Upload 4 files

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+hf_emr_explorer/data.json filter=lfs diff=lfs merge=lfs -text

hf_emr_explorer/.gitattributes

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+data.json filter=lfs diff=lfs merge=lfs -text

hf_emr_explorer/README.md

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+---
+title: EMR Explorer
+sdk: static
+---
+
+# EMR Explorer (CDA channels 650-1018)
+
+Interactive Hugging Face Space for exploring the **VQ-VAE latent space** of Cassini
+Cosmic Dust Analyzer (CDA) TOF mass spectra in the high-mass / **Extended Mass Range**
+region (channels 650-1018). Built as a **static** Space: a single `index.html` that
+loads its data from `data.json` at runtime.
+
+## Features
+- **Projections:** toggle between t-SNE and UMAP of the latent space.
+- **Coloring:** by Base Model Error, Error Bands, or Outlier score.
+- **Top-outliers strip:** one-click jump to the highest-outlier samples.
+- **Interactive spectra:** click any point to view its raw, processed, and
+  reconstructed spectrum (channels 650-1018).
+
+## Files (all required -- do not skip `data.json`)
+- `index.html` -- the app (does `fetch('data.json')` on load).
+- `data.json` (~60 MB) -- 10,000 sub-sampled spectra, latent coordinates, and scores.
+  This is a large file and is tracked with **Git LFS**.
+- `README.md` -- this file (defines the Space; `sdk: static`).
+- `.gitattributes` -- marks `data.json` for Git LFS.
+
+## Run locally
+```bash
+cd hf_emr_explorer
+python -m http.server 8000
+# open http://localhost:8000
+```
+
+## Upload to a Hugging Face Space
+1. Go to https://huggingface.co/spaces and click **New Space**.
+2. Name it (e.g. `emr-explorer`) and set the SDK to **Static** (taken from this README).
+3. In the Space's **Files** tab, upload **all four**: `index.html`, `data.json`,
+   `README.md`, and `.gitattributes`.
+   - Or via CLI (from inside this folder):
+     `huggingface-cli upload <you>/emr-explorer . --repo-type space`
+4. `data.json` (~60 MB) is tracked with Git LFS, so the Space takes a moment to build.
+
+> The app shows "Error loading data.json" if `data.json` is missing -- always upload it.

hf_emr_explorer/data.json

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+version https://git-lfs.github.com/spec/v1
+oid sha256:e2fd39df31f94bea13a99a8e221e864aeec7b02b82a1831518b47f20a2e69ceb
+size 60363321

hf_emr_explorer/index.html

@@ -0,0 +1,383 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<meta name="viewport" content="width=device-width, initial-scale=1">
+<title>EMR Explorer &mdash; CDA 650-1018</title>
+<script src="https://cdn.plot.ly/plotly-2.32.0.min.js" charset="utf-8"></script>
+<style>
+  *{box-sizing:border-box;margin:0;padding:0;}
+  html,body{height:100%;overflow:hidden;}
+  body{
+    font-family:"Segoe UI",system-ui,Arial,sans-serif;
+    background:#0d0f1a;color:#d8dce8;
+    display:flex;flex-direction:column;
+  }
+  #hdr{
+    flex-shrink:0;
+    display:flex;align-items:center;gap:14px;
+    padding:9px 18px;
+    background:#111422;
+    border-bottom:1px solid #232640;
+  }
+  #hdr h1{font-size:1rem;font-weight:700;color:#7fa8f7;letter-spacing:.02em;}
+  .sub{font-size:.75rem;color:#555e7a;}
+  .ctrls{display:flex;gap:6px;margin-left:auto;align-items:center;flex-wrap:wrap;}
+  .lbl{font-size:.72rem;color:#555e7a;}
+  .sep{width:1px;height:18px;background:#232640;margin:0 4px;}
+  .btn{
+    padding:4px 11px;border-radius:5px;
+    border:1px solid #2d3355;background:#181b2e;
+    color:#9ba8d0;font-size:.72rem;cursor:pointer;
+    transition:background .15s,color .15s;
+  }
+  .btn:hover{background:#222744;}
+  .btn.on{background:#2e3d7a;border-color:#4a5da8;color:#c0ccff;}
+  #main{flex:1;display:flex;min-height:0;min-width:0;}
+  #left{
+    flex:0 0 60%;display:flex;flex-direction:column;
+    border-right:1px solid #232640;
+    position: relative;min-width:0;
+  }
+  #loading{
+    position: absolute; top:0; left:0; width:100%; height:100%;
+    background: rgba(13, 15, 26, 0.9); display:flex;
+    justify-content:center; align-items:center; z-index:10;
+    font-size: 1.2rem; font-weight: bold; color: #7fa8f7;
+  }
+  #right{flex:1;display:flex;flex-direction:column;min-width:0;}
+  .ptitle{
+    flex-shrink:0;font-size:.65rem;letter-spacing:.08em;text-transform:uppercase;
+    padding:5px 12px;background:#0f1120;color:#454d6a;border-bottom:1px solid #1c1f35;
+  }
+  #scatter{flex:1;min-height:0;min-width:0;overflow:hidden;}
+  #spec-wrap{flex:1;min-height:0;min-width:0;display:flex;flex-direction:column;gap:0;}
+  #spec-orig{flex:1;min-height:0;min-width:0;border-bottom:1px solid #1c1f35;overflow:hidden;}
+  #spec-overlay{flex:1;min-height:0;min-width:0;overflow:hidden;}
+  #info{
+    flex-shrink:0;padding:6px 14px;background:#0f1120;
+    border-top:1px solid #1c1f35;font-size:.73rem;color:#6b7280;min-height:28px;
+  }
+  #hint{
+    display:flex;flex-direction:column;align-items:center;justify-content:center;
+    height:100%;gap:10px;color:#2a3050;font-size:.88rem;pointer-events:none;
+  }
+  #hint svg{width:44px;height:44px;}
+  #topout-strip{
+    flex-shrink:0; height:36px; overflow-x:auto; overflow-y:hidden; white-space:nowrap;
+    background:#0f1120; border-top:1px solid #1c1f35;
+    display:flex; align-items:center; gap:6px; padding:0 10px;
+  }
+  #topout-strip > *{flex-shrink:0;}
+  #topout-strip .lbl{white-space:nowrap;}
+  .tchip{
+    padding:2px 8px;border-radius:4px;border:1px solid #2d3355;background:#181b2e;
+    color:#9ba8d0;font-size:.7rem;cursor:pointer;white-space:nowrap;
+  }
+  .tchip:hover{background:#2e3d7a;color:#c0ccff;}
+</style>
+</head>
+<body>
+
+<div id="hdr">
+  <h1>EMR Explorer &mdash; CDA channels 650-1018</h1>
+  <span class="sub">n=10,000 random samples &nbsp;&middot;&nbsp; 368-pt spectra</span>
+  <div class="ctrls">
+    <span class="lbl">Proj.</span>
+    <button class="btn on" id="bt-tsne" onclick="setProj('tsne')">t-SNE</button>
+    <button class="btn"    id="bt-umap" onclick="setProj('umap')">UMAP</button>
+    <div class="sep"></div>
+    <span class="lbl">Colour</span>
+    <button class="btn on" id="bt-base-err" onclick="setCol('base-err')">Base Err</button>
+    <button class="btn"    id="bt-base-band" onclick="setCol('base-band')">Base Band</button>
+    <button class="btn"    id="bt-outlier" onclick="setCol('outlier')">Outlier</button>
+    <div class="sep"></div>
+    <span class="lbl">Highlight top</span>
+    <select id="sel-topn" class="btn" onchange="setTopN(this.value)">
+      <option value="0" selected>off</option>
+      <option value="50">50</option>
+      <option value="100">100</option>
+      <option value="500">500</option>
+    </select>
+    <div class="sep"></div>
+    <span class="lbl">Colormap</span>
+    <button class="btn on" id="bt-cmap-def" onclick="setCmap('default')">Default</button>
+    <button class="btn"    id="bt-cmap-cb"  onclick="setCmap('cb')">Colorblind</button>
+  </div>
+</div>
+
+<div id="main">
+  <div id="left">
+    <div id="loading">Loading embedded data... please wait.</div>
+    <div class="ptitle">Latent Space &mdash; click a point to inspect its spectrum</div>
+    <div id="scatter"></div>
+    <div id="topout-strip"></div>
+  </div>
+  <div id="right">
+    <div class="ptitle">Spectrum Viewer</div>
+    <div id="spec-wrap">
+      <div id="spec-orig">
+        <div id="hint">
+          <svg viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="1.4">
+            <circle cx="11" cy="11" r="8"/><line x1="21" y1="21" x2="16.65" y2="16.65"/>
+          </svg>
+          Click any point in the scatter plot
+        </div>
+      </div>
+      <div id="spec-overlay"></div>
+    </div>
+    <div id="info">&mdash;</div>
+  </div>
+</div>
+
+<script>
+let D = null;
+let rawFlat    = null;
+let origFlat   = null;
+let reconFlat  = null;
+let N = 0;
+let C = 0;
+
+function decodeF32(b64) {
+  const bin = window.atob(b64);
+  const buf = new ArrayBuffer(bin.length);
+  const u8  = new Uint8Array(buf);
+  for (let i = 0; i < bin.length; i++) u8[i] = bin.charCodeAt(i);
+  return new Float32Array(buf);
+}
+
+function spectrum(flat, i) {
+  return Array.from(flat.subarray(i * C, (i + 1) * C));
+}
+
+let proj = 'tsne', col = 'base-err', cmap = 'default', topN = 0;
+let specInited = false;
+const scDiv     = document.getElementById('scatter');
+const spOrig    = document.getElementById('spec-orig');
+const spOverlay = document.getElementById('spec-overlay');
+
+const BAND_NAMES      = ['0-20% (Best)','20-40%','40-60%','60-80%','80-100% (Worst)'];
+const BAND_COLORS_DEF = ['#27ae60','#3498db','#f1c40f','#e67e22','#e74c3c'];
+const BAND_COLORS_CB  = ['#009E73','#56B4E9','#F0E442','#E69F00','#D55E00'];
+
+const CSCALE_DEF = 'Plasma';
+const CSCALE_CB  = 'Cividis';
+
+function activeBand()   { return cmap === 'cb' ? BAND_COLORS_CB : BAND_COLORS_DEF; }
+function activeCscale() { return cmap === 'cb' ? CSCALE_CB      : CSCALE_DEF;     }
+
+function topNIdx(n) {
+  return D.outlier_score
+    .map((s,i) => [s,i])
+    .sort((a,b) => b[0]-a[0])
+    .slice(0, n)
+    .map(p => p[1]);
+}
+
+function scatterTraces() {
+  const xs = proj === 'tsne' ? D.tsne_x : D.umap_x;
+  const ys = proj === 'tsne' ? D.tsne_y : D.umap_y;
+
+  const cd = D.base_err.map((e,i) => [i, e, D.base_band_label[i], D.sclk[i], D.outlier_score[i]]);
+  let htpl = '<b>sample %{customdata[0]}</b><br>';
+  const traces = [];
+
+  if (col === 'base-err') {
+    const logE = D.base_err.map(v => Math.log10(Math.max(v, 1e-12)));
+    htpl += 'MSE: %{customdata[1]:.3e}<br>Outlier: %{customdata[4]:.3f}<br>SCLK: %{customdata[3]}<extra></extra>';
+    traces.push({
+      type:'scattergl', mode:'markers', x:xs, y:ys,
+      marker:{
+        size:3, opacity:.72, color:logE, colorscale:activeCscale(), showscale:true,
+        colorbar:{
+          title:{text:'log₁₀(MSE)',side:'right',font:{color:'#7a82a0',size:10}},
+          tickfont:{color:'#7a82a0',size:9},
+          bgcolor:'rgba(0,0,0,0)', bordercolor:'rgba(0,0,0,0)',
+          len:.75, thickness:14,
+        },
+      },
+      customdata:cd, hovertemplate:htpl,
+    });
+  }
+
+  if (col === 'outlier') {
+    htpl += 'Outlier: %{customdata[4]:.3f}<br>MSE: %{customdata[1]:.3e}<br>SCLK: %{customdata[3]}<extra></extra>';
+    traces.push({
+      type:'scattergl', mode:'markers', x:xs, y:ys,
+      marker:{
+        size:3, opacity:.72, color:D.outlier_score, colorscale:'Inferno', showscale:true,
+        cmin:0, cmax:1,
+        colorbar:{
+          title:{text:'Outlier score',side:'right',font:{color:'#7a82a0',size:10}},
+          tickfont:{color:'#7a82a0',size:9},
+          bgcolor:'rgba(0,0,0,0)', bordercolor:'rgba(0,0,0,0)',
+          len:.75, thickness:14,
+        },
+      },
+      customdata:cd, hovertemplate:htpl,
+    });
+  }
+
+  if (col === 'base-band') {
+    htpl += 'Band: %{customdata[2]}<br>Outlier: %{customdata[4]:.3f}<br>MSE: %{customdata[1]:.3e}<extra></extra>';
+    BAND_NAMES.forEach((name, b) => {
+      const bx=[], by=[], bcd=[];
+      D.base_band.forEach((eb,i) => {
+        if(eb===b){ bx.push(xs[i]); by.push(ys[i]); bcd.push(cd[i]); }
+      });
+      traces.push({
+        type:'scattergl', mode:'markers', name, x:bx, y:by,
+        marker:{size:3, color:activeBand()[b], opacity:.75},
+        customdata:bcd, hovertemplate:htpl,
+      });
+    });
+  }
+
+  if (topN > 0) {
+    const hi = topNIdx(topN);
+    traces.push({
+      type:'scattergl', mode:'markers', name:`Top-${topN} outliers`,
+      x:hi.map(i => xs[i]), y:hi.map(i => ys[i]),
+      marker:{size:5.5, color:'#22d3ee', opacity:.95,
+               line:{color:'rgba(255,255,255,.65)', width:.5}},
+      customdata:hi.map(i => cd[i]),
+      hovertemplate:htpl,
+    });
+  }
+
+  return traces;
+}
+
+function scatterLayout() {
+  const isCont = (col === 'base-err' || col === 'outlier');
+  return {
+    paper_bgcolor:'#0d0f1a', plot_bgcolor:'#0d0f1a',
+    margin:{l:45, r:isCont?80:10, t:30, b:45},
+    xaxis:{title:proj.toUpperCase() + ' 1', titlefont:{color:'#555e7a',size:10}, tickfont:{color:'#454d6a',size:9}, gridcolor:'#181b2e', zeroline:false, showline:false},
+    yaxis:{title:proj.toUpperCase() + ' 2', titlefont:{color:'#555e7a',size:10}, tickfont:{color:'#454d6a',size:9}, gridcolor:'#181b2e', zeroline:false, showline:false},
+    legend:{font:{color:'#8a93b0',size:10}, bgcolor:'rgba(0,0,0,0)', x:.01, y:.99},
+    hovermode:'closest',
+    uirevision: proj + col + cmap,
+  };
+}
+
+function renderScatter() {
+  if(!D) return;
+  Plotly.react(scDiv, scatterTraces(), scatterLayout(), {
+    responsive:true, displayModeBar:true, modeBarButtonsToRemove:['lasso2d','select2d','toImage'], displaylogo:false,
+  });
+  scDiv.on('plotly_click', onPointClick);
+}
+
+function onPointClick(evt) {
+  if (!evt?.points?.length) return;
+  showSample(evt.points[0].customdata[0]);
+}
+
+function showSample(si) {
+  const base_err    = D.base_err[si];
+  const base_band_l = D.base_band_label[si];
+  const sclk        = D.sclk[si];
+  const out_score   = D.outlier_score[si];
+
+  const raw   = spectrum(rawFlat,   si);
+  const proc  = spectrum(origFlat,  si);
+  const recon = spectrum(reconFlat, si);
+  const xs    = D.channel_indices;
+
+  const commonLayout = {
+    paper_bgcolor:'#0d0f1a', plot_bgcolor:'#111220',
+    margin:{l:55, r:20, t:32, b:38},
+    xaxis:{ title:'m/z', titlefont:{color:'#555e7a',size:10}, tickfont:{color:'#454d6a',size:9}, gridcolor:'#181b2e', zeroline:false },
+    yaxis:{ title:'Intensity', titlefont:{color:'#555e7a',size:10}, tickfont:{color:'#454d6a',size:9}, gridcolor:'#181b2e', zeroline:false },
+    legend:{ font:{color:'#8a93b0',size:10}, bgcolor:'rgba(16,18,32,.8)', bordercolor:'#2a2d45', borderwidth:1, x:.01, y:.99 },
+    hovermode:'x unified',
+  };
+
+  const layoutOrig = Object.assign({}, commonLayout, {
+    title:{
+      text:`Sample #${si} &nbsp;<span style="font-size:10px;color:#555e7a">&mdash; SCLK ${sclk} | ${base_band_l} | outlier ${out_score.toFixed(3)}</span>`,
+      font:{color:'#8a93b0',size:11}, x:.04,
+    },
+  });
+
+  const layoutOverlay = Object.assign({}, commonLayout, {
+    title:{ text:'Processed vs Reconstructed', font:{color:'#8a93b0',size:11}, x:.04 },
+    legend:{ font:{color:'#8a93b0',size:10}, bgcolor:'rgba(16,18,32,.8)', bordercolor:'#2a2d45', borderwidth:1, x:.99, y:.99, xanchor:'right', yanchor:'top' },
+  });
+
+  if (!specInited) { spOrig.innerHTML = ''; specInited = true; }
+
+  Plotly.react(spOrig, [
+    {type:'scatter', mode:'lines', name:'Raw', x:xs, y:raw, line:{color:'#6eadf5', width:1.6}},
+  ], layoutOrig, {responsive:true, displayModeBar:false});
+
+  Plotly.react(spOverlay, [
+    {type:'scatter', mode:'lines', name:'Processed', x:xs, y:proc, line:{color:'#6eadf5', width:1.6, opacity:0.5}},
+    {type:'scatter', mode:'lines', name:'Reconstructed', x:xs, y:recon, line:{color:'#fb923c', width:1.5, dash:'dash'}},
+  ], layoutOverlay, {responsive:true, displayModeBar:false});
+
+  document.getElementById('info').innerHTML =
+    `<b style="color:#d8dce8">Sample #${si}</b>` +
+    `&nbsp;&nbsp;SCLK: <b style="color:#cccccc">${sclk}</b>` +
+    `&nbsp;&nbsp;Band: <b style="color:#cccccc">${base_band_l}</b>` +
+    `&nbsp;&nbsp;Recon MSE: <b style="color:#fb923c">${base_err.toExponential(3)}</b>` +
+    `&nbsp;&nbsp;Outlier: <b style="color:#22d3ee">${out_score.toFixed(3)}</b>`;
+}
+
+function buildTopOutStrip() {
+  const el = document.getElementById('topout-strip');
+  if (!el) return;
+  const order = D.outlier_score.map((s,i) => [s,i]).sort((a,b) => b[0]-a[0]).slice(0, 20);
+  el.innerHTML = '<span class="lbl">Top outliers (click to inspect):</span>' +
+    order.map(([s,i], k) =>
+      `<span class="tchip" onclick="showSample(${i})" title="outlier score ${s.toFixed(3)}">#${k+1} SCLK ${D.sclk[i]} (${s.toFixed(3)})</span>`
+    ).join('');
+}
+
+function setProj(p) {
+  proj = p;
+  document.getElementById('bt-tsne').classList.toggle('on', p==='tsne');
+  document.getElementById('bt-umap').classList.toggle('on', p==='umap');
+  renderScatter();
+}
+function setCol(c) {
+  col = c;
+  ['base-err','base-band','outlier'].forEach(x => {
+    document.getElementById('bt-'+x).classList.toggle('on', c===x);
+  });
+  renderScatter();
+}
+function setTopN(v) {
+  topN = parseInt(v, 10) || 0;
+  renderScatter();
+}
+function setCmap(m) {
+  cmap = m;
+  document.getElementById('bt-cmap-def').classList.toggle('on', m==='default');
+  document.getElementById('bt-cmap-cb' ).classList.toggle('on', m==='cb');
+  renderScatter();
+}
+
+fetch('data.json')
+  .then(res => res.json())
+  .then(data => {
+    D = data;
+    N = D.n_samples;
+    C = D.n_channels;
+    rawFlat   = decodeF32(D.raw_b64);
+    origFlat  = decodeF32(D.orig_b64);
+    reconFlat = decodeF32(D.recon_b64);
+
+    document.getElementById('loading').style.display = 'none';
+    buildTopOutStrip();
+    renderScatter();
+  })
+  .catch(err => {
+    document.getElementById('loading').innerText = "Error loading data.json: " + err.message;
+    console.error(err);
+  });
+
+</script>
+</body>
+</html>