feat: Enhance dashboard with charts, study report viewer, and pruning tracking

- Add ConvergencePlot component with running best, statistics, gradient fill - Add ParameterImportanceChart with Pearson correlation analysis - Add StudyReportViewer with KaTeX math rendering and full markdown support - Update pruning endpoint to query Optuna database directly - Add /report endpoint for STUDY_REPORT.md files - Fix chart data transformation for single/multi-objective studies - Update Protocol 13 documentation with new components - Update generate-report skill with dashboard integration 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
2025-12-02 22:01:49 -05:00
parent ec5e42d733
commit 75d7036193
10 changed files with 2917 additions and 66 deletions
--- a/docs/04_USER_GUIDES/DASHBOARD.md
+++ b/docs/04_USER_GUIDES/DASHBOARD.md
@@ -1,6 +1,6 @@
 # Atomizer Dashboard

-**Last Updated**: November 23, 2025
+**Last Updated**: December 3, 2025

 ---

@@ -83,23 +83,50 @@ Displays algorithm information:
 - **Objectives Count**: Number of optimization objectives
 - **Design Variables Count**: Number of design parameters

-### 3. Convergence Monitoring
- **Convergence Plot**: Best value vs. trial number
- **Real-time Updates**: WebSocket-driven live updates
- **Pruned Trials**: Visual indication of pruned trials
+### 3. Convergence Plot (Enhanced)
+**File**: `atomizer-dashboard/frontend/src/components/ConvergencePlot.tsx`

-### 4. Parameter Space Exploration
- **2D Scatter Plot**: Design variable relationships
- **Color Mapping**: Objective values mapped to color intensity
- **Interactive Tooltips**: Trial details on hover
+Advanced convergence visualization:
+- **Dual-line plot**: Individual trial values + running best trajectory
+- **Area fill**: Gradient under trial values curve
+- **Statistics panel**: Best value, improvement %, 90% convergence trial
+- **Summary footer**: First value, mean, std dev, total trials
+- **Step-after interpolation**: Running best shown as step function

-### 5. Trial History Table
+### 4. Parameter Importance Chart
+**File**: `atomizer-dashboard/frontend/src/components/ParameterImportanceChart.tsx`
+
+Correlation-based parameter analysis:
+- **Pearson correlation**: Calculates correlation between each parameter and objective
+- **Horizontal bar chart**: Parameters ranked by absolute importance
+- **Color coding**: Green (negative correlation - helps minimize), Red (positive - hurts minimize)
+- **Tooltip**: Shows percentage importance and raw correlation coefficient (r)
+- **Minimum 3 trials**: Required for statistical significance
+
+### 5. Study Report Viewer
+**File**: `atomizer-dashboard/frontend/src/components/StudyReportViewer.tsx`
+
+Full-featured markdown report viewer:
+- **Modal overlay**: Full-screen report viewing
+- **Math equations**: KaTeX support for LaTeX math (`$...$` inline, `$$...$$` block)
+- **GitHub-flavored markdown**: Tables, code blocks, task lists
+- **Custom styling**: Dark theme with proper typography
+- **Syntax highlighting**: Code blocks with language detection
+- **Refresh button**: Re-fetch report for live updates
+- **External link**: Open in system editor
+
+### 6. Trial History Table
 - Comprehensive list of all trials
 - Sortable columns
 - Status indicators (COMPLETE, PRUNED, FAIL)
 - Parameter values and objective values
 - User attributes (constraints)

+### 7. Pruned Trials Tracking
+- **Real-time count**: Fetched directly from Optuna database
+- **Pruning diagnostics**: Tracks pruned trial params and causes
+- **Database query**: Uses SQLite `state = 'PRUNED'` filter
+
 ---

 ## API Endpoints
@@ -286,6 +313,9 @@ atomizer-dashboard/
 │   │   │   ├── ParallelCoordinatesPlot.tsx    # Multi-objective visualization
 │   │   │   ├── ParetoPlot.tsx                  # Pareto front scatter plot
 │   │   │   ├── OptimizerPanel.tsx              # Strategy information
+│   │   │   ├── ConvergencePlot.tsx             # Enhanced convergence chart
+│   │   │   ├── ParameterImportanceChart.tsx    # Correlation-based importance
+│   │   │   ├── StudyReportViewer.tsx           # Markdown report viewer
 │   │   │   ├── common/
 │   │   │   │   └── Card.tsx                    # Reusable card component
 │   │   │   └── dashboard/
@@ -307,6 +337,15 @@ atomizer-dashboard/
            └── optimization.py                  # Optimization endpoints
 ```

+## NPM Dependencies
+
+The frontend uses these key packages:
+- `react-markdown` - Markdown rendering
+- `remark-gfm` - GitHub-flavored markdown support
+- `remark-math` - Math equation parsing
+- `rehype-katex` - KaTeX math rendering
+- `recharts` - Interactive charts
+
 ---

 ## Data Flow
@@ -368,7 +407,16 @@ if (!objectives || !designVariables) return <EmptyState />;

 ---

-## Future Enhancements
+## Recent Updates (December 2025)
+
+### Completed
+- [x] **Convergence Plot**: Enhanced with running best, statistics, and gradient fill
+- [x] **Parameter Importance Chart**: Correlation analysis with color-coded bars
+- [x] **Study Report Viewer**: Full markdown rendering with KaTeX math support
+- [x] **Pruned Trials**: Real-time count from Optuna database (not JSON file)
+- [x] **Chart Data Transformation**: Fixed `values` array mapping for single/multi-objective
+
+### Future Enhancements

 - [ ] 3D Pareto front visualization for 3+ objectives
 - [ ] Advanced filtering and search in trial history
--- a/docs/06_PROTOCOLS_DETAILED/protocol_13_dashboard.md
+++ b/docs/06_PROTOCOLS_DETAILED/protocol_13_dashboard.md
@@ -1,7 +1,7 @@
 # Protocol 13: Real-Time Dashboard Tracking

-**Status**: ✅ COMPLETED
-**Date**: November 21, 2025
+**Status**: ✅ COMPLETED (Enhanced December 2025)
+**Date**: November 21, 2025 (Last Updated: December 3, 2025)
 **Priority**: P1 (Critical)

 ## Overview
@@ -130,7 +130,39 @@ Stiffness    Mass    support_angle    tip_thickness
   |  ╱                  ╲                  |
 ```

-#### 4. Dashboard Integration
+#### 4. ConvergencePlot Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/ConvergencePlot.tsx`
+
+**Features**:
+- Dual-line visualization: trial values + running best
+- Area fill gradient under trial curve
+- Statistics header: Best value, Improvement %, 90% convergence trial
+- Summary footer: First value, Mean, Std Dev, Total trials
+- Step-after interpolation for running best line
+- Reference line at best value
+
+#### 5. ParameterImportanceChart Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/ParameterImportanceChart.tsx`
+
+**Features**:
+- Pearson correlation between parameters and objectives
+- Horizontal bar chart sorted by absolute importance
+- Color coding: Green (negative correlation), Red (positive correlation)
+- Tooltip with percentage and raw correlation coefficient
+- Requires minimum 3 trials for statistical analysis
+
+#### 6. StudyReportViewer Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/StudyReportViewer.tsx`
+
+**Features**:
+- Full-screen modal for viewing STUDY_REPORT.md
+- KaTeX math equation rendering (`$...$` inline, `$$...$$` block)
+- GitHub-flavored markdown (tables, code blocks, task lists)
+- Custom dark theme styling for all markdown elements
+- Refresh button for live updates
+- External link to open in system editor
+
+#### 7. Dashboard Integration
 **File**: `atomizer-dashboard/frontend/src/pages/Dashboard.tsx`

 **Layout Structure**:
@@ -292,6 +324,28 @@ npm run dev  # Runs on port 3001
 - **Real-time writes**: <5ms per trial (JSON serialization)
 - **Dashboard load time**: <500ms initial render

+## December 2025 Enhancements
+
+### Completed
+- [x] **ConvergencePlot**: Enhanced with running best, statistics panel, gradient fill
+- [x] **ParameterImportanceChart**: Pearson correlation analysis with color-coded bars
+- [x] **StudyReportViewer**: Full markdown rendering with KaTeX math equation support
+- [x] **Pruning endpoint**: Now queries Optuna SQLite directly instead of JSON file
+- [x] **Report endpoint**: New `/studies/{id}/report` endpoint for STUDY_REPORT.md
+- [x] **Chart data fix**: Proper `values` array transformation for single/multi-objective
+
+### API Endpoint Additions (December 2025)
+
+4. **GET `/api/optimization/studies/{study_id}/pruning`** (Enhanced)
+   - Now queries Optuna database directly for PRUNED trials
+   - Returns params, timing, and pruning cause for each trial
+   - Fallback to legacy JSON file if database unavailable
+
+5. **GET `/api/optimization/studies/{study_id}/report`** (NEW)
+   - Returns STUDY_REPORT.md content as JSON
+   - Searches in 2_results/, 3_results/, and study root
+   - Returns 404 if no report found
+
 ## Future Enhancements (P3)

 - [ ] WebSocket support for instant updates (currently polling)
@@ -300,7 +354,6 @@ npm run dev  # Runs on port 3001
 - [ ] Strategy performance comparison charts
 - [ ] Historical phase duration analysis
 - [ ] Mobile-responsive design
- [ ] Dark/light theme toggle

 ## Troubleshooting