vivo while osteogenic priming led to mineralized matrix, no vascularization, and poor cell viability. Unprimed control conditions yielded no bone. Mineralized chondrogenic priming severely diminished production of inductive growth factors.
Janicki et al.662010BMSCsbeta-TCP or Hydroxyapatite (HA/TCP)Isolated human BMSCs were primed in chondrogenic medium (6 weeks), in osteogenic medium, or unprimed in control medium.Implanted subcutaneously in nude mice.Osteogenic priming led to poor bone formation. Unprimed hBMSCs on beta-TCP exhibited IM ossification. With chondrogenic priming, hBMSCs formed bone via EC ossification, while hematopoietic marrow formed from murine origin. This was hypothesized to be the result of direct osteogenesis of cartilage-resident hBMSCs or transdifferentiation from chondrocytes to osteoblasts.
Scotti et al.742010BMSCsNone, direct pellet implantationIsolated human BMSCs were primed to prechondrogenic, early hypertrophic, and late hypertrophic phase tissuesImplanted subcutaneously in nude mice.Hypertrophic cartilage templates were required to form bone trabeculae. Prehypertrophic hBMSCs resorbed quickly and did not form bone. Results indicate that no external scaffolding was required to undergo EC ossification.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Yamada et al.1042003BMSCsFibrin and beta-TCPIsolated rat BMSCs were chondrogenically primed on beta-TCP blocks and implanted with fibrin glue.Implanted subcutaneously in nude mice.EC ossification was only seen in primed rBMSC constructs. Noncellular and unprimed rBMSC scaffolds did not produce EC ossification.
Simmons et al.1052004BMSCsAlginate Matrix (RGD conjugation)Isolated rat BMSCs were chondrogenically primed and implanted with dual growth factor encapsulation (BMP-2 and TGF- $ \\beta $).Implanted subcutaneously in nude mice.Significantly higher amount of EC ossification was seen in scaffolds with dual GF compared with single GF and nonloaded controls.
Peltari et al.722006BMSCsFibrin MatrixIsolated human BMSCs were primed in chondrogenic medium for 4 to 7 weeks. Human ACs were isolated for implantation, and a portion of hACs were expanded in chondrogenic medium.Implanted subcutaneously in nude mice.hBMSCs exhibited extensive EC ossification, while hACs remained stable cartilage. Chondrogenically expanded hACs did not undergo EC ossification, suggesting that they are locked into a stable cartilage phase.
Farrell et al.642009BMSCsCollagen and GAGIsolated human BMSCs were cultured for 21 days in chondrogenic medium. Three groups were cultured for 14 extra days in (a) the same medium, (b) mineralizing chondrogenic medium, or (c) osteogenic medium. Unprimed control medium was also used.Implanted subcutaneously in nude mice.Chondrogenic priming led to collagen II and X production along with vessel ingrowth in vivo while osteogenic priming led to mineralized matrix, no vascularization, and poor cell viability. Unprimed control conditions yielded no bone. Mineralized chondrogenic priming severely diminished production of inductive growth factors.
Janicki et al.662010BMSCsbeta-TCP or Hydroxyapatite (HA/TCP)Isolated human BMSCs were primed in chondrogenic medium (6 weeks), in osteogenic medium, or unprimed in control medium.Implanted subcutaneously in nude mice.Osteogenic priming led to poor bone formation. Unprimed hBMSCs on beta-TCP exhibited IM ossification. With chondrogenic priming, hBMSCs formed bone via EC ossification, while hematopoietic marrow formed from murine origin. This was hypothesized to be the result of direct osteogenesis of cartilage-resident hBMSCs or transdifferentiation from chondrocytes to osteoblasts.
Scotti et al.742010BMSCsNone, direct pellet implantationIsolated human BMSCs were primed to prechondrogenic, early hypertrophic, and late hypertrophic phase tissuesImplanted subcutaneously in nude mice.Hypertrophic cartilage templates were required to form bone trabeculae. Prehypertrophic hBMSCs resorbed quickly and did not form bone. Results indicate that no external scaffolding was required to undergo EC ossification.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Yamada et al.1042003BMSCsFibrin and beta-TCPIsolated rat BMSCs were chondrogenically primed on beta-TCP blocks and implanted with fibrin glue.Implanted subcutaneously in nude mice.EC ossification was only seen in primed rBMSC constructs. Noncellular and unprimed rBMSC scaffolds did not produce EC ossification.
Simmons et al.1052004BMSCsAlginate Matrix (RGD conjugation)Isolated rat BMSCs were chondrogenically primed and implanted with dual growth factor encapsulation (BMP-2 and TGF- $ \\beta $).Implanted subcutaneously in nude mice.Significantly higher amount of EC ossification was seen in scaffolds with dual GF compared with single GF and nonloaded controls.
Peltari et al.722006BMSCsFibrin MatrixIsolated human BMSCs were primed in chondrogenic medium for 4 to 7 weeks. Human ACs were isolated for implantation, and a portion of hACs were expanded in chondrogenic medium.Implanted subcutaneously in nude mice.hBMSCs exhibited extensive EC ossification, while hACs remained stable cartilage. Chondrogenically expanded hACs did not undergo EC ossification, suggesting that they are locked into a stable cartilage phase.
Farrell et al.642009BMSCsCollagen and GAGIsolated human BMSCs were cultured for 21 days in chondrogenic medium. Three groups were cultured for 14 extra days in (a) the same medium, (b) mineralizing chondrogenic medium, or (c) osteogenic medium. Unprimed control medium was also used.Implanted subcutaneously in nude mice.Chondrogenic priming led to collagen II and X production along with vessel ingrowth in vivo while osteogenic priming led to mineralized matrix, no vascularization, and poor cell viability. Unprimed control conditions yielded no bone. Mineralized chondrogenic priming severely diminished production of inductive growth factors.
Janicki et al.662010BMSCsbeta-TCP or Hydroxyapatite (HA/TCP)Isolated human BMSCs were primed in chondrogenic medium (6 weeks), in osteogenic medium, or unprimed in control medium.Implanted subcutaneously in nude mice.Osteogenic priming led to poor bone formation. Unprimed hBMSCs on beta-TCP exhibited IM ossification. With chondrogenic priming, hBMSCs formed bone via EC ossification, while hematopoietic marrow formed from murine origin. This was hypothesized to be the result of direct osteogenesis of cartilage-resident hBMSCs or transdifferentiation from chondrocytes to osteoblasts.
Scotti et al.742010BMSCsNone, direct pellet implantationIsolated human BMSCs were primed to prechondrogenic, early hypertrophic, and late hypertrophic phase tissuesImplanted subcutaneously in nude mice.Hypertrophic cartilage templates were required to form bone trabeculae. Prehypertrophic hBMSCs resorbed quickly and did not form bone. Results indicate that no external scaffolding was required to undergo EC ossification.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Farrell et al. $ ^{63} $2011BMSCsCollagen and GAGIsolated human BMSCs and rat BMSCs were cultured in osteogenic, chondrogenic, or control medium (28 days). In some cases, induced mineralization in chondrogenic medium lasted for 7 days.Implanted subcutaneously in nude co-isogenic hPLAP-transgenic F344 ratsBone and bone marrow was observed in chondrogenic primed constructs but not in unprimed control and osteogenic primed constructs. Late switching (last 7 days) to osteogenic medium prevented bone formation, but beta-glycophosphate-induced mineralization did not prevent bone formation in chondrogenic primed constructs. Osteoblasts in formed bone were almost entirely of host origin, but osteocytes were of both host and donor origin.
Scotti et al. $ ^{73} $2013BMSCsCollagen Type I MeshesIsolated human BMSCs were primed to hypertrophic stage and seeded onto collagen type I meshes.Implanted subcutaneously in nude mice.Functional bone was formed heterotopically with cortical-like bone originating from host murine cells, and inner trabecular-like bone from EC ossification and originating from hBMSC primed hypertrophic cartilage constructs.
Sheehy et al. $ ^{60} $2013BMSCsAgaroseIsolated porcine chondrocytes and BMSCs were cultured and chondrogenically primed before seeding on bilayer osteochondral scaffolds.Implanted subcutaneously in nude mice.EC ossification was restricted to the BMSC primed layer of the scaffold in vivo, while primed chondrocytes maintained chondrogenic phenotype. This led to a bilayer osteochondral construct.
Sheehy et al. $ ^{107} $2014BMSCsAgarose and “Channeled” AgaroseIsolated porcine BMSCs were chondrogenically primed for 5 weeks followed by hypertrophic priming for an additional week.Implanted subcutaneously in nude mice.EC ossification was observed in hypertrophic primed pBMSCs encapsulated in agarose gel. In addition, chameled agarose gels with pBMSCs showed increased vascularization and mineralization compared with solid agarose counterparts, which indicated that EC ossification may be enhanced with improved vascular support.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Farrell et al. $ ^{63} $2011BMSCsCollagen and GAGIsolated human BMSCs and rat BMSCs were cultured in osteogenic, chondrogenic, or control medium (28 days). In some cases, induced mineralization in chondrogenic medium lasted for 7 days.Implanted subcutaneously in nude co-isogenic hPLAP-transgenic F344 ratsBone and bone marrow was observed in chondrogenic primed constructs but not in unprimed control and osteogenic primed constructs. Late switching (last 7 days) to osteogenic medium prevented bone formation, but beta-glycophosphate-induced mineralization did not prevent bone formation in chondrogenic primed constructs. Osteoblasts in formed bone were almost entirely of host origin, but osteocytes were of both host and donor origin.
Scotti et al. $ ^{73} $2013BMSCsCollagen Type I MeshesIsolated human BMSCs were primed to hypertrophic stage and seeded onto collagen type I meshes.Implanted subcutaneously in nude mice.Functional bone was formed heterotopically with cortical-like bone originating from host murine cells, and inner trabecular-like bone from EC ossification and originating from hBMSC primed hypertrophic cartilage constructs.
Sheehy et al. $ ^{60} $2013BMSCsAgaroseIsolated porcine chondrocytes and BMSCs were cultured and chondrogenically primed before seeding on bilayer osteochondral scaffolds.Implanted subcutaneously in nude mice.EC ossification was restricted to the BMSC primed layer of the scaffold in vivo, while primed chondrocytes maintained chondrogenic phenotype. This led to a bilayer osteochondral construct.
Sheehy et al. $ ^{107} $2014BMSCsAgarose and “Channeled” AgaroseIsolated porcine BMSCs were chondrogenically primed for 5 weeks followed by hypertrophic priming for an additional week.Implanted subcutaneously in nude mice.EC ossification was observed in hypertrophic primed pBMSCs encapsulated in agarose gel. In addition, chameled agarose gels with pBMSCs showed increased vascularization and mineralization compared with solid agarose counterparts, which indicated that EC ossification may be enhanced with improved vascular support.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Farrell et al. $ ^{63} $2011BMSCsCollagen and GAGIsolated human BMSCs and rat BMSCs were cultured in osteogenic, chondrogenic, or control medium (28 days). In some cases, induced mineralization in chondrogenic medium lasted for 7 days.Implanted subcutaneously in nude co-isogenic hPLAP-transgenic F344 ratsBone and bone marrow was observed in chondrogenic primed constructs but not in unprimed control and osteogenic primed constructs. Late switching (last 7 days) to osteogenic medium prevented bone formation, but beta-glycophosphate-induced mineralization did not prevent bone formation in chondrogenic primed constructs. Osteoblasts in formed bone were almost entirely of host origin, but osteocytes were of both host and donor origin.
Scotti et al. $ ^{73} $2013BMSCsCollagen Type I MeshesIsolated human BMSCs were primed to hypertrophic stage and seeded onto collagen type I meshes.Implanted subcutaneously in nude mice.Functional bone was formed heterotopically with cortical-like bone originating from host murine cells, and inner trabecular-like bone from EC ossification and originating from hBMSC primed hypertrophic cartilage constructs.
Sheehy et al. $ ^{60} $2013BMSCsAgaroseIsolated porcine chondrocytes and BMSCs were cultured and chondrogenically primed before seeding on bilayer osteochondral scaffolds.Implanted subcutaneously in nude mice.EC ossification was restricted to the BMSC primed layer of the scaffold in vivo, while primed chondrocytes maintained chondrogenic phenotype. This led to a bilayer osteochondral construct.
Sheehy et al. $ ^{107} $2014BMSCsAgarose and “Channeled” AgaroseIsolated porcine BMSCs were chondrogenically primed for 5 weeks followed by hypertrophic priming for an additional week.Implanted subcutaneously in nude mice.EC ossification was observed in hypertrophic primed pBMSCs encapsulated in agarose gel. In addition, chameled agarose gels with pBMSCs showed increased vascularization and mineralization compared with solid agarose counterparts, which indicated that EC ossification may be enhanced with improved vascular support.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Bahney et al. 1102014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks. In addition, cartilage grafts were isolated from healing callus at 7 days after fracture and re-implanted in vivo. Implants were compared with living isografts, devitalized allografts, and sham groups.Implanted into mid-tibia diaphysis osteotomy in nude mice.Cartilage grafts and primed hBMSC pellets produce well vascularized and integrated bone regenerate via EC ossification; however, hBMSC pellets did not integrate with each other in vivo. Cartilage graft was equally likely to integrate with adjacent bone as bone isografts and outperformed devitalized allografts. Osteocytes in regenerated bone were primarily of donor origin rather than host recruited cells.
van der Stok et al. 1062014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks and compared with hBMSCs cultured in chondrogenic media for only 3 days.Implanted in 6 mm mid-femur diaphysis defects in Rowett nude rats.Significantly higher EC ossification was observed in 21 day chondrogenically primed hBMSC pellets compared with 3 day undifferentiated hBMSC controls. Primed hBMSC can result in complete bridging of the 6 mm defect; however, the effect was donor dependent.
Harada et al. 1052014BMSCsPLGAIsolated rat BMSCs were chondrogenically primed for 21 days and compared with rBMSCs that were cultured in standard medium. Implants were also compared with cell-free scaffolds and contralateral femur controls.Implanted into 5 and 15 mm mid-femur diaphysis defects in Fischer 344 rats.Significantly higher EC ossification was observed in chondrogenically primed rBMSCs seeded onto PLGA scaffolds compared with undifferentiated hBMSC controls. Histological, micro-CT, and mechanical analysis of primed cell scaffolds revealed functionalized bone regeneration as early as 2 weeks after implantation in both 5 and 15 mm defect models. By 8 weeks, mechanical strength of primed cell scaffolds was statistically equivalent to contralateral femur controls in 5 mm defects, while scaffolds implanted in 15 mm defects exhibited 75% of the mean strength of native bone.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Bahney et al. 1102014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks. In addition, cartilage grafts were isolated from healing callus at 7 days after fracture and re-implanted in vivo. Implants were compared with living isografts, devitalized allografts, and sham groups.Implanted into mid-tibia diaphysis osteotomy in nude mice.Cartilage grafts and primed hBMSC pellets produce well vascularized and integrated bone regenerate via EC ossification; however, hBMSC pellets did not integrate with each other in vivo. Cartilage graft was equally likely to integrate with adjacent bone as bone isografts and outperformed devitalized allografts. Osteocytes in regenerated bone were primarily of donor origin rather than host recruited cells.
van der Stok et al. 1062014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks and compared with hBMSCs cultured in chondrogenic media for only 3 days.Implanted in 6 mm mid-femur diaphysis defects in Rowett nude rats.Significantly higher EC ossification was observed in 21 day chondrogenically primed hBMSC pellets compared with 3 day undifferentiated hBMSC controls. Primed hBMSC can result in complete bridging of the 6 mm defect; however, the effect was donor dependent.
Harada et al. 1052014BMSCsPLGAIsolated rat BMSCs were chondrogenically primed for 21 days and compared with rBMSCs that were cultured in standard medium. Implants were also compared with cell-free scaffolds and contralateral femur controls.Implanted into 5 and 15 mm mid-femur diaphysis defects in Fischer 344 rats.Significantly higher EC ossification was observed in chondrogenically primed rBMSCs seeded onto PLGA scaffolds compared with undifferentiated hBMSC controls. Histological, micro-CT, and mechanical analysis of primed cell scaffolds revealed functionalized bone regeneration as early as 2 weeks after implantation in both 5 and 15 mm defect models. By 8 weeks, mechanical strength of primed cell scaffolds was statistically equivalent to contralateral femur controls in 5 mm defects, while scaffolds implanted in 15 mm defects exhibited 75% of the mean strength of native bone.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Bahney et al. 1102014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks. In addition, cartilage grafts were isolated from healing callus at 7 days after fracture and re-implanted in vivo. Implants were compared with living isografts, devitalized allografts, and sham groups.Implanted into mid-tibia diaphysis osteotomy in nude mice.Cartilage grafts and primed hBMSC pellets produce well vascularized and integrated bone regenerate via EC ossification; however, hBMSC pellets did not integrate with each other in vivo. Cartilage graft was equally likely to integrate with adjacent bone as bone isografts and outperformed devitalized allografts. Osteocytes in regenerated bone were primarily of donor origin rather than host recruited cells.
van der Stok et al. 1062014BMSCsNone, direct pellet implantationIsolated human BMSCs were chondrogenically primed for three weeks and compared with hBMSCs cultured in chondrogenic media for only 3 days.Implanted in 6 mm mid-femur diaphysis defects in Rowett nude rats.Significantly higher EC ossification was observed in 21 day chondrogenically primed hBMSC pellets compared with 3 day undifferentiated hBMSC controls. Primed hBMSC can result in complete bridging of the 6 mm defect; however, the effect was donor dependent.
Harada et al. 1052014BMSCsPLGAIsolated rat BMSCs were chondrogenically primed for 21 days and compared with rBMSCs that were cultured in standard medium. Implants were also compared with cell-free scaffolds and contralateral femur controls.Implanted into 5 and 15 mm mid-femur diaphysis defects in Fischer 344 rats.Significantly higher EC ossification was observed in chondrogenically primed rBMSCs seeded onto PLGA scaffolds compared with undifferentiated hBMSC controls. Histological, micro-CT, and mechanical analysis of primed cell scaffolds revealed functionalized bone regeneration as early as 2 weeks after implantation in both 5 and 15 mm defect models. By 8 weeks, mechanical strength of primed cell scaffolds was statistically equivalent to contralateral femur controls in 5 mm defects, while scaffolds implanted in 15 mm defects exhibited 75% of the mean strength of native bone.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Montufar-Solis et al. $ ^{27} $2004ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted adjacent to and within murine skull defects of same lineage.Implants placed both adjacently and directly into skull defects exhibited EC ossification, while control groups without primed implants did not.
Doan et al. $ ^{62} $2010ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted into murine skull defects of same lineage.EC Ossification was only seen in rBMSC primed cartilage implants.
Shoji et al. $ ^{108} $2010ADSCsCollagenIsolated human ADSCs expanded from SVFImplanted in nude rat femurshADSCs exhibited greater EC ossification than PBS and hFB (fibroblast) implant controls in collagen matrix.
Case et al. $ ^{61} $2003ACsPGAIsolated rabbit chondrocytes from patellar groove and femoral condyles were chondrogenically primed on PGA scaffolds for 4 weeks.Implanted into empty bone chambers in rabbit femoral metaphyses.Cell-loaded constructs exhibited EC ossification and led to increased bone formation compared with devitalized constructs. Thus, cells had a significant impact on outcome.
Oliveira et al. $ ^{70,71} $2009ACsChitosan SpongeIsolated chondrocytes from chicken embryo stroma expanded on chitosan sponge and hypertrophically primed for 3 weeks. Control chondrocytes were taken from caudal region of sternum, while transient chondrocytes were taken from cephalic region of sternum.Implanted subcutaneously in nude mice.Maturation and hypertrophy seen in treated chondrocyte-chitosan scaffolds. EC ossification was only seen in transient cartilage templates compared with permanent cartilage scaffold (control).
Tam et al. $ ^{109} $2014iChonsCopiOs (Zimmer) Bone Void FillerInduced chondrocytes (iChons) were directly reprogrammed from murine dermal fibroblasts by two methods: iChon (Con) and iChon (Ind). After induction, cells were chondrogenically primed for 7 days, and hypertrophically primed for 14 days.Implanted subcutaneously in nude mice.Both induced cell sources underwent chondrogenic differentiation in vitro, but hypertrophic differentiation was only seen in iChon (Ind) cells. In vivo, iChon (Con) cells formed stable cartilage, while iChon (Ind) cells exhibited EC ossification markers. Osteoblasts in formed bone were of host origin, while chondrocytes were of both donor and host origin.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Montufar-Solis et al. $ ^{27} $2004ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted adjacent to and within murine skull defects of same lineage.Implants placed both adjacently and directly into skull defects exhibited EC ossification, while control groups without primed implants did not.
Doan et al. $ ^{62} $2010ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted into murine skull defects of same lineage.EC Ossification was only seen in rBMSC primed cartilage implants.
Shoji et al. $ ^{108} $2010ADSCsCollagenIsolated human ADSCs expanded from SVFImplanted in nude rat femurshADSCs exhibited greater EC ossification than PBS and hFB (fibroblast) implant controls in collagen matrix.
Case et al. $ ^{61} $2003ACsPGAIsolated rabbit chondrocytes from patellar groove and femoral condyles were chondrogenically primed on PGA scaffolds for 4 weeks.Implanted into empty bone chambers in rabbit femoral metaphyses.Cell-loaded constructs exhibited EC ossification and led to increased bone formation compared with devitalized constructs. Thus, cells had a significant impact on outcome.
Oliveira et al. $ ^{70,71} $2009ACsChitosan SpongeIsolated chondrocytes from chicken embryo stroma expanded on chitosan sponge and hypertrophically primed for 3 weeks. Control chondrocytes were taken from caudal region of sternum, while transient chondrocytes were taken from cephalic region of sternum.Implanted subcutaneously in nude mice.Maturation and hypertrophy seen in treated chondrocyte-chitosan scaffolds. EC ossification was only seen in transient cartilage templates compared with permanent cartilage scaffold (control).
Tam et al. $ ^{109} $2014iChonsCopiOs (Zimmer) Bone Void FillerInduced chondrocytes (iChons) were directly reprogrammed from murine dermal fibroblasts by two methods: iChon (Con) and iChon (Ind). After induction, cells were chondrogenically primed for 7 days, and hypertrophically primed for 14 days.Implanted subcutaneously in nude mice.Both induced cell sources underwent chondrogenic differentiation in vitro, but hypertrophic differentiation was only seen in iChon (Ind) cells. In vivo, iChon (Con) cells formed stable cartilage, while iChon (Ind) cells exhibited EC ossification markers. Osteoblasts in formed bone were of host origin, while chondrocytes were of both donor and host origin.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Montufar-Solis et al. $ ^{27} $2004ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted adjacent to and within murine skull defects of same lineage.Implants placed both adjacently and directly into skull defects exhibited EC ossification, while control groups without primed implants did not.
Doan et al. $ ^{62} $2010ESCsNone, direct pellet implantationIsolated murine ESC constructs were chondrogenically primed for 3 weeks.Implanted into murine skull defects of same lineage.EC Ossification was only seen in rBMSC primed cartilage implants.
Shoji et al. $ ^{108} $2010ADSCsCollagenIsolated human ADSCs expanded from SVFImplanted in nude rat femurshADSCs exhibited greater EC ossification than PBS and hFB (fibroblast) implant controls in collagen matrix.
Case et al. $ ^{61} $2003ACsPGAIsolated rabbit chondrocytes from patellar groove and femoral condyles were chondrogenically primed on PGA scaffolds for 4 weeks.Implanted into empty bone chambers in rabbit femoral metaphyses.Cell-loaded constructs exhibited EC ossification and led to increased bone formation compared with devitalized constructs. Thus, cells had a significant impact on outcome.
Oliveira et al. $ ^{70,71} $2009ACsChitosan SpongeIsolated chondrocytes from chicken embryo stroma expanded on chitosan sponge and hypertrophically primed for 3 weeks. Control chondrocytes were taken from caudal region of sternum, while transient chondrocytes were taken from cephalic region of sternum.Implanted subcutaneously in nude mice.Maturation and hypertrophy seen in treated chondrocyte-chitosan scaffolds. EC ossification was only seen in transient cartilage templates compared with permanent cartilage scaffold (control).
Tam et al. $ ^{109} $2014iChonsCopiOs (Zimmer) Bone Void FillerInduced chondrocytes (iChons) were directly reprogrammed from murine dermal fibroblasts by two methods: iChon (Con) and iChon (Ind). After induction, cells were chondrogenically primed for 7 days, and hypertrophically primed for 14 days.Implanted subcutaneously in nude mice.Both induced cell sources underwent chondrogenic differentiation in vitro, but hypertrophic differentiation was only seen in iChon (Ind) cells. In vivo, iChon (Con) cells formed stable cartilage, while iChon (Ind) cells exhibited EC ossification markers. Osteoblasts in formed bone were of host origin, while chondrocytes were of both donor and host origin.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal moeaChondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation. Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Dickhut et al.772009BMSCs, ADSCs, SDSCs and ACsNone, direct pellet implantationIsolated human BMSCs, ADSCs, SDSCs and ACs were cultured in chondrogenic medium (5 weeks).Implanted subcutaneously in nude mice.Chondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation.
Jukes et al.672008ESCs, BMSCs, and ACsCeramic particlesIsolated goat and human BMSCs were osteogenically primed for 7 or 21 days. In addition, these cells along with murine ESCs and goat ACs were chondrogenically primed for approximately 21 days.Implanted into nude mouse skull defects.Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Tortelli et al.1112009BMSCs and OBsHydroxyapatiteIsolated rate BMSCs and OBs were cultured in standard medium.Implanted subcutaneously in nude mice.The capacity to recruit host cells and the ossification pathway were dependent on donor cell commitment. rBMSC implants led to formation of bone from host cells through the EC ossification pathway, and donor rOBs exhibited direct IM ossification. No studies were conducted with chondrogenically primed cells.
Both et al.762011BMSCs and ESCsBCPIsolated human BMSCs, rat ESCs, and human ESCs were cultured in a series of differentiation mediums, including chondrogenic priming followed by osteogenic priming. Cells were seeded on BCP scaffolds.Implanted subcutaneously in nude mice.ESCs were indistinguishable from BMSCs after in vitro osteogenic priming. Osteogenic priming of BMSCs led to direct IM osteogenesis and extensive bone formation. Both rESCs and hESCs did not form substantial bone but exhibited signs of limited EC ossification.
Vinardell et al.752012BMSCs, FPSCs, SDSCs and ACsAgaroseIsolated porcine BMSCs, SDSCs, FPSCs, and ACs were chondrogenically primed (3 weeks). An additional group was primed in hypertrophic medium for 4 weeks.Implanted subcutaneously in nude mice.Only BMSCs exhibited EC ossification. SDSCs and FPSCs underwent fibrous dedifferentiation and resorption, and ACs appeared to maintain chondrogenic stability.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal moeaChondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation. Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Dickhut et al.772009BMSCs, ADSCs, SDSCs and ACsNone, direct pellet implantationIsolated human BMSCs, ADSCs, SDSCs and ACs were cultured in chondrogenic medium (5 weeks).Implanted subcutaneously in nude mice.Chondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation.
Jukes et al.672008ESCs, BMSCs, and ACsCeramic particlesIsolated goat and human BMSCs were osteogenically primed for 7 or 21 days. In addition, these cells along with murine ESCs and goat ACs were chondrogenically primed for approximately 21 days.Implanted into nude mouse skull defects.Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Tortelli et al.1112009BMSCs and OBsHydroxyapatiteIsolated rate BMSCs and OBs were cultured in standard medium.Implanted subcutaneously in nude mice.The capacity to recruit host cells and the ossification pathway were dependent on donor cell commitment. rBMSC implants led to formation of bone from host cells through the EC ossification pathway, and donor rOBs exhibited direct IM ossification. No studies were conducted with chondrogenically primed cells.
Both et al.762011BMSCs and ESCsBCPIsolated human BMSCs, rat ESCs, and human ESCs were cultured in a series of differentiation mediums, including chondrogenic priming followed by osteogenic priming. Cells were seeded on BCP scaffolds.Implanted subcutaneously in nude mice.ESCs were indistinguishable from BMSCs after in vitro osteogenic priming. Osteogenic priming of BMSCs led to direct IM osteogenesis and extensive bone formation. Both rESCs and hESCs did not form substantial bone but exhibited signs of limited EC ossification.
Vinardell et al.752012BMSCs, FPSCs, SDSCs and ACsAgaroseIsolated porcine BMSCs, SDSCs, FPSCs, and ACs were chondrogenically primed (3 weeks). An additional group was primed in hypertrophic medium for 4 weeks.Implanted subcutaneously in nude mice.Only BMSCs exhibited EC ossification. SDSCs and FPSCs underwent fibrous dedifferentiation and resorption, and ACs appeared to maintain chondrogenic stability.
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Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal moeaChondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation. Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Dickhut et al.772009BMSCs, ADSCs, SDSCs and ACsNone, direct pellet implantationIsolated human BMSCs, ADSCs, SDSCs and ACs were cultured in chondrogenic medium (5 weeks).Implanted subcutaneously in nude mice.Chondrogenic priming led to similar collagen type II vs. type I levels and were positive for type X in all cells. SDSCs and ACs had significantly lower levels of ALP activity after priming, which correlated with poor EC ossification after implantation. While primed BMSCs and ADSCs exhibited EC ossification in vivo, SDSCs and ACs exhibited fibrous dedifferentiation and degradation.
Jukes et al.672008ESCs, BMSCs, and ACsCeramic particlesIsolated goat and human BMSCs were osteogenically primed for 7 or 21 days. In addition, these cells along with murine ESCs and goat ACs were chondrogenically primed for approximately 21 days.Implanted into nude mouse skull defects.Osteogenic priming led only to direct IM ossification. Chondrogenic priming was necessary for EC ossification, but not sufficient as only mESCs underwent EC ossification. Goat and human BMSCs underwent only marginal EC ossification and goat ACs did not exhibit any EC ossification when cultured in a similar fashion.
Tortelli et al.1112009BMSCs and OBsHydroxyapatiteIsolated rate BMSCs and OBs were cultured in standard medium.Implanted subcutaneously in nude mice.The capacity to recruit host cells and the ossification pathway were dependent on donor cell commitment. rBMSC implants led to formation of bone from host cells through the EC ossification pathway, and donor rOBs exhibited direct IM ossification. No studies were conducted with chondrogenically primed cells.
Both et al.762011BMSCs and ESCsBCPIsolated human BMSCs, rat ESCs, and human ESCs were cultured in a series of differentiation mediums, including chondrogenic priming followed by osteogenic priming. Cells were seeded on BCP scaffolds.Implanted subcutaneously in nude mice.ESCs were indistinguishable from BMSCs after in vitro osteogenic priming. Osteogenic priming of BMSCs led to direct IM osteogenesis and extensive bone formation. Both rESCs and hESCs did not form substantial bone but exhibited signs of limited EC ossification.
Vinardell et al.752012BMSCs, FPSCs, SDSCs and ACsAgaroseIsolated porcine BMSCs, SDSCs, FPSCs, and ACs were chondrogenically primed (3 weeks). An additional group was primed in hypertrophic medium for 4 weeks.Implanted subcutaneously in nude mice.Only BMSCs exhibited EC ossification. SDSCs and FPSCs underwent fibrous dedifferentiation and resorption, and ACs appeared to maintain chondrogenic stability.
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However, evidence from Rabie et al. $ ^{28,30,31} $ showed that IM and EC ossification pathways can be utilized, exclusively or in combination, to regenerate parietal defects based entirely on the source of DBM. In addition, the amount of bone regeneration was shown to be source dependent, where grafts favoring IM ossification displayed a significantly higher degree of newly formed bone observed by serial histological sectioning. $ ^{32} $ While these studies collectively support the “same for same” surgical practice in bone regeneration, $ ^{32} $ where DBM from IM and EC sources is matched on a developmental basis to the respective bone defect site, the major limitation of these studies was the short timeframe of healing (14 days) observed after implantation. Since Oakes et al. $ ^{26} $ observed no evidence of a difference in bone regeneration at 16 weeks postimplantation, similar longitudinal studies are necessary to determine whether DBM implants from EC or IM sources display significant regenerative capacities.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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[1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 2, "page": 10, "raw_label": "text", "text": "suggesting that only implants directed toward IM ossification will possess regenerative potential. However, evidence from Rabie et al. $ ^{28,30,31} $ showed that IM and EC ossification pathways can be utilized, exclusively or in combination, to regenerate parietal defects based entirely on the source of DBM. In addition, the amount of bone regeneration was shown to be source dependent, where grafts favoring IM ossification displayed a significantly higher degree of newly formed bone observed by serial histological sectioning. $ ^{32} $ While these studies collectively support the “same for same” surgical practice in bone regeneration, $ ^{32} $ where DBM from IM and EC sources is matched on a developmental basis to the respective bone defect site, the major limitation of these studies was the short timeframe of healing (14 days) observed after implantation. Since Oakes et al. $ ^{26} $ observed no evidence of a difference in bone regeneration at 16 weeks postimplantation, similar longitudinal studies are necessary to determine whether DBM implants from EC or IM sources display significant regenerative capacities.", "bbox": [117, 117, 606, 534], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "suggesting that only implants directed toward IM ossification will possess regenerative potential. However, evidence from Rabie et al. $ ^{28,30,31} $ showed that IM and EC ossification pathways can be utilized, exclusively or in combination, to regenerate parietal defects based entirely on the source of DBM. In addition, the amount of bone regeneration was shown to be source dependent, where grafts favoring IM ossification displayed a significantly higher degree of newly formed bone observed by serial histological sectioning. $ ^{32} $ While these studies collectively support the “same for same” surgical practice in bone regeneration, $ ^{32} $ where DBM from IM and EC sources is matched on a developmental basis to the respective bone defect site, the major limitation of these studies was the short timeframe of healing (14 days) observed after implantation. Since Oakes et al. $ ^{26} $ observed no evidence of a difference in bone regeneration at 16 weeks postimplantation, similar longitudinal studies are necessary to determine whether DBM implants from EC or IM sources display significant regenerative capacities."}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 417, "left": 117, "top": 117, "right": 606, "bottom": 534, "x_center": 361.5, "x_center_bucket": 350, "y_center": 325.5, "x_ratio": 0.2953, "y_ratio": 0.2055, "width_ratio": 0.3995, "height_ratio": 0.2633, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 194}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 10, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [117, 533, 606, 1015], "text": "The differences in regenerative potential and developmental pathways seen in the Rabie studies were attributed to varying inductive and conductive ECM factors within DBM. $ ^{28,30-32} $ Inductive factors such as bone morphogenic proteins (BMPs) have been implicated in bone morphogenesis dating back to their initial isolation from DBM, reviewed in chronological detail by Gruskin et al. $ ^{15} $ Consequently, BMP-2 content, release, and bioactivity has become an important guideline in determining efficacy and quality control of commercially available DBM products. $ ^{15} $ BMPs, however, represent only a fraction of the growth factors in the spatiotemporal cascade of inductive molecules involved during bone healing, extensively reviewed by Mehta et al. $ ^{9} $ Inductive signaling alone could have been responsible for the regenerative effect seen in DBM as well as account for differences seen between DBM from IM and EC sources. However, the conductive proteins present in DBM may also provide key regulatory control, as it has become increasingly evident that structural components of native ECM along with mechanical forces acting on the tissue have a significant influence on cellular and molecular bioactivity. $ ^{21,45} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 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bone morphogenesis dating back to their initial isolation from DBM, reviewed in chronological detail by Gruskin et al. $ ^{15} $ Consequently, BMP-2 content, release, and bioactivity has become an important guideline in determining efficacy and quality control of commercially available DBM products. $ ^{15} $ BMPs, however, represent only a fraction of the growth factors in the spatiotemporal cascade of inductive molecules involved during bone healing, extensively reviewed by Mehta et al. $ ^{9} $ Inductive signaling alone could have been responsible for the regenerative effect seen in DBM as well as account for differences seen between DBM from IM and EC sources. However, the conductive proteins present in DBM may also provide key regulatory control, as it has become increasingly evident that structural components of native ECM along with mechanical forces acting on the tissue have a significant influence on cellular and molecular bioactivity. $ ^{21,45} $", "bbox": [117, 533, 606, 1015], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "The differences in regenerative potential and developmental pathways seen in the Rabie studies were attributed to varying inductive and conductive ECM factors within DBM. $ ^{28,30-32} $ Inductive factors such as bone morphogenic proteins (BMPs) have been implicated in bone morphogenesis dating back to their initial isolation from DBM, reviewed in chronological detail by Gruskin et al. $ ^{15} $ Consequently, BMP-2 content, release, and bioactivity has become an important guideline in determining efficacy and quality control of commercially available DBM products. $ ^{15} $ BMPs, however, represent only a fraction of the growth factors in the spatiotemporal cascade of inductive molecules involved during bone healing, extensively reviewed by Mehta et al. $ ^{9} $ Inductive signaling alone could have been responsible for the regenerative effect seen in DBM as well as account for differences seen between DBM from IM and EC sources. However, the conductive proteins present in DBM may also provide key regulatory control, as it has become increasingly evident that structural components of native ECM along with mechanical forces acting on the tissue have a significant influence on cellular and molecular bioactivity. $ ^{21,45} $"}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 482, "left": 117, "top": 533, "right": 606, "bottom": 1015, "x_center": 361.5, "x_center_bucket": 350, "y_center": 774.0, "x_ratio": 0.2953, "y_ratio": 0.4886, "width_ratio": 0.3995, "height_ratio": 0.3043, "line_count": 1}, "span_signature": {"font_size": 9.79, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 271}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 10, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [117, 1014, 606, 1261], "text": "Collectively, there is significant evidence to suggest that EC ossification can occur within native ECM biomaterials in the form of acellular DBM implants. While there has been extensive research into the bone regenerative capacity of DBM, an underexplored avenue of research is the focus on the developmental pathway's effect on regenerative capacity of these implants. 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While there has been extensive research into the bone regenerative capacity of DBM, an underexplored avenue of research is the focus on the developmental pathway's effect on regenerative capacity of these implants. The characterization of DBM's influence, and perhaps limitation, in stimulating EC ossification should be elucidated in the future to advance the understanding of the bone-healing process and potentially enhance bone regenerative designs.", "bbox": [117, 1014, 606, 1261], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Collectively, there is significant evidence to suggest that EC ossification can occur within native ECM biomaterials in the form of acellular DBM implants. While there has been extensive research into the bone regenerative capacity of DBM, an underexplored avenue of research is the focus on the developmental pathway's effect on regenerative capacity of these implants. 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[618, 205, 1110, 774], "text": "Traditional bone ECM strategies: ABG intrinsically involves the grafting of native bone ECM tissue with associated autologous cells into bone defects, and it remains the gold standard of treatment in bone regeneration due to its inherent osteoconductivity, osteoinductivity, and osteogenic capacity. $ ^{6,12-14} $ It intuitively followed that designs mimicking the native bone ECM (Fig. 1) held potential for bone regeneration, and, as a result, many alternative bone regeneration strategies focused on mimicking portions of the complex composition and bioactive signals present in ABG, which resembles the late reparative stage ECM in bone fracture repair (i.e., “hard” or “bony” callus). $ ^{1-8} $ Some of these strategies were discussed in the previous DBM characterization section where allogeneic tissue was used to elicit bone regeneration. Subsequently, efforts in the bone ECM biomimetic area have yielded dozens of commercially available products. $ ^{15,16} $ Two reviews by Gruskin et al. $ ^{15} $ and Bohner $ ^{16} $ compare an extensive number of these products that can be divided into two broad categories: (1) organic scaffolds (e.g., allografts and xenografts) and (2) inorganic scaffolds (e.g., calcium phosphate cements); however, the majority of orthopedic procedures continue to utilize ABG. $ ^{6,12-14} $ This is likely due to the fact that bone ECM biomimetic strategies fail to sufficiently mimic the complex three-dimensional (3D) physical, chemical, and cellular composition of healthy autologous bone. $ ^{6,12-14} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 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"raw_label": "text", "raw_order": 8, "bbox": [618, 972, 1110, 1258], "text": "Alternative ECM biomaterial strategies for EC ossification: By instead leveraging the concepts of both developmental engineering and the spatiotemporal dynamics of ECM in bone healing, there may be potential to enhance the extent and quality of EC ossification. Specifically, native ECM biomaterials that mimic the initial inflammatory stage ECM or fibrocartilaginous ECM (i.e., “pro-” or “soft” callus) in the early reparative stage of bone fracture healing may be selected instead of materials which mimic the composition of bone ECM. These scaffolds or grafts based on inflammatory or fibrocartilaginous ECM may harness the path-dependent, robust, and semi-autonomous nature of EC ossification, potentially leading to extensive bone regeneration.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, 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Specifically, native ECM biomaterials that mimic the initial inflammatory stage ECM or fibrocartilaginous ECM (i.e., “pro-” or “soft” callus) in the early reparative stage of bone fracture healing may be selected instead of materials which mimic the composition of bone ECM. These scaffolds or grafts based on inflammatory or fibrocartilaginous ECM may harness the path-dependent, robust, and semi-autonomous nature of EC ossification, potentially leading to extensive bone regeneration.", "bbox": [618, 972, 1110, 1258], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Alternative ECM biomaterial strategies for EC ossification: By instead leveraging the concepts of both developmental engineering and the spatiotemporal dynamics of ECM in bone healing, there may be potential to enhance the extent and quality of EC ossification. Specifically, native ECM biomaterials that mimic the initial inflammatory stage ECM or fibrocartilaginous ECM (i.e., “pro-” or “soft” callus) in the early reparative stage of bone fracture healing may be selected instead of materials which mimic the composition of bone ECM. 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modulating signaling activity of soluble bioactive molecules. $ ^{21,45} $ Furthermore, the native ECM's integrated approach to combine the traditional signaling and scaffolding components of the tissue engineering triad suggests that acellular designs may obviate the need for burdensome cell expansion protocols and additional bioactive signal incorporation which introduce major challenges that threaten commercial success in bone regeneration. $ ^{24,25} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 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signaling activity of soluble bioactive molecules. $ ^{21,45} $ Furthermore, the native ECM's integrated approach to combine the traditional signaling and scaffolding components of the tissue engineering triad suggests that acellular designs may obviate the need for burdensome cell expansion protocols and additional bioactive signal incorporation which introduce major challenges that threaten commercial success in bone regeneration. $ ^{24,25} $", "bbox": [111, 161, 602, 511], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Native ECM biomaterials possess both conductive and inductive potential that are difficult to match with synthetic designs (e.g., non-native polymers). $ ^{17-20} $ In addition, it is increasingly evident that the structural components of native ECM also provide a regulatory role for key processes in cellular development and tissue regeneration. $ ^{21,45} $ These processes include cell adhesion, proliferation, differentiation, migration, and survival along with modulating signaling activity of soluble bioactive molecules. $ ^{21,45} $ Furthermore, the native ECM's integrated approach to combine the traditional signaling and scaffolding components of the tissue engineering triad suggests that acellular designs may obviate the need for burdensome cell expansion protocols and additional bioactive signal incorporation which introduce major challenges that threaten commercial success in bone regeneration. $ ^{24,25} $"}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 350, "left": 111, "top": 161, "right": 602, "bottom": 511, "x_center": 356.5, "x_center_bucket": 350, "y_center": 336.0, "x_ratio": 0.2913, "y_ratio": 0.2121, "width_ratio": 0.4011, "height_ratio": 0.221, "line_count": 1}, "span_signature": {"font_size": 9.79, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 200}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 11, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [112, 511, 602, 666], "text": "To date, a few studies have attempted to coordinate developmental bone engineering strategies with acellular native ECM biomaterials (Figs. 1 and 2). Subsequent sections will address key features of existing technology and more importantly focus on worthwhile areas of future investigation for the purpose of enhancing EC ossification and bone regeneration.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": 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Subsequent sections will address key features of existing technology and more importantly focus on worthwhile areas of future investigation for the purpose of enhancing EC ossification and bone regeneration.", "bbox": [112, 511, 602, 666], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "To date, a few studies have attempted to coordinate developmental bone engineering strategies with acellular native ECM biomaterials (Figs. 1 and 2). Subsequent sections will address key features of existing technology and more importantly focus on worthwhile areas of future investigation for the purpose of enhancing EC ossification and bone regeneration."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 155, "left": 112, "top": 511, "right": 602, "bottom": 666, "x_center": 357.0, "x_center_bucket": 350, "y_center": 588.5, "x_ratio": 0.2917, "y_ratio": 0.3715, "width_ratio": 0.4003, "height_ratio": 0.0979, "line_count": 1}, "span_signature": {"font_size": 9.84, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 101}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 11, "block_id": 5, "raw_label": "text", "raw_order": 4, "bbox": [111, 665, 602, 1038], "text": "Inflammatory stage ECM strategies for EC ossification: Since most tissues primarily rely on broken vasculature to supply damaged areas with inflammatory signals and cells, modulating the body's initial inflammatory response after any tissue trauma has been well studied. $ ^{46,47} $ As a result, many regenerative design strategies have focused on isolating and concentrating portions of human blood such as platelets and plasma (e.g., platelet-rich plasma [PRP]) or pro-coagulation molecules (e.g., fibrin sealants) to enhance endogenous healing responses. $ ^{48-54} $ It remains to be seen whether a scaffold with only inflammation-related chemical and mechanical cues can elicit enough of an EC ossification response to heal critical-sized bone defects. Pure fibrin scaffolds and PRP alone do not appear to exhibit sufficient cartilage $ ^{48-50,52} $ and bone $ ^{51,53,54} $ regeneration in critical-sized defects, which suggests that additional regenerative stimuli such as bioactive molecules and progenitor stem cells may be required.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 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remains to be seen whether a scaffold with only inflammation-related chemical and mechanical cues can elicit enough of an EC ossification response to heal critical-sized bone defects. Pure fibrin scaffolds and PRP alone do not appear to exhibit sufficient cartilage $ ^{48-50,52} $ and bone $ ^{51,53,54} $ regeneration in critical-sized defects, which suggests that additional regenerative stimuli such as bioactive molecules and progenitor stem cells may be required.", "bbox": [111, 665, 602, 1038], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Inflammatory stage ECM strategies for EC ossification: Since most tissues primarily rely on broken vasculature to supply damaged areas with inflammatory signals and cells, modulating the body's initial inflammatory response after any tissue trauma has been well studied. $ ^{46,47} $ As a result, many regenerative design strategies have focused on isolating and concentrating portions of human blood such as platelets and plasma (e.g., platelet-rich plasma [PRP]) or pro-coagulation molecules (e.g., fibrin sealants) to enhance endogenous healing responses. $ ^{48-54} $ It remains to be seen whether a scaffold with only inflammation-related chemical and mechanical cues can elicit enough of an EC ossification response to heal critical-sized bone defects. Pure fibrin scaffolds and PRP alone do not appear to exhibit sufficient cartilage $ ^{48-50,52} $ and bone $ ^{51,53,54} $ regeneration in critical-sized defects, which suggests that additional regenerative stimuli such as bioactive molecules and progenitor stem cells may be required."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 373, "left": 111, "top": 665, "right": 602, "bottom": 1038, "x_center": 356.5, "x_center_bucket": 350, "y_center": 851.5, "x_ratio": 0.2913, "y_ratio": 0.5376, "width_ratio": 0.4011, "height_ratio": 0.2355, "line_count": 1}, "span_signature": {"font_size": 9.8, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 243}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 11, "block_id": 6, "raw_label": "text", "raw_order": 5, "bbox": [111, 1038, 603, 1481], "text": "One strategy to enhance the regenerative response in inflammatory stage ECM strategies has been to supply the fracture space with stem cells from bone marrow aspirate, as fractured bone is supplied with bone marrow intrusion when the inner marrow space is disrupted. $ ^{1-9} $ This intrusion of marrow allows supplementary signaling molecules and progenitor cells, including BMSCs, to infiltrate the fracture space. However, hypoxic conditions within the mechanically unstable fracture lead to significant cell mortality, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to actively participate in subsequent tissue regeneration. $ ^{1-9} $ Jakob et al. $ ^{25} $ reviewed some bone engineering strategies which included isolated and concentrated bone marrow aspirate to enhance regeneration, but concluded that the fraction of BMSCs present in bone marrow (1 in 10,000 nucleated cells) limited the regenerative capacity of these designs. Extensive work has also been conducted to additionally isolate, differentiate, and expand the BMSCs within bone marrow to enhance the regenerative capacity of engineered bone implants, discussed in subsequent sections on SCBT strategies (Tables 2–4). However, the expansion of BMSCs requires financially burdensome and time-consuming protocols that limit the commercial application of these strategies. $ ^{24,25} $ Therefore, cell expansion should likely be considered a contingent reserve to cell recruitment strategies.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": 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^{1-9} $ This intrusion of marrow allows supplementary signaling molecules and progenitor cells, including BMSCs, to infiltrate the fracture space. However, hypoxic conditions within the mechanically unstable fracture lead to significant cell mortality, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to actively participate in subsequent tissue regeneration. $ ^{1-9} $ Jakob et al. $ ^{25} $ reviewed some bone engineering strategies which included isolated and concentrated bone marrow aspirate to enhance regeneration, but concluded that the fraction of BMSCs present in bone marrow (1 in 10,000 nucleated cells) limited the regenerative capacity of these designs. Extensive work has also been conducted to additionally isolate, differentiate, and expand the BMSCs within bone marrow to enhance the regenerative capacity of engineered bone implants, discussed in subsequent sections on SCBT strategies (Tables 2–4). However, the expansion of BMSCs requires financially burdensome and time-consuming protocols that limit the commercial application of these strategies. $ ^{24,25} $ Therefore, cell expansion should likely be considered a contingent reserve to cell recruitment strategies.", "bbox": [111, 1038, 603, 1481], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "One strategy to enhance the regenerative response in inflammatory stage ECM strategies has been to supply the fracture space with stem cells from bone marrow aspirate, as fractured bone is supplied with bone marrow intrusion when the inner marrow space is disrupted. $ ^{1-9} $ This intrusion of marrow allows supplementary signaling molecules and progenitor cells, including BMSCs, to infiltrate the fracture space. However, hypoxic conditions within the mechanically unstable fracture lead to significant cell mortality, and it remains unclear whether enough of these stem cells survive the initial inflammatory phase to actively participate in subsequent tissue regeneration. $ ^{1-9} $ Jakob et al. $ ^{25} $ reviewed some bone engineering strategies which included isolated and concentrated bone marrow aspirate to enhance regeneration, but concluded that the fraction of BMSCs present in bone marrow (1 in 10,000 nucleated cells) limited the regenerative capacity of these designs. Extensive work has also been conducted to additionally isolate, differentiate, and expand the BMSCs within bone marrow to enhance the regenerative capacity of engineered bone implants, discussed in subsequent sections on SCBT strategies (Tables 2–4). 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As the native bone healing process continues into the reparative stages of healing, the exposed periosteum and bone marrow continue to serve as reservoirs of progenitor cells that subsequently migrate into the fracture space. $ ^{6,9,33,34} $ Several important reviews have focused on physical (e.g., osmotic gradients and hydrodynamic forces) and chemical (e.g., chemokines) cellular recruitment strategies for tissue regeneration. $ ^{55,56} $ Within the realm of developmental engineering and native ECM biomaterials, the subsequent differentiation pathway should also be emphasized with regard to overall cellular recruitment strategy. Since critical-sized defects are primarily avascular and hypoxic. $ ^{2,5,6} $ Initial chondrogenesis involved in EC ossification may be a more favorable condition to exploit in this lower oxygen tension environment compared with direct osteogenesis in IM ossification. $ ^{39-43} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 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As the native bone healing process continues into the reparative stages of healing, the exposed periosteum and bone marrow continue to serve as reservoirs of progenitor cells that subsequently migrate into the fracture space. $ ^{6,9,33,34} $ Several important reviews have focused on physical (e.g., osmotic gradients and hydrodynamic forces) and chemical (e.g., chemokines) cellular recruitment strategies for tissue regeneration. $ ^{55,56} $ Within the realm of developmental engineering and native ECM biomaterials, the subsequent differentiation pathway should also be emphasized with regard to overall cellular recruitment strategy. Since critical-sized defects are primarily avascular and hypoxic. $ ^{2,5,6} $ Initial chondrogenesis involved in EC ossification may be a more favorable condition to exploit in this lower oxygen tension environment compared with direct osteogenesis in IM ossification. $ ^{39-43} $", "bbox": [614, 248, 1105, 665], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Coupling the evidence of low progenitor count with poor cell survival rate observed in hypoxic bone defects suggests the importance of spatiotemporal cellular recruitment strategies for bone regeneration. As the native bone healing process continues into the reparative stages of healing, the exposed periosteum and bone marrow continue to serve as reservoirs of progenitor cells that subsequently migrate into the fracture space. $ ^{6,9,33,34} $ Several important reviews have focused on physical (e.g., osmotic gradients and hydrodynamic forces) and chemical (e.g., chemokines) cellular recruitment strategies for tissue regeneration. $ ^{55,56} $ Within the realm of developmental engineering and native ECM biomaterials, the subsequent differentiation pathway should also be emphasized with regard to overall cellular recruitment strategy. Since critical-sized defects are primarily avascular and hypoxic. $ ^{2,5,6} $ Initial chondrogenesis involved in EC ossification may be a more favorable condition to exploit in this lower oxygen tension environment compared with direct osteogenesis in IM ossification. $ ^{39-43} $"}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 417, "left": 614, "top": 248, "right": 1105, "bottom": 665, "x_center": 859.5, "x_center_bucket": 850, "y_center": 456.5, "x_ratio": 0.7022, "y_ratio": 0.2882, "width_ratio": 0.4011, "height_ratio": 0.2633, "line_count": 1}, "span_signature": {"font_size": 9.8, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 261}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 11, "block_id": 9, "raw_label": "text", "raw_order": 8, "bbox": [614, 665, 1105, 863], "text": "Collectively, the evidence surrounding the use of inflammatory stage ECM scaffolds, signals, and recruited cells indicates that current designs remain insufficient in regenerating bone in critical-sized defects. To date, no studies have focused on controlling the recruitment and differentiation of BMSCs down the EC ossification pathway within the realm of inflammatory stage ECM strategies. 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To date, no studies have focused on controlling the recruitment and differentiation of BMSCs down the EC ossification pathway within the realm of inflammatory stage ECM strategies. This underexplored area may be an advantageous condition to exploit in future bone regeneration strategies.", "bbox": [614, 665, 1105, 863], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Collectively, the evidence surrounding the use of inflammatory stage ECM scaffolds, signals, and recruited cells indicates that current designs remain insufficient in regenerating bone in critical-sized defects. To date, no studies have focused on controlling the recruitment and differentiation of BMSCs down the EC ossification pathway within the realm of inflammatory stage ECM strategies. This underexplored area may be an advantageous condition to exploit in future bone regeneration strategies."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 198, "left": 614, "top": 665, "right": 1105, "bottom": 863, "x_center": 859.5, "x_center_bucket": 850, "y_center": 764.0, "x_ratio": 0.7022, "y_ratio": 0.4823, "width_ratio": 0.4011, "height_ratio": 0.125, "line_count": 1}, "span_signature": {"font_size": 9.84, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 109}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 11, "block_id": 10, "raw_label": "text", "raw_order": 9, "bbox": [614, 863, 1105, 1479], "text": "Procallus stage ECM strategies for EC ossification: An intuitive source for enhancing stimulation of EC ossification is the procallus ECM, as natural bone healing progresses to this stage early in the regenerative process. $ ^{1-9} $ Insights into the conductive and inductive biomolecules that control EC ossification have been essential to tissue engineering strategies focusing on cartilage formation, $ ^{57,58} $ osteochondral defects, $ ^{59,60} $ and, more recently, bone regeneration (Tables 2–4). $ ^{27,43,57,58,61-76} $ While cartilage tissue engineering strategies have focused on inducing and maintaining chondrogenic phenotypes, the induction and modulation of cartilage hypertrophy is critical to the progression of EC ossification in bone regeneration designs. $ ^{9,33,54,37-43,72,77-85} $ The key transcription factor involved in initial chondrogenesis is SOX9, whereas the primary hypertrophy associated factors are run-related transcription factor 2 (Runx2) and myocyte enhancer factor 2C (MEF2C). $ ^{33,34,41,78} $ In this critical maturation stage of EC ossification, chondrocytes experience a large increase in volume ( $ \\sim $5- to 10-fold), and downstream proteins activated by Runx2 and MEF2C transcription factors begin to remodel the surrounding ECM. $ ^{33,34,41,78} $ These targets include matrix metalloproteinases that degrade cartilaginous ECM, $ ^{1-8} $ Indian Hedgehog (Ihh) that induces proliferation of non-hypertrophic chondrocytes, $ ^{33,34,41,78} $ angiogenic factors such as vascular endothelial growth factor (VEGF) to promote neo-vascularization $ ^{34,35,72,77,78} $ along with collagen type X, alkaline phosphatase (ALP), and matrix vesicles for ECM mineralization. $ ^{86-88} $ While several in vitro studies have shown", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 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cartilage formation, $ ^{57,58} $ osteochondral defects, $ ^{59,60} $ and, more recently, bone regeneration (Tables 2–4). $ ^{27,43,57,58,61-76} $ While cartilage tissue engineering strategies have focused on inducing and maintaining chondrogenic phenotypes, the induction and modulation of cartilage hypertrophy is critical to the progression of EC ossification in bone regeneration designs. $ ^{9,33,54,37-43,72,77-85} $ The key transcription factor involved in initial chondrogenesis is SOX9, whereas the primary hypertrophy associated factors are run-related transcription factor 2 (Runx2) and myocyte enhancer factor 2C (MEF2C). $ ^{33,34,41,78} $ In this critical maturation stage of EC ossification, chondrocytes experience a large increase in volume ( $ \\sim $5- to 10-fold), and downstream proteins activated by Runx2 and MEF2C transcription factors begin to remodel the surrounding ECM. $ ^{33,34,41,78} $ These targets include matrix metalloproteinases that degrade cartilaginous ECM, $ ^{1-8} $ Indian Hedgehog (Ihh) that induces proliferation of non-hypertrophic chondrocytes, $ ^{33,34,41,78} $ angiogenic factors such as vascular endothelial growth factor (VEGF) to promote neo-vascularization $ ^{34,35,72,77,78} $ along with collagen type X, alkaline phosphatase (ALP), and matrix vesicles for ECM mineralization. $ ^{86-88} $ While several in vitro studies have shown", "bbox": [614, 863, 1105, 1479], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Procallus stage ECM strategies for EC ossification: An intuitive source for enhancing stimulation of EC ossification is the procallus ECM, as natural bone healing progresses to this stage early in the regenerative process. $ ^{1-9} $ Insights into the conductive and inductive biomolecules that control EC ossification have been essential to tissue engineering strategies focusing on cartilage formation, $ ^{57,58} $ osteochondral defects, $ ^{59,60} $ and, more recently, bone regeneration (Tables 2–4). $ ^{27,43,57,58,61-76} $ While cartilage tissue engineering strategies have focused on inducing and maintaining chondrogenic phenotypes, the induction and modulation of cartilage hypertrophy is critical to the progression of EC ossification in bone regeneration designs. $ ^{9,33,54,37-43,72,77-85} $ The key transcription factor involved in initial chondrogenesis is SOX9, whereas the primary hypertrophy associated factors are run-related transcription factor 2 (Runx2) and myocyte enhancer factor 2C (MEF2C). $ ^{33,34,41,78} $ In this critical maturation stage of EC ossification, chondrocytes experience a large increase in volume ( $ \\sim $5- to 10-fold), and downstream proteins activated by Runx2 and MEF2C transcription factors begin to remodel the surrounding ECM. $ ^{33,34,41,78} $ These targets include matrix metalloproteinases that degrade cartilaginous ECM, $ ^{1-8} $ Indian Hedgehog (Ihh) that 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Differentiation pathwayChemicalPhysicalMechanical
ChondrogenesisTGF- $ \\beta $, BMPs, DexamethasoneLow oxygen tensionLower stiffness and adhesion, intermittent and cyclic compression load conditions
Hypertrophy and osteogenesisVitamin D3, Retinoic acid, Leptin, Insulin, Thyroxine, $ \\beta $-glycerophosphate, BMPs, MMPs, IL-1 $ \\beta $, Calcium ionsNormal oxygen tensionHigher stiffness and adhesion, lower magnitude, and higher fluid shear load conditions
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Differentiation pathwayChemicalPhysicalMechanical
ChondrogenesisTGF- $ \\beta $, BMPs, DexamethasoneLow oxygen tensionLower stiffness and adhesion, intermittent and cyclic compression load conditions
Hypertrophy and osteogenesisVitamin D3, Retinoic acid, Leptin, Insulin, Thyroxine, $ \\beta $-glycerophosphate, BMPs, MMPs, IL-1 $ \\beta $, Calcium ionsNormal oxygen tensionHigher stiffness and adhesion, lower magnitude, and higher fluid shear load conditions
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Differentiation pathwayChemicalPhysicalMechanical
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Coupling these results with the previously discussed evidence regarding DBM's influence on EC ossification $ ^{26-32} $ provides a potent array of strategies for future bone regeneration designs. Furthermore, it is evident that the selection of appropriate native ECM components is essential for exploiting the advantages of EC ossification. However, strategies to efficiently and feasibly incorporate these biomolecules into bone regenerative implant designs require consideration and, thus, will be further discussed next.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 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Coupling these results with the previously discussed evidence regarding DBM's influence on EC ossification $ ^{26-32} $ provides a potent array of strategies for future bone regeneration designs. Furthermore, it is evident that the selection of appropriate native ECM components is essential for exploiting the advantages of EC ossification. However, strategies to efficiently and feasibly incorporate these biomolecules into bone regenerative implant designs require consideration and, thus, will be further discussed next.", "bbox": [117, 533, 607, 843], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "In summary, the success of in vivo developmental engineering designs for EC ossification will likely depend on the incorporation of physiologically relevant bioactive chemical mediators along with physical and mechanical cues drawn from these important in vitro studies. Coupling these results with the previously discussed evidence regarding DBM's influence on EC ossification $ ^{26-32} $ provides a potent array of strategies for future bone regeneration designs. Furthermore, it is evident that the selection of appropriate native ECM components is essential for exploiting the advantages of EC ossification. 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Strategies to design scaffolds with incorporated native ECM components can be divided into two main categories: (1) Bottom-up approach or (2) Top-down approach (i.e., step-wise designs) (Fig. 3). While the former aims at mimicking native ECM with complex biomaterial re-synthesis strategies (e.g., collagen polymerization), the latter step-wise approach attempts to process native ECM from autologous, allogeneic, or xenogeneic sources without completely compromising tissue structure and function (e.g., decellularization and demineralization). Two extensive reviews by Badylak $ ^{17} $ and Renth et al. $ ^{20} $ provided detailed experimental outcomes and current clinical products utilizing “raw” native ECM biomaterials for tissue regeneration, which include both bottom-up and step-wise strategies. In general, nearly all step-wise design approaches described in these reviews, with the exception of autologous tissue harvesting, require some form of processing to avoid immunogenicity with host (i.e., recipient) tissue, as allogeneic and xenogeneic cellular antigens are recognized as foreign. $ ^{17-19,91} $ To address this immunogenicity, a variety of physical, chemical, and enzymatic processing methods have demonstrated the possibility of sufficiently devitalizing or decellularizing these tissues to suppress host rejection without compromising the conductive, inductive, and mechanical components of the ECM. $ ^{17-19,91} $\nIn a comprehensive review of current tissue and whole organ decellularization methods by Crapo et al. $ ^{91} $, it was recognized that all current techniques cause some degree of ECM disruption. As manufacturing requirements increase, the complex physical and chemical components of the native ECM tissue decrease along with corresponding mechanical structures and functions. $ ^{17-21,91} $ At the extreme end of this spectrum, where individual “raw” ECM components are isolated (e.g., collagen, glycosaminoglycans, and soluble growth factors), $ ^{20} $ designs necessarily require some form of bottom-up re-synthesis to regain a portion of the physiologically relevant ECM structure and functionality; however, it poorly resembles the initial native ECM tissue (Fig. 3). $ ^{17} $ The main advantage of using", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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Strategies to design scaffolds with incorporated native ECM components can be divided into two main categories: (1) Bottom-up approach or (2) Top-down approach (i.e., step-wise designs) (Fig. 3). While the former aims at mimicking native ECM with complex biomaterial re-synthesis strategies (e.g., collagen polymerization), the latter step-wise approach attempts to process native ECM from autologous, allogeneic, or xenogeneic sources without completely compromising tissue structure and function (e.g., decellularization and demineralization). Two extensive reviews by Badylak $ ^{17} $ and Renth et al. $ ^{20} $ provided detailed experimental outcomes and current clinical products utilizing “raw” native ECM biomaterials for tissue regeneration, which include both bottom-up and step-wise strategies. 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independently. As a result, each component can be characterized for its contribution to the process as a whole in a full-factorial experimental design (e.g., scaffolding protein vs. soluble factor vs. scaffolding protein + soluble factor). Nevertheless, the problem with modular re-synthesis-based designs is that mimicking complex environments, such as the complex cascade of signaling events involved in bone healing, $ ^{6,9,33,34} $ is nearly impossible in addition to being economically infeasible. $ ^{92} $ This is compounded by the fact that the characterization of the complex 3D structures and functions of native ECM remains incomplete. $ ^{17,91} $ A modular design coupling both conductive and inductive biomolecules present in native bone ECM yields nearly infinite permutations; however, this has remained entrenched as the primary philosophy of bone tissue engineering over the past three decades. $ ^{92} $ Even with current sophisticated manufacturing technology, including 3D printing, complex polymerization, and chemical conjugation techniques, artificial re-synthesis of this biological material remains physiologically dissimilar compared with its native tissue counterpart in terms of relevant physicochemical composition. $ ^{17-21} $ Although future technological advances may someday improve bottom-up re-synthesis designs, the main consequence is that step-wise design strategies may currently represent the more favorable option when attempting to mimic native ECM. $ ^{91} $", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": 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"text", "text": "“raw” biomaterial re-synthesis, however, is that designs can be modular, which means that separate elements of the design can be tested independently. As a result, each component can be characterized for its contribution to the process as a whole in a full-factorial experimental design (e.g., scaffolding protein vs. soluble factor vs. scaffolding protein + soluble factor). Nevertheless, the problem with modular re-synthesis-based designs is that mimicking complex environments, such as the complex cascade of signaling events involved in bone healing, $ ^{6,9,33,34} $ is nearly impossible in addition to being economically infeasible. $ ^{92} $ This is compounded by the fact that the characterization of the complex 3D structures and functions of native ECM remains incomplete. $ ^{17,91} $ A modular design coupling both conductive and inductive biomolecules present in native bone ECM yields nearly infinite permutations; however, this has remained entrenched as the primary philosophy of bone tissue engineering over the past three decades. $ ^{92} $ Even with current sophisticated manufacturing technology, including 3D printing, complex polymerization, and chemical conjugation techniques, artificial re-synthesis of this biological material remains physiologically dissimilar compared with its native tissue counterpart in terms of relevant physicochemical composition. $ ^{17-21} $ Although future technological advances may someday improve bottom-up re-synthesis designs, the main consequence is that step-wise design strategies may currently represent the more favorable option when attempting to mimic native ECM. $ ^{91} $", "bbox": [112, 120, 602, 751], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "“raw” biomaterial re-synthesis, however, is that designs can be modular, which means that separate elements of the design can be tested independently. As a result, each component can be characterized for its contribution to the process as a whole in a full-factorial experimental design (e.g., scaffolding protein vs. soluble factor vs. scaffolding protein + soluble factor). Nevertheless, the problem with modular re-synthesis-based designs is that mimicking complex environments, such as the complex cascade of signaling events involved in bone healing, $ ^{6,9,33,34} $ is nearly impossible in addition to being economically infeasible. $ ^{92} $ This is compounded by the fact that the characterization of the complex 3D structures and functions of native ECM remains incomplete. $ ^{17,91} $ A modular design coupling both conductive and inductive biomolecules present in native bone ECM yields nearly infinite permutations; however, this has remained entrenched as the primary philosophy of bone tissue engineering over the past three decades. $ ^{92} $ Even with current sophisticated manufacturing technology, including 3D printing, complex polymerization, and chemical conjugation techniques, artificial re-synthesis of this biological material remains physiologically dissimilar compared with its native tissue counterpart in terms of relevant physicochemical composition. $ ^{17-21} $ Although future technological advances may someday improve bottom-up re-synthesis designs, the main consequence is that step-wise design strategies may currently represent the more favorable option when attempting to mimic native ECM. $ ^{91} $"}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 631, "left": 112, "top": 120, "right": 602, "bottom": 751, "x_center": 357.0, "x_center_bucket": 350, "y_center": 435.5, "x_ratio": 0.2917, "y_ratio": 0.2749, "width_ratio": 0.4003, "height_ratio": 0.3984, "line_count": 1}, "span_signature": {"font_size": 9.79, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 358}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 13, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [112, 752, 602, 1041], "text": "Step-wise designs from both allogeneic and xenogeneic tissue sources have been utilized clinically for cartilage and bone tissue engineering along with dermal, vascular, nerve, and urogenital tissue. $ ^{[15,17,18,20,93]} $ Furthermore, previous evidence was presented as linking step-wise-derived DBM to extensive bone regeneration via IM and EC ossification, $ ^{[26-32]} $ an attribute that likely contributes to its role as a key protagonist in the bone graft substitute market. $ ^{[15]} $ If alternative ECM biomaterials are to be used to enhance bone regeneration as proposed in the current review, then key technical, regulatory, and commercial features surrounding the use and approval of DBM should be utilized as a guiding template for potential success.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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"flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 3, "page": 13, "raw_label": "text", "text": "Step-wise designs from both allogeneic and xenogeneic tissue sources have been utilized clinically for cartilage and bone tissue engineering along with dermal, vascular, nerve, and urogenital tissue. $ ^{[15,17,18,20,93]} $ Furthermore, previous evidence was presented as linking step-wise-derived DBM to extensive bone regeneration via IM and EC ossification, $ ^{[26-32]} $ an attribute that likely contributes to its role as a key protagonist in the bone graft substitute market. $ ^{[15]} $ If alternative ECM biomaterials are to be used to enhance bone regeneration as proposed in the current review, then key technical, regulatory, and commercial features surrounding the use and approval of DBM should be utilized as a guiding template for potential success.", "bbox": [112, 752, 602, 1041], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Step-wise designs from both allogeneic and xenogeneic tissue sources have been utilized clinically for cartilage and bone tissue engineering along with dermal, vascular, nerve, and urogenital tissue. $ ^{[15,17,18,20,93]} $ Furthermore, previous evidence was presented as linking step-wise-derived DBM to extensive bone regeneration via IM and EC ossification, $ ^{[26-32]} $ an attribute that likely contributes to its role as a key protagonist in the bone graft substitute market. $ ^{[15]} $ If alternative ECM biomaterials are to be used to enhance bone regeneration as proposed in the current review, then key technical, regulatory, and commercial features surrounding the use and approval of DBM should be utilized as a guiding template for potential success."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 289, "left": 112, "top": 752, "right": 602, "bottom": 1041, "x_center": 357.0, "x_center_bucket": 350, "y_center": 896.5, "x_ratio": 0.2917, "y_ratio": 0.566, "width_ratio": 0.4003, "height_ratio": 0.1824, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 148}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 13, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [112, 1059, 602, 1480], "text": "Decellularized cartilage for enhancing EC ossification. Intuitively, it follows that designs mimicking the native bone or cartilage ECM hold vast potential for eliciting ossification and chondrogenesis, respectively. Therefore, it is understandable that for many years, bone and cartilage tissue engineering strategies have focused primarily on treating these two tissues as separate regenerative endeavors. Although a pivotal review by Singh et al. $ ^{55} $ established chemical and mechanical-based spatial gradients as an advantageous design approach in osteochondral interfacial tissue regeneration, these strategies still involve a binary differentiation pathway, where the transition zone is only a spatial gradient formed by a gradual change in either chondrogenic or osteogenic cues. EC ossification, however, is a spatiotemporal transition process where cartilage precursor gradually transitions to bone over extended periods of time. $ ^{1,2,9,33} $ Thus, the chondrogenic signaling cues initially present in a scaffold may be required to transition over time to influence hypertrophy and osteogenesis.\nPreviously mentioned in this review was emerging evidence which has shown the potential of DBM to prompt EC ossification in vivo, $ ^{26-32} $ and subsequent sections will discuss evidence that in vitro primed cartilage constructs may also prompt EC ossification in vivo (Tables 2–4). Coupling this evidence with motifs in developmental engineering, including path dependence, robustness, and semi-autonomy, suggests that decellularized cartilage (DCC), which mimics portions of the native procallus ECM, may provide extensive potential in prompting EC ossification within an implant and could be a worthwhile focus of future investigation in bone regeneration.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 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Intuitively, it follows that designs mimicking the native bone or cartilage ECM hold vast potential for eliciting ossification and chondrogenesis, respectively. Therefore, it is understandable that for many years, bone and cartilage tissue engineering strategies have focused primarily on treating these two tissues as separate regenerative endeavors. Although a pivotal review by Singh et al. $ ^{55} $ established chemical and mechanical-based spatial gradients as an advantageous design approach in osteochondral interfacial tissue regeneration, these strategies still involve a binary differentiation pathway, where the transition zone is only a spatial gradient formed by a gradual change in either chondrogenic or osteogenic cues. EC ossification, however, is a spatiotemporal transition process where cartilage precursor gradually transitions to bone over extended periods of time. $ ^{1,2,9,33} $ Thus, the chondrogenic signaling cues initially present in a scaffold may be required to transition over time to influence hypertrophy and osteogenesis.\nPreviously mentioned in this review was emerging evidence which has shown the potential of DBM to prompt EC ossification in vivo, $ ^{26-32} $ and subsequent sections will discuss evidence that in vitro primed cartilage constructs may also prompt EC ossification in vivo (Tables 2–4). Coupling this evidence with motifs in developmental engineering, including path dependence, robustness, and semi-autonomy, suggests that decellularized cartilage (DCC), which mimics portions of the native procallus ECM, may provide extensive potential in prompting EC ossification within an implant and could be a worthwhile focus of future investigation in bone regeneration.", "bbox": [112, 1059, 602, 1480], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Decellularized cartilage for enhancing EC ossification. Intuitively, it follows that designs mimicking the native bone or cartilage ECM hold vast potential for eliciting ossification and chondrogenesis, respectively. Therefore, it is understandable that for many years, bone and cartilage tissue engineering strategies have focused primarily on treating these two tissues as separate regenerative endeavors. Although a pivotal review by Singh et al. $ ^{55} $ established chemical and mechanical-based spatial gradients as an advantageous design approach in osteochondral interfacial tissue regeneration, these strategies still involve a binary differentiation pathway, where the transition zone is only a spatial gradient formed by a gradual change in either chondrogenic or osteogenic cues. EC ossification, however, is a spatiotemporal transition process where cartilage precursor gradually transitions to bone over extended periods of time. $ ^{1,2,9,33} $ Thus, the chondrogenic signaling cues initially present in a scaffold may be required to transition over time to influence hypertrophy and osteogenesis.\nPreviously mentioned in this review was emerging evidence which has shown the potential of DBM to prompt EC ossification in vivo, $ ^{26-32} $ and subsequent sections will discuss evidence that in vitro primed cartilage constructs may also prompt EC ossification in vivo (Tables 2–4). Coupling this evidence with motifs in developmental engineering, including path dependence, robustness, and semi-autonomy, suggests that decellularized cartilage (DCC), which mimics portions of the native procallus ECM, may provide extensive potential in prompting EC ossification within an implant and could be a worthwhile focus of future investigation in bone regeneration."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 421, "left": 112, "top": 1059, "right": 602, "bottom": 1480, "x_center": 357.0, "x_center_bucket": 350, "y_center": 1269.5, "x_ratio": 0.2917, "y_ratio": 0.8015, "width_ratio": 0.4003, "height_ratio": 0.2658, "line_count": 1}, "span_signature": {"font_size": 9.81, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvP6EC0", "bold": false, "italic": true, "span_count": 200}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": 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"index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "_needs_pdf_fallback": true, "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 13, "block_id": 6, "raw_label": "text", "raw_order": 5, "bbox": [614, 381, 1106, 1171], "text": "DCC, from both allogeneic and xenogeneic sources, is a poorly explored native ECM biomaterial. Recently, it has emerged as a source that is rich in both chondroinductive and chondroconductive potential. $ ^{18,20,21,93-95} $ Current commercially available products utilizing articular cartilage and/or DCC include Biocartilage $ ^{\\circledR} $ (Arthrex), De Novo NT $ ^{\\circledR} $ and ET $ ^{\\circledR} $ Live Graft (Zimmer), and Chondrofix $ ^{\\circledR} $ (Zimmer). However, all of these products use cartilage ECM for the purpose of regenerating only cartilage tissue. In the framework of developmental engineering, DCC provides a source for modulating and enhancing EC ossification; however, there remains an extreme deficiency in both fundamental research and translatable products incorporating this material. Hyaline cartilage is avascular in nature, which may be advantageous to pursue for critical-sized bone defects, as chondrocytes are better suited for hypoxic environments compared with osteoblasts. Moreover, an avascular tissue may minimize potential developmental disturbance from unintended external perturbations. $ ^{1-9,22,23} $ An additional consequence of this isolation is that the progression of cartilage to bone during EC ossification is primarily dictated within the tissue by intercellular signaling, incorporating semi-autonomous control into the process. $ ^{1-9,22,23} $ Furthermore, many forms of cartilage exist in the body, including hyaline cartilage (e.g., femoral condyles and tibial plateau), fibrocartilage (e.g., temporomandibular joint disc and knee meniscus), elastic cartilage (e.g., nose and ear), and even hypertrophic cartilage (e.g., fetal bones and growth plates). $ ^{4} $ Fibrocartilage may provide an even better procallus mimetic tissue than hyaline cartilage, as the procallus is fibrocartilaginous in nature. In addition, fetal bones undergoing EC ossification during skeletogenesis may provide primed hypertrophic cartilage that could facilitate rapid ossification in a bone defect. Thus, there exists a range of DCC-derived tissues that may be explored in relation to EC ossification.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 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Recently, it has emerged as a source that is rich in both chondroinductive and chondroconductive potential. $ ^{18,20,21,93-95} $ Current commercially available products utilizing articular cartilage and/or DCC include Biocartilage $ ^{\\circledR} $ (Arthrex), De Novo NT $ ^{\\circledR} $ and ET $ ^{\\circledR} $ Live Graft (Zimmer), and Chondrofix $ ^{\\circledR} $ (Zimmer). However, all of these products use cartilage ECM for the purpose of regenerating only cartilage tissue. In the framework of developmental engineering, DCC provides a source for modulating and enhancing EC ossification; however, there remains an extreme deficiency in both fundamental research and translatable products incorporating this material. Hyaline cartilage is avascular in nature, which may be advantageous to pursue for critical-sized bone defects, as chondrocytes are better suited for hypoxic environments compared with osteoblasts. Moreover, an avascular tissue may minimize potential developmental disturbance from unintended external perturbations. $ ^{1-9,22,23} $ An additional consequence of this isolation is that the progression of cartilage to bone during EC ossification is primarily dictated within the tissue by intercellular signaling, incorporating semi-autonomous control into the process. $ ^{1-9,22,23} $ Furthermore, many forms of cartilage exist in the body, including hyaline cartilage (e.g., femoral condyles and tibial plateau), fibrocartilage (e.g., temporomandibular joint disc and knee meniscus), elastic cartilage (e.g., nose and ear), and even hypertrophic cartilage (e.g., fetal bones and growth plates). $ ^{4} $ Fibrocartilage may provide an even better procallus mimetic tissue than hyaline cartilage, as the procallus is fibrocartilaginous in nature. In addition, fetal bones undergoing EC ossification during skeletogenesis may provide primed hypertrophic cartilage that could facilitate rapid ossification in a bone defect. Thus, there exists a range of DCC-derived tissues that may be explored in relation to EC ossification.", "bbox": [614, 381, 1106, 1171], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "DCC, from both allogeneic and xenogeneic sources, is a poorly explored native ECM biomaterial. Recently, it has emerged as a source that is rich in both chondroinductive and chondroconductive potential. $ ^{18,20,21,93-95} $ Current commercially available products utilizing articular cartilage and/or DCC include Biocartilage $ ^{\\circledR} $ (Arthrex), De Novo NT $ ^{\\circledR} $ and ET $ ^{\\circledR} $ Live Graft (Zimmer), and Chondrofix $ ^{\\circledR} $ (Zimmer). However, all of these products use cartilage ECM for the purpose of regenerating only cartilage tissue. In the framework of developmental engineering, DCC provides a source for modulating and enhancing EC ossification; however, there remains an extreme deficiency in both fundamental research and translatable products incorporating this material. Hyaline cartilage is avascular in nature, which may be advantageous to pursue for critical-sized bone defects, as chondrocytes are better suited for hypoxic environments compared with osteoblasts. Moreover, an avascular tissue may minimize potential developmental disturbance from unintended external perturbations. $ ^{1-9,22,23} $ An additional consequence of this isolation is that the progression of cartilage to bone during EC ossification is primarily dictated within the tissue by intercellular signaling, incorporating semi-autonomous control into the process. $ ^{1-9,22,23} $ Furthermore, many forms of cartilage exist in the body, including hyaline cartilage (e.g., femoral condyles and tibial plateau), fibrocartilage (e.g., temporomandibular joint disc and knee meniscus), elastic cartilage (e.g., nose and ear), and even hypertrophic cartilage (e.g., fetal bones and growth plates). $ ^{4} $ Fibrocartilage may provide an even better procallus mimetic tissue than hyaline cartilage, as the procallus is fibrocartilaginous in nature. In addition, fetal bones undergoing EC ossification during skeletogenesis may provide primed hypertrophic cartilage that could facilitate rapid ossification in a bone defect. Thus, there exists a range of DCC-derived tissues that may be explored in relation to EC ossification."}, "layout_signature": {"width": 492, "width_bucket": 500, "height": 790, "left": 614, "top": 381, "right": 1106, "bottom": 1171, "x_center": 860.0, "x_center_bucket": 850, "y_center": 776.0, "x_ratio": 0.7026, "y_ratio": 0.4899, "width_ratio": 0.402, "height_ratio": 0.4987, "line_count": 1}, "span_signature": {"font_size": 9.79, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 434}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 13, "block_id": 7, "raw_label": "text", "raw_order": 6, "bbox": [614, 1191, 1106, 1479], "text": "Delivery strategies for decellularized tissues. Crucial to the future success of these ECM materials will be the strategies used to incorporate and deliver them within engineered implants. If maximum retention of native inductive, conductive, and mechanical potential of ECM is desired, then minimal required processing is preferred to keep the microarchitecture of the native tissue intact. $ ^{17-21} $ However, this severely limits native ECM's potential to be incorporated within an engineered implant or delivered surgically to a defect site. Large sections of native ECM tissue have been broken down by various morselization and solubilization strategies, which can be used to enhance decellularization efficiency. $ ^{15,18-20} $ However, the effect of", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, 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Crucial to the future success of these ECM materials will be the strategies used to incorporate and deliver them within engineered implants. If maximum retention of native inductive, conductive, and mechanical potential of ECM is desired, then minimal required processing is preferred to keep the microarchitecture of the native tissue intact. $ ^{17-21} $ However, this severely limits native ECM's potential to be incorporated within an engineered implant or delivered surgically to a defect site. Large sections of native ECM tissue have been broken down by various morselization and solubilization strategies, which can be used to enhance decellularization efficiency. $ ^{15,18-20} $ However, the effect of", "bbox": [614, 1191, 1106, 1479], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Delivery strategies for decellularized tissues. Crucial to the future success of these ECM materials will be the strategies used to incorporate and deliver them within engineered implants. If maximum retention of native inductive, conductive, and mechanical potential of ECM is desired, then minimal required processing is preferred to keep the microarchitecture of the native tissue intact. $ ^{17-21} $ However, this severely limits native ECM's potential to be incorporated within an engineered implant or delivered surgically to a defect site. Large sections of native ECM tissue have been broken down by various morselization and solubilization strategies, which can be used to enhance decellularization efficiency. $ ^{15,18-20} $ However, the effect of"}, "layout_signature": {"width": 492, "width_bucket": 500, "height": 288, "left": 614, "top": 1191, "right": 1106, "bottom": 1479, "x_center": 860.0, "x_center_bucket": 850, "y_center": 1335.0, "x_ratio": 0.7026, "y_ratio": 0.8428, "width_ratio": 0.402, "height_ratio": 0.1818, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvP6EC0", "bold": false, "italic": true, "span_count": 202}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", 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A recent review of DBM clinical products and procurement by Gruskin et al. $ ^{15} $ indicated that larger particles of DBM (420–840 $ \\mu $m) might be more osteoinductive than smaller particles (<250 $ \\mu $m) but warned readers that the majority of preclinical data regarding particle-size effects are inconsistent due to varying animal models and subjective outcome measures. Furthermore, the authors of this article are not aware of any studies that analyze chondrogenesis as a function of DCC particle size or EC ossification as a function of ECM particle size.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", 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"particle size on regenerative capacity of these materials remains unclear. A recent review of DBM clinical products and procurement by Gruskin et al. $ ^{15} $ indicated that larger particles of DBM (420–840 $ \\mu $m) might be more osteoinductive than smaller particles (<250 $ \\mu $m) but warned readers that the majority of preclinical data regarding particle-size effects are inconsistent due to varying animal models and subjective outcome measures. Furthermore, the authors of this article are not aware of any studies that analyze chondrogenesis as a function of DCC particle size or EC ossification as a function of ECM particle size.", "bbox": [116, 117, 606, 358], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "particle size on regenerative capacity of these materials remains unclear. A recent review of DBM clinical products and procurement by Gruskin et al. $ ^{15} $ indicated that larger particles of DBM (420–840 $ \\mu $m) might be more osteoinductive than smaller particles (<250 $ \\mu $m) but warned readers that the majority of preclinical data regarding particle-size effects are inconsistent due to varying animal models and subjective outcome measures. Furthermore, the authors of this article are not aware of any studies that analyze chondrogenesis as a function of DCC particle size or EC ossification as a function of ECM particle size."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 241, "left": 116, "top": 117, "right": 606, "bottom": 358, "x_center": 361.0, "x_center_bucket": 350, "y_center": 237.5, "x_ratio": 0.2949, "y_ratio": 0.1499, "width_ratio": 0.4003, "height_ratio": 0.1521, "line_count": 1}, "span_signature": {"font_size": 9.83, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 190}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [116, 359, 606, 622], "text": "While morselization strategies most often include some form of mechanical breakdown (e.g., pulverization or cyro-grinding), solubilization uses chemical and enzymatic methods (e.g., demineralization and collagenase) to break down ECM. $ ^{[18,19]} $ The primary advantage of breaking down native ECM into micron- or sub-micron-sized particles is an increased relative surface area per volume of material. This can be exploited to improve decellularization efficiency, but it may also be essential in exposing cellular adhesion proteins, modulating growth factor release, and uncovering potential cross-linking moieties to facilitate synthetic reconstruction strategies (e.g., polymerization).", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 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This can be exploited to improve decellularization efficiency, but it may also be essential in exposing cellular adhesion proteins, modulating growth factor release, and uncovering potential cross-linking moieties to facilitate synthetic reconstruction strategies (e.g., polymerization).", "bbox": [116, 359, 606, 622], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "While morselization strategies most often include some form of mechanical breakdown (e.g., pulverization or cyro-grinding), solubilization uses chemical and enzymatic methods (e.g., demineralization and collagenase) to break down ECM. $ ^{[18,19]} $ The primary advantage of breaking down native ECM into micron- or sub-micron-sized particles is an increased relative surface area per volume of material. This can be exploited to improve decellularization efficiency, but it may also be essential in exposing cellular adhesion proteins, modulating growth factor release, and uncovering potential cross-linking moieties to facilitate synthetic reconstruction strategies (e.g., polymerization)."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 263, "left": 116, "top": 359, "right": 606, "bottom": 622, "x_center": 361.0, "x_center_bucket": 350, "y_center": 490.5, "x_ratio": 0.2949, "y_ratio": 0.3097, "width_ratio": 0.4003, "height_ratio": 0.166, "line_count": 1}, "span_signature": {"font_size": 9.82, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 139}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [116, 622, 607, 931], "text": "In summary, the extent of native ECM processing required to enhance the regenerative capacity of a bone implant will be application specific. These specifications will include issues such as load-bearing requirements, defect geometry (e.g., irregular vs. machined defects), bone architecture (e.g., cortical vs. cancellous), and vulnerable surrounding tissues (e.g., the spinal cord in vertebral fusion or brain tissue in calvarial repair). Existing design paradigms already used to support DBM particles, such as solid scaffolding or chemically cross-linked hydrogels $ ^{15} $ along with emerging design paradigms such as shear-responsive and self-assembling colloidal gels, $ ^{96-100} $ will likely yield an extensive array of application-specific bone regenerative scaffolds with EC ossification potential.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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implant will be application specific. These specifications will include issues such as load-bearing requirements, defect geometry (e.g., irregular vs. machined defects), bone architecture (e.g., cortical vs. cancellous), and vulnerable surrounding tissues (e.g., the spinal cord in vertebral fusion or brain tissue in calvarial repair). Existing design paradigms already used to support DBM particles, such as solid scaffolding or chemically cross-linked hydrogels $ ^{15} $ along with emerging design paradigms such as shear-responsive and self-assembling colloidal gels, $ ^{96-100} $ will likely yield an extensive array of application-specific bone regenerative scaffolds with EC ossification potential.", "bbox": [116, 622, 607, 931], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "In summary, the extent of native ECM processing required to enhance the regenerative capacity of a bone implant will be application specific. These specifications will include issues such as load-bearing requirements, defect geometry (e.g., irregular vs. machined defects), bone architecture (e.g., cortical vs. cancellous), and vulnerable surrounding tissues (e.g., the spinal cord in vertebral fusion or brain tissue in calvarial repair). Existing design paradigms already used to support DBM particles, such as solid scaffolding or chemically cross-linked hydrogels $ ^{15} $ along with emerging design paradigms such as shear-responsive and self-assembling colloidal gels, $ ^{96-100} $ will likely yield an extensive array of application-specific bone regenerative scaffolds with EC ossification potential."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 309, "left": 116, "top": 622, "right": 607, "bottom": 931, "x_center": 361.5, "x_center_bucket": 350, "y_center": 776.5, "x_ratio": 0.2953, "y_ratio": 0.4902, "width_ratio": 0.4011, "height_ratio": 0.1951, "line_count": 1}, "span_signature": {"font_size": 9.81, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 204}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 5, "raw_label": "paragraph_title", "raw_order": 4, "bbox": [120, 961, 421, 983], "text": "Incorporating SCBTs into the design", "page_width": 1224, "page_height": 1584, "role": "subsection_heading", "role_confidence": 0.6, "evidence": ["unnumbered paragraph_title, inferred level subsection_heading: Incorporating SCBTs into the design"], "seed_role": "subsection_heading", "seed_confidence": 0.6, "seed_evidence": ["unnumbered paragraph_title, inferred level subsection_heading: Incorporating SCBTs into the design"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 5, "page": 14, "raw_label": "paragraph_title", "text": "Incorporating SCBTs into the design", "bbox": [120, 961, 421, 983], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Incorporating SCBTs into the design"}, "layout_signature": {"width": 301, "width_bucket": 300, "height": 22, "left": 120, "top": 961, "right": 421, "bottom": 983, "x_center": 270.5, "x_center_bucket": 275, "y_center": 972.0, "x_ratio": 0.221, "y_ratio": 0.6136, "width_ratio": 0.2459, "height_ratio": 0.0139, "line_count": 1}, "span_signature": {"font_size": 8.97, "font_size_median": 8.97, "font_size_bucket": 9.0, "font_family_norm": "AdvP6ECA", "bold": false, "italic": true, "span_count": 9}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "accepted_heading", "role_evidence": ["heading verified by heading artifact"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 6, "raw_label": "text", "raw_order": 5, "bbox": [117, 992, 606, 1410], "text": "Priming chondrogenesis in vitro for EC ossification. While acellular ECM design strategies possess great conductive and inductive potential for eliciting in vivo EC ossification, SCBTs may provide advantageous osteo- and chondrogenic capacity within bone implants. Without the incorporation of donor cells, acellular implants such as allografts, xenografts, or synthetic scaffolds should rely solely on recruited cells from the peripheral host tissue. Recruitment strategies often involve biochemical agents (e.g., chemokines) or induced physical migration (e.g., osmotic gradients or hydrodynamic forces), which may be insufficient for some indications with limited access to progenitor cell reservoirs in the bone marrow and periosteum. BMSC recruitment also involves successful cellular migration into the scaffold, which may be limited by physical constraints within the implant (e.g., small pore size, limited pore connectivity). $ ^{101} $ By incorporating a donor stem cell population within an implant instead, these cellular recruitment challenges may be overcome.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6ECA", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 8.966300010681152, "font": "AdvP6EC0", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": 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"role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 9, "raw_label": "text", "raw_order": 8, "bbox": [618, 448, 1110, 1039], "text": "Within the realm of SCBTs for bone regeneration, a majority of strategies have focused on stimulating cell populations to undergo direct osteogenesis rather than chondrogenesis. However, as previously mentioned, the EC ossification pathway holds key advantages over IM ossification. This is especially true in critical-sized defects that are inherently large avascular spaces and favor intermediate chondrogenesis of tissue rather than direct ossification. $ ^{1-9} $ An emerging group of successful research efforts have focused on exploiting this condition over the past decade. These recent publications (Tables 2–4) have demonstrated the capacity of cartilage tissue constructs to promote EC ossification in vivo after in vitro priming with seeded BMSCs, $ ^{60,63,64,66,67,72-76,103-107} $ ESCs, $ ^{27,62,67,76} $ ADSCs, $ ^{108} $ iPSCs, $ ^{109} $ and articular chondrocytes (ACs). $ ^{61,67,70,71,75} $ Most of these studies utilized a heterotopic bone formation model in immunocompromised animals to provide evidence of osteo- and chondro-conductivity and inductivity. However, more recent studies by Bahney et al., $ ^{110} $ van der Stok et al., $ ^{106} $ Harada et al., $ ^{105} $ and Shoji et al. $ ^{108} $ (Table 2) showed critical-size defect regeneration in rat femurs and mice tibias via EC ossification. Likewise, studies by Montufar-Solis et al. $ ^{27} $ and Doan et al. $ ^{62} $ (Table 3) showed critical-sized defect regeneration in murine calvaria. Collectively, these studies indicated that primed cartilage constructs can regenerate bone through EC ossification regardless of fetal developmental origin.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, 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4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 9, "page": 14, "raw_label": "text", "text": "Within the realm of SCBTs for bone regeneration, a majority of strategies have focused on stimulating cell populations to undergo direct osteogenesis rather than chondrogenesis. However, as previously mentioned, the EC ossification pathway holds key advantages over IM ossification. This is especially true in critical-sized defects that are inherently large avascular spaces and favor intermediate chondrogenesis of tissue rather than direct ossification. $ ^{1-9} $ An emerging group of successful research efforts have focused on exploiting this condition over the past decade. These recent publications (Tables 2–4) have demonstrated the capacity of cartilage tissue constructs to promote EC ossification in vivo after in vitro priming with seeded BMSCs, $ ^{60,63,64,66,67,72-76,103-107} $ ESCs, $ ^{27,62,67,76} $ ADSCs, $ ^{108} $ iPSCs, $ ^{109} $ and articular chondrocytes (ACs). $ ^{61,67,70,71,75} $ Most of these studies utilized a heterotopic bone formation model in immunocompromised animals to provide evidence of osteo- and chondro-conductivity and inductivity. However, more recent studies by Bahney et al., $ ^{110} $ van der Stok et al., $ ^{106} $ Harada et al., $ ^{105} $ and Shoji et al. $ ^{108} $ (Table 2) showed critical-size defect regeneration in rat femurs and mice tibias via EC ossification. Likewise, studies by Montufar-Solis et al. $ ^{27} $ and Doan et al. $ ^{62} $ (Table 3) showed critical-sized defect regeneration in murine calvaria. Collectively, these studies indicated that primed cartilage constructs can regenerate bone through EC ossification regardless of fetal developmental origin.", "bbox": [618, 448, 1110, 1039], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Within the realm of SCBTs for bone regeneration, a majority of strategies have focused on stimulating cell populations to undergo direct osteogenesis rather than chondrogenesis. However, as previously mentioned, the EC ossification pathway holds key advantages over IM ossification. This is especially true in critical-sized defects that are inherently large avascular spaces and favor intermediate chondrogenesis of tissue rather than direct ossification. $ ^{1-9} $ An emerging group of successful research efforts have focused on exploiting this condition over the past decade. These recent publications (Tables 2–4) have demonstrated the capacity of cartilage tissue constructs to promote EC ossification in vivo after in vitro priming with seeded BMSCs, $ ^{60,63,64,66,67,72-76,103-107} $ ESCs, $ ^{27,62,67,76} $ ADSCs, $ ^{108} $ iPSCs, $ ^{109} $ and articular chondrocytes (ACs). $ ^{61,67,70,71,75} $ Most of these studies utilized a heterotopic bone formation model in immunocompromised animals to provide evidence of osteo- and chondro-conductivity and inductivity. However, more recent studies by Bahney et al., $ ^{110} $ van der Stok et al., $ ^{106} $ Harada et al., $ ^{105} $ and Shoji et al. $ ^{108} $ (Table 2) showed critical-size defect regeneration in rat femurs and mice tibias via EC ossification. Likewise, studies by Montufar-Solis et al. $ ^{27} $ and Doan et al. $ ^{62} $ (Table 3) showed critical-sized defect regeneration in murine calvaria. Collectively, these studies indicated that primed cartilage constructs can regenerate bone through EC ossification regardless of fetal developmental origin."}, "layout_signature": {"width": 492, "width_bucket": 500, "height": 591, "left": 618, "top": 448, "right": 1110, "bottom": 1039, "x_center": 864.0, "x_center_bucket": 875, "y_center": 743.5, "x_ratio": 0.7059, "y_ratio": 0.4694, "width_ratio": 0.402, "height_ratio": 0.3731, "line_count": 1}, "span_signature": {"font_size": 9.75, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 379}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 14, "block_id": 10, "raw_label": "text", "raw_order": 9, "bbox": [618, 1039, 1111, 1479], "text": "While the majority of the tissue priming research aimed at establishing feasibility from a particular cell population (Tables 2 and 3), several studies compared various cell sources to elucidate differences in their capacity to stimulate EC ossification (Table 4). $ ^{67,75,76} $ Most of these comparative studies concluded that only certain cell sources, most often ESCs or BMSCs, were capable of inducing EC ossification in animal models $ ^{67,75-77,111} $; however, other studies clearly showed significant EC ossification with ADSCs, $ ^{108} $ iPSCs, $ ^{109} $ and even ACs in vivo. $ ^{61,70,71} $ The only stem cell population that did not exhibit EC ossification were SDSCs, which instead went through fibrous degradation and resorption in vivo. $ ^{75,77} $ This contradicting evidence highlights the fact that the spatiotemporal control of cell culture priming conditions is essential in determining implant fate in vivo. A review by Gawlitta et al. $ ^{41} $ focused on the modulation of these conditions to optimize the in vitro priming of BMSCs for EC ossification. However, a comprehensive overview of modulating EC priming conditions between comparative sources of stem cells has not been addressed.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], 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clearly showed significant EC ossification with ADSCs, $ ^{108} $ iPSCs, $ ^{109} $ and even ACs in vivo. $ ^{61,70,71} $ The only stem cell population that did not exhibit EC ossification were SDSCs, which instead went through fibrous degradation and resorption in vivo. $ ^{75,77} $ This contradicting evidence highlights the fact that the spatiotemporal control of cell culture priming conditions is essential in determining implant fate in vivo. A review by Gawlitta et al. $ ^{41} $ focused on the modulation of these conditions to optimize the in vitro priming of BMSCs for EC ossification. 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A review by Gawlitta et al. $ ^{41} $ focused on the modulation of these conditions to optimize the in vitro priming of BMSCs for EC ossification. 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vitro cell priming and expansion, previous evidence was already presented as linking EC ossification to acellular DBM grafts. $ ^{26-32} $ This evidence directly contradicts the notion that priming is necessary to elicit an EC response (Tables 2–4) and instead only represents a sufficient condition which can also be addressed by acellular native ECM biomaterials.", "bbox": [111, 489, 601, 688], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "While the collective evidence from these studies suggested that EC ossification remains necessarily tethered to the burden of in vitro cell priming and expansion, previous evidence was already presented as linking EC ossification to acellular DBM grafts. $ ^{26-32} $ This evidence directly contradicts the notion that priming is necessary to elicit an EC response (Tables 2–4) and instead only represents a sufficient condition which can also 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Extensive supporting evidence has been previously presented in this review to suggest that native, acellular ECM biomaterials (e.g., DCC) mimicking the procallus healing microenvironment may be a worthwhile focus for future investigation in this underexplored design space for bone regeneration.", "bbox": [111, 688, 601, 976], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Consequently, this contradictory evidence suggests that an intermediate and underexplored strategy for bone regeneration may exist which incorporates advantages exhibited by both DBM biomaterials and primed cartilage constructs, such as the enhancement of EC ossification, and possibly minimizes their limitations, for example the extensive costs, risks, and time-consuming manufacturing practices associated with in vitro cell expansion. Extensive supporting evidence has been previously presented in this review to suggest that native, acellular ECM biomaterials (e.g., DCC) mimicking the procallus healing microenvironment may be a worthwhile focus for future investigation in this underexplored design space for bone regeneration."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 288, "left": 111, "top": 688, "right": 601, "bottom": 976, "x_center": 356.0, "x_center_bucket": 350, "y_center": 832.0, "x_ratio": 0.2908, "y_ratio": 0.5253, "width_ratio": 0.4003, "height_ratio": 0.1818, "line_count": 1}, "span_signature": {"font_size": 9.84, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 167}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 15, "block_id": 11, "raw_label": "text", "raw_order": 10, "bbox": [112, 992, 602, 1300], "text": "Intraoperative SCBT strategies with native ECM biomaterials. An emerging strategy to streamline SCBTs is to consolidate necessary cell protocols, including the harvesting, isolation, stimulation, and implantation of autologous cells, into one surgical (i.e., intraoperative) setting. Intraoperative SCBTs usually involve the use of multiple surgical sites (e.g., a bone defect site and a bone marrow aspiration site) but obviates the need for cell expansion protocols. By definition, ABG falls under the description of an intraoperative SCBT, as autologous stem cells are harvested and implanted within one surgical setting. 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"Intraoperative SCBT strategies with native ECM biomaterials. An emerging strategy to streamline SCBTs is to consolidate necessary cell protocols, including the harvesting, isolation, stimulation, and implantation of autologous cells, into one surgical (i.e., intraoperative) setting. Intraoperative SCBTs usually involve the use of multiple surgical sites (e.g., a bone defect site and a bone marrow aspiration site) but obviates the need for cell expansion protocols. By definition, ABG falls under the description of an intraoperative SCBT, as autologous stem cells are harvested and implanted within one surgical setting. Recent intraoperative strategies aim at minimizing the limitations associated with traditional stem cell expansion protocols and ABG while also maximizing stem cell efficacy.", "bbox": [112, 992, 602, 1300], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Intraoperative SCBT strategies with native ECM biomaterials. An emerging strategy to streamline SCBTs is to consolidate necessary cell protocols, including the harvesting, isolation, stimulation, and implantation of autologous cells, into one surgical (i.e., intraoperative) setting. Intraoperative SCBTs usually involve the use of multiple surgical sites (e.g., a bone defect site and a bone marrow aspiration site) but obviates the need for cell expansion protocols. By definition, ABG falls under the description of an intraoperative SCBT, as autologous stem cells are harvested and implanted within one surgical setting. Recent intraoperative strategies aim at minimizing the limitations associated with traditional stem cell expansion protocols and ABG while also maximizing stem cell efficacy."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 308, "left": 112, "top": 992, "right": 602, "bottom": 1300, "x_center": 357.0, "x_center_bucket": 350, "y_center": 1146.0, "x_ratio": 0.2917, "y_ratio": 0.7235, "width_ratio": 0.4003, "height_ratio": 0.1944, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvP6EC0", "bold": false, "italic": true, "span_count": 199}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "unknown_like", "style_family_authority": "fallback", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 15, "block_id": 12, "raw_label": "text", "raw_order": 11, "bbox": [112, 1300, 602, 1479], "text": "To date, however, no intraoperative SCBT approaches using either BMSCs or ADSCs derived from the stromal vascular fraction (SVF) have been able to regenerate bone in critical-sized defects without the inclusion of additional stimulatory factors. $ ^{25} $ In a study by Helder et al., $ ^{112} $ isolated SVF cells failed to generate bone when implanted in a goat intervertebral model. Likewise, Follmar et al. $ ^{113} $ saw limited angiogenesis and no evidence of ossification in ADSCs-loaded fibrin glues implanted subcutaneously in rabbits. Muller et al. $ ^{114} $ observed some evidence of combined angiogenesis and osteoid structures, identified with histology and immunostaining for bone sialoprotein and osteocalcin, in human ADSC-loaded fibrin glues combined with betatricalcium phosphate, hydroxyapatite, and acellular bone xenografts implanted subcutaneously in nude mice. However, the authors found no evidence of murine derived bone structures in the implants, indicating a lack of osteoinductivity. $ ^{114} $ More recent data from the same group indicated that SVF combined with 250ng of BMP-2 and encapsulated in a fibrin and porous calcium phosphate composite gel could form heterotropic bone when injected subcutaneously in nude mice. $ ^{115} $ Overall, this combined evidence suggests that additional inductive stimulation of stem cells within the brief surgical time frame may be crucial in improving efficacy of intraoperative designs.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, 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using either BMSCs or ADSCs derived from the stromal vascular fraction (SVF) have been able to regenerate bone in critical-sized defects without the inclusion of additional stimulatory factors. $ ^{25} $ In a study by Helder et al., $ ^{112} $ isolated SVF cells failed to generate bone when implanted in a goat intervertebral model. Likewise, Follmar et al. $ ^{113} $ saw limited angiogenesis and no evidence of ossification in ADSCs-loaded fibrin glues implanted subcutaneously in rabbits. Muller et al. $ ^{114} $ observed some evidence of combined angiogenesis and osteoid structures, identified with histology and immunostaining for bone sialoprotein and osteocalcin, in human ADSC-loaded fibrin glues combined with betatricalcium phosphate, hydroxyapatite, and acellular bone xenografts implanted subcutaneously in nude mice. However, the authors found no evidence of murine derived bone structures in the implants, indicating a lack of osteoinductivity. $ ^{114} $ More recent data from the same group indicated that SVF combined with 250ng of BMP-2 and encapsulated in a fibrin and porous calcium phosphate composite gel could form heterotropic bone when injected subcutaneously in nude mice. $ ^{115} $ Overall, this combined evidence suggests that additional inductive stimulation of stem cells within the brief surgical time frame may be crucial in improving efficacy of intraoperative designs.", "bbox": [112, 1300, 602, 1479], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "To date, however, no intraoperative SCBT approaches using either BMSCs or ADSCs derived from the stromal vascular fraction (SVF) have been able to regenerate bone in critical-sized defects without the inclusion of additional stimulatory factors. $ ^{25} $ In a study by Helder et al., $ ^{112} $ isolated SVF cells failed to generate bone when implanted in a goat intervertebral model. Likewise, Follmar et al. $ ^{113} $ saw limited angiogenesis and no evidence of ossification in ADSCs-loaded fibrin glues implanted subcutaneously in rabbits. Muller et al. $ ^{114} $ observed some evidence of combined angiogenesis and osteoid structures, identified with histology and immunostaining for bone sialoprotein and osteocalcin, in human ADSC-loaded fibrin glues combined with betatricalcium phosphate, hydroxyapatite, and acellular bone xenografts implanted subcutaneously in nude mice. 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"page": 15, "block_id": 15, "raw_label": "text", "raw_order": 14, "bbox": [614, 730, 1104, 1017], "text": "Meanwhile, it should be reiterated and emphasized that native ECM biomaterials from allogeneic and xenogeneic sources possess both conductive and inductive biomolecules. $ ^{17,18,20,21} $ These biomaterials alone may have the potential to stimulate stem cells in an intraoperative setting. 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"Meanwhile, it should be reiterated and emphasized that native ECM biomaterials from allogeneic and xenogeneic sources possess both conductive and inductive biomolecules. $ ^{17,18,20,21} $ These biomaterials alone may have the potential to stimulate stem cells in an intraoperative setting. As previously discussed, native ECM representing both the early and late stages of bone repair have the ability to induce both chondro- and osteogenesis by seeded stem cells. $ ^{26-29,93} $ A critical area of future investigation, therefore, should be devoted to examining the capacity of these biomaterials to stimulate stem cell differentiation and gene expression within the time constrained intraoperative setting for the purpose of enhancing bone regeneration.", "bbox": [614, 730, 1104, 1017], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Meanwhile, it should be reiterated and emphasized that native ECM biomaterials from allogeneic and xenogeneic sources possess both conductive and inductive biomolecules. $ ^{17,18,20,21} $ These biomaterials alone may have the potential to stimulate stem cells in an intraoperative setting. As previously discussed, native ECM representing both the early and late stages of bone repair have the ability to induce both chondro- and osteogenesis by seeded stem cells. $ ^{26-29,93} $ A critical area of future investigation, therefore, should be devoted to examining the capacity of these biomaterials to stimulate stem cell differentiation and gene expression within the time constrained intraoperative setting for the purpose of enhancing bone regeneration."}, "layout_signature": {"width": 490, "width_bucket": 500, "height": 287, "left": 614, "top": 730, "right": 1104, "bottom": 1017, "x_center": 859.0, "x_center_bucket": 850, "y_center": 873.5, "x_ratio": 0.7018, "y_ratio": 0.5515, "width_ratio": 0.4003, "height_ratio": 0.1812, "line_count": 1}, "span_signature": {"font_size": 9.8, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 145}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "unknown_like", "style_family_authority": "fallback", "reading_band_id": "band_073", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 15, "block_id": 16, "raw_label": "text", "raw_order": 15, "bbox": [614, 1015, 1105, 1237], "text": "In summary, establishing the regenerative potential of acellular ECM biomaterial designs will help elucidate the additional benefits of incorporating either SCBTs or other purified inductive and conductive biomolecules into intraoperative manufacturing strategies for bone tissue engineering. 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Evidence to support this claim of utility resides in two evolving arenas of bone tissue engineering: (1) in vitro primed chondrogenic constructs (Tables 2–4) and (2) native DBM allografts and xenografts. $ ^{26-32} $ Both strategies have been shown to elicit EC ossification in heterotopic animal models and, more importantly, regenerate critical-sized defects in bone that originated during fetal development from EC ossification (e.g., femur) and IM ossification (e.g., cranium). 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Evidence to support this claim of utility resides in two evolving arenas of bone tissue engineering: (1) in vitro primed chondrogenic constructs (Tables 2–4) and (2) native DBM allografts and xenografts. $ ^{26-32} $ Both strategies have been shown to elicit EC ossification in heterotopic animal models and, more importantly, regenerate critical-sized defects in bone that originated during fetal development from EC ossification (e.g., femur) and IM ossification (e.g., cranium). This latter evidence gives credence to the potential versatility of strategies enhancing EC ossification for a vast array of clinical orthopedic indications.", "bbox": [117, 117, 606, 402], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "intervention but can potentially be enhanced by combining in vivo developmental engineering strategies with biomimetic ECM biomaterials. Evidence to support this claim of utility resides in two evolving arenas of bone tissue engineering: (1) in vitro primed chondrogenic constructs (Tables 2–4) and (2) native DBM allografts and xenografts. $ ^{26-32} $ Both strategies have been shown to elicit EC ossification in heterotopic animal models and, more importantly, regenerate critical-sized defects in bone that originated during fetal development from EC ossification (e.g., femur) and IM ossification (e.g., cranium). This latter evidence gives credence to the potential versatility of strategies enhancing EC ossification for a vast array of clinical orthopedic indications."}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 285, "left": 117, "top": 117, "right": 606, "bottom": 402, "x_center": 361.5, "x_center_bucket": 350, "y_center": 259.5, "x_ratio": 0.2953, "y_ratio": 0.1638, "width_ratio": 0.3995, "height_ratio": 0.1799, "line_count": 1}, "span_signature": {"font_size": 9.83, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 170}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 16, "block_id": 3, "raw_label": "text", "raw_order": 2, "bbox": [117, 402, 606, 600], "text": "Currently, however, both in vitro priming and DBM strategies face formidable technical, business, and regulatory challenges that limit their feasibility as commercially competitive alternatives to the standard of treatment, ABG. While the former approach remains tethered to burdensome, costly, and commercially inhibitive in vitro cell expansion protocols, the latter may elicit an insufficient EC ossification response due to its primarily osteoinductive and osteoconductive ECM cues, which instead favor IM ossification.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, 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"raw_observation": {"block_id": 3, "page": 16, "raw_label": "text", "text": "Currently, however, both in vitro priming and DBM strategies face formidable technical, business, and regulatory challenges that limit their feasibility as commercially competitive alternatives to the standard of treatment, ABG. While the former approach remains tethered to burdensome, costly, and commercially inhibitive in vitro cell expansion protocols, the latter may elicit an insufficient EC ossification response due to its primarily osteoinductive and osteoconductive ECM cues, which instead favor IM ossification.", "bbox": [117, 402, 606, 600], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Currently, however, both in vitro priming and DBM strategies face formidable technical, business, and regulatory challenges that limit their feasibility as commercially competitive alternatives to the standard of treatment, ABG. While the former approach remains tethered to burdensome, costly, and commercially inhibitive in vitro cell expansion protocols, the latter may elicit an insufficient EC ossification response due to its primarily osteoinductive and osteoconductive ECM cues, which instead favor IM ossification."}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 198, "left": 117, "top": 402, "right": 606, "bottom": 600, "x_center": 361.5, "x_center_bucket": 350, "y_center": 501.0, "x_ratio": 0.2953, "y_ratio": 0.3163, "width_ratio": 0.3995, "height_ratio": 0.125, "line_count": 1}, "span_signature": {"font_size": 9.84, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 105}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 16, "block_id": 4, "raw_label": "text", "raw_order": 3, "bbox": [117, 601, 606, 1170], "text": "In addition, regulatory challenges exist for both strategies. $ ^{118} $ The in vitro expansion of autologous stem cells inherently involves a high level of manufacturing risk that should meet stringent quality assurance and control for approval by the U.S. Food and Drug Administration (FDA), $ ^{118} $ potentially resulting in an expensive premarket approval (PMA) process for each orthopedic indication. Furthermore, off-site facilities may be required to expand cells, which add to the associated risks involved in maintaining viability and preventing contamination of cells. Meanwhile, native ECM biomaterials also face regulatory approval challenges outlined by the FDA and American Association of Tissue Banks (AATB). $ ^{15} $ Allogeneic tissue (e.g., DBM or DCC) by itself is not considered a medical device by the FDA unless it is combined with a carrier material, such as hyaluronic acid (e.g., DBX $ ^{\\circledR} $; MTF/Synthes), in which case it should go through 510(k) approval. Instead, these materials (e.g., Puros $ ^{\\circledR} $ DBM; Zimmer) are categorized under the heading of human cells, tissues, and cellular and tissue-based products (HCT/P). However, the majority of orthopedic DBM products have undergone 510(k) approval by the FDA. $ ^{15} $ Based on this knowledge of the regulatory landscape surrounding these strategies, it is evident that acellular ECM biomaterials face fewer challenges than SBCT strategies for approval and, therefore, may represent the more favorable route to clinical translation.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, 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Furthermore, off-site facilities may be required to expand cells, which add to the associated risks involved in maintaining viability and preventing contamination of cells. Meanwhile, native ECM biomaterials also face regulatory approval challenges outlined by the FDA and American Association of Tissue Banks (AATB). $ ^{15} $ Allogeneic tissue (e.g., DBM or DCC) by itself is not considered a medical device by the FDA unless it is combined with a carrier material, such as hyaluronic acid (e.g., DBX $ ^{\\circledR} $; MTF/Synthes), in which case it should go through 510(k) approval. Instead, these materials (e.g., Puros $ ^{\\circledR} $ DBM; Zimmer) are categorized under the heading of human cells, tissues, and cellular and tissue-based products (HCT/P). However, the majority of orthopedic DBM products have undergone 510(k) approval by the FDA. $ ^{15} $ Based on this knowledge of the regulatory landscape surrounding these strategies, it is evident that acellular ECM biomaterials face fewer challenges than SBCT strategies for approval and, therefore, may represent the more favorable route to clinical translation.", "bbox": [117, 601, 606, 1170], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "In addition, regulatory challenges exist for both strategies. $ ^{118} $ The in vitro expansion of autologous stem cells inherently involves a high level of manufacturing risk that should meet stringent quality assurance and control for approval by the U.S. Food and Drug Administration (FDA), $ ^{118} $ potentially resulting in an expensive premarket approval (PMA) process for each orthopedic indication. Furthermore, off-site facilities may be required to expand cells, which add to the associated risks involved in maintaining viability and preventing contamination of cells. Meanwhile, native ECM biomaterials also face regulatory approval challenges outlined by the FDA and American Association of Tissue Banks (AATB). $ ^{15} $ Allogeneic tissue (e.g., DBM or DCC) by itself is not considered a medical device by the FDA unless it is combined with a carrier material, such as hyaluronic acid (e.g., DBX $ ^{\\circledR} $; MTF/Synthes), in which case it should go through 510(k) approval. Instead, these materials (e.g., Puros $ ^{\\circledR} $ DBM; Zimmer) are categorized under the heading of human cells, tissues, and cellular and tissue-based products (HCT/P). However, the majority of orthopedic DBM products have undergone 510(k) approval by the FDA. $ ^{15} $ Based on this knowledge of the regulatory landscape surrounding these strategies, it is evident that acellular ECM biomaterials face fewer challenges than SBCT strategies for approval and, therefore, may represent the more favorable route to clinical translation."}, "layout_signature": {"width": 489, "width_bucket": 500, "height": 569, "left": 117, "top": 601, "right": 606, "bottom": 1170, "x_center": 361.5, "x_center_bucket": 350, "y_center": 885.5, "x_ratio": 0.2953, "y_ratio": 0.559, "width_ratio": 0.3995, "height_ratio": 0.3592, "line_count": 1}, "span_signature": {"font_size": 9.78, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 293}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_family_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 16, "block_id": 5, "raw_label": "text", "raw_order": 4, "bbox": [117, 1169, 607, 1479], "text": "An alternative, and underexplored, developmental engineering strategy integrates the advantages of these two EC ossification approaches with a new class of ECM biomaterials that instead resemble the early fibrocartilaginous bone-healing microenvironment and may enhance the EC ossification response from damaged host tissue. The primary native ECM candidates proposed to potentially elicit such a response are decellularized biomaterials originating from articular, fibrocartilaginous, or hypertrophic cartilage sources. These tissues inherently possess relevant chondroconductive and chondroinductive biomolecules that may potentially modulate EC ossification within an implant. In addition, decellularized ECM constructs may reduce or remove the need for time- and cost-consuming in vitro cell expansion protocols, expanding the developmental engineering paradigm $ ^{22,23} $ to include in vivo design strategies. Likewise, the FDA regulatory approval associated with this new class of ECM biomaterials may possibly avoid the more costly and time-consuming PMA process and instead follow a less stringent 510(k) approval process due to its similarity to existing commercially available DBM products.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 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The primary native ECM candidates proposed to potentially elicit such a response are decellularized biomaterials originating from articular, fibrocartilaginous, or hypertrophic cartilage sources. These tissues inherently possess relevant chondroconductive and chondroinductive biomolecules that may potentially modulate EC ossification within an implant. In addition, decellularized ECM constructs may reduce or remove the need for time- and cost-consuming in vitro cell expansion protocols, expanding the developmental engineering paradigm $ ^{22,23} $ to include in vivo design strategies. Likewise, the FDA regulatory approval associated with this new class of ECM biomaterials may possibly avoid the more costly and time-consuming PMA process and instead follow a less stringent 510(k) approval process due to its similarity to existing commercially available DBM products.", "bbox": [117, 1169, 607, 1479], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "An alternative, and underexplored, developmental engineering strategy integrates the advantages of these two EC ossification approaches with a new class of ECM biomaterials that instead resemble the early fibrocartilaginous bone-healing microenvironment and may enhance the EC ossification response from damaged host tissue. The primary native ECM candidates proposed to potentially elicit such a response are decellularized biomaterials originating from articular, fibrocartilaginous, or hypertrophic cartilage sources. These tissues inherently possess relevant chondroconductive and chondroinductive biomolecules that may potentially modulate EC ossification within an implant. In addition, decellularized ECM constructs may reduce or remove the need for time- and cost-consuming in vitro cell expansion protocols, expanding the developmental engineering paradigm $ ^{22,23} $ to include in vivo design strategies. 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While the reviewed chondrogenic priming studies collectively concluded that in vitro stimulation was a necessary step to elicit EC ossification, contradicting evidence with acellular DBM implants suggests that the inclusion and priming of stem cells is not a requirement and may be obviated with the proper inclusion of native ECM components. $ ^{26-32} $ Regardless of this contradiction, SCBT strategies provided evidence that modulating hypertrophic signals in bone regenerative implants may lead to a significant enhancement of EC ossification (Tables 2–4). Furthermore, SCBTs provide additional chondrogenic and osteogenic potential within implants compared with acellular ECM biomaterials that alternatively rely on stem cell recruitment from surrounding host tissue. It is not clear whether current orthopedic products in the preclinical and clinical development phase utilize in vitro expansion strategies, but according to Jaklenec et al., $ ^{11} $ a majority of SCBTs across the entire area of tissue engineering and regenerative medicine favor autologous cells (59%) compared with allogeneic (39%) and xenogeneic (2%) cell sources. This indicates the industry's growing interest in developing SCBTs, but it should be emphasized that regulatory approval is not a guarantee of commercial success. Intraoperative SCBT strategies may address these concerns by reducing or removing the burden of in vitro cell expansion without compromising the chondrogenic and osteogenic potential of incorporated stem cells, thus furthering the bone regenerative potential of ECM implants along with overall commercial feasibility.", "page_width": 1224, "page_height": 1584, "role": "body_paragraph", "role_confidence": 0.6, "evidence": ["default body_paragraph for text label"], "seed_role": "body_paragraph", "seed_confidence": 0.6, "seed_evidence": ["default body_paragraph for text label"], "span_metadata": [{"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": 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4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}, {"size": 9.843000411987305, "font": "AdvTimRomLiebert", "flags": 4, "color": 2301728, "dir": [1.0, 0.0], "wmode": 0}], "raw_observation": {"block_id": 7, "page": 16, "raw_label": "text", "text": "Although significant focus was given to acellular ECM strategies, critical perspectives on SCBTs were also discussed. While the reviewed chondrogenic priming studies collectively concluded that in vitro stimulation was a necessary step to elicit EC ossification, contradicting evidence with acellular DBM implants suggests that the inclusion and priming of stem cells is not a requirement and may be obviated with the proper inclusion of native ECM components. $ ^{26-32} $ Regardless of this contradiction, SCBT strategies provided evidence that modulating hypertrophic signals in bone regenerative implants may lead to a significant enhancement of EC ossification (Tables 2–4). Furthermore, SCBTs provide additional chondrogenic and osteogenic potential within implants compared with acellular ECM biomaterials that alternatively rely on stem cell recruitment from surrounding host tissue. It is not clear whether current orthopedic products in the preclinical and clinical development phase utilize in vitro expansion strategies, but according to Jaklenec et al., $ ^{11} $ a majority of SCBTs across the entire area of tissue engineering and regenerative medicine favor autologous cells (59%) compared with allogeneic (39%) and xenogeneic (2%) cell sources. This indicates the industry's growing interest in developing SCBTs, but it should be emphasized that regulatory approval is not a guarantee of commercial success. Intraoperative SCBT strategies may address these concerns by reducing or removing the burden of in vitro cell expansion without compromising the chondrogenic and osteogenic potential of incorporated stem cells, thus furthering the bone regenerative potential of ECM implants along with overall commercial feasibility.", "bbox": [619, 269, 1110, 930], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "Although significant focus was given to acellular ECM strategies, critical perspectives on SCBTs were also discussed. While the reviewed chondrogenic priming studies collectively concluded that in vitro stimulation was a necessary step to elicit EC ossification, contradicting evidence with acellular DBM implants suggests that the inclusion and priming of stem cells is not a requirement and may be obviated with the proper inclusion of native ECM components. $ ^{26-32} $ Regardless of this contradiction, SCBT strategies provided evidence that modulating hypertrophic signals in bone regenerative implants may lead to a significant enhancement of EC ossification (Tables 2–4). Furthermore, SCBTs provide additional chondrogenic and osteogenic potential within implants compared with acellular ECM biomaterials that alternatively rely on stem cell recruitment from surrounding host tissue. It is not clear whether current orthopedic products in the preclinical and clinical development phase utilize in vitro expansion strategies, but according to Jaklenec et al., $ ^{11} $ a majority of SCBTs across the entire area of tissue engineering and regenerative medicine favor autologous cells (59%) compared with allogeneic (39%) and xenogeneic (2%) cell sources. This indicates the industry's growing interest in developing SCBTs, but it should be emphasized that regulatory approval is not a guarantee of commercial success. Intraoperative SCBT strategies may address these concerns by reducing or removing the burden of in vitro cell expansion without compromising the chondrogenic and osteogenic potential of incorporated stem cells, thus furthering the bone regenerative potential of ECM implants along with overall commercial feasibility."}, "layout_signature": {"width": 491, "width_bucket": 500, "height": 661, "left": 619, "top": 269, "right": 1110, "bottom": 930, "x_center": 864.5, "x_center_bucket": 875, "y_center": 599.5, "x_ratio": 0.7063, "y_ratio": 0.3785, "width_ratio": 0.4011, "height_ratio": 0.4173, "line_count": 1}, "span_signature": {"font_size": 9.83, "font_size_median": 9.84, "font_size_bucket": 10.0, "font_family_norm": "AdvTimRomLiebert", "bold": false, "italic": true, "span_count": 405}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "body_zone", "style_family": "body_like", "style_family_authority": "body_zone_with_anchor", "reading_band_id": "band_072", "display_cluster_candidate_id": "", "layout_region": "reference_candidate", "boundary_before": "weak", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} +{"paper_id": "37LK5T97", "page": 16, "block_id": 8, "raw_label": "text", "raw_order": 7, "bbox": [619, 929, 1109, 1194], "text": "In summary, native ECM biomaterials inherently possessing ideal conductive, inductive, and mechanical properties have yet to be considered with regard to EC ossification and developmental engineering principles in general. 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A variety of ECM biomaterial criteria have been reviewed here, which are promising for regenerative investigations spanning bone, cartilage, and osteochondral defects. In the future, in vivo comparisons will be necessary to provide substantial evidence that native ECM biomaterials mimicking aspects of the reparative procellus microenvironment will provide superior performance compared with traditional tissue engineering strategies and current standards of treatment.", "bbox": [619, 929, 1109, 1194], "page_width": 1224, "page_height": 1584}, "marker_signature": {"type": "none", "raw_marker": null, "number": null, "kind": "generic_text", "normalized_text": "In summary, native ECM biomaterials inherently possessing ideal conductive, inductive, and mechanical properties have yet to be considered with regard to EC ossification and developmental engineering principles in general. A variety of ECM biomaterial criteria have been reviewed here, which are promising for regenerative investigations spanning bone, cartilage, and osteochondral defects. 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"bold": false, "italic": true, "span_count": 25}, "_in_visual_container": null, "_container_bbox": null, "_container_text": null, "_text_source": null, "_ocr_raw_status": null, "_ocr_raw_error_type": null, "render_default": true, "index_default": true, "zone": "tail_nonref_hold_zone", "style_family": "unknown_like", "style_family_authority": "fallback", "reading_band_id": "band_074", "display_cluster_candidate_id": "", "layout_region": "tail_candidate", "boundary_before": "none", "boundary_after": "none", "bridge_eligible": false, "insert_score": {"score": 0.15, "decision": "body", "evidence": ["narrow_width"]}, "role_verification_status": "ACCEPT", "role_source": "non_structural_normalized_role", "role_evidence": ["pre-gate normalized non-structural role preserved"]} diff --git a/tests/test_ocr_figures.py b/tests/test_ocr_figures.py index e5dbc1c1..67baed31 100644 --- a/tests/test_ocr_figures.py +++ b/tests/test_ocr_figures.py @@ -272,11 +272,56 @@ def test_build_figure_inventory_exposes_mixed_local_pairing_hypotheses() -> None from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"paper_id": "MX", "page": 1, "block_id": "a1", "role": "media_asset", "raw_label": "image", "bbox": [520, 80, 1040, 360], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX", "page": 1, "block_id": "a2", "role": "media_asset", "raw_label": "image", "bbox": [520, 410, 1040, 690], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX", "page": 1, "block_id": "a3", "role": "media_asset", "raw_label": "image", "bbox": [520, 760, 1040, 980], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX", "page": 1, "block_id": "a4", "role": "media_asset", "raw_label": "image", "bbox": [120, 820, 1080, 1080], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX", "page": 1, "block_id": "body_sep", "role": "body_paragraph", "text": "This body text separates the sidecar pair from the lower figure.", "bbox": [120, 700, 1080, 790], "page_width": 1200, "page_height": 1600}, + { + "paper_id": "MX", + "page": 1, + "block_id": "a1", + "role": "media_asset", + "raw_label": "image", + "bbox": [520, 80, 1040, 360], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX", + "page": 1, + "block_id": "a2", + "role": "media_asset", + "raw_label": "image", + "bbox": [520, 410, 1040, 690], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX", + "page": 1, + "block_id": "a3", + "role": "media_asset", + "raw_label": "image", + "bbox": [520, 760, 1040, 980], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX", + "page": 1, + "block_id": "a4", + "role": "media_asset", + "raw_label": "image", + "bbox": [120, 820, 1080, 1080], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX", + "page": 1, + "block_id": "body_sep", + "role": "body_paragraph", + "text": "This body text separates the sidecar pair from the lower figure.", + "bbox": [120, 700, 1080, 790], + "page_width": 1200, + "page_height": 1600, + }, { "paper_id": "MX", "page": 1, @@ -401,6 +446,7 @@ def test_media_clusters_ignores_non_media_assets() -> None: def test_rect_intersection_area() -> None: from paperforge.worker.ocr_figures import _rect_intersection_area + a = [0, 0, 10, 10] b = [5, 5, 15, 15] assert _rect_intersection_area(a, b) == 25.0 @@ -409,6 +455,7 @@ def test_rect_intersection_area() -> None: def test_has_text_separator_detects_body_between_stacked_assets() -> None: from paperforge.worker.ocr_figures import _has_text_separator + a = {"bbox": [0, 0, 100, 50], "page": 1} b = {"bbox": [0, 150, 100, 200], "page": 1} body = {"bbox": [10, 70, 90, 130], "page": 1, "role": "body_paragraph", "text": "some body text here"} @@ -417,6 +464,7 @@ def test_has_text_separator_detects_body_between_stacked_assets() -> None: def test_has_text_separator_no_block_returns_false() -> None: from paperforge.worker.ocr_figures import _has_text_separator + a = {"bbox": [0, 0, 100, 50], "page": 1} b = {"bbox": [0, 150, 100, 200], "page": 1} assert _has_text_separator(a, b, []) is False @@ -424,6 +472,7 @@ def test_has_text_separator_no_block_returns_false() -> None: def test_has_text_separator_side_by_side_body_between() -> None: from paperforge.worker.ocr_figures import _has_text_separator + a = {"bbox": [0, 0, 100, 200], "page": 1} b = {"bbox": [300, 0, 400, 200], "page": 1} body = {"bbox": [130, 50, 270, 150], "page": 1, "role": "body_paragraph", "text": "column text separator"} @@ -432,6 +481,7 @@ def test_has_text_separator_side_by_side_body_between() -> None: def test_has_text_separator_short_text_ignored() -> None: from paperforge.worker.ocr_figures import _has_text_separator + a = {"bbox": [0, 0, 100, 50], "page": 1} b = {"bbox": [0, 150, 100, 200], "page": 1} short = {"bbox": [10, 70, 90, 130], "page": 1, "role": "body_paragraph", "text": "short"} @@ -440,6 +490,7 @@ def test_has_text_separator_short_text_ignored() -> None: def test_has_text_separator_diagonal_no_false_positive() -> None: from paperforge.worker.ocr_figures import _has_text_separator + a = {"bbox": [0, 0, 100, 100], "page": 1} b = {"bbox": [300, 300, 400, 400], "page": 1} assert _has_text_separator(a, b, []) is False @@ -447,6 +498,7 @@ def test_has_text_separator_diagonal_no_false_positive() -> None: def test_filter_figure_assets() -> None: from paperforge.worker.ocr_figures import _filter_figure_assets + assets = [ {"block_id": "fig", "role": "figure_asset", "raw_label": "image"}, {"block_id": "chart", "role": "media_asset", "raw_label": "chart"}, @@ -462,6 +514,7 @@ def test_filter_figure_assets() -> None: def test_cluster_page_assets_2x2_grid() -> None: from paperforge.worker.ocr_figures import _cluster_page_assets + assets = [ {"bbox": [0, 0, 100, 100], "page": 1, "role": "figure_asset"}, {"bbox": [120, 0, 220, 100], "page": 1, "role": "figure_asset"}, @@ -475,6 +528,7 @@ def test_cluster_page_assets_2x2_grid() -> None: def test_cluster_page_assets_wide_separation_no_irregular() -> None: from paperforge.worker.ocr_figures import _cluster_page_assets + assets = [ {"bbox": [0, 0, 100, 100], "page": 1, "role": "figure_asset"}, {"bbox": [500, 0, 600, 100], "page": 1, "role": "figure_asset"}, @@ -485,17 +539,24 @@ def test_cluster_page_assets_wide_separation_no_irregular() -> None: def test_cluster_page_assets_text_separator_splits() -> None: from paperforge.worker.ocr_figures import _cluster_page_assets + assets = [ {"bbox": [0, 0, 100, 100], "page": 1, "role": "figure_asset"}, {"bbox": [0, 200, 100, 300], "page": 1, "role": "figure_asset"}, ] - body = {"bbox": [10, 120, 90, 180], "page": 1, "role": "body_paragraph", "text": "some body text here between figures"} + body = { + "bbox": [10, 120, 90, 180], + "page": 1, + "role": "body_paragraph", + "text": "some body text here between figures", + } clusters = _cluster_page_assets(assets, [body], 1, 1000, 1000) assert len(clusters) == 2 def test_cluster_page_assets_irregular_merge() -> None: from paperforge.worker.ocr_figures import _cluster_page_assets + assets = [ {"bbox": [0, 0, 100, 300], "page": 1, "role": "figure_asset"}, {"bbox": [200, 0, 300, 100], "page": 1, "role": "figure_asset"}, @@ -509,6 +570,7 @@ def test_cluster_page_assets_irregular_merge() -> None: def test_cluster_page_assets_no_irregular_when_multi_legend() -> None: from paperforge.worker.ocr_figures import _cluster_page_assets + assets = [ {"bbox": [0, 0, 100, 300], "page": 1, "role": "figure_asset"}, {"bbox": [300, 0, 400, 100], "page": 1, "role": "figure_asset"}, @@ -545,11 +607,29 @@ def test_semantic_grouping_topology_is_caption_count_independent() -> None: {"block_id": "a4", "page": 1, "role": "figure_asset", "bbox": [320, 420, 520, 560]}, ] one_caption_blocks = assets + [ - {"block_id": "cap1", "page": 1, "role": "figure_caption", "text": "Figure 1. Caption.", "bbox": [100, 600, 520, 660]}, + { + "block_id": "cap1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Caption.", + "bbox": [100, 600, 520, 660], + }, ] two_caption_blocks = assets + [ - {"block_id": "cap1", "page": 1, "role": "figure_caption", "text": "Figure 1. Caption.", "bbox": [100, 280, 520, 340]}, - {"block_id": "cap2", "page": 1, "role": "figure_caption", "text": "Figure 2. Caption.", "bbox": [100, 600, 520, 660]}, + { + "block_id": "cap1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Caption.", + "bbox": [100, 280, 520, 340], + }, + { + "block_id": "cap2", + "page": 1, + "role": "figure_caption", + "text": "Figure 2. Caption.", + "bbox": [100, 600, 520, 660], + }, ] one_caption = _build_semantic_figure_groups_from_assets(assets, one_caption_blocks, page_width=1200) @@ -613,8 +693,20 @@ def test_candidate_groups_do_not_include_caption_band_local_groups() -> None: {"block_id": "a4", "page": 1, "role": "figure_asset", "bbox": [320, 420, 520, 560]}, ] legends = [ - {"block_id": "cap1", "page": 1, "role": "figure_caption", "text": "Figure 1. Caption.", "bbox": [100, 280, 520, 340]}, - {"block_id": "cap2", "page": 1, "role": "figure_caption", "text": "Figure 2. Caption.", "bbox": [100, 600, 520, 660]}, + { + "block_id": "cap1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Caption.", + "bbox": [100, 280, 520, 340], + }, + { + "block_id": "cap2", + "page": 1, + "role": "figure_caption", + "text": "Figure 2. Caption.", + "bbox": [100, 600, 520, 660], + }, ] candidate_groups = _build_candidate_figure_groups_from_assets(assets, assets + legends, legends, page_width=1200) @@ -848,6 +940,7 @@ def test_unmatched_assets_are_preserved() -> None: assert len(inventory["matched_figures"]) == 0 assert len(inventory["unmatched_assets"]) == 1 + def test_extract_figure_number_basic() -> None: from paperforge.worker.ocr_figures import _extract_figure_number @@ -1088,7 +1181,12 @@ def test_legend_does_not_steal_offpage_asset() -> None: # and p2_b1 asset may stay unmatched. Accept either outcome. if inventory["matched_figures"]: mf_flags = inventory["matched_figures"][0].get("flags", []) - assert "sequential_match" in mf_flags or "group_sequential_match" in mf_flags or "cross_page_match" in mf_flags or "cross_page_reserved" in mf_flags + assert ( + "sequential_match" in mf_flags + or "group_sequential_match" in mf_flags + or "cross_page_match" in mf_flags + or "cross_page_reserved" in mf_flags + ) else: # In vnext, cross-page may not match; legend may be in unmatched_legends assert any(ul.get("block_id") == "p1_b1" for ul in inventory.get("unmatched_legends", [])) @@ -1184,16 +1282,12 @@ def test_unresolved_clusters_in_inventory() -> None: assert len(inventory["matched_figures"]) == 0 assert len(inventory["rejected_legends"]) == 1 - assert "unresolved_clusters" in inventory, ( - "unresolved_clusters key must exist in inventory" - ) + assert "unresolved_clusters" in inventory, "unresolved_clusters key must exist in inventory" assert len(inventory["unresolved_clusters"]) == 1, ( "One unresolved cluster expected for six panels with rejected legend" ) cluster = inventory["unresolved_clusters"][0] - assert len(cluster["media_block_ids"]) == 6, ( - "Cluster must contain all six media block ids" - ) + assert len(cluster["media_block_ids"]) == 6, "Cluster must contain all six media block ids" for bid in ["p9_b2", "p9_b3", "p9_b4", "p9_b5", "p9_b6", "p9_b7"]: assert bid in cluster["media_block_ids"], f"Cluster missing {bid}" assert len(inventory["unmatched_assets"]) == 0, ( @@ -1317,6 +1411,7 @@ PAGE1_AUTHOR_BIO_FIXTURE = [ def test_non_body_insert_media_not_in_figure_assets() -> None: from paperforge.worker.ocr_figures import build_figure_inventory + inventory = build_figure_inventory(PAGE1_AUTHOR_BIO_FIXTURE) # vnext: no figure_assets key; use matched_figures' matched_assets asset_ids = [a.get("block_id") for fig in inventory["matched_figures"] for a in fig.get("matched_assets", [])] @@ -1339,7 +1434,9 @@ def test_non_body_insert_media_not_in_unmatched_assets() -> None: inventory = build_figure_inventory(PAGE1_AUTHOR_BIO_FIXTURE) unmatched_ids = [a.get("block_id") for a in inventory["unmatched_assets"]] # vnext: author bio media may appear in unmatched_assets; just verify it's not matched - matched_asset_ids = [a.get("block_id") for fig in inventory["matched_figures"] for a in fig.get("matched_assets", [])] + matched_asset_ids = [ + a.get("block_id") for fig in inventory["matched_figures"] for a in fig.get("matched_assets", []) + ] assert "p1_b3" not in matched_asset_ids, "Author bio image must not be in matched figure assets" @@ -1451,14 +1548,29 @@ def test_resolved_figure_caption_not_rejected_by_inventory(): from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "m1", "role": "media_asset", "bbox": [100, 500, 400, 800], "page": 5, "page_width": 1200, "page_height": 1700, "text": ""}, - {"block_id": "c1", "role": "figure_caption", "text": "Fig. 7. Expression of mRNA in tissue sections.", "bbox": [100, 450, 500, 490], "page": 5, "page_width": 1200, "page_height": 1700, "render_default": True}, + { + "block_id": "m1", + "role": "media_asset", + "bbox": [100, 500, 400, 800], + "page": 5, + "page_width": 1200, + "page_height": 1700, + "text": "", + }, + { + "block_id": "c1", + "role": "figure_caption", + "text": "Fig. 7. Expression of mRNA in tissue sections.", + "bbox": [100, 450, 500, 490], + "page": 5, + "page_width": 1200, + "page_height": 1700, + "render_default": True, + }, ] inventory = build_figure_inventory(blocks) - assert len(inventory["matched_figures"]) == 1, ( - f"Expected 1 matched figure, got {len(inventory['matched_figures'])}" - ) + assert len(inventory["matched_figures"]) == 1, f"Expected 1 matched figure, got {len(inventory['matched_figures'])}" # === SAN9AYVR guard tests (Task 7 -- preserve figure mainline) === @@ -1471,10 +1583,10 @@ SAN9AYVR_BODY_AND_FIGURES = [ "role": "figure_caption_candidate", "block_label": "text", "text": "Fig. 26c addresses the limiting case of the mathematical model where " - "the field strength approaches zero. The trend reverses at higher " - "concentrations as the system enters a regime where nonlinear effects " - "dominate the observed dynamics. This pattern is consistent with " - "prior observations in similar experimental systems.", + "the field strength approaches zero. The trend reverses at higher " + "concentrations as the system enters a regime where nonlinear effects " + "dominate the observed dynamics. This pattern is consistent with " + "prior observations in similar experimental systems.", "bbox": [50, 700, 550, 760], "page_width": 1200, "page_height": 1700, @@ -1485,9 +1597,9 @@ SAN9AYVR_BODY_AND_FIGURES = [ "block_id": "p3_b2", "role": "figure_caption", "text": "Figure 26. Quantitative analysis of cell migration under " - "applied DC electric field stimulation over 48 hours. " - "Data represent mean plus/minus standard deviation from " - "three independent experiments performed in triplicate.", + "applied DC electric field stimulation over 48 hours. " + "Data represent mean plus/minus standard deviation from " + "three independent experiments performed in triplicate.", "bbox": [50, 420, 550, 480], "page_width": 1200, "page_height": 1700, @@ -1508,9 +1620,9 @@ SAN9AYVR_BODY_AND_FIGURES = [ "block_id": "p3_b4", "role": "figure_caption", "text": "Figure 27. Expression levels of key proteins under " - "different experimental conditions. Error bars " - "represent standard deviation from three independent " - "biological replicates measured in duplicate.", + "different experimental conditions. Error bars " + "represent standard deviation from three independent " + "biological replicates measured in duplicate.", "bbox": [600, 420, 1100, 490], "page_width": 1200, "page_height": 1700, @@ -1546,7 +1658,9 @@ def test_san9ayvr_fig26c_body_narrative() -> None: # same_number_distinct_legends may not exist in vnext distinct = inventory.get("same_number_distinct_legends", []) or [] if distinct: - assert any(d.get("figure_number") == 26 for d in distinct), "Fig 26c narrative must appear in same_number_distinct_legends when populated" + assert any(d.get("figure_number") == 26 for d in distinct), ( + "Fig 26c narrative must appear in same_number_distinct_legends when populated" + ) def test_san9ayvr_fig26_fig27_remain_formal() -> None: @@ -1559,9 +1673,7 @@ def test_san9ayvr_fig26_fig27_remain_formal() -> None: assert 26 in fig_numbers, "Figure 26 must be a matched figure" assert 27 in fig_numbers, "Figure 27 must be a matched figure" for m in inventory["matched_figures"]: - assert len(m["matched_assets"]) == 1, ( - f"Figure {m['figure_number']} must retain its media asset" - ) + assert len(m["matched_assets"]) == 1, f"Figure {m['figure_number']} must retain its media asset" def test_same_number_distinct_legends_can_both_match_separate_assets() -> None: @@ -1655,7 +1767,13 @@ def test_figure_inventory_marks_close_asset_candidates_ambiguous() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "cap1", "role": "figure_caption", "page": 1, "text": "Figure 1. Assay result", "bbox": [100, 500, 700, 540]}, + { + "block_id": "cap1", + "role": "figure_caption", + "page": 1, + "text": "Figure 1. Assay result", + "bbox": [100, 500, 700, 540], + }, {"block_id": "asset1", "role": "figure_asset", "page": 1, "bbox": [100, 100, 700, 470]}, {"block_id": "asset2", "role": "figure_asset", "page": 1, "bbox": [110, 560, 710, 900]}, ] @@ -1673,7 +1791,13 @@ def test_figure_inventory_does_not_confidently_match_low_caption_score() -> None from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "cap1", "role": "figure_caption_candidate", "page": 1, "text": "Experimental results demonstrating cellular response over time with treatment.", "bbox": [100, 500, 700, 540]}, + { + "block_id": "cap1", + "role": "figure_caption_candidate", + "page": 1, + "text": "Experimental results demonstrating cellular response over time with treatment.", + "bbox": [100, 500, 700, 540], + }, {"block_id": "asset1", "role": "figure_asset", "page": 1, "bbox": [100, 100, 700, 470]}, ] @@ -2108,8 +2232,7 @@ def test_no_candidate_sequential_fallback_no_longer_manufactures_match() -> None assert inv["matched_figures"] == [] assert all( - figure.get("match_score", {}).get("decision") != "matched_fallback" - for figure in inv.get("matched_figures", []) + figure.get("match_score", {}).get("decision") != "matched_fallback" for figure in inv.get("matched_figures", []) ) ambiguous = inv.get("ambiguous_figures", []) assert len(ambiguous) == 0 or (ambiguous[0]["legend_block_id"] == "p6_b1") @@ -2138,12 +2261,18 @@ def test_rejected_legend_caption_score_evidence() -> None: def test_inline_figure_mention_is_rejected_as_formal_caption(): from paperforge.worker.ocr_figures import build_figure_inventory + blocks = [ - {"block_id": "cap1", "role": "figure_caption_candidate", "page": 1, - "text": "Figure 2 shows that cells migrated significantly under electrical stimulation conditions.", - "bbox": [100, 100, 700, 130], "page_width": 1200, "page_height": 1700}, - {"block_id": "asset1", "role": "figure_asset", "page": 1, - "bbox": [100, 200, 700, 500]}, + { + "block_id": "cap1", + "role": "figure_caption_candidate", + "page": 1, + "text": "Figure 2 shows that cells migrated significantly under electrical stimulation conditions.", + "bbox": [100, 100, 700, 130], + "page_width": 1200, + "page_height": 1700, + }, + {"block_id": "asset1", "role": "figure_asset", "page": 1, "bbox": [100, 200, 700, 500]}, ] inventory = build_figure_inventory(blocks) assert len(inventory["matched_figures"]) >= 1 @@ -2153,12 +2282,18 @@ def test_inline_figure_mention_is_rejected_as_formal_caption(): def test_frontiers_caption_not_affected_by_inline_detector(): from paperforge.worker.ocr_figures import build_figure_inventory + blocks = [ - {"block_id": "cap1", "role": "figure_caption", "page": 1, - "text": "FIGURE 1 | Expression of irisin is downregulated in OA cartilage", - "bbox": [100, 500, 700, 540], "page_width": 1200, "page_height": 1700}, - {"block_id": "asset1", "role": "figure_asset", "page": 1, - "bbox": [100, 50, 700, 450]}, + { + "block_id": "cap1", + "role": "figure_caption", + "page": 1, + "text": "FIGURE 1 | Expression of irisin is downregulated in OA cartilage", + "bbox": [100, 500, 700, 540], + "page_width": 1200, + "page_height": 1700, + }, + {"block_id": "asset1", "role": "figure_asset", "page": 1, "bbox": [100, 50, 700, 450]}, ] inventory = build_figure_inventory(blocks) assert len(inventory["matched_figures"]) >= 1 @@ -2166,12 +2301,18 @@ def test_frontiers_caption_not_affected_by_inline_detector(): def test_as_shown_in_figure_mention_rejected(): from paperforge.worker.ocr_figures import build_figure_inventory + blocks = [ - {"block_id": "cap1", "role": "figure_caption_candidate", "page": 1, - "text": "As shown in Figure 3, the scaffold promotes cell attachment.", - "bbox": [100, 100, 700, 130], "page_width": 1200, "page_height": 1700}, - {"block_id": "asset1", "role": "figure_asset", "page": 1, - "bbox": [100, 200, 700, 500]}, + { + "block_id": "cap1", + "role": "figure_caption_candidate", + "page": 1, + "text": "As shown in Figure 3, the scaffold promotes cell attachment.", + "bbox": [100, 100, 700, 130], + "page_width": 1200, + "page_height": 1700, + }, + {"block_id": "asset1", "role": "figure_asset", "page": 1, "bbox": [100, 200, 700, 500]}, ] inventory = build_figure_inventory(blocks) assert len(inventory["matched_figures"]) >= 1 @@ -2198,25 +2339,35 @@ def test_completeness_all_legends_accounted_matched() -> None: blocks = [ { - "paper_id": "K001", "page": 1, "block_id": "p1_b1", + "paper_id": "K001", + "page": 1, + "block_id": "p1_b1", "role": "figure_caption", "text": "Figure 1. Migration under DC field.", "bbox": [50, 420, 550, 460], }, { - "paper_id": "K001", "page": 1, "block_id": "p1_b2", - "role": "figure_asset", "text": "", + "paper_id": "K001", + "page": 1, + "block_id": "p1_b2", + "role": "figure_asset", + "text": "", "bbox": [50, 50, 550, 400], }, { - "paper_id": "K001", "page": 2, "block_id": "p2_b1", + "paper_id": "K001", + "page": 2, + "block_id": "p2_b1", "role": "figure_caption", "text": "Figure 2. Expression levels.", "bbox": [50, 420, 550, 460], }, { - "paper_id": "K001", "page": 2, "block_id": "p2_b2", - "role": "figure_asset", "text": "", + "paper_id": "K001", + "page": 2, + "block_id": "p2_b2", + "role": "figure_asset", + "text": "", "bbox": [50, 50, 550, 400], }, ] @@ -2238,7 +2389,9 @@ def test_completeness_legend_only_no_asset_is_ambiguous() -> None: blocks = [ { - "paper_id": "K001", "page": 3, "block_id": "p3_b1", + "paper_id": "K001", + "page": 3, + "block_id": "p3_b1", "role": "figure_caption", "text": "Figure 5. Caption with no asset on this page.", "bbox": [50, 700, 550, 750], @@ -2260,20 +2413,28 @@ def test_completeness_held_legend_is_accounted() -> None: blocks = [ { - "paper_id": "K001", "page": 10, "block_id": "p10_b1", - "zone": "body_zone", "style_family": "legend_like", + "paper_id": "K001", + "page": 10, + "block_id": "p10_b1", + "zone": "body_zone", + "style_family": "legend_like", "text": "Figure 1", "marker_signature": {"type": "figure_number", "number": 1}, "bbox": [50, 50, 300, 90], - "page_width": 1200, "page_height": 1600, + "page_width": 1200, + "page_height": 1600, }, { - "paper_id": "K001", "page": 10, "block_id": "p10_b2", - "zone": "body_zone", "style_family": "body_like", + "paper_id": "K001", + "page": 10, + "block_id": "p10_b2", + "zone": "body_zone", + "style_family": "body_like", "text": "Narrative prose", "marker_signature": {"type": "none"}, "bbox": [50, 100, 900, 140], - "page_width": 1200, "page_height": 1600, + "page_width": 1200, + "page_height": 1600, }, ] @@ -2292,7 +2453,9 @@ def test_completeness_low_score_legend_is_unmatched_not_gap() -> None: blocks = [ { - "paper_id": "K001", "page": 1, "block_id": "p1_b1", + "paper_id": "K001", + "page": 1, + "block_id": "p1_b1", "role": "figure_caption", "text": "Total cells", "bbox": [50, 700, 200, 720], @@ -2313,8 +2476,11 @@ def test_completeness_rejected_legend_not_in_count() -> None: blocks = [ { - "paper_id": "K001", "page": 9, "block_id": "p9_b8", - "role": "figure_caption", "raw_label": "figure_title", + "paper_id": "K001", + "page": 9, + "block_id": "p9_b8", + "role": "figure_caption", + "raw_label": "figure_title", "text": "Days post culture in osteogenic differentiation supplemented medium", "bbox": [374, 1046, 1143, 1077], }, @@ -2332,26 +2498,35 @@ def test_completeness_mixed_outcomes_all_accounted() -> None: blocks = [ # Figure 1: matched { - "paper_id": "K001", "page": 1, "block_id": "p1_b1", + "paper_id": "K001", + "page": 1, + "block_id": "p1_b1", "role": "figure_caption", "text": "Figure 1. Migration under DC field.", "bbox": [50, 420, 550, 460], }, { - "paper_id": "K001", "page": 1, "block_id": "p1_b2", - "role": "figure_asset", "text": "", + "paper_id": "K001", + "page": 1, + "block_id": "p1_b2", + "role": "figure_asset", + "text": "", "bbox": [50, 50, 550, 400], }, # Figure 5: no asset on same page -> ambiguous { - "paper_id": "K001", "page": 2, "block_id": "p2_b1", + "paper_id": "K001", + "page": 2, + "block_id": "p2_b1", "role": "figure_caption", "text": "Figure 5. Expression levels without asset.", "bbox": [50, 700, 550, 750], }, # Non-numbered caption (axis label) -> not counted by completeness { - "paper_id": "K001", "page": 3, "block_id": "p3_b1", + "paper_id": "K001", + "page": 3, + "block_id": "p3_b1", "role": "figure_caption", "text": "Days post culture", "bbox": [50, 700, 200, 720], @@ -2377,13 +2552,17 @@ def test_compute_figure_legend_completeness_directly() -> None: structured_blocks = [ { - "paper_id": "K001", "page": 1, "block_id": "leg_A", + "paper_id": "K001", + "page": 1, + "block_id": "leg_A", "role": "figure_caption", "text": "Figure 1. Test.", "bbox": [50, 420, 550, 460], }, { - "paper_id": "K001", "page": 2, "block_id": "leg_B", + "paper_id": "K001", + "page": 2, + "block_id": "leg_B", "role": "figure_caption", "text": "Figure 2. Test.", "bbox": [50, 420, 550, 460], @@ -2417,34 +2596,42 @@ def test_strict_layer_promotes_contiguous_legends_with_ordered_assets() -> None: blocks = [ # Fig 1: legend + asset on page 3 — direct match - {"block_id": 10, "role": "figure_caption", - "text": "Figure 1. Experimental setup for biomechanical testing.", - "page": 3, "bbox": [100, 700, 500, 720], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 11, "role": "figure_asset", - "page": 3, "bbox": [100, 400, 500, 680]}, - + { + "block_id": 10, + "role": "figure_caption", + "text": "Figure 1. Experimental setup for biomechanical testing.", + "page": 3, + "bbox": [100, 700, 500, 720], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 11, "role": "figure_asset", "page": 3, "bbox": [100, 400, 500, 680]}, # Fig 2: legend on page 4, no asset — ambiguous (no_asset_match) - {"block_id": 12, "role": "figure_caption", - "text": "Figure 2. Histological analysis of tissue sections.", - "page": 4, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - + { + "block_id": 12, + "role": "figure_caption", + "text": "Figure 2. Histological analysis of tissue sections.", + "page": 4, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, # Fig 3: legend + asset on page 5 — direct match - {"block_id": 13, "role": "figure_caption", - "text": "Figure 3. Gene expression analysis results.", - "page": 5, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 14, "role": "figure_asset", - "page": 5, "bbox": [100, 50, 500, 280]}, - + { + "block_id": 13, + "role": "figure_caption", + "text": "Figure 3. Gene expression analysis results.", + "page": 5, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 14, "role": "figure_asset", "page": 5, "bbox": [100, 50, 500, 280]}, # Body paragraph on page 3 - {"block_id": 15, "role": "body_paragraph", - "text": "Body text here.", - "page": 3, "bbox": [100, 750, 500, 770]}, + {"block_id": 15, "role": "body_paragraph", "text": "Body text here.", "page": 3, "bbox": [100, 750, 500, 770]}, ] inventory = build_figure_inventory(blocks) @@ -2454,8 +2641,7 @@ def test_strict_layer_promotes_contiguous_legends_with_ordered_assets() -> None: # Fig 2 must NOT be promoted — it has no assets assert 2 not in fig_numbers, ( - f"Fig 2 must NOT be promoted to SEQUENCE_MATCH without assets. " - f"Matched fig nums: {fig_numbers}" + f"Fig 2 must NOT be promoted to SEQUENCE_MATCH without assets. Matched fig nums: {fig_numbers}" ) # Fig 1 and Fig 3 should still be matched directly assert 1 in fig_numbers @@ -2468,8 +2654,11 @@ def test_compute_figure_legend_completeness_skips_body_mentions() -> None: structured_blocks = [ { - "paper_id": "K001", "page": 1, "block_id": "body1", - "role": "body_paragraph", "raw_role": "body_paragraph", + "paper_id": "K001", + "page": 1, + "block_id": "body1", + "role": "body_paragraph", + "raw_role": "body_paragraph", "text": "Figure 2 shows the results.", "bbox": [50, 100, 550, 140], "marker_signature": {"type": "figure_number", "number": 2}, @@ -2497,29 +2686,40 @@ def test_sequence_match_requires_at_least_one_asset_block_id() -> None: blocks = [ # Fig 1: legend + asset on page 3 — direct match - {"block_id": 10, "role": "figure_caption", - "text": "Figure 1. Experimental setup for biomechanical testing.", - "page": 3, "bbox": [100, 700, 500, 720], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 11, "role": "figure_asset", - "page": 3, "bbox": [100, 400, 500, 680]}, - + { + "block_id": 10, + "role": "figure_caption", + "text": "Figure 1. Experimental setup for biomechanical testing.", + "page": 3, + "bbox": [100, 700, 500, 720], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 11, "role": "figure_asset", "page": 3, "bbox": [100, 400, 500, 680]}, # Fig 2: legend on page 4, no asset — ambiguous (no_asset_match) - {"block_id": 12, "role": "figure_caption", - "text": "Figure 2. Histological analysis of tissue sections.", - "page": 4, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - + { + "block_id": 12, + "role": "figure_caption", + "text": "Figure 2. Histological analysis of tissue sections.", + "page": 4, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, # Fig 3: legend + asset on page 5 — direct match - {"block_id": 13, "role": "figure_caption", - "text": "Figure 3. Gene expression analysis results.", - "page": 5, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 14, "role": "figure_asset", - "page": 5, "bbox": [100, 50, 500, 280]}, + { + "block_id": 13, + "role": "figure_caption", + "text": "Figure 3. Gene expression analysis results.", + "page": 5, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 14, "role": "figure_asset", "page": 5, "bbox": [100, 50, 500, 280]}, ] inventory = build_figure_inventory(blocks) @@ -2529,8 +2729,7 @@ def test_sequence_match_requires_at_least_one_asset_block_id() -> None: # Fig 2 should NOT be promoted — it has no assets assert 2 not in fig_numbers, ( - f"Fig 2 must NOT be promoted to SEQUENCE_MATCH without assets. " - f"Matched fig nums: {fig_numbers}" + f"Fig 2 must NOT be promoted to SEQUENCE_MATCH without assets. Matched fig nums: {fig_numbers}" ) # Fig 1 and Fig 3 should still be matched directly assert 1 in fig_numbers @@ -2661,19 +2860,49 @@ def test_assetless_sequence_shell_never_increments_official_count() -> None: promoted = _promote_sequence_matches(inventory, blocks=[]) matched_count = len(promoted.get("matched_figures", [])) official = promoted.get("official_figure_count", matched_count) - assert official == 1, ( - f"Official count must not include assetless sequence shell, got {official}" - ) + assert official == 1, f"Official count must not include assetless sequence shell, got {official}" def test_bundle_source_duplicate_loser_is_accounted_not_gap() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "dup_legend", "page": 10, "role": "figure_caption", "text": "Figure 3. Caption list duplicate.", "bbox": [100, 100, 900, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "dup_peer_1", "page": 10, "role": "figure_caption", "text": "Figure 1. Caption list.", "bbox": [100, 200, 900, 250], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "dup_peer_2", "page": 10, "role": "figure_caption", "text": "Figure 2. Caption list.", "bbox": [100, 300, 900, 350], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "real_legend", "page": 12, "role": "figure_caption", "text": "Figure 3. Real legend.", "bbox": [100, 100, 900, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, + { + "block_id": "dup_legend", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Caption list duplicate.", + "bbox": [100, 100, 900, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "dup_peer_1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Caption list.", + "bbox": [100, 200, 900, 250], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "dup_peer_2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. Caption list.", + "bbox": [100, 300, 900, 350], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "real_legend", + "page": 12, + "role": "figure_caption", + "text": "Figure 3. Real legend.", + "bbox": [100, 100, 900, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, {"block_id": "asset_3", "page": 11, "role": "figure_asset", "raw_label": "image", "bbox": [100, 120, 700, 520]}, ] @@ -2691,29 +2920,40 @@ def test_reader_figures_never_include_empty_visual_groups() -> None: blocks = [ # Fig 1: legend + asset — direct match - {"block_id": 10, "role": "figure_caption", - "text": "Figure 1. Experimental setup.", - "page": 3, "bbox": [100, 700, 500, 720], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 11, "role": "figure_asset", - "page": 3, "bbox": [100, 400, 500, 680]}, - + { + "block_id": 10, + "role": "figure_caption", + "text": "Figure 1. Experimental setup.", + "page": 3, + "bbox": [100, 700, 500, 720], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 11, "role": "figure_asset", "page": 3, "bbox": [100, 400, 500, 680]}, # Fig 2: legend only, no asset - {"block_id": 12, "role": "figure_caption", - "text": "Figure 2. Histological analysis.", - "page": 4, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - + { + "block_id": 12, + "role": "figure_caption", + "text": "Figure 2. Histological analysis.", + "page": 4, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, # Fig 3: legend + asset — direct match - {"block_id": 13, "role": "figure_caption", - "text": "Figure 3. Gene expression results.", - "page": 5, "bbox": [100, 300, 500, 320], - "marker_signature": {"type": "figure_number"}, - "zone": "body_zone", "style_family": "legend_like"}, - {"block_id": 14, "role": "figure_asset", - "page": 5, "bbox": [100, 50, 500, 280]}, + { + "block_id": 13, + "role": "figure_caption", + "text": "Figure 3. Gene expression results.", + "page": 5, + "bbox": [100, 300, 500, 320], + "marker_signature": {"type": "figure_number"}, + "zone": "body_zone", + "style_family": "legend_like", + }, + {"block_id": 14, "role": "figure_asset", "page": 5, "bbox": [100, 50, 500, 280]}, ] inventory = build_figure_inventory(blocks) @@ -2721,9 +2961,7 @@ def test_reader_figures_never_include_empty_visual_groups() -> None: for figure in reader.get("reader_figures", []): vg = figure.get("visual_groups") - assert vg, ( - f"Reader figure {figure.get('reader_figure_id')} has empty visual_groups: {figure}" - ) + assert vg, f"Reader figure {figure.get('reader_figure_id')} has empty visual_groups: {figure}" # === group-first matching (Task 1: Red test) === @@ -2762,10 +3000,28 @@ def test_sequential_fallback_does_not_split_grouped_assets() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": 1, "role": "figure_caption", "text": "Fig. 2 A and B, paired figure.", "page": 3, "bbox": [80, 120, 420, 210], "marker_signature": {"type": "figure_number"}, "zone": "display_zone", "style_family": "legend_like"}, + { + "block_id": 1, + "role": "figure_caption", + "text": "Fig. 2 A and B, paired figure.", + "page": 3, + "bbox": [80, 120, 420, 210], + "marker_signature": {"type": "figure_number"}, + "zone": "display_zone", + "style_family": "legend_like", + }, {"block_id": 2, "role": "media_asset", "raw_label": "image", "page": 3, "bbox": [450, 120, 780, 520]}, {"block_id": 3, "role": "media_asset", "raw_label": "image", "page": 3, "bbox": [805, 120, 1130, 520]}, - {"block_id": 4, "role": "figure_caption", "text": "Fig. 3 Single figure.", "page": 4, "bbox": [80, 120, 420, 210], "marker_signature": {"type": "figure_number"}, "zone": "display_zone", "style_family": "legend_like"}, + { + "block_id": 4, + "role": "figure_caption", + "text": "Fig. 3 Single figure.", + "page": 4, + "bbox": [80, 120, 420, 210], + "marker_signature": {"type": "figure_number"}, + "zone": "display_zone", + "style_family": "legend_like", + }, ] inventory = build_figure_inventory(blocks, page_width=1200) @@ -2773,15 +3029,11 @@ def test_sequential_fallback_does_not_split_grouped_assets() -> None: assert [a["block_id"] for a in matched[2]["matched_assets"]] == [2, 3] assert 3 not in matched fig3_buckets = [ - af["figure_number"] - for af in inventory.get("ambiguous_figures", []) - if af.get("figure_number") == 3 + af["figure_number"] for af in inventory.get("ambiguous_figures", []) if af.get("figure_number") == 3 ] # vnext: ambiguous_figures is always empty if inventory.get("ambiguous_figures", []): - assert fig3_buckets, ( - "Fig 3 with no same-page asset should appear in ambiguous_figures" - ) + assert fig3_buckets, "Fig 3 with no same-page asset should appear in ambiguous_figures" def test_fallback_eligible_asset_page_ids_rejects_preowned_assets() -> None: @@ -2833,20 +3085,39 @@ def test_fallback_eligible_groups_rejects_preowned_groups() -> None: def test_fallback_can_consume_rejects_blocked_assets() -> None: from paperforge.worker.ocr_figures import _fallback_can_consume - assert _fallback_can_consume( - [(7, "asset_1")], - used_asset_page_ids=set(), - blocked_asset_page_ids={(7, "asset_1")}, - ) is False + assert ( + _fallback_can_consume( + [(7, "asset_1")], + used_asset_page_ids=set(), + blocked_asset_page_ids={(7, "asset_1")}, + ) + is False + ) def test_sequential_fallback_skips_preowned_bare_asset() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "cap1", "page": 1, "role": "figure_caption", "text": "Figure 1. Same-page figure.", "bbox": [100, 420, 800, 470], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, + { + "block_id": "cap1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Same-page figure.", + "bbox": [100, 420, 800, 470], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, {"block_id": "asset_1", "page": 1, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 380]}, - {"block_id": "cap2", "page": 2, "role": "figure_caption", "text": "Figure 2. Later caption.", "bbox": [100, 120, 800, 170], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, + { + "block_id": "cap2", + "page": 2, + "role": "figure_caption", + "text": "Figure 2. Later caption.", + "bbox": [100, 120, 800, 170], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, ] inv = build_figure_inventory(blocks) @@ -2914,11 +3185,11 @@ def test_matched_figure_assets_preserve_asset_family_hints() -> None: def test_ownership_conflicts_persisted_in_figure_inventory_json(tmp_path) -> None: """P0-A: ownership_conflicts must be in the written figure_inventory.json.""" + from paperforge.core.io import read_json from paperforge.worker.ocr_figures import ( attach_ownership_conflicts, write_figure_inventory, ) - from paperforge.core.io import read_json figure_inventory: dict = { "matched_figures": [ @@ -2984,14 +3255,70 @@ def test_local_figure_expansion_absorbs_adjacent_same_page_stack() -> None: from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"paper_id": "KX", "page": 2, "block_id": 3, "role": "media_asset", "raw_label": "image", "bbox": [101, 155, 401, 349]}, - {"paper_id": "KX", "page": 2, "block_id": 4, "role": "media_asset", "raw_label": "chart", "bbox": [448, 154, 699, 360]}, - {"paper_id": "KX", "page": 2, "block_id": 5, "role": "media_asset", "raw_label": "chart", "bbox": [102, 379, 399, 646]}, - {"paper_id": "KX", "page": 2, "block_id": 6, "role": "media_asset", "raw_label": "chart", "bbox": [415, 375, 695, 642]}, - {"paper_id": "KX", "page": 2, "block_id": 7, "role": "media_asset", "raw_label": "chart", "bbox": [709, 158, 1079, 634]}, - {"paper_id": "KX", "page": 2, "block_id": 8, "role": "media_asset", "raw_label": "chart", "bbox": [118, 662, 395, 929]}, - {"paper_id": "KX", "page": 2, "block_id": 9, "role": "media_asset", "raw_label": "chart", "bbox": [415, 663, 691, 933]}, - {"paper_id": "KX", "page": 2, "block_id": 10, "role": "media_asset", "raw_label": "chart", "bbox": [715, 638, 1063, 936]}, + { + "paper_id": "KX", + "page": 2, + "block_id": 3, + "role": "media_asset", + "raw_label": "image", + "bbox": [101, 155, 401, 349], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 4, + "role": "media_asset", + "raw_label": "chart", + "bbox": [448, 154, 699, 360], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 5, + "role": "media_asset", + "raw_label": "chart", + "bbox": [102, 379, 399, 646], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 6, + "role": "media_asset", + "raw_label": "chart", + "bbox": [415, 375, 695, 642], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 7, + "role": "media_asset", + "raw_label": "chart", + "bbox": [709, 158, 1079, 634], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 8, + "role": "media_asset", + "raw_label": "chart", + "bbox": [118, 662, 395, 929], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 9, + "role": "media_asset", + "raw_label": "chart", + "bbox": [415, 663, 691, 933], + }, + { + "paper_id": "KX", + "page": 2, + "block_id": 10, + "role": "media_asset", + "raw_label": "chart", + "bbox": [715, 638, 1063, 936], + }, { "paper_id": "KX", "page": 2, @@ -3018,10 +3345,38 @@ def test_local_figure_expansion_does_not_cross_second_formal_caption_boundary() from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"paper_id": "KX", "page": 4, "block_id": 1, "role": "media_asset", "raw_label": "image", "bbox": [100, 100, 500, 280]}, - {"paper_id": "KX", "page": 4, "block_id": 2, "role": "media_asset", "raw_label": "image", "bbox": [100, 300, 500, 500]}, - {"paper_id": "KX", "page": 4, "block_id": 3, "role": "media_asset", "raw_label": "image", "bbox": [100, 560, 500, 760]}, - {"paper_id": "KX", "page": 4, "block_id": 4, "role": "media_asset", "raw_label": "image", "bbox": [100, 780, 500, 980]}, + { + "paper_id": "KX", + "page": 4, + "block_id": 1, + "role": "media_asset", + "raw_label": "image", + "bbox": [100, 100, 500, 280], + }, + { + "paper_id": "KX", + "page": 4, + "block_id": 2, + "role": "media_asset", + "raw_label": "image", + "bbox": [100, 300, 500, 500], + }, + { + "paper_id": "KX", + "page": 4, + "block_id": 3, + "role": "media_asset", + "raw_label": "image", + "bbox": [100, 560, 500, 760], + }, + { + "paper_id": "KX", + "page": 4, + "block_id": 4, + "role": "media_asset", + "raw_label": "image", + "bbox": [100, 780, 500, 980], + }, { "paper_id": "KX", "page": 4, @@ -3068,7 +3423,16 @@ def test_full_width_caption_does_not_enter_sidecar_partition() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"paper_id": "FW", "page": 1, "block_id": 1, "role": "media_asset", "raw_label": "image", "bbox": [80, 80, 1080, 700], "page_width": 1200, "page_height": 1600}, + { + "paper_id": "FW", + "page": 1, + "block_id": 1, + "role": "media_asset", + "raw_label": "image", + "bbox": [80, 80, 1080, 700], + "page_width": 1200, + "page_height": 1600, + }, { "paper_id": "FW", "page": 1, @@ -3095,9 +3459,36 @@ def test_narrow_same_column_captions_partition_same_page_figures() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"paper_id": "SC", "page": 3, "block_id": 3, "role": "media_asset", "raw_label": "image", "bbox": [470, 80, 980, 360], "page_width": 1200, "page_height": 1600}, - {"paper_id": "SC", "page": 3, "block_id": 4, "role": "media_asset", "raw_label": "image", "bbox": [470, 400, 980, 680], "page_width": 1200, "page_height": 1600}, - {"paper_id": "SC", "page": 3, "block_id": 8, "role": "media_asset", "raw_label": "image", "bbox": [470, 720, 980, 1040], "page_width": 1200, "page_height": 1600}, + { + "paper_id": "SC", + "page": 3, + "block_id": 3, + "role": "media_asset", + "raw_label": "image", + "bbox": [470, 80, 980, 360], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "SC", + "page": 3, + "block_id": 4, + "role": "media_asset", + "raw_label": "image", + "bbox": [470, 400, 980, 680], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "SC", + "page": 3, + "block_id": 8, + "role": "media_asset", + "raw_label": "image", + "bbox": [470, 720, 980, 1040], + "page_width": 1200, + "page_height": 1600, + }, { "paper_id": "SC", "page": 3, @@ -3162,11 +3553,71 @@ def test_panel_labels_do_not_form_sidecar_caption_column() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"paper_id": "PL", "page": 1, "block_id": 1, "role": "media_asset", "raw_label": "image", "bbox": [100, 80, 420, 320], "page_width": 1200, "page_height": 1600}, - {"paper_id": "PL", "page": 1, "block_id": 2, "role": "media_asset", "raw_label": "image", "bbox": [460, 80, 780, 320], "page_width": 1200, "page_height": 1600}, - {"paper_id": "PL", "page": 1, "block_id": 3, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "a", "bbox": [95, 60, 120, 78], "page_width": 1200, "page_height": 1600, "zone": "body_zone", "style_family": "unknown_like", "marker_signature": {"type": "short_fragment"}}, - {"paper_id": "PL", "page": 1, "block_id": 4, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "b", "bbox": [455, 60, 480, 78], "page_width": 1200, "page_height": 1600, "zone": "body_zone", "style_family": "unknown_like", "marker_signature": {"type": "short_fragment"}}, - {"paper_id": "PL", "page": 1, "block_id": 5, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "Figure 1. Full caption.", "bbox": [120, 340, 760, 420], "page_width": 1200, "page_height": 1600, "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, + { + "paper_id": "PL", + "page": 1, + "block_id": 1, + "role": "media_asset", + "raw_label": "image", + "bbox": [100, 80, 420, 320], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "PL", + "page": 1, + "block_id": 2, + "role": "media_asset", + "raw_label": "image", + "bbox": [460, 80, 780, 320], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "PL", + "page": 1, + "block_id": 3, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "a", + "bbox": [95, 60, 120, 78], + "page_width": 1200, + "page_height": 1600, + "zone": "body_zone", + "style_family": "unknown_like", + "marker_signature": {"type": "short_fragment"}, + }, + { + "paper_id": "PL", + "page": 1, + "block_id": 4, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "b", + "bbox": [455, 60, 480, 78], + "page_width": 1200, + "page_height": 1600, + "zone": "body_zone", + "style_family": "unknown_like", + "marker_signature": {"type": "short_fragment"}, + }, + { + "paper_id": "PL", + "page": 1, + "block_id": 5, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "Figure 1. Full caption.", + "bbox": [120, 340, 760, 420], + "page_width": 1200, + "page_height": 1600, + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, ] inventory = build_figure_inventory(blocks) @@ -3178,13 +3629,90 @@ def test_mixed_page_keeps_sidecar_and_ordinary_below_pairs_separate() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"paper_id": "MX2", "page": 1, "block_id": "a1", "role": "media_asset", "raw_label": "image", "bbox": [520, 80, 960, 280], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX2", "page": 1, "block_id": "a2", "role": "media_asset", "raw_label": "image", "bbox": [520, 340, 960, 540], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX2", "page": 1, "block_id": "body_sep", "role": "body_paragraph", "text": "Body separator between local layouts.", "bbox": [120, 620, 1080, 760], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX2", "page": 1, "block_id": "a3", "role": "media_asset", "raw_label": "image", "bbox": [140, 820, 1060, 1080], "page_width": 1200, "page_height": 1600}, - {"paper_id": "MX2", "page": 1, "block_id": "cap1", "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "Figure 1. Sidecar top.", "bbox": [80, 90, 320, 150], "page_width": 1200, "page_height": 1600, "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"paper_id": "MX2", "page": 1, "block_id": "cap2", "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "Figure 2. Sidecar lower.", "bbox": [80, 350, 320, 410], "page_width": 1200, "page_height": 1600, "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"paper_id": "MX2", "page": 1, "block_id": "cap3", "role": "figure_caption", "raw_label": "figure_title", "text": "Figure 3. Ordinary caption below.", "bbox": [160, 1100, 1040, 1170], "page_width": 1200, "page_height": 1600, "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, + { + "paper_id": "MX2", + "page": 1, + "block_id": "a1", + "role": "media_asset", + "raw_label": "image", + "bbox": [520, 80, 960, 280], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "a2", + "role": "media_asset", + "raw_label": "image", + "bbox": [520, 340, 960, 540], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "body_sep", + "role": "body_paragraph", + "text": "Body separator between local layouts.", + "bbox": [120, 620, 1080, 760], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "a3", + "role": "media_asset", + "raw_label": "image", + "bbox": [140, 820, 1060, 1080], + "page_width": 1200, + "page_height": 1600, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "cap1", + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "Figure 1. Sidecar top.", + "bbox": [80, 90, 320, 150], + "page_width": 1200, + "page_height": 1600, + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "cap2", + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "Figure 2. Sidecar lower.", + "bbox": [80, 350, 320, 410], + "page_width": 1200, + "page_height": 1600, + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "paper_id": "MX2", + "page": 1, + "block_id": "cap3", + "role": "figure_caption", + "raw_label": "figure_title", + "text": "Figure 3. Ordinary caption below.", + "bbox": [160, 1100, 1040, 1170], + "page_width": 1200, + "page_height": 1600, + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, ] inventory = build_figure_inventory(blocks) @@ -3255,9 +3783,21 @@ def test_main_and_supplementary_figures_do_not_dedup_into_one_number() -> None: from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"page": 3, "block_id": "p3_c1", "role": "figure_caption", "text": "Figure 1. Migration assay under DC electric field stimulation over 48 hours.", "bbox": [100, 420, 600, 460]}, + { + "page": 3, + "block_id": "p3_c1", + "role": "figure_caption", + "text": "Figure 1. Migration assay under DC electric field stimulation over 48 hours.", + "bbox": [100, 420, 600, 460], + }, {"page": 3, "block_id": "p3_a1", "role": "figure_asset", "bbox": [100, 100, 600, 400], "text": ""}, - {"page": 4, "block_id": "p4_c1", "role": "figure_caption", "text": "Supplementary Figure 1. Gene expression analysis under supplemental treatment conditions.", "bbox": [100, 420, 600, 460]}, + { + "page": 4, + "block_id": "p4_c1", + "role": "figure_caption", + "text": "Supplementary Figure 1. Gene expression analysis under supplemental treatment conditions.", + "bbox": [100, 420, 600, 460], + }, {"page": 4, "block_id": "p4_a1", "role": "figure_asset", "bbox": [100, 100, 600, 400], "text": ""}, ] inventory = build_figure_inventory(structured_blocks) @@ -3270,11 +3810,48 @@ def test_page_assets_does_not_strict_match_when_page_has_competing_captions() -> from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"page": 5, "block_id": "p5_a1", "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 300, 260], "text": ""}, - {"page": 5, "block_id": "p5_a2", "role": "figure_asset", "raw_label": "image", "bbox": [320, 100, 520, 260], "text": ""}, - {"page": 5, "block_id": "p5_a3", "role": "figure_asset", "raw_label": "image", "bbox": [540, 100, 740, 260], "text": ""}, - {"page": 5, "block_id": "p5_c1", "role": "figure_caption", "text": "Figure 1. Left.", "bbox": [100, 280, 320, 320], "zone": "display_zone", "style_family": "legend_like"}, - {"page": 5, "block_id": "p5_c2", "role": "figure_caption", "text": "Figure 2. Right.", "bbox": [420, 280, 740, 320], "zone": "display_zone", "style_family": "legend_like"}, + { + "page": 5, + "block_id": "p5_a1", + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 300, 260], + "text": "", + }, + { + "page": 5, + "block_id": "p5_a2", + "role": "figure_asset", + "raw_label": "image", + "bbox": [320, 100, 520, 260], + "text": "", + }, + { + "page": 5, + "block_id": "p5_a3", + "role": "figure_asset", + "raw_label": "image", + "bbox": [540, 100, 740, 260], + "text": "", + }, + { + "page": 5, + "block_id": "p5_c1", + "role": "figure_caption", + "text": "Figure 1. Left.", + "bbox": [100, 280, 320, 320], + "zone": "display_zone", + "style_family": "legend_like", + }, + { + "page": 5, + "block_id": "p5_c2", + "role": "figure_caption", + "text": "Figure 2. Right.", + "bbox": [420, 280, 740, 320], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inventory = build_figure_inventory(structured_blocks) for fig in inventory["matched_figures"]: @@ -3287,9 +3864,31 @@ def test_build_figure_inventory_uses_distance_cluster_for_irregular_pair() -> No from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"page": 5, "block_id": "a1", "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 300, 260], "text": ""}, - {"page": 5, "block_id": "a2", "role": "figure_asset", "raw_label": "image", "bbox": [315, 110, 525, 270], "text": ""}, - {"page": 5, "block_id": "c1", "role": "figure_caption", "text": "Figure 1. Irregular pair.", "bbox": [100, 290, 520, 330], "zone": "display_zone", "style_family": "legend_like"}, + { + "page": 5, + "block_id": "a1", + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 300, 260], + "text": "", + }, + { + "page": 5, + "block_id": "a2", + "role": "figure_asset", + "raw_label": "image", + "bbox": [315, 110, 525, 270], + "text": "", + }, + { + "page": 5, + "block_id": "c1", + "role": "figure_caption", + "text": "Figure 1. Irregular pair.", + "bbox": [100, 290, 520, 330], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inventory = build_figure_inventory(structured_blocks) @@ -3302,9 +3901,31 @@ def test_display_cluster_keeps_empty_bridge_between_asset_and_caption() -> None: from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"page": 9, "block_id": "asset_1", "role": "figure_asset", "bbox": [100, 100, 520, 360], "text": "", "layout_region": "display_zone"}, - {"page": 9, "block_id": "gap_1", "role": "unknown_structural", "bbox": [530, 110, 900, 360], "text": "", "layout_region": "display_zone", "bridge_eligible": True}, - {"page": 9, "block_id": "cap_1", "role": "figure_caption", "bbox": [120, 380, 880, 430], "text": "Figure 2. Multi-panel reconstruction.", "layout_region": "display_zone"}, + { + "page": 9, + "block_id": "asset_1", + "role": "figure_asset", + "bbox": [100, 100, 520, 360], + "text": "", + "layout_region": "display_zone", + }, + { + "page": 9, + "block_id": "gap_1", + "role": "unknown_structural", + "bbox": [530, 110, 900, 360], + "text": "", + "layout_region": "display_zone", + "bridge_eligible": True, + }, + { + "page": 9, + "block_id": "cap_1", + "role": "figure_caption", + "bbox": [120, 380, 880, 430], + "text": "Figure 2. Multi-panel reconstruction.", + "layout_region": "display_zone", + }, ] inventory = build_figure_inventory(structured_blocks) @@ -3322,7 +3943,12 @@ def test_caption_group_assignments_does_not_cross_page() -> None: blocks = [ {"block_label": "image", "page": 12, "block_bbox": [100, 100, 400, 300], "block_content": ""}, - {"block_label": "figure_title", "page": 13, "block_bbox": [100, 400, 500, 440], "block_content": "Figure 4. Test caption."}, + { + "block_label": "figure_title", + "page": 13, + "block_bbox": [100, 400, 500, 440], + "block_content": "Figure 4. Test caption.", + }, ] figure_map, _ = caption_group_assignments(blocks) assert len(figure_map) == 0, "caption_group_assignments must NOT match cross-page image/caption" @@ -3332,7 +3958,15 @@ def test_caption_group_assignments_does_not_cross_page() -> None: def test_strong_numbered_legend_weak_truncated_not_strong() -> None: from paperforge.worker.ocr_figures import _is_strong_numbered_legend - block = {"block_id": "b1", "page": 1, "role": "figure_caption", "text": "Figure 1.", "bbox": [0, 0, 100, 50], "marker_signature": {"type": "figure_number", "number": 1}, "style_family": "legend_like"} + block = { + "block_id": "b1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1.", + "bbox": [0, 0, 100, 50], + "marker_signature": {"type": "figure_number", "number": 1}, + "style_family": "legend_like", + } score = {"score": 0.9, "decision": "figure_caption", "evidence": ["figure_number"]} assert _is_strong_numbered_legend(block, caption_score=score) is False @@ -3340,7 +3974,13 @@ def test_strong_numbered_legend_weak_truncated_not_strong() -> None: def test_strong_numbered_legend_full_legend_is_strong() -> None: from paperforge.worker.ocr_figures import _is_strong_numbered_legend - block = {"block_id": "b1", "page": 1, "role": "figure_caption", "text": "Figure 1. Quantitative analysis of cell migration under DC electric field stimulation.", "bbox": [0, 0, 500, 50]} + block = { + "block_id": "b1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Quantitative analysis of cell migration under DC electric field stimulation.", + "bbox": [0, 0, 500, 50], + } score = {"score": 0.9, "decision": "figure_caption", "evidence": ["figure_number"]} assert _is_strong_numbered_legend(block, caption_score=score) is True @@ -3348,7 +3988,13 @@ def test_strong_numbered_legend_full_legend_is_strong() -> None: def test_strong_numbered_legend_low_score_not_strong() -> None: from paperforge.worker.ocr_figures import _is_strong_numbered_legend - block = {"block_id": "b1", "page": 1, "role": "figure_caption", "text": "Figure 1. Some text.", "bbox": [0, 0, 500, 50]} + block = { + "block_id": "b1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Some text.", + "bbox": [0, 0, 500, 50], + } score = {"score": 0.2, "decision": "ambiguous", "evidence": ["weak"]} assert _is_strong_numbered_legend(block, caption_score=score) is False @@ -3357,15 +4003,22 @@ def test_strong_numbered_legend_validation_first_needs_anchor() -> None: from paperforge.worker.ocr_figures import _is_strong_numbered_legend block = { - "block_id": "b1", "page": 1, "role": "unknown_structural", - "zone": "body_zone", "style_family": "legend_like", "style_family_authority": "figure_family_anchor", + "block_id": "b1", + "page": 1, + "role": "unknown_structural", + "zone": "body_zone", + "style_family": "legend_like", + "style_family_authority": "figure_family_anchor", "text": "Figure 1. Quantitative analysis of cell migration.", "bbox": [0, 0, 500, 50], "marker_signature": {"type": "figure_number", "number": 1}, } score = {"score": 0.9, "decision": "figure_caption", "evidence": ["figure_number"]} assert _is_strong_numbered_legend(block, caption_score=score, anchor_supported=True) is True - assert _is_strong_numbered_legend(block, caption_score=score, anchor_supported=False, caption_text_supported=False) is False + assert ( + _is_strong_numbered_legend(block, caption_score=score, anchor_supported=False, caption_text_supported=False) + is False + ) def test_structurally_matchable_empty_group_not_matchable() -> None: @@ -3385,7 +4038,13 @@ def test_structurally_matchable_valid_group() -> None: def test_structurally_matchable_page_assets_on_competing_page_not_matchable() -> None: from paperforge.worker.ocr_figures import _is_structurally_matchable_group - group = {"group_id": "g1", "page": 13, "group_type": "page_assets", "asset_block_ids": ["a1", "a2"], "cluster_bbox": [0, 0, 500, 500]} + group = { + "group_id": "g1", + "page": 13, + "group_type": "page_assets", + "asset_block_ids": ["a1", "a2"], + "cluster_bbox": [0, 0, 500, 500], + } assert _is_structurally_matchable_group(group, competing_caption_pages={13}) is False @@ -3435,7 +4094,7 @@ def test_residual_ledger_balanced() -> None: def test_residual_legend_surplus_positive() -> None: - from paperforge.worker.ocr_figures import _build_residual_ledger, _residual_legend_surplus + from paperforge.worker.ocr_figures import _build_residual_ledger legends = [ {"block_id": "c1", "page": 1, "text": "Figure 1. First.", "bbox": [0, 0, 100, 50]}, @@ -3447,7 +4106,7 @@ def test_residual_legend_surplus_positive() -> None: def test_residual_group_surplus_positive() -> None: - from paperforge.worker.ocr_figures import _build_residual_ledger, _residual_group_surplus + from paperforge.worker.ocr_figures import _build_residual_ledger legends = [{"block_id": "c1", "page": 2, "text": "Figure 1. Caption.", "bbox": [0, 0, 100, 50]}] groups = [ @@ -3461,20 +4120,51 @@ def test_residual_group_surplus_positive() -> None: # Task 4: reservation def test_reservation_reserves_top_caption_on_caption_surplus_page() -> None: from paperforge.worker.ocr_figures import ( - _build_page_ledger, _build_residual_ledger, _reserve_cross_page_objects, + _build_residual_ledger, + _reserve_cross_page_objects, ) legends = [ - {"block_id": "fig4_cap", "page": 13, "text": "Figure 4. Caption for figure on page 12.", "bbox": [0, 0, 500, 50]}, - {"block_id": "fig5_cap", "page": 13, "text": "Figure 5. Caption for page 13 figure.", "bbox": [0, 100, 500, 150]}, + { + "block_id": "fig4_cap", + "page": 13, + "text": "Figure 4. Caption for figure on page 12.", + "bbox": [0, 0, 500, 50], + }, + { + "block_id": "fig5_cap", + "page": 13, + "text": "Figure 5. Caption for page 13 figure.", + "bbox": [0, 100, 500, 150], + }, ] groups = [ - {"group_id": "g1", "page": 12, "asset_block_ids": ["a1"], "cluster_bbox": [0, 0, 200, 200], "media_blocks": [{"block_id": "a1", "page": 12, "bbox": [0, 0, 200, 200]}], "group_type": "single_asset", "group_evidence": ["single_asset"]}, - {"group_id": "g2", "page": 13, "asset_block_ids": ["a2"], "cluster_bbox": [0, 300, 200, 500], "media_blocks": [{"block_id": "a2", "page": 13, "bbox": [0, 300, 200, 500]}], "group_type": "single_asset", "group_evidence": ["single_asset"]}, + { + "group_id": "g1", + "page": 12, + "asset_block_ids": ["a1"], + "cluster_bbox": [0, 0, 200, 200], + "media_blocks": [{"block_id": "a1", "page": 12, "bbox": [0, 0, 200, 200]}], + "group_type": "single_asset", + "group_evidence": ["single_asset"], + }, + { + "group_id": "g2", + "page": 13, + "asset_block_ids": ["a2"], + "cluster_bbox": [0, 300, 200, 500], + "media_blocks": [{"block_id": "a2", "page": 13, "bbox": [0, 300, 200, 500]}], + "group_type": "single_asset", + "group_evidence": ["single_asset"], + }, ] residual = _build_residual_ledger(legends, groups, competing_caption_pages={13}) reserved_legend_ids, reserved_group_ids = _reserve_cross_page_objects( - legends, groups, residual, competing_caption_pages={13}, sidecar_pages=set(), + legends, + groups, + residual, + competing_caption_pages={13}, + sidecar_pages=set(), ) assert (13, "fig4_cap") in reserved_legend_ids assert "fig5_cap" not in reserved_legend_ids @@ -3482,16 +4172,30 @@ def test_reservation_reserves_top_caption_on_caption_surplus_page() -> None: def test_reservation_skips_sidecar_pages() -> None: from paperforge.worker.ocr_figures import ( - _build_residual_ledger, _reserve_cross_page_objects, + _build_residual_ledger, + _reserve_cross_page_objects, ) + legends = [ {"block_id": "c1", "page": 5, "text": "Figure 1. Narrow sidecar caption.", "bbox": [0, 0, 200, 50]}, {"block_id": "c2", "page": 5, "text": "Figure 2. Another narrow caption.", "bbox": [0, 100, 200, 150]}, ] - groups = [{"group_id": "g1", "page": 5, "asset_block_ids": ["a1"], "cluster_bbox": [0, 0, 100, 100], "group_type": "single_asset"}] + groups = [ + { + "group_id": "g1", + "page": 5, + "asset_block_ids": ["a1"], + "cluster_bbox": [0, 0, 100, 100], + "group_type": "single_asset", + } + ] residual = _build_residual_ledger(legends, groups, competing_caption_pages={5}) reserved_legend_ids, reserved_group_ids = _reserve_cross_page_objects( - legends, groups, residual, competing_caption_pages={5}, sidecar_pages={5}, + legends, + groups, + residual, + competing_caption_pages={5}, + sidecar_pages={5}, ) assert len(reserved_legend_ids) == 0 @@ -3506,12 +4210,56 @@ def test_cross_page_backward_settlement() -> None: # Ledger: page 12 = -1 (0 legends, 1 group), page 13 = +1 (2 strong legends, 1 group) # Reservation: Fig4 caption reserved, matched backward to page 12 group blocks = [ - {"block_id": "p12_a1", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 100, 300, 300]}, - {"block_id": "p12_a2", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 320, 300, 520]}, - {"block_id": "p13_c4", "page": 13, "role": "figure_caption", "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", "bbox": [100, 100, 880, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "p13_f5a", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 300, 500, 370]}, - {"block_id": "p13_f5b", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 390, 500, 460]}, - {"block_id": "p13_c5", "page": 13, "role": "figure_caption", "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", "bbox": [100, 500, 880, 550], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 5}}, + { + "block_id": "p12_a1", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 100, 300, 300], + }, + { + "block_id": "p12_a2", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 320, 300, 520], + }, + { + "block_id": "p13_c4", + "page": 13, + "role": "figure_caption", + "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", + "bbox": [100, 100, 880, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + { + "block_id": "p13_f5a", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 300, 500, 370], + }, + { + "block_id": "p13_f5b", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 390, 500, 460], + }, + { + "block_id": "p13_c5", + "page": 13, + "role": "figure_caption", + "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", + "bbox": [100, 500, 880, 550], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 5}, + }, ] inv = build_figure_inventory(blocks) fig4 = [m for m in inv["matched_figures"] if m.get("figure_number") == 4] @@ -3528,12 +4276,56 @@ def test_reserved_same_page_hypothesis_is_deferred_from_commit() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "p12_a1", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 100, 300, 300]}, - {"block_id": "p12_a2", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 320, 300, 520]}, - {"block_id": "p13_c4", "page": 13, "role": "figure_caption", "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", "bbox": [100, 100, 880, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "p13_f5a", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 300, 500, 370]}, - {"block_id": "p13_f5b", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 390, 500, 460]}, - {"block_id": "p13_c5", "page": 13, "role": "figure_caption", "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", "bbox": [100, 500, 880, 550], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 5}}, + { + "block_id": "p12_a1", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 100, 300, 300], + }, + { + "block_id": "p12_a2", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 320, 300, 520], + }, + { + "block_id": "p13_c4", + "page": 13, + "role": "figure_caption", + "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", + "bbox": [100, 100, 880, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + { + "block_id": "p13_f5a", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 300, 500, 370], + }, + { + "block_id": "p13_f5b", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 390, 500, 460], + }, + { + "block_id": "p13_c5", + "page": 13, + "role": "figure_caption", + "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", + "bbox": [100, 500, 880, 550], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 5}, + }, ] inv = build_figure_inventory(blocks) @@ -3568,9 +4360,7 @@ def test_non_reserved_same_page_pair_still_commits_normally() -> None: matched = [m for m in inv["matched_figures"] if m.get("figure_number") == 1] assert len(matched) == 1 assert matched[0]["settlement_type"] == "same_page" - hypotheses = [ - h for h in inv.get("local_pairing_hypotheses", []) if h.get("legend_block_id") == "cap_1" - ] + hypotheses = [h for h in inv.get("local_pairing_hypotheses", []) if h.get("legend_block_id") == "cap_1"] if hypotheses: assert any(h.get("mode") == "caption_below" for h in hypotheses) assert all("reserved_same_page_commit_deferred" not in h.get("conflicts", []) for h in hypotheses) @@ -3580,8 +4370,20 @@ def test_cross_page_settlement_two_captions_one_group_ambiguous() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 12, "role": "figure_caption", "text": "Figure 4. First caption.", "bbox": [100, 100, 500, 150]}, - {"block_id": "c2", "page": 12, "role": "figure_caption", "text": "Figure 5. Second caption.", "bbox": [100, 200, 500, 250]}, + { + "block_id": "c1", + "page": 12, + "role": "figure_caption", + "text": "Figure 4. First caption.", + "bbox": [100, 100, 500, 150], + }, + { + "block_id": "c2", + "page": 12, + "role": "figure_caption", + "text": "Figure 5. Second caption.", + "bbox": [100, 200, 500, 250], + }, {"block_id": "a1", "page": 12, "role": "figure_asset", "text": "", "bbox": [100, 400, 500, 700]}, ] inv = build_figure_inventory(blocks) @@ -3594,7 +4396,13 @@ def test_legacy_fallback_does_not_consume_grouped_asset() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 10, "role": "figure_caption", "text": "Figure 1. Caption on page before assets.", "bbox": [100, 100, 500, 150]}, + { + "block_id": "c1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Caption on page before assets.", + "bbox": [100, 100, 500, 150], + }, {"block_id": "a1", "page": 11, "role": "figure_asset", "text": "", "bbox": [100, 100, 500, 400]}, {"block_id": "a2", "page": 11, "role": "figure_asset", "text": "", "bbox": [100, 500, 500, 800]}, ] @@ -3609,9 +4417,27 @@ def test_legend_bundle_fallback_does_not_consume_grouped_assets() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 10, "role": "figure_caption", "text": "Figure 1. First caption.", "bbox": [100, 100, 700, 150]}, - {"block_id": "c2", "page": 10, "role": "figure_caption", "text": "Figure 2. Second caption.", "bbox": [100, 180, 700, 230]}, - {"block_id": "c3", "page": 10, "role": "figure_caption", "text": "Figure 3. Third caption.", "bbox": [100, 260, 700, 310]}, + { + "block_id": "c1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. First caption.", + "bbox": [100, 100, 700, 150], + }, + { + "block_id": "c2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. Second caption.", + "bbox": [100, 180, 700, 230], + }, + { + "block_id": "c3", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Third caption.", + "bbox": [100, 260, 700, 310], + }, {"block_id": "a11_1", "page": 11, "role": "figure_asset", "text": "", "bbox": [100, 100, 420, 320]}, {"block_id": "a11_2", "page": 11, "role": "figure_asset", "text": "", "bbox": [100, 340, 420, 560]}, {"block_id": "a12_1", "page": 12, "role": "figure_asset", "text": "", "bbox": [100, 100, 420, 320]}, @@ -3619,28 +4445,73 @@ def test_legend_bundle_fallback_does_not_consume_grouped_assets() -> None: inv = build_figure_inventory(blocks) - legend_bundle_matches = [ - m for m in inv["matched_figures"] if m.get("settlement_type") == "legend_bundle" - ] + legend_bundle_matches = [m for m in inv["matched_figures"] if m.get("settlement_type") == "legend_bundle"] bundled_asset_ids = { - str(asset.get("block_id", "")) - for match in legend_bundle_matches - for asset in match.get("matched_assets", []) + str(asset.get("block_id", "")) for match in legend_bundle_matches for asset in match.get("matched_assets", []) } - def test_legend_bundle_fallback_skips_preowned_asset_pages() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "pre_cap", "page": 9, "role": "figure_caption", "text": "Figure 1. Same-page owned figure.", "bbox": [100, 100, 700, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "pre_asset", "page": 9, "role": "figure_asset", "raw_label": "image", "bbox": [100, 180, 700, 500]}, - {"block_id": "c2", "page": 10, "role": "figure_caption", "text": "Figure 2. First bundled caption.", "bbox": [100, 100, 700, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "c3", "page": 10, "role": "figure_caption", "text": "Figure 3. Second bundled caption.", "bbox": [100, 200, 700, 250], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "c4", "page": 10, "role": "figure_caption", "text": "Figure 4. Third bundled caption.", "bbox": [100, 300, 700, 350], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "future_1", "page": 11, "role": "figure_asset", "raw_label": "image", "bbox": [100, 200, 600, 500]}, - {"block_id": "future_2", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 200, 600, 500]}, + { + "block_id": "pre_cap", + "page": 9, + "role": "figure_caption", + "text": "Figure 1. Same-page owned figure.", + "bbox": [100, 100, 700, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "pre_asset", + "page": 9, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 180, 700, 500], + }, + { + "block_id": "c2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. First bundled caption.", + "bbox": [100, 100, 700, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "c3", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Second bundled caption.", + "bbox": [100, 200, 700, 250], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "c4", + "page": 10, + "role": "figure_caption", + "text": "Figure 4. Third bundled caption.", + "bbox": [100, 300, 700, 350], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + { + "block_id": "future_1", + "page": 11, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 200, 600, 500], + }, + { + "block_id": "future_2", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 200, 600, 500], + }, ] inv = build_figure_inventory(blocks) @@ -3654,13 +4525,61 @@ def test_legend_bundle_fallback_respects_body_interruption() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c2", "page": 10, "role": "figure_caption", "text": "Figure 2. First bundled caption.", "bbox": [100, 100, 700, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "c3", "page": 10, "role": "figure_caption", "text": "Figure 3. Second bundled caption.", "bbox": [100, 200, 700, 250], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "c4", "page": 10, "role": "figure_caption", "text": "Figure 4. Third bundled caption.", "bbox": [100, 300, 700, 350], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "body_break", "page": 11, "role": "body_paragraph", "text": "This body text interrupts bundle recovery.", "bbox": [100, 100, 1000, 240]}, - {"block_id": "future_1", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 200, 600, 500]}, - {"block_id": "future_2", "page": 13, "role": "figure_asset", "raw_label": "image", "bbox": [100, 200, 600, 500]}, - {"block_id": "future_3", "page": 14, "role": "figure_asset", "raw_label": "image", "bbox": [100, 200, 600, 500]}, + { + "block_id": "c2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. First bundled caption.", + "bbox": [100, 100, 700, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "c3", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Second bundled caption.", + "bbox": [100, 200, 700, 250], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "c4", + "page": 10, + "role": "figure_caption", + "text": "Figure 4. Third bundled caption.", + "bbox": [100, 300, 700, 350], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + { + "block_id": "body_break", + "page": 11, + "role": "body_paragraph", + "text": "This body text interrupts bundle recovery.", + "bbox": [100, 100, 1000, 240], + }, + { + "block_id": "future_1", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 200, 600, 500], + }, + { + "block_id": "future_2", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 200, 600, 500], + }, + { + "block_id": "future_3", + "page": 14, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 200, 600, 500], + }, ] inv = build_figure_inventory(blocks) @@ -3672,12 +4591,56 @@ def test_dwqq_style_duplicate_legend_prefers_real_cross_page_instance() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 35, "role": "figure_caption", "text": "Figure 1. Caption list peer.", "bbox": [100, 100, 900, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "c2", "page": 35, "role": "figure_caption", "text": "Figure 2. Caption list peer.", "bbox": [100, 200, 900, 250], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "dup_fig3", "page": 35, "role": "figure_caption", "text": "Figure 3. Caption list duplicate.", "bbox": [100, 300, 900, 350], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "asset_39a", "page": 39, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 400]}, - {"block_id": "asset_39b", "page": 39, "role": "figure_asset", "raw_label": "image", "bbox": [520, 100, 920, 400]}, - {"block_id": "real_fig3", "page": 40, "role": "figure_caption", "text": "Figure 3. Real cross-page legend.", "bbox": [100, 100, 900, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, + { + "block_id": "c1", + "page": 35, + "role": "figure_caption", + "text": "Figure 1. Caption list peer.", + "bbox": [100, 100, 900, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "c2", + "page": 35, + "role": "figure_caption", + "text": "Figure 2. Caption list peer.", + "bbox": [100, 200, 900, 250], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "dup_fig3", + "page": 35, + "role": "figure_caption", + "text": "Figure 3. Caption list duplicate.", + "bbox": [100, 300, 900, 350], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "asset_39a", + "page": 39, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 500, 400], + }, + { + "block_id": "asset_39b", + "page": 39, + "role": "figure_asset", + "raw_label": "image", + "bbox": [520, 100, 920, 400], + }, + { + "block_id": "real_fig3", + "page": 40, + "role": "figure_caption", + "text": "Figure 3. Real cross-page legend.", + "bbox": [100, 100, 900, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, ] inv = build_figure_inventory(blocks) @@ -3689,21 +4652,62 @@ def test_dwqq_style_duplicate_legend_prefers_real_cross_page_instance() -> None: assert fig3[0].get("page") == 40 assert fig3[0]["settlement_type"] == "cross_page_backward" assert {a["block_id"] for a in fig3[0]["matched_assets"]} == {"asset_39a", "asset_39b"} - assert any( - item.get("block_id") == "dup_fig3" and item.get("dedup_reason") == "bundle_source_duplicate_loser" - for item in inv.get("deduped_legend_ids", []) - ) or True # vnext: deduped_legend_ids may be empty + assert ( + any( + item.get("block_id") == "dup_fig3" and item.get("dedup_reason") == "bundle_source_duplicate_loser" + for item in inv.get("deduped_legend_ids", []) + ) + or True + ) # vnext: deduped_legend_ids may be empty def test_same_page_real_legend_outranks_bundle_duplicate() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 10, "role": "figure_caption", "text": "Figure 1. Caption list peer.", "bbox": [100, 100, 700, 150], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "dup_fig2", "page": 10, "role": "figure_caption", "text": "Figure 2. Caption list duplicate.", "bbox": [100, 200, 700, 250], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "c3", "page": 10, "role": "figure_caption", "text": "Figure 3. Caption list peer.", "bbox": [100, 300, 700, 350], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "real_fig2", "page": 20, "role": "figure_caption", "text": "Figure 2. Real same-page legend.", "bbox": [100, 500, 800, 560], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "asset_20", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 700, 460]}, + { + "block_id": "c1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Caption list peer.", + "bbox": [100, 100, 700, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "dup_fig2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. Caption list duplicate.", + "bbox": [100, 200, 700, 250], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "c3", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Caption list peer.", + "bbox": [100, 300, 700, 350], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "real_fig2", + "page": 20, + "role": "figure_caption", + "text": "Figure 2. Real same-page legend.", + "bbox": [100, 500, 800, 560], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "asset_20", + "page": 20, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 700, 460], + }, ] inv = build_figure_inventory(blocks) @@ -3717,8 +4721,21 @@ def test_final_unmatched_assets_recomputed_after_late_fallback_match() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 1, "role": "figure_caption", "text": "Figure 1. Caption with no same-page asset.", "bbox": [100, 100, 700, 150]}, - {"block_id": "a2", "page": 2, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [100, 120, 500, 420]}, + { + "block_id": "c1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Caption with no same-page asset.", + "bbox": [100, 100, 700, 150], + }, + { + "block_id": "a2", + "page": 2, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [100, 120, 500, 420], + }, ] inv = build_figure_inventory(blocks) @@ -3737,38 +4754,55 @@ def test_bundle_only_source_legends_remain_eligible_for_legend_bundle_fallback() blocks = [ # Bundle-source page (p10): three captions, zero assets - {"block_id": "bs_fig1", "page": 10, "role": "figure_caption", - "text": "Figure 1. Bundle caption.", "bbox": [100, 100, 700, 140], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "bs_fig2", "page": 10, "role": "figure_caption", - "text": "Figure 2. Bundle-only caption.", "bbox": [100, 160, 700, 200], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "bs_fig3", "page": 10, "role": "figure_caption", - "text": "Figure 3. Bundle caption.", "bbox": [100, 220, 700, 260], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, + { + "block_id": "bs_fig1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Bundle caption.", + "bbox": [100, 100, 700, 140], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "bs_fig2", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. Bundle-only caption.", + "bbox": [100, 160, 700, 200], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "bs_fig3", + "page": 10, + "role": "figure_caption", + "text": "Figure 3. Bundle caption.", + "bbox": [100, 220, 700, 260], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, # Real duplicate for Fig 1 on page 11 (outranks bundle) - {"block_id": "real_fig1", "page": 11, "role": "figure_caption", - "text": "Figure 1. Real legend on asset page.", "bbox": [100, 520, 700, 560], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "a11", "page": 11, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 700, 500]}, + { + "block_id": "real_fig1", + "page": 11, + "role": "figure_caption", + "text": "Figure 1. Real legend on asset page.", + "bbox": [100, 520, 700, 560], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "a11", "page": 11, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 700, 500]}, # Asset for Fig 2 on page 12 (no same-page caption) - {"block_id": "a12", "page": 12, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 700, 500]}, + {"block_id": "a12", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 700, 500]}, # Asset for Fig 3 on page 13 (no same-page caption) - {"block_id": "a13", "page": 13, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 700, 500]}, + {"block_id": "a13", "page": 13, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 700, 500]}, ] inv = build_figure_inventory(blocks) matched = {m.get("figure_number"): m for m in inv["matched_figures"]} - assert 2 in matched, ( - "Fig 2 (bundle-only) must be matched via legend_bundle fallback" - ) - assert 3 in matched, ( - "Fig 3 (bundle-only) must be matched via legend_bundle fallback" - ) + assert 2 in matched, "Fig 2 (bundle-only) must be matched via legend_bundle fallback" + assert 3 in matched, "Fig 3 (bundle-only) must be matched via legend_bundle fallback" fig2 = matched[2] assert fig2["settlement_type"] == "legend_bundle" assert fig2["legend_block_id"] == "bs_fig2" @@ -3782,12 +4816,12 @@ def test_bundle_only_source_legends_remain_eligible_for_legend_bundle_fallback() item.get("block_id") == "bs_fig1" and item.get("dedup_reason") == "bundle_source_duplicate_loser" for item in deduped ), "Fig 1 bundle-source must be deduped loser" - assert not any( - item.get("block_id") == "bs_fig3" for item in deduped - ), "Fig 3 must NOT be deduped (no stronger duplicate exists)" - assert not any( - item.get("block_id") == "bs_fig2" for item in deduped - ), "Fig 2 must NOT be deduped (bundle-only, no stronger duplicate)" + assert not any(item.get("block_id") == "bs_fig3" for item in deduped), ( + "Fig 3 must NOT be deduped (no stronger duplicate exists)" + ) + assert not any(item.get("block_id") == "bs_fig2" for item in deduped), ( + "Fig 2 must NOT be deduped (bundle-only, no stronger duplicate)" + ) # vnext: no gap_count in completeness _ = inv["completeness"] @@ -3798,7 +4832,13 @@ def test_matched_figure_has_legend_page_and_asset_pages_and_settlement_type() -> from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 1, "role": "figure_caption", "text": "Figure 1. Test caption.", "bbox": [100, 420, 500, 460]}, + { + "block_id": "c1", + "page": 1, + "role": "figure_caption", + "text": "Figure 1. Test caption.", + "bbox": [100, 420, 500, 460], + }, {"block_id": "a1", "page": 1, "role": "figure_asset", "text": "", "bbox": [100, 50, 500, 400]}, ] inv = build_figure_inventory(blocks) @@ -3818,12 +4858,56 @@ def test_2heud5p9_ownership_pattern() -> None: # Page 12: 2 Fig4 panels close together (1 distance_cluster) # Page 13: wide Fig4 caption (top), 2 Fig5 panels stacked in Fig5's caption band (1 group), wide Fig5 caption (bottom) blocks = [ - {"block_id": "p12_a1", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [50, 50, 300, 350]}, - {"block_id": "p12_a2", "page": 12, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [50, 370, 300, 670]}, - {"block_id": "p13_c4", "page": 13, "role": "figure_caption", "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", "bbox": [50, 50, 800, 100], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "p13_f5a", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [50, 220, 500, 340]}, - {"block_id": "p13_f5b", "page": 13, "role": "figure_asset", "raw_label": "image", "text": "", "bbox": [50, 360, 500, 470]}, - {"block_id": "p13_c5", "page": 13, "role": "figure_caption", "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", "bbox": [50, 520, 800, 570], "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 5}}, + { + "block_id": "p12_a1", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [50, 50, 300, 350], + }, + { + "block_id": "p12_a2", + "page": 12, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [50, 370, 300, 670], + }, + { + "block_id": "p13_c4", + "page": 13, + "role": "figure_caption", + "text": "Figure 4. DC electric field stimulation results showing cell migration patterns over 48 hours.", + "bbox": [50, 50, 800, 100], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + { + "block_id": "p13_f5a", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [50, 220, 500, 340], + }, + { + "block_id": "p13_f5b", + "page": 13, + "role": "figure_asset", + "raw_label": "image", + "text": "", + "bbox": [50, 360, 500, 470], + }, + { + "block_id": "p13_c5", + "page": 13, + "role": "figure_caption", + "text": "Figure 5. Quantitative analysis of migration speed under different field strengths.", + "bbox": [50, 520, 800, 570], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 5}, + }, ] inv = build_figure_inventory(blocks) fig4 = [m for m in inv["matched_figures"] if m.get("figure_number") == 4] @@ -3855,17 +4939,25 @@ def test_composite_parent_candidates_appear_for_dense_grid_page() -> None: # produces separate single_asset groups. Composite parent should re-group them. # Column A at x=[100,500]: pan_a (top), pan_b (bottom) # Column B at x=[600,1000]: pan_c (wider top-right), fig2_asset (separate) - {"block_id": "leg_1a", "page": 5, "role": "figure_caption", - "text": "Figure 1. Composite figure legend.", "bbox": [100, 880, 700, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "pan_a", "page": 5, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 250]}, - {"block_id": "pan_b", "page": 5, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 380, 500, 530]}, - {"block_id": "pan_c", "page": 5, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 100, 1000, 350]}, - {"block_id": "fig2_asset", "page": 5, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 480, 1000, 800]}, + { + "block_id": "leg_1a", + "page": 5, + "role": "figure_caption", + "text": "Figure 1. Composite figure legend.", + "bbox": [100, 880, 700, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "pan_a", "page": 5, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 250]}, + {"block_id": "pan_b", "page": 5, "role": "figure_asset", "raw_label": "image", "bbox": [100, 380, 500, 530]}, + {"block_id": "pan_c", "page": 5, "role": "figure_asset", "raw_label": "image", "bbox": [600, 100, 1000, 350]}, + { + "block_id": "fig2_asset", + "page": 5, + "role": "figure_asset", + "raw_label": "image", + "bbox": [600, 480, 1000, 800], + }, ] inv = build_figure_inventory(blocks) @@ -3886,15 +4978,18 @@ def test_composite_parent_candidates_for_stacked_vertical_panels() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_stacked", "page": 6, "role": "figure_caption", - "text": "Figure 1. Stacked panels.", "bbox": [100, 800, 700, 840], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "top", "page": 6, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 800, 250]}, - {"block_id": "mid", "page": 6, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 380, 800, 530]}, - {"block_id": "bot", "page": 6, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 660, 800, 810]}, + { + "block_id": "leg_stacked", + "page": 6, + "role": "figure_caption", + "text": "Figure 1. Stacked panels.", + "bbox": [100, 800, 700, 840], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "top", "page": 6, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 800, 250]}, + {"block_id": "mid", "page": 6, "role": "figure_asset", "raw_label": "image", "bbox": [100, 380, 800, 530]}, + {"block_id": "bot", "page": 6, "role": "figure_asset", "raw_label": "image", "bbox": [100, 660, 800, 810]}, ] inv = build_figure_inventory(blocks) @@ -3909,7 +5004,7 @@ def test_composite_parent_candidates_for_stacked_vertical_panels() -> None: assert panel_ids <= child_asset_ids, f"Parent must cover all panels, got {child_asset_ids}" break else: - assert False, "No composite parent candidate covers all 3 stacked panels" + raise AssertionError("No composite parent candidate covers all 3 stacked panels") def test_ordinary_multi_figure_page_does_not_mega_merge() -> None: @@ -3917,16 +5012,26 @@ def test_ordinary_multi_figure_page_does_not_mega_merge() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_7a", "page": 7, "role": "figure_caption", - "text": "Figure 1. Top-left figure.", "bbox": [100, 420, 400, 450], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "a7_1", "page": 7, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 400, 400]}, - {"block_id": "leg_7b", "page": 7, "role": "figure_caption", - "text": "Figure 2. Bottom-right figure.", "bbox": [520, 780, 900, 810], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "a7_2", "page": 7, "role": "figure_asset", "raw_label": "image", - "bbox": [520, 520, 900, 760]}, + { + "block_id": "leg_7a", + "page": 7, + "role": "figure_caption", + "text": "Figure 1. Top-left figure.", + "bbox": [100, 420, 400, 450], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "a7_1", "page": 7, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 400, 400]}, + { + "block_id": "leg_7b", + "page": 7, + "role": "figure_caption", + "text": "Figure 2. Bottom-right figure.", + "bbox": [520, 780, 900, 810], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "a7_2", "page": 7, "role": "figure_asset", "raw_label": "image", "bbox": [520, 520, 900, 760]}, ] inv = build_figure_inventory(blocks) @@ -3945,20 +5050,28 @@ def test_composite_parent_detection_preserves_ownership_counts() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "c1", "page": 8, "role": "figure_caption", - "text": "Figure 1. Grid layout.", "bbox": [100, 850, 700, 890], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "g1_a", "page": 8, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 450, 250]}, - {"block_id": "g1_b", "page": 8, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 380, 450, 530]}, - {"block_id": "g1_c", "page": 8, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 660, 450, 810]}, - {"block_id": "c2", "page": 8, "role": "figure_caption", - "text": "Figure 2. Simple single figure.", "bbox": [600, 850, 1000, 890], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "g2", "page": 8, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 100, 1000, 600]}, + { + "block_id": "c1", + "page": 8, + "role": "figure_caption", + "text": "Figure 1. Grid layout.", + "bbox": [100, 850, 700, 890], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "g1_a", "page": 8, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 450, 250]}, + {"block_id": "g1_b", "page": 8, "role": "figure_asset", "raw_label": "image", "bbox": [100, 380, 450, 530]}, + {"block_id": "g1_c", "page": 8, "role": "figure_asset", "raw_label": "image", "bbox": [100, 660, 450, 810]}, + { + "block_id": "c2", + "page": 8, + "role": "figure_caption", + "text": "Figure 2. Simple single figure.", + "bbox": [600, 850, 1000, 890], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "g2", "page": 8, "role": "figure_asset", "raw_label": "image", "bbox": [600, 100, 1000, 600]}, ] inv = build_figure_inventory(blocks) @@ -3969,9 +5082,7 @@ def test_composite_parent_detection_preserves_ownership_counts() -> None: # Verify the composite parent hasn't consumed assets that should be matched matched_asset_ids = { - str(a.get("block_id", "")) - for mf in inv["matched_figures"] - for a in mf.get("matched_assets", []) + str(a.get("block_id", "")) for mf in inv["matched_figures"] for a in mf.get("matched_assets", []) } # Figure 1 legend should own its composite 4-panel group fig1 = [mf for mf in inv["matched_figures"] if mf.get("figure_number") == 1] @@ -3992,15 +5103,18 @@ def test_composite_parent_acceptance_consumes_children() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_cp", "page": 10, "role": "figure_caption", - "text": "Figure 1. Composite multi-panel legend.", "bbox": [100, 880, 700, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "top", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 800, 250]}, - {"block_id": "mid", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 380, 800, 530]}, - {"block_id": "bot", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 660, 800, 810]}, + { + "block_id": "leg_cp", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Composite multi-panel legend.", + "bbox": [100, 880, 700, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "top", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 800, 250]}, + {"block_id": "mid", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 380, 800, 530]}, + {"block_id": "bot", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 660, 800, 810]}, ] inv = build_figure_inventory(blocks) @@ -4016,9 +5130,7 @@ def test_composite_parent_acceptance_consumes_children() -> None: assert "bot" in all_assets, "Bot panel must be owned" # Accept any settlement type (vnext may use same_page instead of composite_parent) settlement = fig1[0].get("settlement_type") - assert settlement in ("composite_parent", "same_page", "sidecar"), ( - f"Unexpected settlement type: {settlement}" - ) + assert settlement in ("composite_parent", "same_page", "sidecar"), f"Unexpected settlement type: {settlement}" def test_scoped_composite_parent_keeps_neighboring_single_figure_separate() -> None: @@ -4026,13 +5138,65 @@ def test_scoped_composite_parent_keeps_neighboring_single_figure_separate() -> N from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "asset_fig3", "page": 18, "role": "figure_asset", "raw_label": "image", "bbox": [377, 155, 813, 440]}, - {"block_id": "leg_fig3", "page": 18, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "图 3 AIHIP 系统自动匹配假体型号", "bbox": [436, 466, 754, 493], "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "asset_fig4_a", "page": 18, "role": "figure_asset", "raw_label": "image", "bbox": [381, 556, 573, 742]}, - {"block_id": "asset_fig4_b", "page": 18, "role": "figure_asset", "raw_label": "image", "bbox": [618, 554, 811, 742]}, - {"block_id": "asset_fig4_c", "page": 18, "role": "figure_asset", "raw_label": "image", "bbox": [381, 753, 573, 942]}, - {"block_id": "asset_fig4_d", "page": 18, "role": "figure_asset", "raw_label": "image", "bbox": [618, 754, 811, 941]}, - {"block_id": "leg_fig4", "page": 18, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "图 4 AIHIP 系统安放髋臼假体并展示三维模拟位置", "bbox": [360, 963, 828, 990], "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, + { + "block_id": "asset_fig3", + "page": 18, + "role": "figure_asset", + "raw_label": "image", + "bbox": [377, 155, 813, 440], + }, + { + "block_id": "leg_fig3", + "page": 18, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "图 3 AIHIP 系统自动匹配假体型号", + "bbox": [436, 466, 754, 493], + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "asset_fig4_a", + "page": 18, + "role": "figure_asset", + "raw_label": "image", + "bbox": [381, 556, 573, 742], + }, + { + "block_id": "asset_fig4_b", + "page": 18, + "role": "figure_asset", + "raw_label": "image", + "bbox": [618, 554, 811, 742], + }, + { + "block_id": "asset_fig4_c", + "page": 18, + "role": "figure_asset", + "raw_label": "image", + "bbox": [381, 753, 573, 942], + }, + { + "block_id": "asset_fig4_d", + "page": 18, + "role": "figure_asset", + "raw_label": "image", + "bbox": [618, 754, 811, 941], + }, + { + "block_id": "leg_fig4", + "page": 18, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "图 4 AIHIP 系统安放髋臼假体并展示三维模拟位置", + "bbox": [360, 963, 828, 990], + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, ] inv = build_figure_inventory(blocks, page_width=1191) @@ -4042,9 +5206,14 @@ def test_scoped_composite_parent_keeps_neighboring_single_figure_separate() -> N assert matched[4].get("settlement_type") in ("composite_parent", "sidecar"), ( f"Expected composite_parent or sidecar, got {matched[4].get('settlement_type')}" ) - assert {str(a.get('block_id', '')) for a in matched[3].get('matched_assets', [])} == {"asset_fig3"} + assert {str(a.get("block_id", "")) for a in matched[3].get("matched_assets", [])} == {"asset_fig3"} assert matched[3].get("settlement_type") == "same_page" - assert {str(a.get('block_id', '')) for a in matched[4].get('matched_assets', [])} == {"asset_fig4_a", "asset_fig4_b", "asset_fig4_c", "asset_fig4_d"} + assert {str(a.get("block_id", "")) for a in matched[4].get("matched_assets", [])} == { + "asset_fig4_a", + "asset_fig4_b", + "asset_fig4_c", + "asset_fig4_d", + } def test_caption_nearest_trap_prefers_interval_scoped_composite() -> None: @@ -4052,21 +5221,78 @@ def test_caption_nearest_trap_prefers_interval_scoped_composite() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "asset_top", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [380, 120, 820, 400]}, - {"block_id": "leg_top", "page": 30, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "图 3 上方单图", "bbox": [430, 430, 760, 460], "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "asset_bl", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [390, 520, 575, 720]}, - {"block_id": "asset_br", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [620, 520, 805, 720]}, - {"block_id": "asset_cl", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [390, 740, 575, 930]}, - {"block_id": "asset_cr", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [620, 740, 805, 930]}, - {"block_id": "leg_bottom", "page": 30, "role": "figure_caption_candidate", "seed_role": "figure_caption", "raw_label": "figure_title", "text": "图 4 下方复合图", "bbox": [360, 955, 830, 985], "zone": "display_zone", "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 4}}, + { + "block_id": "asset_top", + "page": 30, + "role": "figure_asset", + "raw_label": "image", + "bbox": [380, 120, 820, 400], + }, + { + "block_id": "leg_top", + "page": 30, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "图 3 上方单图", + "bbox": [430, 430, 760, 460], + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + { + "block_id": "asset_bl", + "page": 30, + "role": "figure_asset", + "raw_label": "image", + "bbox": [390, 520, 575, 720], + }, + { + "block_id": "asset_br", + "page": 30, + "role": "figure_asset", + "raw_label": "image", + "bbox": [620, 520, 805, 720], + }, + { + "block_id": "asset_cl", + "page": 30, + "role": "figure_asset", + "raw_label": "image", + "bbox": [390, 740, 575, 930], + }, + { + "block_id": "asset_cr", + "page": 30, + "role": "figure_asset", + "raw_label": "image", + "bbox": [620, 740, 805, 930], + }, + { + "block_id": "leg_bottom", + "page": 30, + "role": "figure_caption_candidate", + "seed_role": "figure_caption", + "raw_label": "figure_title", + "text": "图 4 下方复合图", + "bbox": [360, 955, 830, 985], + "zone": "display_zone", + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, ] inv = build_figure_inventory(blocks, page_width=1191) matched = {m.get("figure_number"): m for m in inv.get("matched_figures", [])} - assert {str(a.get('block_id', '')) for a in matched[3].get('matched_assets', [])} == {"asset_top"} + assert {str(a.get("block_id", "")) for a in matched[3].get("matched_assets", [])} == {"asset_top"} assert matched[3].get("settlement_type") == "same_page" - assert {str(a.get('block_id', '')) for a in matched[4].get('matched_assets', [])} == {"asset_bl", "asset_br", "asset_cl", "asset_cr"} + assert {str(a.get("block_id", "")) for a in matched[4].get("matched_assets", [])} == { + "asset_bl", + "asset_br", + "asset_cl", + "asset_cr", + } assert matched[4].get("settlement_type") in ("composite_parent", "sidecar"), ( f"Expected composite_parent or sidecar, got {matched[4].get('settlement_type')}" ) @@ -4077,13 +5303,17 @@ def test_weak_parent_candidate_does_not_consume_children() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_wp", "page": 11, "role": "figure_caption", - "text": "Figure 1. Weak parent legend.", "bbox": [100, 880, 700, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "wp_a", "page": 11, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 250]}, - {"block_id": "wp_b", "page": 11, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 380, 1000, 530]}, + { + "block_id": "leg_wp", + "page": 11, + "role": "figure_caption", + "text": "Figure 1. Weak parent legend.", + "bbox": [100, 880, 700, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "wp_a", "page": 11, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 250]}, + {"block_id": "wp_b", "page": 11, "role": "figure_asset", "raw_label": "image", "bbox": [600, 380, 1000, 530]}, ] inv = build_figure_inventory(blocks) @@ -4104,18 +5334,27 @@ def test_competing_caption_veto_blocks_parent_promotion() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_cv_1", "page": 12, "role": "figure_caption", - "text": "Figure 1. First caption in shared region.", "bbox": [100, 880, 400, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "leg_cv_2", "page": 12, "role": "figure_caption", - "text": "Figure 2. Second caption in shared region.", "bbox": [500, 880, 800, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "cv_a", "page": 12, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 450, 250]}, - {"block_id": "cv_b", "page": 12, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 380, 450, 530]}, - {"block_id": "cv_c", "page": 12, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 660, 450, 810]}, + { + "block_id": "leg_cv_1", + "page": 12, + "role": "figure_caption", + "text": "Figure 1. First caption in shared region.", + "bbox": [100, 880, 400, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "leg_cv_2", + "page": 12, + "role": "figure_caption", + "text": "Figure 2. Second caption in shared region.", + "bbox": [500, 880, 800, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "cv_a", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 450, 250]}, + {"block_id": "cv_b", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 380, 450, 530]}, + {"block_id": "cv_c", "page": 12, "role": "figure_asset", "raw_label": "image", "bbox": [100, 660, 450, 810]}, ] inv = build_figure_inventory(blocks) @@ -4129,15 +5368,11 @@ def test_competing_caption_veto_blocks_parent_promotion() -> None: assert all(m.get("settlement_type") != "composite_parent" for m in fig2) # Cross-caption composite_parent is not allowed: any composite_parent here should # be band-scoped within one caption's legend interval - _composite_parents = [ - m for m in inv["matched_figures"] - if m.get("settlement_type") == "composite_parent" - ] + _composite_parents = [m for m in inv["matched_figures"] if m.get("settlement_type") == "composite_parent"] if _composite_parents: - assert all( - m.get("flags") == ["composite_parent_match"] - for m in _composite_parents - ), "Composite parent must have composite_parent_match flag" + assert all(m.get("flags") == ["composite_parent_match"] for m in _composite_parents), ( + "Composite parent must have composite_parent_match flag" + ) def test_parent_candidate_never_enters_legacy_fallback_directly() -> None: @@ -4145,15 +5380,18 @@ def test_parent_candidate_never_enters_legacy_fallback_directly() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_nl", "page": 13, "role": "figure_caption", - "text": "Figure 1. Legend for composite.", "bbox": [100, 880, 700, 920], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "nl_a", "page": 13, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 300]}, - {"block_id": "nl_b", "page": 13, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 430, 500, 630]}, - {"block_id": "nl_c", "page": 13, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 760, 500, 960]}, + { + "block_id": "leg_nl", + "page": 13, + "role": "figure_caption", + "text": "Figure 1. Legend for composite.", + "bbox": [100, 880, 700, 920], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "nl_a", "page": 13, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 300]}, + {"block_id": "nl_b", "page": 13, "role": "figure_asset", "raw_label": "image", "bbox": [100, 430, 500, 630]}, + {"block_id": "nl_c", "page": 13, "role": "figure_asset", "raw_label": "image", "bbox": [100, 760, 500, 960]}, ] inv = build_figure_inventory(blocks) @@ -4176,11 +5414,16 @@ def test_page_local_grammar_annotations_include_status_reason_evidence() -> None from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_ga", "page": 20, "role": "figure_caption", - "text": "Figure 1. Consistent grammar page.", "bbox": [100, 700, 700, 740], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "ga_1", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 700, 650]}, + { + "block_id": "leg_ga", + "page": 20, + "role": "figure_caption", + "text": "Figure 1. Consistent grammar page.", + "bbox": [100, 700, 700, 740], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "ga_1", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 700, 650]}, ] inv = build_figure_inventory(blocks) @@ -4205,16 +5448,26 @@ def test_incompatible_local_grammar_marks_conflict() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_mx1", "page": 21, "role": "figure_caption", - "text": "Figure 1. Mixed-grammar page A.", "bbox": [100, 400, 450, 440], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "mx1_a", "page": 21, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 450, 380]}, - {"block_id": "leg_mx2", "page": 21, "role": "figure_caption", - "text": "Fig 2. Different grammar style.", "bbox": [550, 400, 900, 440], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "mx2_a", "page": 21, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 100, 900, 380]}, + { + "block_id": "leg_mx1", + "page": 21, + "role": "figure_caption", + "text": "Figure 1. Mixed-grammar page A.", + "bbox": [100, 400, 450, 440], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "mx1_a", "page": 21, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 450, 380]}, + { + "block_id": "leg_mx2", + "page": 21, + "role": "figure_caption", + "text": "Fig 2. Different grammar style.", + "bbox": [550, 400, 900, 440], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "mx2_a", "page": 21, "role": "figure_asset", "raw_label": "image", "bbox": [550, 100, 900, 380]}, ] inv = build_figure_inventory(blocks) @@ -4229,16 +5482,26 @@ def test_mixed_page_can_be_self_consistent_without_one_global_mode() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_u1", "page": 22, "role": "figure_caption", - "text": "Figure 1. Uniform style.", "bbox": [100, 400, 450, 440], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "u1_a", "page": 22, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 450, 380]}, - {"block_id": "leg_u2", "page": 22, "role": "figure_caption", - "text": "Figure 2. Same style family.", "bbox": [550, 400, 900, 440], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "u2_a", "page": 22, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 100, 900, 380]}, + { + "block_id": "leg_u1", + "page": 22, + "role": "figure_caption", + "text": "Figure 1. Uniform style.", + "bbox": [100, 400, 450, 440], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "u1_a", "page": 22, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 450, 380]}, + { + "block_id": "leg_u2", + "page": 22, + "role": "figure_caption", + "text": "Figure 2. Same style family.", + "bbox": [550, 400, 900, 440], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "u2_a", "page": 22, "role": "figure_asset", "raw_label": "image", "bbox": [550, 100, 900, 380]}, ] inv = build_figure_inventory(blocks) @@ -4258,13 +5521,17 @@ def test_asset_family_hint_populated_on_figure_assets() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_ah", "page": 30, "role": "figure_caption", - "text": "Figure 1. Asset family test.", "bbox": [100, 700, 700, 740], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "img1", "page": 30, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 600]}, - {"block_id": "img2", "page": 30, "role": "media_asset", "raw_label": "chart", - "bbox": [520, 100, 900, 600]}, + { + "block_id": "leg_ah", + "page": 30, + "role": "figure_caption", + "text": "Figure 1. Asset family test.", + "bbox": [100, 700, 700, 740], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "img1", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 600]}, + {"block_id": "img2", "page": 30, "role": "media_asset", "raw_label": "chart", "bbox": [520, 100, 900, 600]}, ] inv = build_figure_inventory(blocks) @@ -4281,13 +5548,9 @@ def test_asset_family_hint_populated_on_figure_assets() -> None: ) # vnext: asset_family_confidence/evidence may not be present on matched assets conf = a.get("asset_family_confidence") - assert conf is None or isinstance(conf, (int, float)), ( - f"asset_family_confidence missing or not numeric" - ) + assert conf is None or isinstance(conf, (int, float)), "asset_family_confidence missing or not numeric" ev = a.get("asset_family_evidence") - assert ev is None or isinstance(ev, list), ( - f"asset_family_evidence missing or not list" - ) + assert ev is None or isinstance(ev, list), "asset_family_evidence missing or not list" # === P3B/P3C: Figure/Table Separator Veto === @@ -4298,14 +5561,26 @@ def test_figure_matcher_skips_strong_table_like_region() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_fv", "page": 31, "role": "figure_caption", - "text": "Figure 1. Should NOT own table assets.", "bbox": [100, 700, 700, 740], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "img", "page": 31, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 400, 600]}, - {"block_id": "tbl_like", "page": 31, "role": "figure_asset", "raw_label": "table", - "bbox": [500, 100, 900, 600], "asset_family_hint": "table_like", - "asset_family_confidence": 0.85, "asset_family_evidence": ["raw_label:table"]}, + { + "block_id": "leg_fv", + "page": 31, + "role": "figure_caption", + "text": "Figure 1. Should NOT own table assets.", + "bbox": [100, 700, 700, 740], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "img", "page": 31, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 400, 600]}, + { + "block_id": "tbl_like", + "page": 31, + "role": "figure_asset", + "raw_label": "table", + "bbox": [500, 100, 900, 600], + "asset_family_hint": "table_like", + "asset_family_confidence": 0.85, + "asset_family_evidence": ["raw_label:table"], + }, ] inv = build_figure_inventory(blocks) @@ -4313,9 +5588,7 @@ def test_figure_matcher_skips_strong_table_like_region() -> None: fig1 = [m for m in inv["matched_figures"] if m.get("figure_number") == 1] assert fig1, "Figure 1 must be matched" matched_assets = {str(a.get("block_id", "")) for a in fig1[0].get("matched_assets", [])} - assert "tbl_like" not in matched_assets, ( - "Table-like asset with strong hint must NOT be claimed by figure matcher" - ) + assert "tbl_like" not in matched_assets, "Table-like asset with strong hint must NOT be claimed by figure matcher" def test_ambiguous_region_is_not_hard_forced() -> None: @@ -4323,12 +5596,25 @@ def test_ambiguous_region_is_not_hard_forced() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_amb", "page": 32, "role": "figure_caption", - "text": "Figure 1. Ambiguous region test.", "bbox": [100, 700, 700, 740], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "amb_img", "page": 32, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 600], "asset_family_hint": "ambiguous", - "asset_family_confidence": 0.40, "asset_family_evidence": []}, + { + "block_id": "leg_amb", + "page": 32, + "role": "figure_caption", + "text": "Figure 1. Ambiguous region test.", + "bbox": [100, 700, 700, 740], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "amb_img", + "page": 32, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 500, 600], + "asset_family_hint": "ambiguous", + "asset_family_confidence": 0.40, + "asset_family_evidence": [], + }, ] inv = build_figure_inventory(blocks) @@ -4336,9 +5622,7 @@ def test_ambiguous_region_is_not_hard_forced() -> None: fig1 = [m for m in inv["matched_figures"] if m.get("figure_number") == 1] assert fig1, "Figure 1 must be matched" matched_assets = {str(a.get("block_id", "")) for a in fig1[0].get("matched_assets", [])} - assert "amb_img" in matched_assets, ( - "Ambiguous asset must NOT be hard-excluded from figure matching" - ) + assert "amb_img" in matched_assets, "Ambiguous asset must NOT be hard-excluded from figure matching" def test_table_labeled_img_figure_grids_still_separate_by_caption_when_caption_is_figure() -> None: @@ -4519,10 +5803,9 @@ def test_same_number_internal_punctuation_difference_stays_distinct() -> None: assert {m.get("legend_block_id") for m in matched} == {"fig7_range", "fig7_plain"} distinct = inv.get("same_number_distinct_legends", []) if distinct: - assert any( - item.get("block_id") in {"fig7_range", "fig7_plain"} - for item in distinct - ), "One Figure 7 caption should remain surfaced as same_number_distinct" + assert any(item.get("block_id") in {"fig7_range", "fig7_plain"} for item in distinct), ( + "One Figure 7 caption should remain surfaced as same_number_distinct" + ) # === P1B: Panel-Title Suppression (Task 3) === @@ -4534,14 +5817,31 @@ def test_short_unnumbered_panel_title_does_not_compete_with_numbered_caption() - from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "fig1_legend", "page": 10, "role": "figure_caption", - "text": "Figure 1. Main experimental results.", "bbox": [100, 900, 900, 950], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "fig1_asset", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 900, 500]}, - {"block_id": "panel_title", "page": 10, "role": "figure_caption_candidate", - "text": "RND", "bbox": [100, 520, 500, 540], - "zone": "display_zone", "style_family": "legend_like"}, + { + "block_id": "fig1_legend", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Main experimental results.", + "bbox": [100, 900, 900, 950], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + { + "block_id": "fig1_asset", + "page": 10, + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 900, 500], + }, + { + "block_id": "panel_title", + "page": 10, + "role": "figure_caption_candidate", + "text": "RND", + "bbox": [100, 520, 500, 540], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inv = build_figure_inventory(blocks) @@ -4566,14 +5866,25 @@ def test_suppressed_panel_title_not_emitted_as_matched_or_ambiguous() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_1", "page": 20, "role": "figure_caption", - "text": "Figure 2. Group analysis.", "bbox": [100, 900, 900, 950], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "ast_1", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 900, 500]}, - {"block_id": "fake_cap", "page": 20, "role": "figure_caption_candidate", - "text": "Basal respiration rate", "bbox": [100, 520, 500, 550], - "zone": "display_zone", "style_family": "legend_like"}, + { + "block_id": "leg_1", + "page": 20, + "role": "figure_caption", + "text": "Figure 2. Group analysis.", + "bbox": [100, 900, 900, 950], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "ast_1", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 900, 500]}, + { + "block_id": "fake_cap", + "page": 20, + "role": "figure_caption_candidate", + "text": "Basal respiration rate", + "bbox": [100, 520, 500, 550], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inv = build_figure_inventory(blocks) @@ -4597,14 +5908,25 @@ def test_suppressed_panel_title_remains_accounted_not_body() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_k", "page": 30, "role": "figure_caption", - "text": "Figure 3. Analysis.", "bbox": [100, 900, 900, 950], - "style_family": "legend_like", "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "ast_k", "page": 30, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 900, 500]}, - {"block_id": "panel_k", "page": 30, "role": "figure_caption_candidate", - "text": "COL II", "bbox": [100, 520, 500, 540], - "zone": "display_zone", "style_family": "legend_like"}, + { + "block_id": "leg_k", + "page": 30, + "role": "figure_caption", + "text": "Figure 3. Analysis.", + "bbox": [100, 900, 900, 950], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + {"block_id": "ast_k", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 900, 500]}, + { + "block_id": "panel_k", + "page": 30, + "role": "figure_caption_candidate", + "text": "COL II", + "bbox": [100, 520, 500, 540], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inv = build_figure_inventory(blocks) @@ -4619,7 +5941,6 @@ def test_suppressed_panel_title_remains_accounted_not_body() -> None: assert "panel_k" not in rejected_ids, "Suppressed title must not be in rejected_legends" - # === Dense Composite Parent Candidate Hardening === @@ -4629,28 +5950,26 @@ def test_dense_fragmented_page_emits_composite_parent_candidate() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "d_leg", "page": 20, "role": "figure_caption", - "text": "Figure 1. Dense multi-panel composite figure showing expression profiles.", - "bbox": [100, 750, 900, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "d_a1", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 350, 300]}, - {"block_id": "d_a2", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 100, 650, 300]}, - {"block_id": "d_a3", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [700, 100, 950, 300]}, - {"block_id": "d_a4", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 350, 350, 550]}, - {"block_id": "d_a5", "page": 20, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 350, 650, 550]}, + { + "block_id": "d_leg", + "page": 20, + "role": "figure_caption", + "text": "Figure 1. Dense multi-panel composite figure showing expression profiles.", + "bbox": [100, 750, 900, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "d_a1", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 350, 300]}, + {"block_id": "d_a2", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [400, 100, 650, 300]}, + {"block_id": "d_a3", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [700, 100, 950, 300]}, + {"block_id": "d_a4", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [100, 350, 350, 550]}, + {"block_id": "d_a5", "page": 20, "role": "figure_asset", "raw_label": "image", "bbox": [400, 350, 650, 550]}, ] inv = build_figure_inventory(blocks, page_width=1100) dense_parents = [ - p for p in inv.get("composite_parent_candidates", []) - if p.get("parent_subtype") == "dense_composite" + p for p in inv.get("composite_parent_candidates", []) if p.get("parent_subtype") == "dense_composite" ] # vnext: composite_parent_candidates not emitted; accept empty @@ -4661,29 +5980,34 @@ def test_ordinary_multi_figure_page_does_not_emit_dense_parent() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "ord_leg1", "page": 30, "role": "figure_caption", - "text": "Figure 2. First independent figure.", "bbox": [100, 350, 500, 390], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "ord_a1", "page": 30, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 300]}, - {"block_id": "ord_leg2", "page": 30, "role": "figure_caption", - "text": "Figure 3. Second independent figure.", "bbox": [600, 350, 1000, 390], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "ord_a2", "page": 30, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 100, 1000, 300]}, + { + "block_id": "ord_leg1", + "page": 30, + "role": "figure_caption", + "text": "Figure 2. First independent figure.", + "bbox": [100, 350, 500, 390], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "ord_a1", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 300]}, + { + "block_id": "ord_leg2", + "page": 30, + "role": "figure_caption", + "text": "Figure 3. Second independent figure.", + "bbox": [600, 350, 1000, 390], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + {"block_id": "ord_a2", "page": 30, "role": "figure_asset", "raw_label": "image", "bbox": [600, 100, 1000, 300]}, ] inv = build_figure_inventory(blocks, page_width=1100) dense_parents = [ - p for p in inv.get("composite_parent_candidates", []) - if p.get("parent_subtype") == "dense_composite" + p for p in inv.get("composite_parent_candidates", []) if p.get("parent_subtype") == "dense_composite" ] - assert not dense_parents, ( - "Ordinary multi-figure page must NOT emit a dense parent candidate" - ) + assert not dense_parents, "Ordinary multi-figure page must NOT emit a dense parent candidate" def test_dense_parent_candidate_records_unresolved_cluster_ids() -> None: @@ -4692,30 +6016,27 @@ def test_dense_parent_candidate_records_unresolved_cluster_ids() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "u_leg", "page": 25, "role": "figure_caption", - "text": "Figure 4. Dense composite with orphaned sub-panels.", - "bbox": [100, 750, 900, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 4}}, - {"block_id": "u_a1", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 350, 300]}, - {"block_id": "u_a2", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 100, 650, 300]}, - {"block_id": "u_a3", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [700, 100, 950, 300]}, - {"block_id": "u_a4", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 350, 350, 550]}, - {"block_id": "u_a5", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 350, 650, 550]}, - {"block_id": "u_a6", "page": 25, "role": "figure_asset", "raw_label": "image", - "bbox": [700, 350, 950, 550]}, + { + "block_id": "u_leg", + "page": 25, + "role": "figure_caption", + "text": "Figure 4. Dense composite with orphaned sub-panels.", + "bbox": [100, 750, 900, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 4}, + }, + {"block_id": "u_a1", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 350, 300]}, + {"block_id": "u_a2", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [400, 100, 650, 300]}, + {"block_id": "u_a3", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [700, 100, 950, 300]}, + {"block_id": "u_a4", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [100, 350, 350, 550]}, + {"block_id": "u_a5", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [400, 350, 650, 550]}, + {"block_id": "u_a6", "page": 25, "role": "figure_asset", "raw_label": "image", "bbox": [700, 350, 950, 550]}, ] inv = build_figure_inventory(blocks, page_width=1100) dense_parents = [ - p for p in inv.get("composite_parent_candidates", []) - if p.get("parent_subtype") == "dense_composite" + p for p in inv.get("composite_parent_candidates", []) if p.get("parent_subtype") == "dense_composite" ] # vnext: composite_parent_candidates not emitted; accept empty if dense_parents: @@ -4724,28 +6045,26 @@ def test_dense_parent_candidate_records_unresolved_cluster_ids() -> None: assert uids is not None, "unresolved_cluster_ids field must exist" assert isinstance(uids, list), "unresolved_cluster_ids must be a list" blocks = [ - {"block_id": "c_leg", "page": 35, "role": "figure_caption", - "text": "Figure 5. Composite caption with orphaned fragments.", - "bbox": [100, 750, 900, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 5}}, - {"block_id": "c_a1", "page": 35, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 350, 300]}, - {"block_id": "c_a2", "page": 35, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 100, 650, 300]}, - {"block_id": "c_a3", "page": 35, "role": "figure_asset", "raw_label": "image", - "bbox": [700, 100, 950, 300]}, - {"block_id": "c_a4", "page": 35, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 350, 350, 550]}, - {"block_id": "c_a5", "page": 35, "role": "figure_asset", "raw_label": "image", - "bbox": [400, 350, 650, 550]}, + { + "block_id": "c_leg", + "page": 35, + "role": "figure_caption", + "text": "Figure 5. Composite caption with orphaned fragments.", + "bbox": [100, 750, 900, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 5}, + }, + {"block_id": "c_a1", "page": 35, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 350, 300]}, + {"block_id": "c_a2", "page": 35, "role": "figure_asset", "raw_label": "image", "bbox": [400, 100, 650, 300]}, + {"block_id": "c_a3", "page": 35, "role": "figure_asset", "raw_label": "image", "bbox": [700, 100, 950, 300]}, + {"block_id": "c_a4", "page": 35, "role": "figure_asset", "raw_label": "image", "bbox": [100, 350, 350, 550]}, + {"block_id": "c_a5", "page": 35, "role": "figure_asset", "raw_label": "image", "bbox": [400, 350, 650, 550]}, ] inv = build_figure_inventory(blocks, page_width=1100) dense_parents = [ - p for p in inv.get("composite_parent_candidates", []) - if p.get("parent_subtype") == "dense_composite" + p for p in inv.get("composite_parent_candidates", []) if p.get("parent_subtype") == "dense_composite" ] # vnext: composite_parent_candidates not emitted; accept empty if dense_parents: @@ -4768,31 +6087,38 @@ def test_dense_parent_candidate_records_unresolved_cluster_ids() -> None: # --- Task 5: construction-time vs arbitration-time separation --- + def test_dense_parent_candidate_can_be_constructed_from_visual_fragment_count_only() -> None: from paperforge.worker.ocr_figures import _build_dense_composite_parent_candidates groups = [ { - "group_id": "g1", "page": 10, + "group_id": "g1", + "page": 10, "asset_block_ids": ["a1", "a2"], "cluster_bbox": [100, 100, 400, 400], }, { - "group_id": "g2", "page": 10, + "group_id": "g2", + "page": 10, "asset_block_ids": ["a3", "a4"], "cluster_bbox": [500, 100, 800, 400], }, ] clusters = [ { - "cluster_id": "uc1", "page": 10, + "cluster_id": "uc1", + "page": 10, "media_block_ids": ["a5", "a6"], "cluster_bbox": [100, 500, 400, 800], }, ] parents = _build_dense_composite_parent_candidates( - groups, clusters, {10}, page_width=1000, + groups, + clusters, + {10}, + page_width=1000, ) assert parents, "dense parent must be constructed from visual fragments only" p = parents[0] @@ -4823,12 +6149,16 @@ def test_dense_parent_arbitration_uses_leftover_mass_to_outrank_partial_same_pag "construction_reason": ["dense_fragment_page", "6_visual_fragments", "1_unresolved_clusters"], } - owned = {"a5"} # one asset already owned on page + owned = {"a5"} # one asset already owned on page score_high = _score_dense_parent_candidate_against_local_ownership( - parent, owned_asset_ids=owned, unresolved_asset_ids={"a1", "a2", "a3", "a4", "a6", "a7"}, + parent, + owned_asset_ids=owned, + unresolved_asset_ids={"a1", "a2", "a3", "a4", "a6", "a7"}, ) score_low = _score_dense_parent_candidate_against_local_ownership( - parent, owned_asset_ids=owned, unresolved_asset_ids={"a1"}, + parent, + owned_asset_ids=owned, + unresolved_asset_ids={"a1"}, ) assert score_high["coverage_gain"] > score_low["coverage_gain"], ( @@ -4841,26 +6171,26 @@ def test_dense_parent_arbitration_uses_leftover_mass_to_outrank_partial_same_pag # --- Task 7: dense page arbitration regression --- + def test_dense_composite_parent_collects_large_fragment_set() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg", "page": 10, "role": "figure_caption", - "text": "Figure 1. Multi-panel expression atlas.", "bbox": [100, 830, 900, 880], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "a1", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 80, 450, 230]}, - {"block_id": "a2", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 280, 450, 430]}, - {"block_id": "a3", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 480, 450, 630]}, - {"block_id": "a4", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 80, 900, 230]}, - {"block_id": "a5", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 280, 900, 430]}, - {"block_id": "a6", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 480, 900, 630]}, + { + "block_id": "leg", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Multi-panel expression atlas.", + "bbox": [100, 830, 900, 880], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "a1", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 80, 450, 230]}, + {"block_id": "a2", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 280, 450, 430]}, + {"block_id": "a3", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 480, 450, 630]}, + {"block_id": "a4", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [550, 80, 900, 230]}, + {"block_id": "a5", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [550, 280, 900, 430]}, + {"block_id": "a6", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [550, 480, 900, 630]}, ] inv = build_figure_inventory(blocks, page_width=1000) @@ -4882,26 +6212,29 @@ def test_dense_parent_does_not_swallow_neighboring_ordinary_figure() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg_dense", "page": 10, "role": "figure_caption", - "text": "Figure 1. Dense composite with 6 panels.", - "bbox": [100, 750, 500, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "d1", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 250, 300]}, - {"block_id": "d2", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [300, 100, 450, 300]}, - {"block_id": "d3", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 350, 250, 550]}, - {"block_id": "d4", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [300, 350, 450, 550]}, - {"block_id": "leg_ord", "page": 10, "role": "figure_caption", - "text": "Figure 2. Independent figure on same page.", - "bbox": [600, 750, 1000, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "n1", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 100, 900, 500]}, + { + "block_id": "leg_dense", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Dense composite with 6 panels.", + "bbox": [100, 750, 500, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "d1", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 250, 300]}, + {"block_id": "d2", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [300, 100, 450, 300]}, + {"block_id": "d3", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 350, 250, 550]}, + {"block_id": "d4", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [300, 350, 450, 550]}, + { + "block_id": "leg_ord", + "page": 10, + "role": "figure_caption", + "text": "Figure 2. Independent figure on same page.", + "bbox": [600, 750, 1000, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + {"block_id": "n1", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [600, 100, 900, 500]}, ] inv = build_figure_inventory(blocks, page_width=1100) @@ -4926,25 +6259,22 @@ def test_partial_same_page_claim_becomes_provisional_when_large_same_zone_leftov from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg", "page": 10, "role": "figure_caption", - "text": "Figure 1. Dense multi-panel composite with orphaned sub-panels.", - "bbox": [100, 750, 900, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "ma1", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 300, 300]}, - {"block_id": "ma2", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [350, 100, 550, 300]}, - {"block_id": "ma3", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 100, 800, 300]}, - {"block_id": "ma4", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 350, 300, 550]}, - {"block_id": "ma5", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [350, 350, 550, 550]}, - {"block_id": "ma6", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [600, 350, 800, 550]}, - {"block_id": "ma7", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [850, 350, 950, 400]}, + { + "block_id": "leg", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Dense multi-panel composite with orphaned sub-panels.", + "bbox": [100, 750, 900, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "ma1", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 300, 300]}, + {"block_id": "ma2", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [350, 100, 550, 300]}, + {"block_id": "ma3", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [600, 100, 800, 300]}, + {"block_id": "ma4", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 350, 300, 550]}, + {"block_id": "ma5", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [350, 350, 550, 550]}, + {"block_id": "ma6", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [600, 350, 800, 550]}, + {"block_id": "ma7", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [850, 350, 950, 400]}, ] inv = build_figure_inventory(blocks, page_width=1050) @@ -4974,14 +6304,17 @@ def test_unresolved_clusters_deduped_against_matched_figures() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "leg1", "page": 10, "role": "figure_caption", - "text": "Figure 1. Test figure.", "bbox": [100, 600, 500, 650], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "ast1", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 500]}, - {"block_id": "ast2", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [550, 100, 900, 500]}, + { + "block_id": "leg1", + "page": 10, + "role": "figure_caption", + "text": "Figure 1. Test figure.", + "bbox": [100, 600, 500, 650], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "ast1", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 500]}, + {"block_id": "ast2", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [550, 100, 900, 500]}, ] inv = build_figure_inventory(blocks, page_width=1000) @@ -4998,23 +6331,20 @@ def test_unresolved_clusters_deduped_against_matched_figures() -> None: uc_page = uc.get("page", 0) for bid in uc.get("media_block_ids", []): assert (uc_page, str(bid)) not in { - (mf.get("page", 0), b) for mf in matched for b in mf.get("asset_block_ids", []) - if str(b) == str(bid) + (mf.get("page", 0), b) for mf in matched for b in mf.get("asset_block_ids", []) if str(b) == str(bid) }, f"block {bid} in unresolved_cluster must not also be in matched_figures" # --- Sidecar: outlier-tolerant narrow column + raw band --- + def test_narrow_caption_column_ignores_x_center_outlier() -> None: from paperforge.worker.ocr_figures import _same_page_narrow_caption_column captions = [ - {"block_id": 2, "page": 3, "text": "Fig. 2. Left-column caption.", - "bbox": [103, 140, 422, 312]}, - {"block_id": 5, "page": 3, "text": "Fig. 3. Another left-column caption.", - "bbox": [105, 802, 419, 838]}, - {"block_id": 14, "page": 3, "text": "Fig. 6 body mention right column.", - "bbox": [799, 963, 1132, 1052]}, + {"block_id": 2, "page": 3, "text": "Fig. 2. Left-column caption.", "bbox": [103, 140, 422, 312]}, + {"block_id": 5, "page": 3, "text": "Fig. 3. Another left-column caption.", "bbox": [105, 802, 419, 838]}, + {"block_id": 14, "page": 3, "text": "Fig. 6 body mention right column.", "bbox": [799, 963, 1132, 1052]}, ] result = _same_page_narrow_caption_column(captions, page_width=1133) @@ -5029,10 +6359,8 @@ def test_narrow_caption_column_requires_two_aligned_captions_after_outlier_filte # Only 1 left-column caption + 1 right outlier → no valid cluster captions = [ - {"block_id": 2, "page": 3, "text": "Fig. 2. Left-column caption.", - "bbox": [103, 140, 422, 312]}, - {"block_id": 14, "page": 3, "text": "Fig. 6 body mention right column.", - "bbox": [799, 963, 1132, 1052]}, + {"block_id": 2, "page": 3, "text": "Fig. 2. Left-column caption.", "bbox": [103, 140, 422, 312]}, + {"block_id": 14, "page": 3, "text": "Fig. 6 body mention right column.", "bbox": [799, 963, 1132, 1052]}, ] assert _same_page_narrow_caption_column(captions, page_width=1133) == [] @@ -5044,28 +6372,33 @@ def test_sidecar_uses_full_filtered_raw_band_not_row_coupled_subset() -> None: # All assets cluster into one group, same_page gives it all to Fig 2. # Fig 3 is unresolved → violation → sidecar fires and redistributes. blocks = [ - {"block_id": "leg2", "page": 10, "role": "figure_caption", - "text": "Fig. 2. Left column caption.", "bbox": [100, 80, 400, 150], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "leg3", "page": 10, "role": "figure_caption", - "text": "Fig. 3. Second left caption.", "bbox": [100, 600, 400, 650], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "a2a", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 80, 700, 250]}, - {"block_id": "a2b", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 280, 700, 450]}, - {"block_id": "a3a", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 550, 700, 750]}, - {"block_id": "a3b", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 800, 700, 1000]}, + { + "block_id": "leg2", + "page": 10, + "role": "figure_caption", + "text": "Fig. 2. Left column caption.", + "bbox": [100, 80, 400, 150], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "leg3", + "page": 10, + "role": "figure_caption", + "text": "Fig. 3. Second left caption.", + "bbox": [100, 600, 400, 650], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + {"block_id": "a2a", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 80, 700, 250]}, + {"block_id": "a2b", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 280, 700, 450]}, + {"block_id": "a3a", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 550, 700, 750]}, + {"block_id": "a3b", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 800, 700, 1000]}, ] inv = build_figure_inventory(blocks, page_width=1200) # vnext: only Fig 3 matched (via same_page then sidecar); Fig 2 is unmatched - sidecar_matches = [m for m in inv.get("matched_figures", []) - if m.get("settlement_type") == "sidecar"] + sidecar_matches = [m for m in inv.get("matched_figures", []) if m.get("settlement_type") == "sidecar"] assert len(sidecar_matches) >= 1, "Must have at least one sidecar match" sc = sidecar_matches[0] assert sc.get("settlement_type") == "sidecar" @@ -5079,47 +6412,55 @@ def test_sidecar_raw_band_still_excludes_protected_assets() -> None: from paperforge.worker.ocr_figures import build_figure_inventory blocks = [ - {"block_id": "legA", "page": 10, "role": "figure_caption", - "text": "Fig. 1. Protected below caption.", "bbox": [100, 500, 400, 550], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 1}}, - {"block_id": "aA", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 500, 480]}, - {"block_id": "legB", "page": 10, "role": "figure_caption", - "text": "Fig. 2. Narrow left caption.", "bbox": [100, 600, 400, 650], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 2}}, - {"block_id": "legC", "page": 10, "role": "figure_caption", - "text": "Fig. 3. Narrow left caption.", "bbox": [100, 750, 400, 800], - "style_family": "legend_like", - "marker_signature": {"type": "figure_number", "number": 3}}, - {"block_id": "aB", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 550, 800, 750]}, - {"block_id": "aC", "page": 10, "role": "figure_asset", "raw_label": "image", - "bbox": [450, 800, 800, 1000]}, + { + "block_id": "legA", + "page": 10, + "role": "figure_caption", + "text": "Fig. 1. Protected below caption.", + "bbox": [100, 500, 400, 550], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 1}, + }, + {"block_id": "aA", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [100, 100, 500, 480]}, + { + "block_id": "legB", + "page": 10, + "role": "figure_caption", + "text": "Fig. 2. Narrow left caption.", + "bbox": [100, 600, 400, 650], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 2}, + }, + { + "block_id": "legC", + "page": 10, + "role": "figure_caption", + "text": "Fig. 3. Narrow left caption.", + "bbox": [100, 750, 400, 800], + "style_family": "legend_like", + "marker_signature": {"type": "figure_number", "number": 3}, + }, + {"block_id": "aB", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 550, 800, 750]}, + {"block_id": "aC", "page": 10, "role": "figure_asset", "raw_label": "image", "bbox": [450, 800, 800, 1000]}, ] inv = build_figure_inventory(blocks, page_width=1200) # vnext: Fig 3 matched via same_page (collects aA,aB,aC) + sidecar (aB,aC). # Fig 1 and Fig 2 are unmatched in vnext. - sidecar_matches = [m for m in inv.get("matched_figures", []) - if m.get("settlement_type") == "sidecar"] + sidecar_matches = [m for m in inv.get("matched_figures", []) if m.get("settlement_type") == "sidecar"] assert len(sidecar_matches) >= 1, "Must have at least one sidecar match" # Verify sidecar does NOT claim Fig 1's protected asset aA for sc in sidecar_matches: sc_asset_ids = {str(a.get("block_id", "")) for a in sc.get("matched_assets", [])} - assert "aA" not in sc_asset_ids, ( - f"Sidecar match must not steal protected asset aA, got {sc_asset_ids}" - ) + assert "aA" not in sc_asset_ids, f"Sidecar match must not steal protected asset aA, got {sc_asset_ids}" # Verify sidecar still captures the band assets all_sidecar_assets = set() for sc in sidecar_matches: - all_sidecar_assets.update( - str(a.get("block_id", "")) for a in sc.get("matched_assets", []) - ) + all_sidecar_assets.update(str(a.get("block_id", "")) for a in sc.get("matched_assets", [])) assert "aB" in all_sidecar_assets, "Sidecar must include asset aB" assert "aC" in all_sidecar_assets, "Sidecar must include asset aC" + # === page_assets safety gate regressions (Task 4) === @@ -5128,8 +6469,7 @@ def test_page_assets_missing_page_context_rejected() -> None: result = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, "media_blocks": [], - "cluster_bbox": [0, 0, 500, 500]}, + {"group_type": "page_assets", "page": 5, "media_blocks": [], "cluster_bbox": [0, 0, 500, 500]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, page_width=1200, ) @@ -5147,18 +6487,17 @@ def test_page_assets_single_legend_compact_group_matched() -> None: {"block_id": "a3", "bbox": [100, 280, 300, 440]}, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], - "text": "Dummy body block for context."}, + {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], "text": "Dummy body block for context."}, ] result = _score_legend_to_group( {"text": "Figure 1. Compact.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 520, 440]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 520, 440]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=1, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=1, ) assert result["decision"] == "matched" @@ -5175,18 +6514,17 @@ def test_page_assets_multiple_numbered_legends_rejected() -> None: {"block_id": "a3", "bbox": [100, 280, 300, 440]}, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], - "text": "Dummy body block for context."}, + {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], "text": "Dummy body block for context."}, ] result = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 520, 440]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 520, 440]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=2, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=2, ) assert result["decision"] == "rejected" @@ -5203,19 +6541,17 @@ def test_page_assets_text_separator_rejected() -> None: {"block_id": "a4", "bbox": [330, 240, 530, 340], "page": 5}, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", - "bbox": [300, 130, 335, 170], - "text": "Body text in horizontal gap."}, + {"page": 5, "role": "body_paragraph", "bbox": [300, 130, 335, 170], "text": "Body text in horizontal gap."}, ] result = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 530, 340]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 530, 340]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=1, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=1, ) assert result["decision"] == "rejected" @@ -5231,18 +6567,17 @@ def test_page_assets_large_coverage_rejected() -> None: {"block_id": "a3", "bbox": [0, 900, 600, 1000]}, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], - "text": "Dummy body block for context."}, + {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], "text": "Dummy body block for context."}, ] result = _score_legend_to_group( {"text": "Figure 1. Large.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [0, 0, 1100, 1000]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [0, 0, 1100, 1000]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=1, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=1, ) assert result["decision"] == "rejected" @@ -5255,22 +6590,25 @@ def test_page_assets_table_like_asset_rejected() -> None: media_blocks = [ {"block_id": "a1", "bbox": [100, 100, 300, 260]}, {"block_id": "a2", "bbox": [320, 100, 520, 260]}, - {"block_id": "t1", "bbox": [100, 280, 600, 500], - "raw_label": "table", "text": "
data
"}, + { + "block_id": "t1", + "bbox": [100, 280, 600, 500], + "raw_label": "table", + "text": "
data
", + }, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], - "text": "Dummy body block for context."}, + {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], "text": "Dummy body block for context."}, ] result = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 600, 500]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 600, 500]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=1, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=1, ) assert result["decision"] == "rejected" @@ -5281,18 +6619,48 @@ def test_build_figure_inventory_no_page_assets_on_multi_legend_page() -> None: from paperforge.worker.ocr_figures import build_figure_inventory structured_blocks = [ - {"page": 5, "block_id": "a1", "role": "figure_asset", "raw_label": "image", - "bbox": [100, 100, 300, 260], "text": ""}, - {"page": 5, "block_id": "a2", "role": "figure_asset", "raw_label": "image", - "bbox": [320, 100, 520, 260], "text": ""}, - {"page": 5, "block_id": "a3", "role": "figure_asset", "raw_label": "image", - "bbox": [540, 100, 740, 260], "text": ""}, - {"page": 5, "block_id": "c1", "role": "figure_caption", - "text": "Figure 1. Left.", "bbox": [100, 280, 320, 320], - "zone": "display_zone", "style_family": "legend_like"}, - {"page": 5, "block_id": "c2", "role": "figure_caption", - "text": "Figure 2. Right.", "bbox": [420, 280, 740, 320], - "zone": "display_zone", "style_family": "legend_like"}, + { + "page": 5, + "block_id": "a1", + "role": "figure_asset", + "raw_label": "image", + "bbox": [100, 100, 300, 260], + "text": "", + }, + { + "page": 5, + "block_id": "a2", + "role": "figure_asset", + "raw_label": "image", + "bbox": [320, 100, 520, 260], + "text": "", + }, + { + "page": 5, + "block_id": "a3", + "role": "figure_asset", + "raw_label": "image", + "bbox": [540, 100, 740, 260], + "text": "", + }, + { + "page": 5, + "block_id": "c1", + "role": "figure_caption", + "text": "Figure 1. Left.", + "bbox": [100, 280, 320, 320], + "zone": "display_zone", + "style_family": "legend_like", + }, + { + "page": 5, + "block_id": "c2", + "role": "figure_caption", + "text": "Figure 2. Right.", + "bbox": [420, 280, 740, 320], + "zone": "display_zone", + "style_family": "legend_like", + }, ] inventory = build_figure_inventory(structured_blocks) @@ -5313,31 +6681,30 @@ def test_page_assets_count_uses_ordered_legends_not_stale_deduped() -> None: {"block_id": "a3", "bbox": [100, 280, 300, 440]}, ] page_blocks = [ - {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], - "text": "Dummy."}, + {"page": 5, "role": "body_paragraph", "bbox": [0, 0, 10, 10], "text": "Dummy."}, ] # With count=1 (correct — post-suppression), compact group must match. result = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 520, 440]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 520, 440]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=1, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=1, ) assert result["decision"] == "matched" # With count=2 (stale deduped_count), same group must reject. result2 = _score_legend_to_group( {"text": "Figure 1. Test.", "block_id": "c1", "page": 5}, - {"group_type": "page_assets", "page": 5, - "media_blocks": media_blocks, - "cluster_bbox": [100, 100, 520, 440]}, + {"group_type": "page_assets", "page": 5, "media_blocks": media_blocks, "cluster_bbox": [100, 100, 520, 440]}, caption_score={"score": 0.5, "decision": "candidate", "evidence": []}, - page_width=1200, page_height=1000, - page_blocks=page_blocks, page_numbered_legend_count=2, + page_width=1200, + page_height=1000, + page_blocks=page_blocks, + page_numbered_legend_count=2, ) assert result2["decision"] == "rejected" assert "multiple_numbered_legends" in result2.get("evidence", []) @@ -5351,6 +6718,7 @@ class TestResolveFigureIdCollisions: def _run(self, figs: list[dict]) -> list[dict]: from paperforge.worker.ocr_figures import _resolve_figure_id_collisions + inventory = {"matched_figures": list(figs), "held_figures": [], "ambiguous_figures": []} _resolve_figure_id_collisions(inventory) return inventory["matched_figures"] @@ -5436,8 +6804,14 @@ class TestResolveFigureIdCollisions: ] result = self._run(figs) assert self._ids(result) == [ - "figure_001", "figure_002", "figure_003", "figure_004", - "figure_s001", "figure_s002", "figure_s003", "figure_s004", + "figure_001", + "figure_002", + "figure_003", + "figure_004", + "figure_s001", + "figure_s002", + "figure_s003", + "figure_s004", ] # Verify originals are untouched assert len({f["figure_id"] for f in result}) == 8 # all unique @@ -5459,24 +6833,71 @@ def test_infer_figure1_leading_gap() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, - {"figure_number": 4, "text": "Figure 4.", "legend_block_id": "leg4", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset4"], - "settlement_type": "same_page", "page": 9, "legend_page": 9, "asset_pages": [9]}, - {"figure_number": 5, "text": "Figure 5.", "legend_block_id": "leg5", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset5"], - "settlement_type": "same_page", "page": 11, "legend_page": 11, "asset_pages": [11]}, - {"figure_number": 6, "text": "Figure 6.", "legend_block_id": "leg6", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset6"], - "settlement_type": "same_page", "page": 13, "legend_page": 13, "asset_pages": [13]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, + { + "figure_number": 4, + "text": "Figure 4.", + "legend_block_id": "leg4", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset4"], + "settlement_type": "same_page", + "page": 9, + "legend_page": 9, + "asset_pages": [9], + }, + { + "figure_number": 5, + "text": "Figure 5.", + "legend_block_id": "leg5", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset5"], + "settlement_type": "same_page", + "page": 11, + "legend_page": 11, + "asset_pages": [11], + }, + { + "figure_number": 6, + "text": "Figure 6.", + "legend_block_id": "leg6", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset6"], + "settlement_type": "same_page", + "page": 13, + "legend_page": 13, + "asset_pages": [13], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5502,21 +6923,60 @@ def test_infer_frontmatter_veto() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Graphical Abstract", "legend_block_id": "leg_veto", - "asset_block_ids": ["asset_veto"], "settlement_type": "same_page", - "page": 1, "legend_page": 1, "asset_pages": [1], "legend_bbox": [0, 0, 100, 100]}, - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, - {"figure_number": 4, "text": "Figure 4.", "legend_block_id": "leg4", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset4"], - "settlement_type": "same_page", "page": 9, "legend_page": 9, "asset_pages": [9]}, + { + "figure_number": None, + "text": "Graphical Abstract", + "legend_block_id": "leg_veto", + "asset_block_ids": ["asset_veto"], + "settlement_type": "same_page", + "page": 1, + "legend_page": 1, + "asset_pages": [1], + "legend_bbox": [0, 0, 100, 100], + }, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, + { + "figure_number": 4, + "text": "Figure 4.", + "legend_block_id": "leg4", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset4"], + "settlement_type": "same_page", + "page": 9, + "legend_page": 9, + "asset_pages": [9], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5541,18 +7001,49 @@ def test_infer_main_supplementary_isolation() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 1, "text": "Figure S1.", "legend_block_id": "leg_s1", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset_s1"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [200, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 9, "legend_page": 9, "asset_pages": [9]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 1, + "text": "Figure S1.", + "legend_block_id": "leg_s1", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset_s1"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [200, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 9, + "legend_page": 9, + "asset_pages": [9], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5577,15 +7068,33 @@ def test_infer_no_eligible_unknowns() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": 1, "text": "Figure 1.", "legend_block_id": "leg1", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset1"], - "settlement_type": "same_page", "page": 1}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 3}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 5}, + { + "figure_number": 1, + "text": "Figure 1.", + "legend_block_id": "leg1", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 1, + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 3, + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 5, + }, ] inventory = { "matched_figures": matched_figures, @@ -5603,18 +7112,49 @@ def test_infer_known_min_not_2() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 1, "legend_page": 1, "asset_pages": [1]}, - {"figure_number": 1, "text": "Figure 1.", "legend_block_id": "leg1_known", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset1_known"], - "settlement_type": "same_page", "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 4, "text": "Figure 4.", "legend_block_id": "leg4", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset4"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 1, + "legend_page": 1, + "asset_pages": [1], + }, + { + "figure_number": 1, + "text": "Figure 1.", + "legend_block_id": "leg1_known", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset1_known"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 4, + "text": "Figure 4.", + "legend_block_id": "leg4", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset4"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5635,18 +7175,48 @@ def test_infer_multiple_eligible_unknowns() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 1, "legend_page": 1, "asset_pages": [1]}, - {"figure_number": None, "text": "Some figure", "legend_block_id": "leg2", - "asset_block_ids": ["asset2"], "settlement_type": "same_page", - "page": 2, "legend_page": 2, "asset_pages": [2]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2_known", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2_known"], - "settlement_type": "same_page", "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 1, + "legend_page": 1, + "asset_pages": [1], + }, + { + "figure_number": None, + "text": "Some figure", + "legend_block_id": "leg2", + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 2, + "legend_page": 2, + "asset_pages": [2], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2_known", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2_known"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5668,15 +7238,38 @@ def test_infer_missing_legend_bbox() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, ] inventory = { "matched_figures": matched_figures, @@ -5694,15 +7287,38 @@ def test_infer_unknown_not_before_first_known() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 5, "legend_page": 5, "asset_pages": [5]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 7, "legend_page": 7, "asset_pages": [7]}, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 7, + "legend_page": 7, + "asset_pages": [7], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5723,18 +7339,49 @@ def test_infer_duplicate_known_numbers_skips() -> None: from paperforge.worker.ocr_figures import _infer_missing_main_figure_numbers matched_figures = [ - {"figure_number": None, "text": "Figure 1.", "legend_block_id": "leg1", - "asset_block_ids": ["asset1"], "settlement_type": "same_page", - "page": 1, "legend_page": 1, "asset_pages": [1]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2"], - "settlement_type": "same_page", "page": 3, "legend_page": 3, "asset_pages": [3]}, - {"figure_number": 2, "text": "Figure 2.", "legend_block_id": "leg2b", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset2b"], - "settlement_type": "same_page", "page": 4, "legend_page": 4, "asset_pages": [4]}, - {"figure_number": 3, "text": "Figure 3.", "legend_block_id": "leg3", - "legend_bbox": [100, 100, 500, 200], "asset_block_ids": ["asset3"], - "settlement_type": "same_page", "page": 5, "legend_page": 5, "asset_pages": [5]}, + { + "figure_number": None, + "text": "Figure 1.", + "legend_block_id": "leg1", + "asset_block_ids": ["asset1"], + "settlement_type": "same_page", + "page": 1, + "legend_page": 1, + "asset_pages": [1], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2"], + "settlement_type": "same_page", + "page": 3, + "legend_page": 3, + "asset_pages": [3], + }, + { + "figure_number": 2, + "text": "Figure 2.", + "legend_block_id": "leg2b", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset2b"], + "settlement_type": "same_page", + "page": 4, + "legend_page": 4, + "asset_pages": [4], + }, + { + "figure_number": 3, + "text": "Figure 3.", + "legend_block_id": "leg3", + "legend_bbox": [100, 100, 500, 200], + "asset_block_ids": ["asset3"], + "settlement_type": "same_page", + "page": 5, + "legend_page": 5, + "asset_pages": [5], + }, ] figure_legends = [ {"block_id": "leg1", "bbox": [100, 100, 500, 200], "text": "Figure 1. Test caption"}, @@ -5762,38 +7409,69 @@ def test_previous_page_locator_bridge_cross_page_full_legend() -> None: blocks = [ # p15: full legend (misclassified as body_paragraph via rejected_legend) - {"block_id": "full_leg", "page": 15, "role": "body_paragraph", - "seed_role": "figure_caption_candidate", - "text": "Fig. 10 Histological scores for evaluation of osteochondral repair. " - "A Scores for overall defect evaluation. B Scores for subchondral bone. " - "C Scores for cartilage evaluation.", - "bbox": [100, 1300, 800, 1400], "page_width": 1191, "page_height": 1582, - "style_family": "legend_like", "zone": "display_zone", - "marker_signature": {"type": "figure_number", "number": 10}}, + { + "block_id": "full_leg", + "page": 15, + "role": "body_paragraph", + "seed_role": "figure_caption_candidate", + "text": "Fig. 10 Histological scores for evaluation of osteochondral repair. " + "A Scores for overall defect evaluation. B Scores for subchondral bone. " + "C Scores for cartilage evaluation.", + "bbox": [100, 1300, 800, 1400], + "page_width": 1191, + "page_height": 1582, + "style_family": "legend_like", + "zone": "display_zone", + "marker_signature": {"type": "figure_number", "number": 10}, + }, # p16: locator caption - {"block_id": "locator", "page": 16, "role": "figure_caption", - "text": "Fig. 10 (See legend on previous page.)", - "bbox": [100, 1380, 700, 1410], "page_width": 1191, "page_height": 1582, - "style_family": "legend_like", "zone": "display_zone", - "marker_signature": {"type": "figure_number", "number": 10}}, + { + "block_id": "locator", + "page": 16, + "role": "figure_caption", + "text": "Fig. 10 (See legend on previous page.)", + "bbox": [100, 1380, 700, 1410], + "page_width": 1191, + "page_height": 1582, + "style_family": "legend_like", + "zone": "display_zone", + "marker_signature": {"type": "figure_number", "number": 10}, + }, # p16: three figure assets (composite visual group) - {"block_id": "a1", "page": 16, "role": "figure_asset", - "bbox": [100, 200, 500, 700], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, - {"block_id": "a2", "page": 16, "role": "figure_asset", - "bbox": [100, 750, 500, 1000], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, - {"block_id": "a3", "page": 16, "role": "figure_asset", - "bbox": [100, 1050, 500, 1360], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, + { + "block_id": "a1", + "page": 16, + "role": "figure_asset", + "bbox": [100, 200, 500, 700], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, + { + "block_id": "a2", + "page": 16, + "role": "figure_asset", + "bbox": [100, 750, 500, 1000], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, + { + "block_id": "a3", + "page": 16, + "role": "figure_asset", + "bbox": [100, 1050, 500, 1360], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, ] inventory = build_figure_inventory(blocks, page_width=1191) # vnext: locator bridge may not fire when full legend is body_paragraph; # Fig 10 is still matched with all 3 assets. - fig10 = [m for m in inventory.get("matched_figures", []) - if str(m.get("figure_number", "")) == "10"] + fig10 = [m for m in inventory.get("matched_figures", []) if str(m.get("figure_number", "")) == "10"] assert len(fig10) >= 1, "Fig 10 must be matched" # Collect all consumed asset ids across all Fig 10 matches consumed = set() @@ -5804,14 +7482,12 @@ def test_previous_page_locator_bridge_cross_page_full_legend() -> None: assert "a2" in consumed, "Fig 10 must consume a2" assert "a3" in consumed, "Fig 10 must consume a3" # Assets not in unmatched_assets - unmatched_asset_ids = {(a.get("block_id"), a.get("page")) - for a in inventory.get("unmatched_assets", [])} + unmatched_asset_ids = {(a.get("block_id"), a.get("page")) for a in inventory.get("unmatched_assets", [])} assert ("a1", 16) not in unmatched_asset_ids assert ("a2", 16) not in unmatched_asset_ids assert ("a3", 16) not in unmatched_asset_ids # Full legend not in unmatched_legends - unmatched_leg_ids = {(l.get("block_id"), l.get("page")) - for l in inventory.get("unmatched_legends", [])} + unmatched_leg_ids = {(leg.get("block_id"), leg.get("page")) for leg in inventory.get("unmatched_legends", [])} assert ("full_leg", 15) not in unmatched_leg_ids @@ -5822,38 +7498,75 @@ def test_previous_page_locator_bridge_does_not_swallow_other_group() -> None: blocks = [ # p7: full legend - {"block_id": "fl8", "page": 7, "role": "figure_caption", - "text": "Fig. 8. Micro-CT analysis for subchondral bone regeneration. " - "A Reconstructed images. B Quantitative analysis.", - "bbox": [100, 1300, 800, 1400], "page_width": 1191, "page_height": 1582, - "marker_signature": {"type": "figure_number", "number": 8}, - "style_family": "legend_like", "zone": "display_zone"}, + { + "block_id": "fl8", + "page": 7, + "role": "figure_caption", + "text": "Fig. 8. Micro-CT analysis for subchondral bone regeneration. " + "A Reconstructed images. B Quantitative analysis.", + "bbox": [100, 1300, 800, 1400], + "page_width": 1191, + "page_height": 1582, + "marker_signature": {"type": "figure_number", "number": 8}, + "style_family": "legend_like", + "zone": "display_zone", + }, # p8: locator - {"block_id": "loc8", "page": 8, "role": "figure_caption", - "text": "Fig. 8 (See legend on previous page.)", - "bbox": [100, 1400, 700, 1430], "page_width": 1191, "page_height": 1582, - "marker_signature": {"type": "figure_number", "number": 8}, - "style_family": "legend_like", "zone": "display_zone"}, + { + "block_id": "loc8", + "page": 8, + "role": "figure_caption", + "text": "Fig. 8 (See legend on previous page.)", + "bbox": [100, 1400, 700, 1430], + "page_width": 1191, + "page_height": 1582, + "marker_signature": {"type": "figure_number", "number": 8}, + "style_family": "legend_like", + "zone": "display_zone", + }, # p8: Fig.8 visual group (3 assets) - {"block_id": "g1a", "page": 8, "role": "figure_asset", - "bbox": [100, 200, 500, 600], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, - {"block_id": "g1b", "page": 8, "role": "figure_asset", - "bbox": [100, 650, 500, 900], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, - {"block_id": "g1c", "page": 8, "role": "figure_asset", - "bbox": [100, 950, 500, 1350], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, + { + "block_id": "g1a", + "page": 8, + "role": "figure_asset", + "bbox": [100, 200, 500, 600], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, + { + "block_id": "g1b", + "page": 8, + "role": "figure_asset", + "bbox": [100, 650, 500, 900], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, + { + "block_id": "g1c", + "page": 8, + "role": "figure_asset", + "bbox": [100, 950, 500, 1350], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, # p8: OTHER unowned group (small figure, not Fig.8) - {"block_id": "other", "page": 8, "role": "figure_asset", - "bbox": [600, 300, 800, 500], "page_width": 1191, "page_height": 1582, - "raw_label": "image"}, + { + "block_id": "other", + "page": 8, + "role": "figure_asset", + "bbox": [600, 300, 800, 500], + "page_width": 1191, + "page_height": 1582, + "raw_label": "image", + }, ] inventory = build_figure_inventory(blocks, page_width=1191) - bridged = [m for m in inventory.get("matched_figures", []) - if "previous_page_locator_match" in m.get("flags", [])] + bridged = [m for m in inventory.get("matched_figures", []) if "previous_page_locator_match" in m.get("flags", [])] assert len(bridged) == 1 bf = bridged[0] @@ -5864,6 +7577,7 @@ def test_previous_page_locator_bridge_does_not_swallow_other_group() -> None: assert "g1c" in consumed_ids assert "other" not in consumed_ids, "Must not swallow competing unowned group" + # ────────────────────────────────────────────── # PR3 Task 1: Cross-column rejection gate # ────────────────────────────────────────────── @@ -5881,10 +7595,15 @@ def test_page_assets_group_rejects_cross_column_media_assets(): legend = {"text": "Figure 1. Example.", "page": 1} safe, evidence = _is_safe_page_assets_group( - group, legend, page_blocks=list(media_blocks), - page_numbered_legend_count=1, page_width=800, page_height=1000, + group, + legend, + page_blocks=list(media_blocks), + page_numbered_legend_count=1, + page_width=800, + page_height=1000, ) + def test_same_column_stacked_assets_still_pass_gate(): from paperforge.worker.ocr_figures import _is_safe_page_assets_group @@ -5897,8 +7616,12 @@ def test_same_column_stacked_assets_still_pass_gate(): legend = {"text": "Figure 1. Example.", "page": 1} safe, evidence = _is_safe_page_assets_group( - group, legend, page_blocks=list(media_blocks), - page_numbered_legend_count=1, page_width=600, page_height=1000, + group, + legend, + page_blocks=list(media_blocks), + page_numbered_legend_count=1, + page_width=600, + page_height=1000, ) assert safe is True assert evidence == [] @@ -5916,8 +7639,12 @@ def test_full_width_group_can_span_columns_without_rejection(): legend = {"text": "Figure 1. Full-width figure.", "page": 1} safe, evidence = _is_safe_page_assets_group( - group, legend, page_blocks=list(media_blocks), - page_numbered_legend_count=1, page_width=600, page_height=1000, + group, + legend, + page_blocks=list(media_blocks), + page_numbered_legend_count=1, + page_width=600, + page_height=1000, ) assert safe is True @@ -5928,22 +7655,32 @@ def test_full_width_group_can_span_columns_without_rejection(): def test_resolve_media_asset_conflicts_prefers_explicit_table_over_weak_figure(): - from paperforge.worker.ocr_figures import resolve_media_asset_conflicts, _build_ownership_conflicts + from paperforge.worker.ocr_figures import _build_ownership_conflicts, resolve_media_asset_conflicts figure_inventory = { - "matched_figures": [{ - "figure_id": "figure_001", "legend_block_id": "figcap", - "text": "Figure 1. Example.", - "match_score": {"score": 0.51, "decision": "matched", "evidence": ["fallback"]}, - "asset_block_ids": ["asset"], "page": 1, - }] + "matched_figures": [ + { + "figure_id": "figure_001", + "legend_block_id": "figcap", + "text": "Figure 1. Example.", + "match_score": {"score": 0.51, "decision": "matched", "evidence": ["fallback"]}, + "asset_block_ids": ["asset"], + "page": 1, + } + ] } table_inventory = { - "tables": [{ - "table_id": "table_001", "caption_block_id": "tabcap", - "caption_text": "Table 1. Example.", "match_status": "matched", - "has_asset": True, "asset_block_id": "asset", "page": 1, - }] + "tables": [ + { + "table_id": "table_001", + "caption_block_id": "tabcap", + "caption_text": "Table 1. Example.", + "match_status": "matched", + "has_asset": True, + "asset_block_id": "asset", + "page": 1, + } + ] } resolutions = resolve_media_asset_conflicts(figure_inventory, table_inventory) @@ -5955,22 +7692,33 @@ def test_resolve_media_asset_conflicts_prefers_explicit_table_over_weak_figure() def test_resolve_media_asset_conflicts_prefers_explicit_figure_over_weak_table(): - from paperforge.worker.ocr_figures import resolve_media_asset_conflicts, _build_ownership_conflicts + from paperforge.worker.ocr_figures import _build_ownership_conflicts, resolve_media_asset_conflicts figure_inventory = { - "matched_figures": [{ - "figure_id": "figure_001", "legend_block_id": "figcap", - "text": "Figure 1. Example.", - "match_score": {"score": 0.92, "decision": "matched", "evidence": ["same_page", "x_overlap"]}, - "asset_block_ids": ["asset"], "matched_assets": [{"block_id": "asset"}], "page": 1, - }] + "matched_figures": [ + { + "figure_id": "figure_001", + "legend_block_id": "figcap", + "text": "Figure 1. Example.", + "match_score": {"score": 0.92, "decision": "matched", "evidence": ["same_page", "x_overlap"]}, + "asset_block_ids": ["asset"], + "matched_assets": [{"block_id": "asset"}], + "page": 1, + } + ] } table_inventory = { - "tables": [{ - "table_id": "table_001", "caption_block_id": "tabcap", - "caption_text": "Table 1", "match_status": "matched_low_confidence", - "has_asset": True, "asset_block_id": "asset", "page": 1, - }] + "tables": [ + { + "table_id": "table_001", + "caption_block_id": "tabcap", + "caption_text": "Table 1", + "match_status": "matched_low_confidence", + "has_asset": True, + "asset_block_id": "asset", + "page": 1, + } + ] } resolutions = resolve_media_asset_conflicts(figure_inventory, table_inventory) @@ -5982,22 +7730,33 @@ def test_resolve_media_asset_conflicts_prefers_explicit_figure_over_weak_table() def test_resolve_media_asset_conflicts_leaves_weak_weak_case_unresolved(): - from paperforge.worker.ocr_figures import resolve_media_asset_conflicts, _build_ownership_conflicts + from paperforge.worker.ocr_figures import _build_ownership_conflicts, resolve_media_asset_conflicts figure_inventory = { - "matched_figures": [{ - "figure_id": "figure_001", "legend_block_id": "figcap", - "text": "Figure 1.", - "match_score": {"score": 0.52, "decision": "matched_low_confidence", "evidence": ["fallback"]}, - "asset_block_ids": ["asset"], "matched_assets": [{"block_id": "asset"}], "page": 1, - }] + "matched_figures": [ + { + "figure_id": "figure_001", + "legend_block_id": "figcap", + "text": "Figure 1.", + "match_score": {"score": 0.52, "decision": "matched_low_confidence", "evidence": ["fallback"]}, + "asset_block_ids": ["asset"], + "matched_assets": [{"block_id": "asset"}], + "page": 1, + } + ] } table_inventory = { - "tables": [{ - "table_id": "table_001", "caption_block_id": "tabcap", - "caption_text": "Table 1", "match_status": "matched_low_confidence", - "has_asset": True, "asset_block_id": "asset", "page": 1, - }] + "tables": [ + { + "table_id": "table_001", + "caption_block_id": "tabcap", + "caption_text": "Table 1", + "match_status": "matched_low_confidence", + "has_asset": True, + "asset_block_id": "asset", + "page": 1, + } + ] } resolutions = resolve_media_asset_conflicts(figure_inventory, table_inventory) @@ -6013,22 +7772,32 @@ def test_resolve_media_asset_conflicts_leaves_weak_weak_case_unresolved(): def test_attach_ownership_conflicts_runs_after_resolution(): - from paperforge.worker.ocr_figures import resolve_media_asset_conflicts, attach_ownership_conflicts + from paperforge.worker.ocr_figures import attach_ownership_conflicts, resolve_media_asset_conflicts figure_inventory = { - "matched_figures": [{ - "figure_id": "figure_001", "legend_block_id": "figcap", - "text": "Figure 1. Example.", - "match_score": {"score": 0.51, "decision": "matched", "evidence": ["fallback"]}, - "asset_block_ids": ["asset"], "page": 1, - }] + "matched_figures": [ + { + "figure_id": "figure_001", + "legend_block_id": "figcap", + "text": "Figure 1. Example.", + "match_score": {"score": 0.51, "decision": "matched", "evidence": ["fallback"]}, + "asset_block_ids": ["asset"], + "page": 1, + } + ] } table_inventory = { - "tables": [{ - "table_id": "table_001", "caption_block_id": "tabcap", - "caption_text": "Table 1. Example.", "match_status": "matched", - "has_asset": True, "asset_block_id": "asset", "page": 1, - }] + "tables": [ + { + "table_id": "table_001", + "caption_block_id": "tabcap", + "caption_text": "Table 1. Example.", + "match_status": "matched", + "has_asset": True, + "asset_block_id": "asset", + "page": 1, + } + ] } resolve_media_asset_conflicts(figure_inventory, table_inventory) @@ -6042,11 +7811,14 @@ def test_final_unmatched_assets_excludes_matched_assets_after_promotion(): from paperforge.worker.ocr_figures import _dedup_unmatched_assets_against_matched_figures inventory = { - "matched_figures": [{ - "page": 9, "asset_pages": [9], - "matched_assets": [{"page": 9, "block_id": "11"}], - "asset_block_ids": ["11"], - }], + "matched_figures": [ + { + "page": 9, + "asset_pages": [9], + "matched_assets": [{"page": 9, "block_id": "11"}], + "asset_block_ids": ["11"], + } + ], "unmatched_assets": [ {"page": 9, "block_id": "11"}, {"page": 9, "block_id": "12"}, @@ -6060,30 +7832,56 @@ def test_final_unmatched_assets_excludes_matched_assets_after_promotion(): def test_collect_matched_figure_asset_ids_uses_asset_page_not_legend_page(): from paperforge.worker.ocr_figures import _collect_matched_figure_asset_ids_from_list - ids = _collect_matched_figure_asset_ids_from_list([{ - "page": 10, "legend_page": 9, "asset_pages": [10], - "matched_assets": [{"page": 10, "block_id": "A"}], - "asset_block_ids": ["A"], - }]) + ids = _collect_matched_figure_asset_ids_from_list( + [ + { + "page": 10, + "legend_page": 9, + "asset_pages": [10], + "matched_assets": [{"page": 10, "block_id": "A"}], + "asset_block_ids": ["A"], + } + ] + ) assert ids == {(10, "A")} + def test_apply_bbox_only_synthetic_vector_fallback_basic(): from paperforge.worker.ocr_figures import ( - _apply_bbox_only_synthetic_vector_fallback, FigureOwnershipRegistry, + _apply_bbox_only_synthetic_vector_fallback, ) + ownership = FigureOwnershipRegistry() - mf, ul, rl, ua = [], [{ - "block_id": "cap1", "page": 5, "role": "figure_caption_candidate", - "text": "Figure 1. Flow Diagram", "bbox": [100, 700, 900, 760], - }], [], [{ - "block_id": "a1", "page": 5, "role": "media_asset", - "raw_label": "chart", "asset_family_hint": "figure_like", - "bbox": [100, 200, 900, 680], - }] + mf, ul, rl, ua = ( + [], + [ + { + "block_id": "cap1", + "page": 5, + "role": "figure_caption_candidate", + "text": "Figure 1. Flow Diagram", + "bbox": [100, 700, 900, 760], + } + ], + [], + [ + { + "block_id": "a1", + "page": 5, + "role": "media_asset", + "raw_label": "chart", + "asset_family_hint": "figure_like", + "bbox": [100, 200, 900, 680], + } + ], + ) _apply_bbox_only_synthetic_vector_fallback( - matched_figures=mf, unmatched_legends=ul, rejected_legends=rl, - unmatched_assets=ua, ownership=ownership, + matched_figures=mf, + unmatched_legends=ul, + rejected_legends=rl, + unmatched_assets=ua, + ownership=ownership, ) assert len(mf) == 1 assert mf[0]["truth_source"] == "vector_bbox" @@ -6096,6 +7894,7 @@ def test_synthetic_fallback_rejects_low_score(): from paperforge.worker.ocr_figures import ( _score_caption_to_unmatched_asset_for_synthetic, ) + # caption far from asset -> vertical_gap > 300 -> reject score = _score_caption_to_unmatched_asset_for_synthetic( {"page": 5, "bbox": [100, 100, 900, 140]}, @@ -6153,14 +7952,87 @@ def test_score_legend_to_group_rotated_prematch_adds_rotation_metadata(): assert "rotated_caption_normalized" in score["evidence"] +def test_enrich_figure_match_rotation_standalone_adds_rotation_metadata() -> None: + """The standalone enrichment function adds rotation_correction_deg and cluster_bbox.""" + from paperforge.worker.ocr_figure_domain import FigureCorpus + from paperforge.worker.ocr_figures import _enrich_figure_match_rotation + from paperforge.worker.ocr_pairing_types import ClaimProposal, ResourceRef + + legend = { + "block_id": "c1", + "page": 8, + "bbox": [984, 136, 1062, 1442], + "text": "Figure 8. A rotated caption.", + "span_metadata": [{"dir": (0.0, -1.0), "wmode": 0}], + } + asset = { + "block_id": "a1", + "page": 8, + "bbox": [105, 134, 967, 1443], + } + blocks = [legend] + raw_assets = [asset] + corpus = FigureCorpus(blocks=blocks, page_width=1200, raw_assets=raw_assets) + + from types import SimpleNamespace + + state = SimpleNamespace(corpus=corpus) + + match_record: dict[str, object] = {} + proposal = ClaimProposal( + pass_name="test", + figure_no=8, + claim_type="match", + legends=[ResourceRef(kind="legend", page=8, block_id="c1")], + assets=[ResourceRef(kind="asset", page=8, block_id="a1")], + groups=[], + confidence=1.0, + evidence_rank=0, + reason="test", + ) + + _enrich_figure_match_rotation(proposal, match_record, state) + + assert "rotation_correction_deg" in match_record + assert "cluster_bbox" in match_record + assert match_record["rotation_correction_deg"] == 270 + + +def test_enrich_figure_match_rotation_skips_when_no_legend() -> None: + """No-op on empty legends should not enrich.""" + from types import SimpleNamespace + + from paperforge.worker.ocr_figures import _enrich_figure_match_rotation + from paperforge.worker.ocr_pairing_types import ClaimProposal + + state = SimpleNamespace(corpus=None) + match_record: dict[str, object] = {} + proposal = ClaimProposal( + pass_name="test", + figure_no=None, + claim_type="match", + legends=[], + assets=[], + groups=[], + confidence=1.0, + evidence_rank=0, + reason="test", + ) + + _enrich_figure_match_rotation(proposal, match_record, state) + + assert "rotation_correction_deg" not in match_record + assert "cluster_bbox" not in match_record + + # === Asset-internal figure number recovery tests === def test_recover_internal_figure_number_basic(): """Scenario 1: synthetic unknown with asset-internal Figure 2 line -> recovers figure_number==2.""" from paperforge.worker.ocr_figures import ( - _recover_missing_figure_numbers_from_assets, _format_figure_id, + _recover_missing_figure_numbers_from_assets, ) fig = { @@ -6229,9 +8101,7 @@ def test_recover_internal_figure_number_duplicate_rejection(): "page": 8, "text": "This figure demonstrates the results.", "flags": ["bbox_only_asset", "synthetic_vector_asset"], - "matched_assets": [ - {"block_id": "asset_2", "bbox": [100, 100, 900, 1400]} - ], + "matched_assets": [{"block_id": "asset_2", "bbox": [100, 100, 900, 1400]}], "asset_block_ids": ["asset_2"], } inventory = { @@ -6314,9 +8184,7 @@ def test_recover_internal_figure_number_conflict_multiple_labels(): "page": 5, "text": "This figure shows the data.", "flags": ["bbox_only_asset", "synthetic_vector_asset"], - "matched_assets": [ - {"block_id": "a1", "bbox": [100, 100, 900, 1400]} - ], + "matched_assets": [{"block_id": "a1", "bbox": [100, 100, 900, 1400]}], "asset_block_ids": ["a1"], } inventory = { @@ -6371,8 +8239,8 @@ def test_recover_internal_figure_number_center_rejection(): def test_recover_internal_figure_number_inside_overlap_gate(): """Scenario 6: coordinate normalization & inside/overlap gate.""" from paperforge.worker.ocr_figures import ( - _line_inside_or_overlaps_asset, _asset_edge_band_score, + _line_inside_or_overlaps_asset, ) # Line fully inside asset @@ -6429,3 +8297,24 @@ def test_vnext_entrypoint_is_callable_without_cutover(): assert isinstance(result, dict) assert result.get("pipeline_mode") == "vnext" assert result.get("matched_figures") == [] + + +# ── Baseline lock: figure entrypoint delegates to vnext ── + + +def test_build_figure_inventory_delegates_to_vnext(monkeypatch): + from paperforge.worker import ocr_figures + + called = {} + + def fake_vnext(structured_blocks, page_width=1200, page_pdf_lines_by_page=None): + called["args"] = (structured_blocks, page_width, page_pdf_lines_by_page) + return {"pipeline_mode": "vnext", "matched_figures": []} + + monkeypatch.setattr(ocr_figures, "build_figure_inventory_vnext", fake_vnext) + + blocks = [{"block_id": "b1", "page": 1, "role": "body_text", "text": "x"}] + result = ocr_figures.build_figure_inventory(blocks, page_width=777, page_pdf_lines_by_page={1: []}) + + assert result["pipeline_mode"] == "vnext" + assert called["args"] == (blocks, 777, {1: []}) diff --git a/tests/test_ocr_pairing_framework.py b/tests/test_ocr_pairing_framework.py new file mode 100644 index 00000000..366bd3ce --- /dev/null +++ b/tests/test_ocr_pairing_framework.py @@ -0,0 +1,246 @@ +from __future__ import annotations + +"""Baseline lock tests for the OCR pairing framework. + +These tests lock the current vnext types/state module surface before extraction. +They verify the framework types are importable and constructable. +""" + + +def test_vnext_types_module_is_currently_generic_surface(): + from paperforge.worker.ocr_figure_vnext_types import ClaimProposal, PassReport, ResourceRef + + assert ResourceRef.__name__ == "ResourceRef" + assert ClaimProposal.__name__ == "ClaimProposal" + assert PassReport.__name__ == "PassReport" + + +def test_vnext_state_module_is_currently_generic_surface(): + from paperforge.worker.ocr_figure_vnext_state import FigurePipelineState, OwnershipLedger + + state = FigurePipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + + assert state.matches == [] + assert state.reservations == [] + assert state.unresolved == [] + + +# ── Task 2: Generic pairing types extraction ── + + +def test_pairing_types_module_exports_generic_types(): + from paperforge.worker.ocr_pairing_types import ClaimProposal, PassReport, ResourceRef + + ref = ResourceRef(kind="legend", page=1, block_id="b1") + proposal = ClaimProposal( + pass_name="p", + figure_no=1, + claim_type="match", + legends=[ref], + assets=[], + groups=[], + confidence=0.9, + evidence_rank=1, + reason="test", + ) + report = PassReport(pass_name="p") + + assert proposal.pass_name == "p" + assert report.pass_name == "p" + assert ref.page == 1 + + +def test_figure_vnext_types_module_reexports_framework_types(): + from paperforge.worker.ocr_figure_vnext_types import ResourceRef as FigureModuleResourceRef + from paperforge.worker.ocr_pairing_types import ResourceRef as FrameworkResourceRef + + assert FigureModuleResourceRef is FrameworkResourceRef + + +def test_resource_ref_rejects_page_agnostic_asset(): + import pytest + + from paperforge.worker.ocr_pairing_types import ResourceRef + + with pytest.raises(ValueError): + ResourceRef(kind="asset", page=None, block_id="a1") + + +def test_resource_ref_normalizes_block_id_type(): + from paperforge.worker.ocr_pairing_types import ResourceRef + + assert ResourceRef(kind="asset", page=1, block_id=1) == ResourceRef(kind="asset", page=1, block_id="1") + + +def test_resource_ref_rejects_group_without_group_id(): + import pytest + + from paperforge.worker.ocr_pairing_types import ResourceRef + + with pytest.raises(ValueError): + ResourceRef(kind="group", page=1, block_id=None) + + +# ── Task 3: Generic state and ledger extraction ── + + +def test_pairing_state_module_exports_ownership_ledger(): + from paperforge.worker.ocr_pairing_state import OwnershipLedger + from paperforge.worker.ocr_pairing_types import ResourceRef + + ledger = OwnershipLedger() + owner = ResourceRef(kind="legend", page=1, block_id="cap") + asset = ResourceRef(kind="asset", page=1, block_id="asset") + + assert ledger.try_claim_assets([asset], owner=owner, reason="test") is None + assert ledger.owner_of_asset(page=1, block_id="asset") == owner + + +def test_figure_vnext_state_module_reexports_framework_ledger(): + from paperforge.worker.ocr_figure_vnext_state import OwnershipLedger as FigureModuleLedger + from paperforge.worker.ocr_pairing_state import OwnershipLedger as FrameworkLedger + + assert FigureModuleLedger is FrameworkLedger + + +# ── Task 4: Pairing framework runner ── + + +def test_run_pairing_passes_executes_in_declared_order(): + from paperforge.worker.ocr_pairing_framework import run_pairing_passes + from paperforge.worker.ocr_pairing_state import FigurePipelineState, OwnershipLedger + from paperforge.worker.ocr_pairing_types import PassReport + + seen = [] + + class FirstPass: + name = "first" + + def run(self, state): + seen.append(self.name) + return PassReport(pass_name=self.name) + + class SecondPass: + name = "second" + + def run(self, state): + seen.append(self.name) + return PassReport(pass_name=self.name) + + state = FigurePipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + reports = run_pairing_passes(state, [FirstPass, SecondPass]) + + assert seen == ["first", "second"] + assert [r.pass_name for r in reports] == ["first", "second"] + + +# ── Task 5: Figure domain module ── + + +def test_figure_domain_module_exports_corpus_and_candidate_index(): + from paperforge.worker.ocr_figure_domain import FigureCandidateIndex, FigureCorpus + + assert FigureCorpus.__name__ == "FigureCorpus" + assert FigureCandidateIndex.__name__ == "FigureCandidateIndex" + + +def test_legacy_vnext_corpus_module_reexports_figure_domain_types(): + from paperforge.worker.ocr_figure_domain import FigureCorpus as DomainFigureCorpus + from paperforge.worker.ocr_figure_vnext_corpus import FigureCorpus as LegacyModuleFigureCorpus + + assert LegacyModuleFigureCorpus is DomainFigureCorpus + + +def test_resource_ref_supports_text_kind_and_role() -> None: + from paperforge.worker.ocr_pairing_types import ResourceRef + + ref = ResourceRef(kind="text", page=5, block_id="note1", role="note") + + assert ref.kind == "text" + assert ref.role == "note" + + +def test_claim_proposal_exposes_entity_no_alias_and_texts() -> None: + from paperforge.worker.ocr_pairing_types import ClaimProposal, ResourceRef + + proposal = ClaimProposal( + pass_name="p", + figure_no=3, + claim_type="attach_text", + legends=[ResourceRef(kind="legend", page=5, block_id="cap1")], + assets=[], + groups=[], + texts=[ResourceRef(kind="text", page=5, block_id="note1", role="note")], + confidence=0.8, + evidence_rank=1, + reason="test", + ) + + assert proposal.entity_no == 3 + assert proposal.texts[0].block_id == "note1" + + +def test_ownership_ledger_journals_text_attachments() -> None: + from paperforge.worker.ocr_pairing_state import OwnershipLedger + from paperforge.worker.ocr_pairing_types import ResourceRef + + ledger = OwnershipLedger() + owner = ResourceRef(kind="legend", page=5, block_id="cap1", figure_no=5) + texts = [ResourceRef(kind="text", page=5, block_id="note1", role="note")] + + ledger.journal_text_attachment(texts, owner=owner, reason="table-notes") + + assert ledger.text_attachments_for(owner) == texts + + +def test_pipeline_state_alias_preserves_figure_state_compatibility() -> None: + from paperforge.worker.ocr_pairing_state import FigurePipelineState, OwnershipLedger, PipelineState + + state = PipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + + assert FigurePipelineState is PipelineState + assert state.matches == [] + assert state.reservations == [] + + +def test_state_accept_match_defaults_to_no_enricher() -> None: + """The generic state must not enrich matches by default (domain-neutral).""" + from paperforge.worker.ocr_pairing_state import OwnershipLedger, PipelineState + + state = PipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + assert state._match_pre_enricher is None + + +def test_state_accept_match_invokes_enricher_when_set() -> None: + """When a _match_pre_enricher hook is wired, accept_match must call it.""" + from paperforge.worker.ocr_pairing_state import FigurePipelineState, OwnershipLedger + from paperforge.worker.ocr_pairing_types import ClaimProposal, ResourceRef + + state = FigurePipelineState(corpus=None, candidate_index=None, ledger=OwnershipLedger()) + called_with: list[tuple] = [] + + def fake_enricher(proposal, match_record, state_obj): + called_with.append((proposal, match_record, state_obj)) + + state._match_pre_enricher = fake_enricher + proposal = ClaimProposal( + pass_name="test", + figure_no=None, + claim_type="match", + legends=[ResourceRef(kind="legend", page=1, block_id="l1")], + assets=[], + groups=[], + confidence=1.0, + evidence_rank=0, + reason="test", + ) + match_record = {"test": True} + state.accept_match(proposal, match_record) + + assert len(called_with) == 1 + assert called_with[0][0] is proposal + assert called_with[0][1] is match_record + assert called_with[0][2] is state + # The match_record should have been appended to state.matches *after* enrichment + assert state.matches[0] is match_record + assert state.matches[0]["test"] is True diff --git a/tests/test_ocr_rebuild.py b/tests/test_ocr_rebuild.py index 20a6958e..f4df9b3c 100644 --- a/tests/test_ocr_rebuild.py +++ b/tests/test_ocr_rebuild.py @@ -188,7 +188,7 @@ def test_run_derived_rebuild_skips_span_backfill_when_valid(tmp_path: Path, monk encoding="utf-8", ) (paper_root / "meta.json").write_text( - '{"source_pdf":"sample.pdf","span_backfill_version":"2026-06-22.1","span_visual_container_version":"2026-06-26.6","span_pdf_fingerprint":"fp-1","span_backfill_coverage":1.0}', + '{"source_pdf":"sample.pdf","span_backfill_version":"2026-07-01.1","span_visual_container_version":"2026-06-26.6","span_pdf_fingerprint":"fp-1","span_backfill_coverage":1.0}', encoding="utf-8", ) pdf_path = tmp_path / "sample.pdf" @@ -242,7 +242,7 @@ def test_run_derived_rebuild_records_unavailable_pdf_missing_without_rerun(tmp_p paper_root = tmp_path / "System" / "PaperForge" / "ocr" / key (paper_root / "canonical").mkdir(parents=True) (paper_root / "raw").mkdir(parents=True) - (paper_root / "meta.json").write_text('{"span_backfill_version":"2026-06-22.1"}', encoding="utf-8") + (paper_root / "meta.json").write_text('{"span_backfill_version":"2026-07-01.1"}', encoding="utf-8") (paper_root / "canonical" / "blocks.raw.jsonl").write_text('{"paper_id":"TESTKEY1","page":1,"block_id":"p1_b1","raw_label":"text","raw_order":0,"text":"A","bbox":[0,0,10,10],"page_width":600,"page_height":800,"span_metadata":[{"size":10}]}\n', encoding="utf-8") (paper_root / "raw" / "source_metadata.json").write_text('{"title":"Example Title"}', encoding="utf-8") @@ -292,8 +292,8 @@ def test_run_derived_rebuild_does_not_skip_when_current_fingerprint_is_unknown() from paperforge.worker.ocr_rebuild import _span_backfill_is_valid meta = { - "span_backfill_version": "2026-06-22.1", - "span_visual_container_version": "2026-06-22.1", + "span_backfill_version": "2026-07-01.1", + "span_visual_container_version": "2026-06-26.6", "span_pdf_fingerprint": "unknown", "span_backfill_coverage": 1.0, } @@ -306,7 +306,7 @@ def test_span_backfill_invalid_when_version_mismatch() -> None: meta = { "span_backfill_version": "old", - "span_visual_container_version": "2026-06-22.1", + "span_visual_container_version": "2026-06-26.6", "span_pdf_fingerprint": "fp-1", } @@ -317,7 +317,7 @@ def test_span_backfill_invalid_when_visual_container_version_mismatch() -> None: from paperforge.worker.ocr_rebuild import _span_backfill_is_valid meta = { - "span_backfill_version": "2026-06-22.1", + "span_backfill_version": "2026-07-01.1", "span_visual_container_version": "old", "span_pdf_fingerprint": "fp-1", } @@ -329,8 +329,8 @@ def test_span_backfill_invalid_when_fingerprint_mismatch() -> None: from paperforge.worker.ocr_rebuild import _span_backfill_is_valid meta = { - "span_backfill_version": "2026-06-22.1", - "span_visual_container_version": "2026-06-22.1", + "span_backfill_version": "2026-07-01.1", + "span_visual_container_version": "2026-06-26.6", "span_pdf_fingerprint": "fp-old", } @@ -341,8 +341,8 @@ def test_span_backfill_invalid_when_coverage_below_threshold() -> None: from paperforge.worker.ocr_rebuild import _span_backfill_is_valid meta = { - "span_backfill_version": "2026-06-22.1", - "span_visual_container_version": "2026-06-22.1", + "span_backfill_version": "2026-07-01.1", + "span_visual_container_version": "2026-06-26.6", "span_pdf_fingerprint": "fp-1", } @@ -422,3 +422,123 @@ doi: 10.1000/example assert meta["authors"] == ["W. H. Marks"] assert meta.get("authors_incomplete") is True assert meta.get("authors_source") == "paper_note.first_author_fallback" + + +# ── Plan A: rebuild compatibility proof (pairing framework) ── + + +def test_run_derived_rebuild_for_keys_still_uses_public_build_figure_inventory(tmp_path: Path, monkeypatch) -> None: + import json + + from paperforge.worker.ocr_rebuild import run_derived_rebuild_for_keys + + key = "TESTKEY1" + paper_root = tmp_path / "System" / "PaperForge" / "ocr" / key + (paper_root / "canonical").mkdir(parents=True) + (paper_root / "raw").mkdir(parents=True) + (paper_root / "structure").mkdir(parents=True) + + (paper_root / "canonical" / "blocks.raw.jsonl").write_text( + json.dumps( + { + "paper_id": key, + "page": 1, + "block_id": "p1_b1", + "raw_label": "text", + "raw_order": 0, + "text": "Example text", + "bbox": [10, 10, 100, 40], + "page_width": 600, + "page_height": 800, + } + ) + + "\n", + encoding="utf-8", + ) + (paper_root / "raw" / "source_metadata.json").write_text( + json.dumps({"title": "Example Title"}), + encoding="utf-8", + ) + (paper_root / "meta.json").write_text(json.dumps({"source_pdf": ""}), encoding="utf-8") + + called = {"count": 0} + + def fake_build_figure_inventory(structured_blocks, page_width=1200, page_pdf_lines_by_page=None): + called["count"] += 1 + return { + "pipeline_mode": "vnext", + "matched_figures": [], + "ambiguous_figures": [], + "unmatched_legends": [], + "unmatched_assets": [], + "unresolved_clusters": [], + "held_figures": [], + "rejected_legends": [], + "page_ledger": {}, + "residual_ledger": {}, + "local_pairing_hypotheses": [], + "pass_reports": [], + "completeness": {"total_numbered_legends": 0, "accounted_for": 0, "details": []}, + } + + monkeypatch.setattr("paperforge.worker.ocr_figures.build_figure_inventory", fake_build_figure_inventory) + monkeypatch.setattr("paperforge.worker.ocr_blocks.write_structured_blocks_jsonl", lambda *args, **kwargs: None) + monkeypatch.setattr( + "paperforge.worker.ocr_metadata.extract_frontmatter_candidates_from_blocks", + lambda structured: {"title": "Example Title", "authors_text": None, "doi_candidates": []}, + ) + + result = run_derived_rebuild_for_keys(tmp_path, [key]) + + assert result["rebuild_count"] == 1 + assert called["count"] > 0 + + +def test_run_derived_rebuild_for_keys_still_uses_public_build_table_inventory(tmp_path: Path, monkeypatch) -> None: + import json + + from paperforge.worker.ocr_rebuild import run_derived_rebuild_for_keys + + key = "TESTKEY1" + paper_root = tmp_path / "System" / "PaperForge" / "ocr" / key + (paper_root / "canonical").mkdir(parents=True) + (paper_root / "raw").mkdir(parents=True) + (paper_root / "structure").mkdir(parents=True) + + (paper_root / "canonical" / "blocks.raw.jsonl").write_text( + json.dumps({"paper_id": key, "page": 1, "block_id": "p1_b1", "raw_label": "text", "raw_order": 0, "text": "text", "bbox": [10, 10, 100, 40], "page_width": 600, "page_height": 800}) + "\n", encoding="utf-8" + ) + (paper_root / "raw" / "source_metadata.json").write_text(json.dumps({"title": "Example Title"}), encoding="utf-8") + (paper_root / "meta.json").write_text(json.dumps({"source_pdf": ""}), encoding="utf-8") + + called = {"count": 0} + + def fake_build_table_inventory(structured_blocks): + called["count"] += 1 + return {"tables": [], "held_tables": [], "unmatched_captions": [], "unmatched_assets": [], "official_table_count": 0} + + monkeypatch.setattr("paperforge.worker.ocr_tables.build_table_inventory", fake_build_table_inventory) + monkeypatch.setattr("paperforge.worker.ocr_blocks.write_structured_blocks_jsonl", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_metadata.extract_frontmatter_candidates_from_blocks", lambda s: {"title": "Example Title", "authors_text": None, "doi_candidates": []}) + monkeypatch.setattr("paperforge.worker.ocr_figures.build_figure_inventory", lambda *a, **kw: {"matched_figures": [], "unmatched_assets": [], "unresolved_clusters": []}) + monkeypatch.setattr("paperforge.worker.ocr_figures.write_back_figure_roles", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_figures.write_figure_inventory", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_figure_reader.synthesize_reader_figures", lambda *a, **kw: {}) + monkeypatch.setattr("paperforge.worker.ocr_tables.write_back_table_roles", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_tables.write_table_inventory", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_objects.extract_and_write_objects", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_render.render_fulltext_markdown", lambda *a, **kw: "") + monkeypatch.setattr("paperforge.worker.ocr_render.write_render_outputs", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_health.build_ocr_health", lambda *a, **kw: {}) + monkeypatch.setattr("paperforge.worker.ocr_health.build_ocr_raw_integrity_health", lambda *a, **kw: {}) + monkeypatch.setattr("paperforge.worker.ocr_health.write_ocr_health", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_decisions.collect_decisions", lambda *a, **kw: []) + monkeypatch.setattr("paperforge.worker.ocr_decisions.write_decision_log", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr_index.build_role_indexes", lambda *a, **kw: {}) + monkeypatch.setattr("paperforge.worker.ocr_index.write_role_index", lambda *a, **kw: None) + monkeypatch.setattr("paperforge.worker.ocr.validate_ocr_meta", lambda *a, **kw: ("done", "")) + + result = run_derived_rebuild_for_keys(tmp_path, [key]) + + assert result["rebuild_count"] == 1 + assert called["count"] > 0 diff --git a/tests/test_ocr_table_pairing_framework.py b/tests/test_ocr_table_pairing_framework.py new file mode 100644 index 00000000..56f8ebeb --- /dev/null +++ b/tests/test_ocr_table_pairing_framework.py @@ -0,0 +1,450 @@ +from __future__ import annotations + + +def test_table_corpus_collects_captions_assets_and_page_context() -> None: + from paperforge.worker.ocr_table_domain import TableCorpus + + blocks = [ + { + "block_id": "cap1", + "page": 5, + "role": "table_caption", + "text": "Table 1. Example", + "bbox": [100, 100, 700, 140], + }, + { + "block_id": "asset1", + "page": 5, + "role": "table_html", + "raw_label": "table", + "text": "
x
", + "bbox": [100, 160, 700, 500], + }, + { + "block_id": "note1", + "page": 5, + "role": "footnote", + "raw_label": "vision_footnote", + "text": "* p < 0.05", + "bbox": [100, 520, 300, 550], + }, + ] + + corpus = TableCorpus.from_blocks(blocks) + + assert [b["block_id"] for b in corpus.raw_captions] == ["cap1"] + assert [b["block_id"] for b in corpus.raw_assets] == ["asset1"] + assert 5 in corpus.page_footnote_prior + assert 5 in corpus.page_max_y + + +def test_table_candidate_index_materializes_caption_records_and_assets_by_page() -> None: + from paperforge.worker.ocr_table_domain import TableCandidateIndex, TableCorpus + + blocks = [ + { + "block_id": "cap2", + "page": 6, + "role": "table_caption_candidate", + "text": "Table 2. (continued)", + "bbox": [100, 100, 700, 130], + }, + { + "block_id": "cap1", + "page": 5, + "role": "table_caption", + "text": "Table 1. Example", + "bbox": [100, 100, 700, 140], + }, + { + "block_id": "asset1", + "page": 5, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 160, 700, 500], + }, + ] + + index = TableCandidateIndex.from_corpus(TableCorpus.from_blocks(blocks)) + + assert [r["caption_block_id"] for r in index.caption_records] == ["cap1", "cap2"] + assert 5 in index.assets_by_page + assert index.caption_records[1]["is_continuation"] is True + + +def test_assemble_table_inventory_preserves_public_shape_for_empty_state() -> None: + from paperforge.worker.ocr_pairing_state import OwnershipLedger, PipelineState + from paperforge.worker.ocr_table_domain import TableCandidateIndex, TableCorpus, assemble_table_inventory + + blocks = [ + {"block_id": "cap1", "page": 1, "role": "table_caption", "text": "Table 1. Example", "bbox": [0, 0, 10, 10]} + ] + corpus = TableCorpus.from_blocks(blocks) + index = TableCandidateIndex.from_corpus(corpus) + state = PipelineState(corpus=corpus, candidate_index=index, ledger=OwnershipLedger()) + + inventory = assemble_table_inventory(state, index) + + assert inventory == { + "official_table_count": 0, + "held_tables": [], + "tables": [ + { + "asset_bbox": [], + "asset_block_id": None, + "assistive_text": "", + "bridge_block_ids": [], + "candidate_assets": [], + "caption_block_id": "cap1", + "caption_text": "Table 1. Example", + "consumed_block_ids": [], + "continuation_of": None, + "formal_table_number": 1, + "has_asset": False, + "is_continuation": False, + "match_score": {"decision": "unmatched", "evidence": [], "matched_asset_id": "", "score": 0.0}, + "match_status": "pending", + "note_band_bbox": [], + "note_bboxes": [], + "note_block_ids": [], + "note_confidence": 0.0, + "note_match_reason": "", + "note_texts": [], + "page": 1, + "render_bbox": None, + "render_rotation_deg": 0, + "segments": [], + "table_number": 1, + "truth_source": "image", + } + ], + "unmatched_assets": [], + "unmatched_captions": [blocks[0]], + } + + +# ── Task 4: vnext matching passes ── + + +def test_build_table_inventory_vnext_matches_same_page_best_asset() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "cap1", + "page": 3, + "role": "table_caption", + "text": "Table 1. Example", + "bbox": [100, 100, 700, 140], + }, + { + "block_id": "asset_good", + "page": 3, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 160, 700, 500], + }, + { + "block_id": "asset_bad", + "page": 3, + "role": "media_asset", + "raw_label": "image", + "text": "", + "bbox": [800, 160, 1100, 300], + }, + ] + + inventory = build_table_inventory_vnext(structured_blocks) + + assert inventory["tables"][0]["asset_block_id"] == "asset_good" + assert inventory["tables"][0]["match_status"] in {"matched", "matched_low_confidence"} + + +def test_build_table_inventory_vnext_holds_validation_first_weak_caption_without_same_page_asset() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "cap1", + "page": 4, + "role": "body_text", + "text": "Table 2", + "bbox": [100, 100, 260, 130], + "zone": "display_zone", + "style_family": "table_caption_like", + "marker_signature": {"type": "table_number"}, + } + ] + + inventory = build_table_inventory_vnext(structured_blocks) + + assert inventory["tables"] == [] + assert inventory["held_tables"][0]["hold_reason"] == "insufficient_caption_evidence" + + +def test_build_table_inventory_vnext_materializes_split_caption_continuation() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + {"block_id": "cap1", "page": 5, "role": "table_caption", "text": "Table 3.", "bbox": [100, 100, 220, 130]}, + {"block_id": "cap2", "page": 5, "role": "body_text", "text": "Continuation text", "bbox": [100, 132, 700, 170]}, + { + "block_id": "asset1", + "page": 5, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 180, 700, 500], + }, + ] + + inventory = build_table_inventory_vnext(structured_blocks) + + assert "cap2" in inventory["tables"][0]["consumed_block_ids"] + assert inventory["tables"][0]["caption_text"].startswith("Table 3.") + + +def test_build_table_inventory_vnext_previous_page_continuation_gets_geometry_elevation() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "asset_prev", + "page": 7, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 1200, 900, 1480], + }, + { + "block_id": "cap1", + "page": 8, + "role": "table_caption", + "text": "Table 4. (continued)", + "bbox": [100, 110, 700, 150], + }, + ] + + inventory = build_table_inventory_vnext(structured_blocks) + + assert inventory["tables"][0]["asset_block_id"] == "asset_prev" + assert "continuation_geometry_elevation" in inventory["tables"][0]["match_score"]["evidence"] + + +# ── Task 5: Notes, accounting, diff tooling ── + + +def test_build_table_inventory_vnext_collects_note_band_and_bridge_blocks() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "cap1", + "page": 5, + "role": "table_caption", + "text": "Table 1. Example", + "bbox": [100, 100, 700, 140], + }, + { + "block_id": "asset1", + "page": 5, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 160, 700, 520], + }, + {"block_id": "note1", "page": 5, "role": "footnote", "text": "* p < 0.05", "bbox": [100, 530, 220, 555]}, + { + "block_id": "bridge1", + "page": 5, + "bridge_eligible": True, + "layout_region": "display_zone", + "text": "", + "bbox": [100, 150, 700, 155], + }, + ] + + tables = build_table_inventory_vnext(structured_blocks)["tables"] + + assert len(tables) == 1 + assert tables[0]["note_block_ids"] == ["note1"] + assert tables[0]["bridge_block_ids"] == ["bridge1"] + assert "note1" in tables[0]["consumed_block_ids"] + + +def test_build_table_inventory_vnext_respects_page_footnote_prior() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "cap1", + "page": 5, + "role": "table_caption", + "text": "Table 1. Example", + "bbox": [100, 100, 700, 140], + }, + { + "block_id": "asset1", + "page": 5, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 160, 700, 1150], + }, + { + "block_id": "note1", + "page": 5, + "role": "footnote", + "text": "* footer-area note", + "bbox": [100, 1180, 300, 1210], + }, + ] + + table = build_table_inventory_vnext(structured_blocks)["tables"][0] + assert table["note_match_reason"] in {"note_band_geometry_match", "outside_vertical_range"} + + +def test_build_table_inventory_vnext_sets_render_rotation_fields_for_rotated_table_asset() -> None: + from paperforge.worker.ocr_tables import build_table_inventory_vnext + + structured_blocks = [ + { + "block_id": "cap1", + "page": 8, + "role": "table_caption", + "text": "Table 2. Caption", + "bbox": [100, 134, 967, 1442], + }, + { + "block_id": "asset1", + "page": 8, + "role": "table_html", + "raw_label": "table", + "text": "
", + "bbox": [100, 100, 880, 1400], + "span_metadata": [{"dir": [0.0, -1.0], "wmode": 0}], + }, + ] + inventory = build_table_inventory_vnext(structured_blocks) + tables = inventory["tables"] + + assert len(tables) >= 1 + assert tables[0]["render_rotation_deg"] in {0, 270} + + +def test_compare_table_inventory_legacy_vs_vnext_smoke_fixture() -> None: + from pathlib import Path + + from scripts.dev.compare_table_inventory_legacy_vs_vnext import compare_table_inventory_legacy_vs_vnext + + result = compare_table_inventory_legacy_vs_vnext(Path("tests/fixtures/ocr_vnext_real_papers/2HEUD5P9")) + + assert "legacy" in result + assert "vnext" in result + assert "diff" in result + + +def test_compare_table_inventory_parity_on_all_real_paper_fixtures() -> None: + """Semantic parity after normalising benign drift (string/int, ordering, None vs ''). + + Runnable fixtures: 2HEUD5P9, 28JLIHLS, YGH7VEX6, DWQQK2YB, 24YKLTHQ, 37LK5T97. + The first five achieve full parity across all fields including consumed_block_ids. + + 37LK5T97 gap: consumed_block_ids in legacy drops caption block_id=0 because + the ``if bid`` filter treats integer 0 as falsy; vnext uses string ``'0'`` + which is truthy. This is a known legacy bug that vnext fixes — the core + fields (caption_block_id, page, formal_table_number, asset_block_id, + match_status, render_rotation_deg) are identical after normalisation. + """ + from pathlib import Path + + from scripts.dev.compare_table_inventory_legacy_vs_vnext import compare_table_inventory_legacy_vs_vnext + + fixtures = [ + ("2HEUD5P9", False), + ("28JLIHLS", False), + ("YGH7VEX6", False), + ("DWQQK2YB", False), + ("24YKLTHQ", False), + ("37LK5T97", True), # True = known consumed_block_ids gap + ] + + core_fields = { + "caption_block_id", + "page", + "formal_table_number", + "asset_block_id", + "match_status", + "render_rotation_deg", + } + + for pid, known_consumed_gap in fixtures: + result = compare_table_inventory_legacy_vs_vnext(Path(f"tests/fixtures/ocr_vnext_real_papers/{pid}")) + + assert len(result["legacy"]) == len(result["vnext"]), ( + f"{pid}: table count mismatch: {len(result['legacy'])} vs {len(result['vnext'])}" + ) + + lo = result["diff"]["legacy_only"] + vo = result["diff"]["vnext_only"] + + # Compare core fields directly: for each fixture paper, every + # legacy table's core fields must appear in the vnext list and + # vice versa. This catches real semantic drift. + legacy_core = {tuple(t.get(k) for k in core_fields) for t in result["legacy"]} + vnext_core = {tuple(t.get(k) for k in core_fields) for t in result["vnext"]} + + legacy_missing = legacy_core - vnext_core + vnext_extra = vnext_core - legacy_core + + assert not legacy_missing and not vnext_extra, ( + f"{pid}: core-field mismatch — " + f"legacy has {legacy_missing} not in vnext, " + f"vnext has {vnext_extra} not in legacy" + ) + + # consumed_block_ids / note / bridge diffs: must be the known gap or absent. + consumed_lo = {tuple(t["consumed_block_ids"]) for t in lo} + consumed_vo = {tuple(t["consumed_block_ids"]) for t in vo} + + if known_consumed_gap: + assert consumed_lo or consumed_vo, f"{pid}: expected consumed_block_ids gap but found none" + # note / bridge must be pair-wise equivalent across lo and vo + # (same empty values for 37LK5T97 — no notes or bridges). + lo_pairs = {(tuple(t.get("note_block_ids")), tuple(t.get("bridge_block_ids"))) for t in lo} + vo_pairs = {(tuple(t.get("note_block_ids")), tuple(t.get("bridge_block_ids"))) for t in vo} + assert lo_pairs == vo_pairs, ( + f"{pid}: note/bridge mismatch beyond consumed_block_ids gap: lo={lo_pairs} vo={vo_pairs}" + ) + else: + assert not consumed_lo and not consumed_vo, ( + f"{pid}: unexpected consumed_block_ids diffs: legacy={consumed_lo}, vnext={consumed_vo}" + ) + + +def test_table_pipeline_does_not_set_figure_enricher() -> None: + """Table pipeline state must not wire the figure-only rotation enricher.""" + from paperforge.worker.ocr_table_domain import TableCandidateIndex, TableCorpus + + # Build a minimal table inventory — the state created internally must not + # have the figure rotation enricher set. + structured_blocks = [ + { + "block_id": "cap1", + "page": 1, + "role": "table_caption", + "text": "Table 1. Results.", + "bbox": [100, 50, 500, 80], + }, + {"block_id": "tab1", "page": 1, "role": "table_asset", "bbox": [100, 100, 500, 400]}, + ] + from paperforge.worker.ocr_pairing_state import OwnershipLedger, PipelineState + + corpus = TableCorpus.from_blocks(structured_blocks) + candidate_index = TableCandidateIndex.from_corpus(corpus) + state = PipelineState(corpus=corpus, candidate_index=candidate_index, ledger=OwnershipLedger()) + + # Table pipeline should never set the figure-only enricher + assert state._match_pre_enricher is None diff --git a/tests/test_ocr_tables.py b/tests/test_ocr_tables.py index 659a6b7b..187ef8cd 100644 --- a/tests/test_ocr_tables.py +++ b/tests/test_ocr_tables.py @@ -1307,22 +1307,16 @@ def test_extract_table_number_supports_roman_and_s_prefix(text, expected_number) assert _extract_table_number(text) == expected_number -def test_build_table_inventory_delegates_to_legacy_during_plan_b(monkeypatch) -> None: +def test_build_table_inventory_delegates_to_vnext_after_cutover(monkeypatch) -> None: from paperforge.worker import ocr_tables called = {} - def fake_legacy(structured_blocks): + def fake_vnext(structured_blocks): called["blocks"] = structured_blocks - return { - "tables": [], - "held_tables": [], - "unmatched_captions": [], - "unmatched_assets": [], - "official_table_count": 0, - } + return {"tables": [], "held_tables": [], "unmatched_captions": [], "unmatched_assets": [], "official_table_count": 0} - monkeypatch.setattr(ocr_tables, "build_table_inventory_legacy", fake_legacy, raising=False) + monkeypatch.setattr(ocr_tables, "build_table_inventory_vnext", fake_vnext) blocks = [{"block_id": "cap1", "page": 1, "role": "table_caption", "text": "Table 1. Example"}] result = ocr_tables.build_table_inventory(blocks)