Initial commit: BIDS neuroimaging viewer

.gitattributes

@@ -15,7 +15,6 @@
 *.npz filter=lfs diff=lfs merge=lfs -text
 *.onnx filter=lfs diff=lfs merge=lfs -text
 *.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
 *.pb filter=lfs diff=lfs merge=lfs -text
 *.pickle filter=lfs diff=lfs merge=lfs -text
 *.pkl filter=lfs diff=lfs merge=lfs -text
@@ -33,3 +32,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+data/train/train-00000-of-00010.parquet filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.13-slim
+
+WORKDIR /app
+
+# Install git (needed for git+ URLs in requirements.txt)
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+
+# Copy requirements first for better caching
+COPY requirements.txt .
+COPY data/ data/
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy application files
+COPY main.py .
+
+EXPOSE 7680
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "7680"]

Makefile

@@ -0,0 +1,5 @@
+build_container:
+	docker build -t bids-neuroimaging .
+
+run_container:
+	docker run --rm -p 7680:7680 bids-neuroimaging

README.md

@@ -9,4 +9,60 @@ license: cc-by-4.0
 short_description: Visualize  Aphasia Recovery Cohort (ARC) Dataset - Mini Samp
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# BIDS Neuroimaging Viewer
+
+A FastAPI-based web application for visualizing neuroimaging data in BIDS format using NiiVue.
+
+## Installation
+
+1. Clone the repository:
+```bash
+git clone <your-repo-url>
+cd bids-neuroimaging
+```
+
+2. Create a virtual environment and install dependencies:
+```bash
+python -m venv .venv
+source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+pip install -r requirements.txt
+```
+
+3. Install the custom datasets fork with BIDS loader:
+```bash
+pip install git+https://github.com/The-Obstacle-Is-The-Way/datasets.git@feat/bids-loader
+```
+
+## Running the Application
+
+Start the FastAPI server with:
+
+```bash
+fastapi dev main.py
+```
+
+Or using uvicorn directly:
+
+```bash
+uvicorn main:app --reload --host 0.0.0.0 --port 8000
+```
+
+Then open your browser and navigate to:
+- **Main viewer**: http://localhost:8000
+- **Health check**: http://localhost:8000/health
+
+## Features
+
+- Interactive 3D visualization of NIfTI files using NiiVue
+- Multiple viewing modes: Multiplanar + 3D, and 3D Render Only
+- Next button to iterate through dataset samples (implement the `/next` endpoint)
+
+## Development
+
+The main application is in `main.py`. To implement the "Next" functionality:
+1. Modify the `/next` endpoint in `main.py` to load and return the next sample
+2. The endpoint should return a JSON with the base64-encoded NIfTI data
+
+## Configuration Reference
+
+For Hugging Face Spaces deployment, check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

data/train/train-00000-of-00010.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:986b9d3b0614d4283a97301e8495ae5cf67968f28c6f85ce46e178fd5bfb1bd2
+size 406159346

main.py

@@ -0,0 +1,484 @@
+from fastapi import FastAPI
+from fastapi.responses import HTMLResponse
+from datasets import load_dataset
+import base64
+import asyncio
+from contextlib import asynccontextmanager
+
+ds_iter = None
+first_sample = None
+nifti_base_url = "data:application/octet-stream;base64,{}"
+initial_metadata = {}
+num_iterations = 0
+
+async def load_dataset_async():
+    global ds_iter
+    dataset = load_dataset("TobiasPitters/ds004884-mini", streaming=True)
+    ds_iter = iter(dataset["train"])
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    global first_sample, initial_metadata
+
+    asyncio.create_task(load_dataset_async())
+
+    yield
+
+app = FastAPI(title="BIDS Neuroimaging Viewer", lifespan=lifespan)
+
+@app.get("/", response_class=HTMLResponse)
+async def root():
+    """Main page with NiiVue viewer"""
+    html_content = f"""<!DOCTYPE html>
+<html>
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>BIDS Neuroimaging Viewer</title>
+    <style>
+        * {{
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }}
+        body {{
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif;
+            background: #1a1a1a;
+            color: #fff;
+        }}
+        .header {{
+            background: #2d2d2d;
+            padding: 20px;
+            border-bottom: 2px solid #3498db;
+        }}
+        .header h1 {{
+            margin: 0;
+            color: #3498db;
+        }}
+        .container {{
+            max-width: 1400px;
+            margin: 0 auto;
+            padding: 20px;
+        }}
+        .main-content {{
+            display: flex;
+            gap: 20px;
+        }}
+        .viewer-section {{
+            flex: 1;
+            min-width: 0;
+        }}
+        .metadata-section {{
+            width: 300px;
+            flex-shrink: 0;
+        }}
+        .metadata-card {{
+            background: #2d2d2d;
+            border-radius: 8px;
+            padding: 20px;
+            position: sticky;
+            top: 20px;
+        }}
+        .metadata-card h3 {{
+            margin: 0 0 15px 0;
+            color: #3498db;
+            font-size: 18px;
+        }}
+        .metadata-item {{
+            margin-bottom: 12px;
+            padding-bottom: 12px;
+            border-bottom: 1px solid #404040;
+        }}
+        .metadata-item:last-child {{
+            border-bottom: none;
+            margin-bottom: 0;
+            padding-bottom: 0;
+        }}
+        .metadata-label {{
+            font-size: 11px;
+            text-transform: uppercase;
+            color: #888;
+            letter-spacing: 0.5px;
+            margin-bottom: 4px;
+        }}
+        .metadata-value {{
+            font-size: 14px;
+            color: #fff;
+            word-break: break-word;
+        }}
+        .viewer-container {{
+            width: 100%;
+            height: 80vh;
+            min-height: 600px;
+            position: relative;
+            background: #000;
+            border-radius: 8px;
+            overflow: hidden;
+        }}
+        #niivue-canvas {{
+            width: 100%;
+            height: 100%;
+            display: block;
+        }}
+        #status {{
+            position: absolute;
+            top: 10px;
+            left: 10px;
+            background: rgba(0, 0, 0, 0.8);
+            color: #fff;
+            font: 14px monospace;
+            padding: 10px 15px;
+            border-radius: 5px;
+            z-index: 100;
+        }}
+        .info {{
+            margin-top: 20px;
+            padding: 15px;
+            background: #2d2d2d;
+            border-radius: 5px;
+        }}
+        .tabs {{
+            display: flex;
+            gap: 10px;
+            margin-bottom: 20px;
+            border-bottom: 2px solid #3498db;
+        }}
+        .tab {{
+            padding: 12px 24px;
+            background: #2d2d2d;
+            border: none;
+            color: #fff;
+            cursor: pointer;
+            font-size: 16px;
+            border-radius: 8px 8px 0 0;
+            transition: all 0.3s;
+        }}
+        .tab:hover {{
+            background: #3d3d3d;
+        }}
+        .tab.active {{
+            background: #3498db;
+            color: #fff;
+        }}
+        .controls {{
+            display: flex;
+            gap: 10px;
+            margin-top: 20px;
+        }}
+        .btn {{
+            padding: 12px 32px;
+            background: #3498db;
+            border: none;
+            color: #fff;
+            cursor: pointer;
+            font-size: 16px;
+            border-radius: 5px;
+            transition: all 0.3s;
+            font-weight: 600;
+        }}
+        .btn:hover {{
+            background: #2980b9;
+            transform: translateY(-2px);
+            box-shadow: 0 4px 8px rgba(52, 152, 219, 0.3);
+        }}
+        .btn:active {{
+            transform: translateY(0);
+        }}
+    </style>
+</head>
+<body>
+    <div class="header">
+        <h1>🧠 BIDS Neuroimaging Viewer</h1>
+        <p>Aphasia Recovery Cohort (ARC) Dataset - Mini Sample</p>
+    </div>
+
+    <div class="container">
+        <div class="main-content">
+            <div class="viewer-section">
+                <div class="tabs">
+                    <button class="tab active" id="tab-multiplanar">Multiplanar + 3D</button>
+                    <button class="tab" id="tab-render3d">3D Render Only</button>
+                </div>
+
+                <div class="viewer-container">
+                    <canvas id="niivue-canvas"></canvas>
+                    <div id="status">Loading NiiVue...</div>
+                </div>
+
+                <div class="controls">
+                    <button class="btn" id="next-btn">Next</button>
+                </div>
+
+                <div class="info">
+                    <h3 id="info-title">Controls:</h3>
+                    <ul id="info-list">
+                        <li><strong>Slice views (3 panels):</strong> Click to move crosshair, drag to pan, scroll to zoom</li>
+                        <li><strong>3D view (bottom-right):</strong> Left-click drag to rotate, scroll to zoom</li>
+                    </ul>
+                </div>
+            </div>
+
+            <div class="metadata-section">
+                <div class="metadata-card">
+                    <h3>Sample Info</h3>
+                    <div id="metadata-content">
+                        <div class="metadata-item">
+                            <div class="metadata-label">Loading...</div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+
+    <script type="module">
+    let nv;
+
+    function updateMetadata(metadata) {{
+        const metadataContent = document.getElementById('metadata-content');
+        const fields = ['subject', 'session', 'datatype', 'suffix', 'task', 'run'];
+
+        metadataContent.innerHTML = fields.map(field => `
+            <div class="metadata-item">
+                <div class="metadata-label">${{field}}</div>
+                <div class="metadata-value">${{metadata[field] || 'N/A'}}</div>
+            </div>
+        `).join('');
+    }}
+
+    function switchView(mode, clickedElement) {{
+        if (!nv) return; // Not initialized yet
+
+        // Update tab styles
+        if (clickedElement) {{
+            document.querySelectorAll('.tab').forEach(tab => tab.classList.remove('active'));
+            clickedElement.classList.add('active');
+        }}
+
+        // Switch view mode
+        if (mode === 'multiplanar') {{
+            nv.setSliceType(nv.sliceTypeMultiplanar);
+            if (nv.setMultiplanarLayout) {{
+                nv.setMultiplanarLayout(2);
+            }}
+            nv.opts.show3Dcrosshair = true;
+
+            document.getElementById('info-list').innerHTML = `
+                <li><strong>Slice views (3 panels):</strong> Click to move crosshair, drag to pan, scroll to zoom</li>
+                <li><strong>3D view (bottom-right):</strong> Left-click drag to rotate, right-click drag to pan, scroll to zoom</li>
+                <li><strong>Double click:</strong> Reset view</li>
+            `;
+        }} else if (mode === 'render3d') {{
+            nv.setSliceType(nv.sliceTypeRender);
+
+            // Enable clip plane in 3D render
+            nv.setClipPlane([0, 270, 0]);  // Show clipping plane
+            nv.opts.clipPlaneHotKey = 'c';  // Press 'c' to toggle clip plane
+
+            document.getElementById('info-list').innerHTML = `
+                <li><strong>Left click + drag:</strong> Rotate the 3D volume</li>
+                <li><strong>Right click + drag:</strong> Pan/move</li>
+                <li><strong>Mouse wheel:</strong> Adjust clip plane depth</li>
+            `;
+        }}
+
+        nv.drawScene();
+    }}
+
+    // Setup tab event listeners
+    document.getElementById('tab-multiplanar').addEventListener('click', function() {{
+        switchView('multiplanar', this);
+    }});
+
+    document.getElementById('tab-render3d').addEventListener('click', function() {{
+        switchView('render3d', this);
+    }});
+
+    // Next button handler
+    document.getElementById('next-btn').addEventListener('click', async function() {{
+        if (!nv) {{
+            alert('Viewer not initialized yet');
+            return;
+        }}
+
+        const statusEl = document.getElementById('status');
+        try {{
+            statusEl.style.display = 'block';
+            statusEl.textContent = 'Loading next sample...';
+            statusEl.style.background = 'rgba(0, 0, 0, 0.8)';
+
+            const response = await fetch('/next');
+            const data = await response.json();
+
+            if (data.status === 'error') {{
+                statusEl.textContent = 'Error: ' + data.message;
+                statusEl.style.background = 'rgba(160, 0, 0, 0.8)';
+                setTimeout(() => {{ statusEl.style.display = 'none'; }}, 3000);
+                return;
+            }}
+
+            console.log('Loading next sample...');
+            await nv.loadVolumes([{{
+                url: data.data_url,
+                name: 'volume.nii.gz'
+            }}]);
+
+            // Update metadata
+            updateMetadata(data.metadata);
+
+            nv.drawScene();
+            statusEl.style.display = 'none';
+            console.log('✓ Next sample loaded!');
+        }} catch (err) {{
+            console.error('Error loading next sample:', err);
+            statusEl.textContent = 'Error: ' + err.message;
+            statusEl.style.background = 'rgba(160, 0, 0, 0.8)';
+            setTimeout(() => {{ statusEl.style.display = 'none'; }}, 3000);
+        }}
+    }});
+
+    (async () => {{
+        const statusEl = document.getElementById('status');
+
+        try {{
+            statusEl.textContent = 'Fetching NiiVue library...';
+
+            const niivueModule = await import('https://unpkg.com/@niivue/[email protected]/dist/index.js');
+            const Niivue = niivueModule.Niivue;
+
+            statusEl.textContent = 'Initializing viewer...';
+            nv = new Niivue({{
+                logging: true,
+                show3Dcrosshair: true,
+                textHeight: 0.04
+            }});
+
+            await nv.attachTo('niivue-canvas');
+
+            statusEl.textContent = 'Loading initial sample...';
+
+            // Fetch initial sample and metadata
+            const initResponse = await fetch('/initial');
+            const initData = await initResponse.json();
+
+            const volumes = [{{
+                url: initData.data_url,
+                name: 'volume.nii.gz'
+            }}];
+
+            await nv.loadVolumes(volumes);
+
+            // Update metadata display
+            updateMetadata(initData.metadata);
+
+            // Start with multiplanar + 3D
+            nv.setSliceType(nv.sliceTypeMultiplanar);
+            if (nv.setMultiplanarLayout) {{
+                nv.setMultiplanarLayout(2);
+            }}
+            nv.setRenderAzimuthElevation(120, 10);
+            nv.opts.show3Dcrosshair = true;
+            nv.opts.crosshairWidth = 2;
+
+            statusEl.textContent = 'Rendering...';
+            setTimeout(() => {{
+                nv.updateGLVolume();
+                nv.drawScene();
+                statusEl.style.display = 'none';
+                console.log('✓✓✓ Viewer ready!');
+            }}, 300);
+
+        }} catch (err) {{
+            console.error('ERROR:', err);
+            console.error('Error message:', err.message);
+            console.error('Error stack:', err.stack);
+            statusEl.textContent = 'Error: ' + err.message;
+            statusEl.style.background = 'rgba(160, 0, 0, 0.8)';
+        }}
+    }})();
+    </script>
+</body>
+</html>
+"""
+    return html_content
+
+@app.get("/initial")
+async def get_initial():
+    print("Loading dataset...")
+    # dataset = load_dataset("TobiasPitters/ds004884-mini", streaming=True)
+    global ds_iter
+    dataset = load_dataset("parquet", data_dir="./data/" ,streaming=True)
+    ds_iter = iter(dataset["train"])
+
+    first_sample = next(ds_iter)
+
+    if isinstance(first_sample['nifti'], dict):
+        nifti_bytes = first_sample['nifti']['bytes']
+    else:
+        nifti_bytes = first_sample['nifti'].to_bytes()
+    nifti_b64 = base64.b64encode(nifti_bytes).decode("utf-8")
+    data_url = nifti_base_url.format(nifti_b64)
+
+    initial_metadata = {
+        'subject': first_sample.get('subject', 'N/A'),
+        'session': first_sample.get('session', 'N/A'),
+        'datatype': first_sample.get('datatype', 'N/A'),
+        'suffix': first_sample.get('suffix', 'N/A'),
+        'task': first_sample.get('task', 'N/A'),
+        'run': first_sample.get('run', 'N/A'),
+        'path': first_sample.get('path', 'N/A')
+    }
+
+    return {
+        "status": "success",
+        "data_url": data_url,
+        "metadata": initial_metadata
+    }
+
+async def load_dataset_iterator():
+    global num_iterations
+    dataset = load_dataset("TobiasPitters/ds004884-mini", streaming=True)
+    ds_iter_new = iter(dataset["train"])
+    for _ in range(num_iterations):
+        next(ds_iter_new)
+
+    global ds_iter
+    ds_iter = ds_iter_new
+
+@app.get("/next")
+async def next_sample():
+    """Load next sample from dataset"""
+    global ds_iter
+    global num_iterations
+    try:
+        ex = next(ds_iter)
+        if isinstance(ex['nifti'], dict):
+            nifti_bytes = ex['nifti']['bytes']
+        else:
+            nifti_bytes = ex['nifti'].to_bytes()
+        nifti_b64 = base64.b64encode(nifti_bytes).decode("utf-8")
+        new_data_url = nifti_base_url.format(nifti_b64)
+
+        metadata = {
+            'subject': ex.get('subject', 'N/A'),
+            'session': ex.get('session', 'N/A'),
+            'datatype': ex.get('datatype', 'N/A'),
+            'suffix': ex.get('suffix', 'N/A'),
+            'task': ex.get('task', 'N/A'),
+            'run': ex.get('run', 'N/A'),
+            'path': ex.get('path', 'N/A')
+        }
+
+        num_iterations += 1
+        return {
+            "status": "success",
+            "data_url": new_data_url,
+            "metadata": metadata
+        }
+    except StopIteration:
+        return {"status": "error", "message": "No more samples in dataset"}
+
+@app.get("/health")
+async def health():
+    """Health check endpoint"""
+    return {"status": "healthy", "dataset_loaded": True}

requirements.txt

@@ -0,0 +1,4 @@
+fastapi
+uvicorn[standard]
+nibabel
+git+https://github.com/The-Obstacle-Is-The-Way/datasets.git@feat/bids-loader