8.2 KiB

Raw Blame History

Bone Quality Assessment Project

Project Overview

Medical AI service for automated assessment of DXA (bone densitometry) study quality. The system analyzes DICOM files and evaluates quality based on standard criteria.

Core Purpose (Hackathon)

Analyze DICOM densitometry studies
Determine anatomical region (spine/hip)
Binary classification: quality (OK/violation)
Detailed violation type detection (motion, artifacts, position, ROI)
Output results in XLSX/CSV format per requirements

Tech Stack

Component	Technology
Backend	Python 3.10, FastAPI, Uvicorn
ML/Deep Learning	PyTorch, torchvision (ResNet18)
Image Processing	PIL, OpenCV, pydicom, scipy
Data Handling	pandas, openpyxl
Containerization	Docker

Project Structure

bone_2026/
├── src/
│   ├── main.py                    # FastAPI app (DXA mode)
│   ├── run.py                     # Server runner
│   ├── dxa/                       # DXA Quality module
│   │   ├── dataset.py            # DXADataset class
│   │   ├── model.py              # ResNet18 classifier
│   │   ├── train.py              # Training script
│   │   ├── inference.py          # Batch inference
│   │   └── __init__.py
│   ├── api/                       # REST endpoints & schemas
│   │   ├── endpoints.py          # Original endpoints
│   │   └── static/               # Web UI
│   │       ├── index.html
│   │       └── js/dxa-app.js
│   ├── core/                     # Orchestrator
│   ├── quality/                  # Quality scoring
│   │   ├── quality_scorer.py     # Base scorer
│   │   ├── detailed_assessment.py # NEW: Detailed assessment
│   │   ├── position_validator.py
│   │   └── artifact_detector.py
│   └── segmentators/             # Segmentation models
├── models/
│   └── dxa_model.pth             # Trained DXA classifier
├── dataset_hack/                  # DICOM datasets
│   ├── Для теста/                # Test data
│   └── НД_для_обучения/         # Training data
├── requirements.txt
├── Dockerfile
├── run.sh
└── README.md

Implemented Features (Current)

✅ API Endpoints

Method	Endpoint	Description
GET	`/`	Web interface
GET	`/api/v1/health`	Health check
POST	`/api/v1/analyze`	Basic analysis
POST	`/api/v1/analyze/detailed`	NEW: Detailed analysis with metrics
POST	`/api/v1/analyze/sr`	NEW: DICOM SR report
POST	`/api/v1/batch`	Batch processing
POST	`/api/v1/export`	Export to XLSX

✅ Detailed Assessment (`src/quality/detailed_assessment.py`)

Motion detection: Laplacian variance, FFT blur analysis
Artifact detection: Metal, implants, cement, calcifications
Spine completeness: Vertebrae count, alignment, spacing
Hip completeness: Full visibility, aspect ratio
Hip rotation: Major axis angle calculation
ROI validation: Boundary check, margin, size
Violation types: correct, position_error, artifact_motion, artifact_other, labeling_error, incomplete_view, roi_error, rotation

✅ Web Interface

Drag-and-drop DICOM upload
Table with results (filter, sort, search)
NEW: Detail panel - click on row to see:
- Violation type
- Reason (human-readable)
- Motion metrics
- Artifact detection
- ROI validation

DXA Module (`src/dxa/`)

Dataset (`dataset.py`)

Loads DICOM files from studies
Parses annotation Excel file
Automatically detects anatomical region from image content
Maps regions: spine, hip_right, hip_left
Quality labels: 0 (OK), 1 (violation)

Model (`model.py`)

Architecture: ResNet18 (pretrained on ImageNet)
Task: Binary classification (quality OK vs violation)
Input: 224x224 RGB images
Output: class probabilities

Training (`train.py`)

python src/dxa/train.py --epochs 10 --batch-size 16

Inference (`inference.py`)

python src/dxa/inference.py \
    --input-path dataset_hack/Для\ теста \
    --output-path results.xlsx \
    --model-path models/dxa_model.pth

Running the Project

Training

python src/dxa/train.py --epochs 10

Inference

python src/dxa/inference.py --input-path file.dcm --output-path result.xlsx

API Server

python -m uvicorn src.main:app --host 0.0.0.0 --port 8000

Web UI: http://localhost:8000

Output Format (per Hackathon Requirements)

Basic Output

Column	Description
path_to_study	Path to study directory
study_uid	StudyInstanceUID from DICOM
image_uid	SOPInstanceUID from DICOM
anatomical_region	spine / hip_left / hip_right / hip
quality_class	0 (OK), 1 (violation)
violation_type	Type of violation (if any)
processing_status	Success / Failure
time_of_processing	Processing time (seconds)

Detailed Output (/api/v1/analyze/detailed)

{
  "anatomical_region": "spine",
  "quality_class": 1,
  "quality_label": "Violation detected",
  "violation_type": "artifact_motion",
  "reason": "Обнаружен артефакт движения (размытие)",
  "confidence": 0.85,
  "confidence_per_class": {
    "correct": 0.15,
    "violation": 0.85
  },
  "view_quality": "full",
  "metrics": {
    "motion": { "motion_detected": true, "severity": "HIGH" },
    "artifacts": { "any_detected": true, "metal_detected": false },
    "roi_check": { "valid": true }
  },
  "overall_quality": "POOR",
  "severity": "HIGH"
}

Anatomical Region Detection

The system automatically determines the anatomical region from the DICOM image content:

Algorithm (`src/dxa/inference.py`)

Spine vs Hip - by bright region shape:
- Extract 95th percentile threshold
- Calculate bounding box aspect ratio
- Spine: bbox_aspect < 1.5 (more square)
- Hip: bbox_aspect > 1.5 (vertically elongated)
Hip Left vs Right - by brightness asymmetry:
- Calculate left/right bright pixel ratio
- hip_left: L/R ratio < 0.7 (left side brighter)
- hip_right: L/R ratio > 1.3 (right side brighter)
- hip: unclear (fallback)

Known Issues & Limitations

Model training - Needs retraining with new violation types
Dataset size - Currently ~100 studies, needs 500+
Segmentation - Uses simple threshold, needs proper model
F1 score - Currently ~0.27, needs improvement with weighted loss
Heatmap visualization - Not implemented (requires model retraining)

Multi-Model Architecture (Planned)

See docs/multi_model_architecture.md for the planned pipeline:

Pipeline:
1. Region Detector → 2. Segmentator → 3. Quality Classifier → 4. Violation Type → 5. Aggregator

Planned Models:

Model	Purpose	File
Region Detector	Spine/Hip detection	`src/models/region_detector.py`
Segmentator	Bone segmentation	`src/models/segmentation/`
Quality Classifier	OK/Violation binary	`src/models/classification/quality.py`
Violation Classifier	7+ violation types	`src/models/classification/violation.py`
Artifact Detector	Motion, metal detection	`src/models/artifacts/detector.py`
Grad-CAM	Attention heatmap	`src/models/visualization/gradcam.py`

Docker

docker build -t dxa-quality .
docker run -v /data:/data -p 8000:8000 dxa-quality

Development Notes

Code Style

Follow existing patterns in src/
Type hints where appropriate
Minimal comments (only for context)

Key Components

DXADataset: Handles DICOM loading + annotation parsing
DXAQualityClassifier: ResNet18-based classifier
process_dicom_files: Batch inference with XLSX output
generate_quality_report: Detailed assessment with metrics

Dependencies

All in requirements.txt:

torch, torchvision - Deep learning
pydicom - DICOM handling
pandas, openpyxl - Data/Excel
fastapi, uvicorn - Web framework
Pillow, opencv-python-headless - Image processing
scipy - Image analysis (blur, artifacts)

8.2 KiB Raw Blame History Unescape Escape