CellProfilerLibraryPyodide/index.html at main · sspathak/CellProfilerLibraryPyodide · GitHub

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<!DOCTYPE html>
<html lang="en">

<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>CellProfiler WebAssembly Demo</title>

    <link rel="stylesheet" href="https://pyscript.net/releases/2024.8.2/core.css">
    <script type="module" src="https://pyscript.net/releases/2024.8.2/core.js"></script>

    <style>
        body {
            font-family: system-ui, -apple-system, sans-serif;
            padding: 20px;
            max-width: 1000px;
            margin: auto;
            background-color: #f9f9f9;
            padding-bottom: 350px;
            /* Space for the floating terminal */
        }

        /* --- Full Screen Loading Overlay --- */
        #loading-overlay {
            position: fixed;
            top: 0;
            left: 0;
            width: 100%;
            height: 100%;
            background: rgba(255, 255, 255, 0.95);
            display: flex;
            flex-direction: column;
            justify-content: center;
            align-items: center;
            z-index: 9999;
            /* High Z-index, but lower than the dock */
            transition: opacity 0.5s ease;
        }

        .spinner {
            width: 50px;
            height: 50px;
            border: 5px solid #f3f3f3;
            border-top: 5px solid #007bff;
            border-radius: 50%;
            animation: spin 1s linear infinite;
            margin-bottom: 20px;
        }

        @keyframes spin {
            0% {
                transform: rotate(0deg);
            }

            100% {
                transform: rotate(360deg);
            }
        }

        /* --- Floating Bottom Dock --- */
        #dev-dock {
            position: fixed;
            bottom: 0;
            left: 0;
            width: 100%;
            height: 350px;
            background: #1e1e1e;
            color: #fff;
            box-shadow: 0 -5px 15px rgba(0, 0, 0, 0.5);
            /* CRITICAL FIX: Z-index 10000 puts it ABOVE the loading screen */
            z-index: 10000;
            transition: transform 0.4s cubic-bezier(0.25, 0.8, 0.25, 1);
            display: flex;
            flex-direction: column;
        }

        #dev-dock.minimized {
            transform: translateY(310px);
        }

        #dock-header {
            background: #2d2d2d;
            padding: 10px 20px;
            cursor: pointer;
            font-weight: bold;
            display: flex;
            justify-content: space-between;
            user-select: none;
            border-top: 3px solid #007bff;
        }

        #dock-header:hover {
            background: #3d3d3d;
        }

        #dock-body {
            display: flex;
            flex: 1;
            overflow: hidden;
        }

        .dock-panel {
            flex: 1;
            padding: 15px;
            overflow-y: auto;
            border-right: 1px solid #444;
        }

        .dock-panel h4 {
            margin-top: 0;
            color: #888;
            text-transform: uppercase;
            font-size: 12px;
            margin-bottom: 10px;
        }

        /* Terminal Logs Formatting */
        #boot-terminal {
            font-family: 'Courier New', monospace;
            font-size: 13px;
            color: #00ff00;
        }

        .log-error {
            color: #ff5555;
        }

        .log-warn {
            color: #ffff55;
        }

        .log-info {
            color: #55ffff;
        }

        /* Remove the old .py-repl-box override and use this instead */
        .repl-wrapper {
            background: #ffffff;
            /* Force a white background for the editor */
            color: #000000;
            padding: 5px;
            border-radius: 4px;
            margin-top: 10px;
        }
    </style>
</head>

<body>

    <div id="loading-overlay">
        <div class="spinner"></div>
        <h2>CellProfiler WebAssembly</h2>
        <p id="loading-status">Downloading library and initializing engine...</p>
    </div>

    <div id="ui-container" style="display: none;">
        <h2>CellProfiler WebAssembly Demo</h2>

        <div
            style="border: 1px solid #ccc; padding: 15px; margin-bottom: 10px; border-radius: 5px; background: white; box-shadow: 0 2px 5px rgba(0,0,0,0.05);">
            <h3>1. Load Image Set</h3>

            <div
                style="margin-bottom: 20px; padding: 10px; background: #f8f9fa; border-radius: 4px; display: flex; gap: 20px;">
                <label style="cursor: pointer;"><input type="radio" name="source-type" value="upload" checked
                        onclick="toggleSourceUI()"> 📂 Local File Upload</label>
                <label style="cursor: pointer;"><input type="radio" name="source-type" value="url"
                        onclick="toggleSourceUI()"> 🌐 Remote Example URLs</label>
            </div>

            <div id="container-upload" style="display: block;">
                <div style="margin-bottom: 10px;"><strong>OrigBlue (DAPI):</strong> <input type="file" id="upload-blue"
                        accept="image/*"></div>
                <div style="margin-bottom: 10px;"><strong>OrigGreen (FITC):</strong> <input type="file"
                        id="upload-green" accept="image/*"></div>
                <div style="margin-bottom: 10px;"><strong>OrigRed (Rhodamine):</strong> <input type="file"
                        id="upload-red" accept="image/*"></div>
            </div>

            <div id="container-url" style="display: none;">
                <p style="font-size: 12px; color: #666; margin-bottom: 15px;">Pre-populated with <i>ExampleFly</i> data
                    from the CellProfiler repository.</p>
                <div style="margin-bottom: 10px; display: flex; flex-direction: row;">
                    <strong>OrigBlue URL:</strong>
                    <input type="text" id="url-blue"
                        value="https://raw.githubusercontent.com/CellProfiler/CellProfiler/main/src/frontend/cellprofiler/data/examples/ExampleFly/images/01_POS002_D.TIF"
                        style="width: max-content; font-family: monospace; font-size: 11px; padding: 5px; margin-left: 10px; flex: 1">
                </div>
                <div style="margin-bottom: 10px; display: flex; flex-direction: row;">
                    <strong>OrigGreen URL:</strong>
                    <input type="text" id="url-green"
                        value="https://raw.githubusercontent.com/CellProfiler/CellProfiler/main/src/frontend/cellprofiler/data/examples/ExampleFly/images/01_POS002_F.TIF"
                        style="width: max-content; font-family: monospace; font-size: 11px; padding: 5px; margin-left: 10px; flex: 1">
                </div>
                <div style="margin-bottom: 10px; display: flex; flex-direction: row;">
                    <strong>OrigRed URL:</strong>
                    <input type="text" id="url-red"
                        value="https://raw.githubusercontent.com/CellProfiler/CellProfiler/main/src/frontend/cellprofiler/data/examples/ExampleFly/images/01_POS002_R.TIF"
                        style="width: max-content; font-family: monospace; font-size: 11px; padding: 5px; margin-left: 10px; flex: 1">
                </div>
            </div>

            <button py-click="on_load_images"
                style="margin-top: 15px; padding: 10px 20px; background: #28a745; color: white; border: none; cursor: pointer; border-radius: 4px; font-weight: bold; width: 100%;">LOAD
                IMAGES</button>
            <div id="out-uploads" style="margin-top: 10px; font-weight: bold; text-align: left;"></div>
        </div>

        <script>
            function toggleSourceUI() {
                const mode = document.querySelector('input[name="source-type"]:checked').value;
                document.getElementById('container-upload').style.display = (mode === 'upload' ? 'block' : 'none');
                document.getElementById('container-url').style.display = (mode === 'url' ? 'block' : 'none');
            }
        </script>

        <div style="border: 1px solid #ccc; padding: 15px; margin-bottom: 10px; border-radius: 5px; background: white;">
            <h3>2. Crop Blue (DAPI)</h3>
            Left: <input type="number" id="crop-b-left" value="501" style="width: 70px;">
            Right: <input type="number" id="crop-b-right" value="700" style="width: 70px;">
            Top: <input type="number" id="crop-b-top" value="251" style="width: 70px;">
            Bottom: <input type="number" id="crop-b-bottom" value="450" style="width: 70px;"><br><br>
            <button py-click="on_crop_b"
                style="padding: 10px 15px; background: #17a2b8; color: white; border: none; cursor: pointer; border-radius: 4px;">Run
                Crop Blue</button>
            <div id="out-crop-b-status" style="margin-top: 10px; font-weight: bold;"></div>

            <details id="details-crop-b" style="margin-top: 10px; padding-top: 10px; border-top: 1px solid #eee;">
                <summary style="cursor: pointer; color: #007bff; font-weight: bold;">👁️ View Output Image</summary>
                <div id="out-crop-b-viz" style="margin-top: 10px; text-align: center;"></div>
            </details>
        </div>

        <div style="border: 1px solid #ccc; padding: 15px; margin-bottom: 10px; border-radius: 5px; background: white;">
            <h3>3. Identify Primary (Nuclei)</h3>
            Min Diam: <input type="number" id="ip-min" value="10" style="width: 70px;">
            Max Diam: <input type="number" id="ip-max" value="40" style="width: 70px;"><br><br>
            <button py-click="on_ip"
                style="padding: 10px 15px; background: #17a2b8; color: white; border: none; cursor: pointer; border-radius: 4px;">Identify
                Nuclei</button>
            <div id="out-ip-status" style="margin-top: 10px; font-weight: bold;"></div>

            <details id="details-ip" style="margin-top: 10px; padding-top: 10px; border-top: 1px solid #eee;">
                <summary style="cursor: pointer; color: #007bff; font-weight: bold;">👁️ View Segmentation</summary>
                <div id="out-ip-viz" style="margin-top: 10px; text-align: center;"></div>
            </details>
        </div>
    </div>

    <div id="dev-dock" class="minimized">
        <div id="dock-header" onclick="toggleDock()">
            <span>🛠️ Developer Console</span>
            <span id="dock-arrow">▲</span>
        </div>

        <div id="dock-body" style="flex-direction: column; padding: 15px; gap: 10px;">

            <div id="boot-terminal"
                style="flex: 1; overflow-y: auto; background: #000; padding: 10px; border-radius: 4px; border: 1px solid #444;">
            </div>

            <div style="display: flex; gap: 10px; height: 50px;">
                <textarea id="repl-input" spellcheck="false"
                    onkeydown="if(event.key === 'Enter' && !event.shiftKey) { event.preventDefault(); document.getElementById('repl-btn').click(); }"
                    style="flex: 1; background: #222; color: #00ff00; font-family: 'Courier New', monospace; font-size: 13px; border: 1px solid #555; border-radius: 4px; padding: 10px; resize: none;"
                    placeholder=">>> Type an expression (e.g., state['OrigBlue'].shape) and press Enter..."></textarea>
                <button id="repl-btn" py-click="on_repl_run"
                    style="padding: 0 20px; background: #28a745; color: white; border: none; cursor: pointer; border-radius: 4px; font-weight: bold; text-transform: uppercase;">▶
                    Run</button>
            </div>

        </div>
    </div>

    <script>
        function toggleDock() {
            const dock = document.getElementById('dev-dock');
            const arrow = document.getElementById('dock-arrow');
            dock.classList.toggle('minimized');
            arrow.innerText = dock.classList.contains('minimized') ? '▲' : '▼';
        }

        const terminal = document.getElementById('boot-terminal');
        function pipeToTerminal(oldFunc, cssClass, prefix) {
            return function (...args) {
                const msg = args.map(a => typeof a === 'object' ? JSON.stringify(a) : a).join(' ');
                terminal.innerHTML += `<div class="${cssClass}">${prefix}${msg}</div>`;
                terminal.parentNode.scrollTop = terminal.parentNode.scrollHeight;
                oldFunc.apply(console, args);
            };
        }
        console.log = pipeToTerminal(console.log, '', '');
        console.info = pipeToTerminal(console.info, 'log-info', '[INFO] ');
        console.warn = pipeToTerminal(console.warn, 'log-warn', '[WARN] ');
        console.error = pipeToTerminal(console.error, 'log-error', '[ERROR] ');
    </script>

    <py-config>
        interpreter = "https://cdn.jsdelivr.net/pyodide/v0.29.3/full/pyodide.mjs"
        packages = ["matplotlib", "numpy", "pydantic"]
    </py-config>

    <py-script src="./main.py"></py-script>

</body>

</html>