structurecc 1.0.4 → 2.0.0

package/README.md

@@ -1,4 +1,4 @@
-<h1 align="center">STRUCTURE</h1>
+<h1 align="center">STRUCTURE v2.0</h1>
 
 <p align="center">
 <strong>Landing AI charges $500/month for agentic document structuring.<br>This is free.</strong>
@@ -19,29 +19,84 @@
 
 ---
 
+## What's New in v2.0
+
+**3-Phase Pipeline with Quality Verification**
+
+```
+Image → [Classify] → [Extract] → [Verify] → Output
+                         ↑_______↻_______↓
+```
+
+| Phase | Agent | Purpose |
+|-------|-------|---------|
+| 1. Classify | `structurecc-classifier` | Fast triage to route to correct extractor |
+| 2. Extract | 6 specialized extractors | Type-specific verbatim extraction |
+| 3. Verify | `structurecc-verifier` | Quality scoring with auto-revision |
+
+**Verbatim Extraction** - Text is copied EXACTLY as shown. No paraphrasing, no "cleanup."
+
+**Quality Scoring** - Each extraction gets a 0.0-1.0 score. Failures auto-retry up to 2x.
+
+**Specialized Extractors** - Tables, charts, heatmaps, diagrams each get dedicated agents.
+
+---
+
 ## The Problem
 
 You have a 50-page PDF with figures, tables, and charts. You need that data.
 
 **Manual approach:** Screenshot each figure. Transcribe tables cell by cell. Spend hours on one document.
 
-**With structurecc:** One command. Walk away. Come back to perfectly structured markdown.
+**With structurecc:** One command. Walk away. Come back to perfectly structured markdown with quality verification.
 
 ```
 /structure paper.pdf
 ```
 
-Spawns parallel AI agents. Each agent analyzes one visual element. All run simultaneously. Done in minutes, not hours.
+Spawns parallel AI agents. Each agent analyzes one visual element. All run simultaneously. Quality verified. Done in minutes, not hours.
 
 ---
 
-## What is this?
+## Specialized Extractors
 
-Give it a document. It extracts every image. Spawns one AI agent per image. Each agent exhaustively analyzes its element—tables become markdown tables, figures get descriptions, charts get data points extracted.
+| Extractor | Handles |
+|-----------|---------|
+| `structurecc-extract-table` | Tables with cell-by-cell accuracy, merged cells, footnotes |
+| `structurecc-extract-chart` | Kaplan-Meier, bar, line, scatter, forest plots with axes, legends, data |
+| `structurecc-extract-heatmap` | Expression heatmaps, correlation matrices with full label extraction |
+| `structurecc-extract-diagram` | CONSORT flows, timelines, network diagrams with all node text |
+| `structurecc-extract-multipanel` | Multi-panel figures (A, B, C, D) with per-panel extraction |
+| `structurecc-extract-generic` | Photographs, schematics, equations, other visuals |
 
-Runs inside **[Claude Code](https://docs.anthropic.com/en/docs/claude-code)** (Anthropic's terminal assistant). One command. ~$0.50-$5 per document.
+---
 
-Like [Landing AI's Agentic Document Extraction](https://landing.ai/agentic-document-extraction), but running locally via Claude Code.
+## Quality Verification
+
+Every extraction is verified against the source image:
+
+```json
+{
+  "scores": {
+    "completeness": 0.95,
+    "accuracy": 0.92,
+    "verbatim_compliance": 0.88,
+    "structure_correctness": 0.97,
+    "overall": 0.93
+  },
+  "pass": true,
+  "threshold": 0.90
+}
+```
+
+| Score | Meaning |
+|-------|---------|
+| **completeness** | Was every visible element captured? |
+| **accuracy** | Are values (numbers, stats) correct? |
+| **verbatim_compliance** | Was text copied exactly as shown? |
+| **structure_correctness** | Is the JSON structure valid? |
+
+**Auto-revision:** If score < 0.90, extraction is re-run with specific feedback. Max 2 attempts.
 
 ---
 
@@ -88,10 +143,6 @@ Copy this command and paste it into your terminal:
 npm install -g @anthropic-ai/claude-code
 ```
 
-<p align="center">
-<img src="assets/screenshots/step0.png" alt="Install Claude Code" width="550">
-</p>
-
 Wait for it to finish.
 
 ---
@@ -104,11 +155,7 @@ Copy and run this:
 npx structurecc
 ```
 
-<p align="center">
-<img src="assets/screenshots/step1.png" alt="Install structurecc" width="420">
-</p>
-
-You will see a STRUCTURE banner. That means it worked. You only do this once.
+You will see a STRUCTURE banner and 8 agents being installed. You only do this once.
 
 ---
 
@@ -116,17 +163,9 @@ You will see a STRUCTURE banner. That means it worked. You only do this once.
 
 Create a folder with your document:
 
-<p align="center">
-<img src="assets/screenshots/step2.png" alt="Folder structure" width="380">
-</p>
-
 ```
 documents/
-├── document.pdf          ← your PDF, DOCX, or image
-└── images/               ← extracted images go here (created automatically)
-    ├── figure_1.png
-    ├── table_2.png
-    └── chart_3.png
+└── document.pdf          ← your PDF, DOCX, or image
 ```
 
 **Put your document in a folder. That's it.**
@@ -142,10 +181,6 @@ cd ~/Desktop/documents
 claude
 ```
 
-<p align="center">
-<img src="assets/screenshots/step3a.png" alt="Start Claude Code" width="460">
-</p>
-
 **Windows users:** Replace `~/Desktop/documents` with your actual path, like `C:\Users\YourName\Desktop\documents`
 
 The first time you run `claude`, it will ask for your API key. Paste it in.
@@ -160,32 +195,53 @@ Now you are inside Claude Code. Type this command:
 /structure document.pdf
 ```
 
-<p align="center">
-<img src="assets/screenshots/step3.png" alt="Run /structure" width="500">
-</p>
-
 **Important:** The `/structure` command only works inside Claude Code. If you type it in your regular terminal, it will not work.
 
 structurecc will:
 1. Extract every image from your document
-2. Spawn one agent per image (all running in parallel)
-3. Each agent exhaustively analyzes its visual element
-4. Combine everything into `STRUCTURED.md`
+2. Classify each image (table, chart, heatmap, diagram, etc.)
+3. Spawn specialized extractors in parallel
+4. Verify each extraction against the source
+5. Auto-revise failed extractions
+6. Combine everything into `STRUCTURED.md`
 
 ---
 
 ## What You Get
 
-A comprehensive markdown file with every visual element extracted:
+A comprehensive output directory with full traceability:
 
 ```
 document_extracted/
-├── images/           # All extracted visuals
-├── elements/         # One markdown file per element
-│   ├── element_1.md  # Table fully extracted
-│   ├── element_2.md  # Figure analyzed
+├── images/                    # All extracted visuals
+├── classifications/           # Phase 1: type detection
+│   ├── element_001_class.json
+│   └── ...
+├── extractions/              # Phase 2: JSON extractions
+│   ├── element_001.json
+│   └── ...
+├── verifications/            # Phase 3: quality scores
+│   ├── element_001_verify.json
 │   └── ...
-└── STRUCTURED.md     # Everything combined
+├── elements/                 # Markdown per element
+│   ├── element_001.md
+│   └── ...
+├── STRUCTURED.md             # Combined output
+└── extraction_report.json    # Quality metrics summary
+```
+
+### Quality Report
+
+```json
+{
+  "document": "clinical_trial.pdf",
+  "pipeline_version": "2.0.0",
+  "elements_total": 15,
+  "elements_passed": 13,
+  "elements_revised": 2,
+  "elements_human_review": 0,
+  "average_quality_score": 0.92
+}
 ```
 
 ### Example: Table Extraction
@@ -196,40 +252,52 @@ document_extracted/
 **Type:** Table
 **Source:** Page 3, clinical_trial.pdf
 
-## Content
+## Data
 
-| Group | N | Age (mean±SD) | Male (%) |
-|-------|---|---------------|----------|
-| Treatment | 245 | 54.3±12.1 | 58.4 |
-| Placebo | 248 | 53.8±11.9 | 56.9 |
-| p-value | - | 0.67 | 0.73 |
+| Characteristic | Treatment (n=245) | Placebo (n=248) | P-value |
+|---|---|---|---|
+| Age, years | 54.3 ± 12.1 | 53.8 ± 11.9 | 0.67 |
+| Male (%) | 58.4 | 56.9 | 0.73 |
+| BMI (kg/m²) | 28.7 ± 4.2 | 28.4 ± 4.1 | 0.42 |
 
-## Notes
-- Confidence level: High
+## Footnotes
 - * Missing data excluded from analysis
+- † Adjusted for baseline
 ```
 
-### Example: Chart Analysis
+### Example: Kaplan-Meier Extraction
 
 ```markdown
 # Kaplan-Meier Survival Curves
 
-**Type:** Chart (Line/Survival)
+**Type:** kaplan_meier
 **Source:** Page 7, clinical_trial.pdf
 
-## Content
+## Axes
+
+- **X-axis:** Time (Days) Since HSV Diagnosis
+  - Range: 0 to 7000
+- **Y-axis:** Cumulative Risk of Dementia
+  - Range: 0 to 0.6
+
+## Legend
+
+- **HSV: Dementia Risk**: purple solid
+- **Control: Dementia Risk**: dark blue solid
+- **HSV: Dementia Risk 95% CI**: light purple shaded area
+- **Control: Dementia Risk 95% CI**: light orange shaded area
 
-Survival curves comparing treatment (blue) vs placebo (red) over 24 months.
+## Statistical Annotations
 
-Key data points:
-- 12-month survival: Treatment 0.89, Placebo 0.78
-- 24-month survival: Treatment 0.76, Placebo 0.61
-- Log-rank p = 0.003
+- p_value: < 0.001
+- hazard_ratio: 1.52 (95% CI: 1.38-1.68)
 
-## Labels & Annotations
-- Y-axis: "Survival Probability"
-- X-axis: "Time (months)"
-- Legend: "Treatment (n=245)", "Placebo (n=248)"
+## Risk Table
+
+| Time (days) | 0 | 1000 | 2000 | 3000 | 4000 | 5000 | 6000 | 7000 |
+|---|---|---|---|---|---|---|---|---|
+| HSV | 8,362 | 7,891 | 6,543 | 5,102 | 3,876 | 2,654 | 1,432 | 521 |
+| Control | 41,810 | 39,765 | 33,421 | 26,543 | 19,876 | 13,543 | 7,654 | 2,876 |
 ```
 
 ---
@@ -238,11 +306,14 @@ Key data points:
 
 | Document | Elements | ~Cost |
 |----------|----------|-------|
-| Simple paper | 5-10 | $0.50-$1 |
-| Full paper | 15-25 | $2-$4 |
-| Dense report | 40+ | $5-$10 |
+| Simple paper | 5-10 | $1-$2 |
+| Full paper | 15-25 | $3-$6 |
+| Dense report | 40+ | $8-$15 |
 
-Uses Claude's multimodal vision. Works best with **Opus 4.5** for complex tables and charts.
+Uses Claude's multimodal vision with model-appropriate routing:
+- **Haiku** for classification (fast, cheap)
+- **Opus** for extraction (highest quality)
+- **Sonnet** for verification (balanced)
 
 ---
 
@@ -268,6 +339,10 @@ You typed `/structure` in your regular terminal. You need to type it inside Clau
 
 Make sure your PDF contains actual images, not just text. Some PDFs render everything as text.
 
+**Low quality scores**
+
+Check `verifications/` for specific issues. Complex tables or poor image quality may need human review.
+
 **Claude Code asks for an API key**
 
 Either get an API key at [console.anthropic.com](https://console.anthropic.com/), or subscribe to Claude Pro/Max at [claude.ai](https://claude.ai/).
@@ -282,6 +357,18 @@ npx structurecc --uninstall
 
 ---
 
+## Upgrade from v1.x
+
+Just run the installer again:
+
+```bash
+npx structurecc
+```
+
+The installer automatically removes the old `structurecc-extractor` and installs the new 8-agent pipeline.
+
+---
+
 ## License
 
 MIT
@@ -289,5 +376,5 @@ MIT
 ---
 
 <p align="center">
-<strong>Unstructured in. Structured out.</strong>
+<strong>Verbatim in. Quality verified out.</strong>
 </p>

package/agents/structurecc-classifier.md

@@ -0,0 +1,135 @@
+---
+name: structurecc-classifier
+description: Phase 1 - Classify visual elements for specialized extraction
+---
+
+# Visual Element Classifier
+
+You are a rapid visual classifier. Your ONLY job is to identify what type of visual element an image contains so the correct specialized extractor can be dispatched.
+
+## Classification Task
+
+Given an image, output a JSON classification. Nothing else.
+
+## Classification Types
+
+| Type | Description |
+|------|-------------|
+| `table_simple` | Standard grid table with clear rows/columns, no merged cells |
+| `table_complex` | Table with merged cells, nested headers, or irregular structure |
+| `chart_kaplan_meier` | Survival curves / time-to-event plots with step functions |
+| `chart_bar` | Bar charts (horizontal or vertical), grouped or stacked |
+| `chart_line` | Line graphs showing trends over continuous x-axis |
+| `chart_scatter` | Scatter plots with individual data points |
+| `chart_box` | Box plots / whisker plots showing distributions |
+| `chart_pie` | Pie charts or donut charts |
+| `chart_area` | Area charts (filled line charts) |
+| `chart_forest` | Forest plots (meta-analysis results) |
+| `chart_volcano` | Volcano plots (differential expression) |
+| `heatmap` | Color-coded matrix (correlation, expression, etc.) |
+| `diagram_flowchart` | Process flows with boxes and arrows |
+| `diagram_timeline` | Temporal sequences, study timelines, CONSORT diagrams |
+| `diagram_network` | Network graphs, pathway diagrams, interaction maps |
+| `diagram_schematic` | Technical schematics, anatomical diagrams |
+| `diagram_venn` | Venn diagrams showing set overlaps |
+| `multi_panel` | Composite figure with labeled panels (A, B, C, D) |
+| `photograph` | Real-world photographs, microscopy images, scans |
+| `equation` | Mathematical equations, formulas |
+| `text_block` | Text-heavy image, caption, or label |
+| `unknown` | Cannot confidently classify |
+
+## Output Format
+
+Return ONLY valid JSON:
+
+```json
+{
+  "classification": {
+    "primary_type": "chart_kaplan_meier",
+    "confidence": 0.95,
+    "secondary_type": null,
+    "is_multi_panel": false,
+    "panel_count": 1,
+    "contains_table": false,
+    "contains_text_annotations": true
+  },
+  "routing": {
+    "extractor": "structurecc-extract-chart",
+    "extraction_hints": ["survival_curve", "two_groups", "has_risk_table"]
+  }
+}
+```
+
+## Field Definitions
+
+### classification
+- `primary_type`: Main visual type from the table above
+- `confidence`: 0.0-1.0 confidence in classification
+- `secondary_type`: If image contains a secondary element (e.g., chart with embedded table)
+- `is_multi_panel`: True if figure has labeled sub-panels (A, B, C...)
+- `panel_count`: Number of panels if multi-panel
+- `contains_table`: True if any tabular data is present
+- `contains_text_annotations`: True if significant text labels/annotations present
+
+### routing
+- `extractor`: Which specialized extractor to use
+- `extraction_hints`: List of specific features to watch for
+
+## Extractor Routing
+
+| Primary Type | Extractor |
+|--------------|-----------|
+| `table_simple`, `table_complex` | `structurecc-extract-table` |
+| `chart_*` | `structurecc-extract-chart` |
+| `heatmap` | `structurecc-extract-heatmap` |
+| `diagram_*` | `structurecc-extract-diagram` |
+| `multi_panel` | `structurecc-extract-multipanel` |
+| `photograph`, `equation`, `text_block`, `unknown` | `structurecc-extract-generic` |
+
+## Rules
+
+1. **Be fast** - This is a triage step, not deep analysis
+2. **Be decisive** - Pick the best match, use confidence to express uncertainty
+3. **Detect multi-panel** - If you see A, B, C, D labels, set `is_multi_panel: true`
+4. **Note secondary elements** - Charts often have risk tables, legends, etc.
+5. **Output ONLY JSON** - No explanations, no markdown, just the JSON object
+
+## Examples
+
+**Kaplan-Meier curve with risk table below:**
+```json
+{
+  "classification": {
+    "primary_type": "chart_kaplan_meier",
+    "confidence": 0.98,
+    "secondary_type": "table_simple",
+    "is_multi_panel": false,
+    "panel_count": 1,
+    "contains_table": true,
+    "contains_text_annotations": true
+  },
+  "routing": {
+    "extractor": "structurecc-extract-chart",
+    "extraction_hints": ["survival_curve", "has_risk_table", "has_confidence_intervals"]
+  }
+}
+```
+
+**Four-panel figure with A=bar chart, B=heatmap, C=box plot, D=table:**
+```json
+{
+  "classification": {
+    "primary_type": "multi_panel",
+    "confidence": 0.99,
+    "secondary_type": null,
+    "is_multi_panel": true,
+    "panel_count": 4,
+    "contains_table": true,
+    "contains_text_annotations": true
+  },
+  "routing": {
+    "extractor": "structurecc-extract-multipanel",
+    "extraction_hints": ["panel_A_bar", "panel_B_heatmap", "panel_C_boxplot", "panel_D_table"]
+  }
+}
+```