@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

package/dist/wsi.direct-6QYNXOBY.js

@@ -1,244 +0,0 @@
-import {
-  Feature_default,
-  MultiPolygon_default,
-  Vector_default,
-  Vector_default2
-} from "./chunk-DKPV7GCZ.js";
-import {
-  Fill_default,
-  Map_default,
-  Stroke_default,
-  Style_default,
-  Tile_default,
-  View_default,
-  Zoomify_default
-} from "./chunk-WZUUWGEU.js";
-import {
-  sayerror
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/w2/wsi.direct.ts
-async function init(opts, holder) {
-  const name = opts.slide ?? opts.label ?? "slide";
-  const loading = holder.append("div").style("margin", "20px").text(`Loading ${name} \u2026`);
-  try {
-    const sq = opts.slideQuery ?? `slide=${encodeURIComponent(opts.slide)}`;
-    const meta = await dofetch3(`wsitiles/meta?${sq}`);
-    if (!meta || meta.error || meta.status === "error") throw meta?.error || "failed to load slide metadata";
-    const [w, h] = meta.slide_dimensions;
-    const host = (sessionStorage.getItem("hostURL") || window.testHost || "").replace(/\/+$/, "");
-    const planes = meta.planes || 1;
-    let plane = Math.floor(planes / 2);
-    const makeSource = (p) => new Zoomify_default({
-      // {z}/{x}/{y} hit wsitiles/tile; unused {TileGroup} satisfies OL's
-      // requirement that a {TileGroup}/{tileIndex} placeholder be present.
-      // v=<slide mtime>: regenerating the slide file in place busts the
-      // browser's immutable tile cache (the server's disk cache keys on it too)
-      url: `${host}/wsitiles/tile/{z}/{x}/{y}?${sq}${planes > 1 ? `&plane=${p}` : ""}&v=${meta.version || 0}&_={TileGroup}`,
-      size: [w, h],
-      // OL derives the tier count from this, same math as wsi_tile.py
-      crossOrigin: "anonymous",
-      // tiles come from the API origin, not the page's
-      zDirection: -1
-      // pick the sharper tier when between two zoom levels
-    });
-    const source = makeSource(plane);
-    const grid = source.getTileGrid();
-    const extent = grid.getExtent();
-    loading.remove();
-    const slideLayer = new Tile_default({ source });
-    if (planes > 1) {
-      const bar = holder.append("div").style("font", "12px system-ui").style("padding", "4px 8px");
-      bar.append("span").text("z-plane: ");
-      const label = () => `${plane + 1}/${planes}`;
-      const planeText = bar.append("span").text(label());
-      bar.append("input").attr("type", "range").attr("min", 0).attr("max", planes - 1).attr("step", 1).property("value", plane).style("vertical-align", "middle").style("margin-left", "8px").style("width", "200px").on("change", function() {
-        plane = Number(this.value);
-        planeText.text(label());
-        slideLayer.setSource(makeSource(plane));
-      });
-    }
-    const mapDiv = holder.append("div").style("width", opts.width ?? "100vw").style("height", opts.height ?? "90vh");
-    const map = new Map_default({
-      target: mapDiv.node(),
-      // mount the map into the holder
-      layers: [slideLayer],
-      // overlays are addLayer'd on top below
-      view: new View_default({ resolutions: grid.getResolutions(), extent })
-      // camera locked to the pyramid
-    });
-    map.getView().fit(extent);
-    holder.append("div").style("font", "12px system-ui").style("padding", "4px 8px").text(
-      `${name} \u2014 ${w}\xD7${h}px${Array.isArray(meta.mpp) && meta.mpp.length === 2 ? `, ${meta.mpp[0].toFixed(3)}\xD7${meta.mpp[1].toFixed(3)} \xB5m/px` : ""}, ${meta.levels} levels`
-    );
-    const [mppX, mppY] = Array.isArray(meta.mpp) && meta.mpp.length === 2 ? meta.mpp : [1, 1];
-    const resolutions = grid.getResolutions();
-    const n = Number(opts.annotationLevel);
-    const maxResolution = Number.isInteger(n) && n > 0 && n < resolutions.length ? resolutions[resolutions.length - 1 - n] : void 0;
-    const overlays = [
-      [opts.cellBoundaries, "rgba(0, 200, 80, 0.9)"],
-      [opts.nucleusBoundaries, "rgba(0, 150, 255, 0.9)"]
-    ];
-    let cellPolys;
-    for (const [file, color] of overlays) {
-      if (!file) continue;
-      try {
-        const polys = await fetchBoundaries(host, sq, file, mppX, mppY);
-        if (file === opts.cellBoundaries) {
-          cellPolys = polys;
-          if (opts.hideCellStrokes) continue;
-        }
-        map.addLayer(strokeLayer(polys, color, maxResolution));
-      } catch (e) {
-        sayerror(holder, `Error loading ${file}: ${e.message || e}`);
-      }
-    }
-    const geneList = (s) => (s || "").split(",").map((t) => t.trim()).filter(Boolean);
-    const exprGenes = geneList(opts.geneExpression);
-    const groupGenes = geneList(opts.geneGroups);
-    if (exprGenes.length || groupGenes.length) {
-      try {
-        if (!opts.geneExpressionFile)
-          throw new Error("gene_expression/gene_groups requires gene_expression_file=<h5 file>");
-        if (!cellPolys) throw new Error("gene_expression/gene_groups requires cell_boundaries=<csv file>");
-        const results = await Promise.all(
-          [...exprGenes, ...groupGenes].map(
-            (gene) => dofetch3(
-              `wsitiles/genecounts?${sq}&file=${encodeURIComponent(opts.geneExpressionFile)}&gene=${encodeURIComponent(
-                gene
-              )}`
-            ).catch((e) => ({ error: e.message || String(e) }))
-          )
-        );
-        let legend;
-        const addLegend = (rgb, name2, max) => {
-          if (!legend) {
-            mapDiv.style("position", "relative");
-            legend = mapDiv.append("div").style("position", "absolute").style("top", "8px").style("right", "8px").style("z-index", "10").style("background", "rgba(255,255,255,0.85)").style("padding", "6px 10px").style("border-radius", "4px").style("font", "12px system-ui");
-          }
-          const row = legend.append("div").style("margin", "2px 0");
-          row.append("span").style("margin-right", "6px").text(name2);
-          row.append("span").style("display", "inline-block").style("width", "80px").style("height", "10px").style("vertical-align", "middle").style("border", "1px solid #ccc").style("background", `linear-gradient(to right, rgba(${rgb}, 0.15), rgba(${rgb}, 0.9))`);
-          row.append("span").style("margin-left", "4px").text(`1\u2013${max}`);
-        };
-        let colorIdx = 0;
-        for (const [i, gene] of exprGenes.entries()) {
-          const r = results[i];
-          if (!r || r.error) {
-            sayerror(holder, `Gene expression error (${gene}): ${r?.error || "failed to load"}`);
-            continue;
-          }
-          const rgb = GENE_COLORS[colorIdx++ % GENE_COLORS.length];
-          map.addLayer(expressionLayer(cellPolys, r.cells, r.max, rgb));
-          addLegend(rgb, gene, r.max);
-        }
-        if (groupGenes.length) {
-          const total = {};
-          const found = [];
-          for (const [i, gene] of groupGenes.entries()) {
-            const r = results[exprGenes.length + i];
-            if (!r || r.error) {
-              sayerror(holder, `Gene expression error (${gene}): ${r?.error || "failed to load"}`);
-              continue;
-            }
-            found.push(gene);
-            for (const id in r.cells) total[id] = (total[id] || 0) + r.cells[id];
-          }
-          if (found.length) {
-            let max = 0;
-            for (const id in total) if (total[id] > max) max = total[id];
-            const rgb = GENE_COLORS[colorIdx++ % GENE_COLORS.length];
-            map.addLayer(expressionLayer(cellPolys, total, max, rgb));
-            addLegend(rgb, found.join("+"), max);
-          }
-        }
-      } catch (e) {
-        sayerror(holder, `Gene expression error: ${e.message || e}`);
-      }
-    }
-  } catch (e) {
-    loading.remove();
-    sayerror(holder, `WSI error: ${e.message || e}`);
-  }
-}
-async function fetchBoundaries(host, sq, file, mppX, mppY) {
-  const res = await fetch(`${host}/wsitiles/boundaries?${sq}&file=${encodeURIComponent(file)}`);
-  if (!res.ok) throw new Error(`${res.status} ${res.statusText}`);
-  const text = await res.text();
-  const cells = [];
-  let ring = [];
-  let curId = "";
-  for (const line of text.split("\n")) {
-    const [id, xs, ys] = line.split(",");
-    const x = Number(xs);
-    if (!xs || Number.isNaN(x)) continue;
-    if (id !== curId) {
-      if (ring.length > 2) cells.push({ id: curId.replace(/"/g, ""), ring });
-      ring = [];
-      curId = id;
-    }
-    ring.push([x / mppX, -Number(ys) / mppY]);
-  }
-  if (ring.length > 2) cells.push({ id: curId.replace(/"/g, ""), ring });
-  return cells;
-}
-function strokeLayer(cells, color, maxResolution) {
-  return new Vector_default({
-    // every ring wrapped into a single MultiPolygon feature
-    source: new Vector_default2({ features: [new Feature_default(new MultiPolygon_default(cells.map((c) => [c.ring])))] }),
-    style: new Style_default({ stroke: new Stroke_default({ color, width: 1 }) }),
-    // outline only, no fill
-    maxResolution
-    // undefined = visible at every zoom
-  });
-}
-var SHADES = 8;
-var GENE_COLORS = ["255, 0, 0", "0, 90, 255", "255, 165, 0", "160, 0, 200", "0, 160, 160", "200, 160, 0"];
-function expressionLayer(cells, counts, max, rgb) {
-  const buckets = Array.from({ length: SHADES }, () => []);
-  for (const c of cells) {
-    const n = counts[c.id];
-    if (!n || !max) continue;
-    buckets[Math.min(SHADES - 1, Math.floor(Math.log1p(n) / Math.log1p(max) * SHADES))].push([c.ring]);
-  }
-  const features = [];
-  for (const [i, polys] of buckets.entries()) {
-    if (!polys.length) continue;
-    const f = new Feature_default(new MultiPolygon_default(polys));
-    const alpha = 0.15 + 0.75 * (i + 1) / SHADES;
-    f.setStyle(new Style_default({ fill: new Fill_default({ color: `rgba(${rgb}, ${alpha.toFixed(2)})` }) }));
-    features.push(f);
-  }
-  return new Vector_default({ source: new Vector_default2({ features }) });
-}
-export {
-  init
-};
-//# sourceMappingURL=wsi.direct-6QYNXOBY.js.map

package/dist/wsi.direct-6QYNXOBY.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/w2/wsi.direct.ts"],
-  "sourcesContent": ["/*\n Direct whole-slide viewer for a single file, launched via runpp URL param:\n   http://localhost:3000/?image_file=SVS/slide.svs\n The format (SVS, OME-TIFF, ...) is deduced from the file extension,\n case-insensitively, by the server (wsi_tile.py open_slide()).\n\n Optional boundary overlays (Xenium segmentation), drawn when these params name\n CSV files; like the slide itself, paths are relative to serverconfig.tpmasterdir:\n   &cell_boundaries=SVS/cell_boundaries.csv&nucleus_boundaries=SVS/nucleus_boundaries.csv\n CSV columns: cell_id, vertex_x, vertex_y (\u00B5m); rows of one cell are contiguous\n and its first vertex is repeated last to close the polygon.\n\n &annotation_level=n limits the boundary strokes to the n most zoomed-in levels\n of the viewer: zoomed out beyond that, the boundaries are hidden. Omit to\n always show. Gene expression fills are not affected \u2014 they show at all zooms.\n\n Gene expression overlay (needs cell_boundaries):\n   &gene_expression_file=SVS/cell_feature_matrix.h5&gene_expression=ACE2,ACTA2\n draws one fill overlay per comma-separated gene, each in its own color (see\n GENE_COLORS), shaded by that gene's transcript count in the cell (10x\n cell_feature_matrix HDF5; cell ids match the boundary CSV's). A legend\n overlaid on the map's top-right corner shows each gene's color gradient and\n count range; cells expressing several genes blend their fills.\n An unknown gene name surfaces an error in the UI (other genes still render).\n\n &gene_groups=g1,g2,g3 instead sums each cell's counts over all listed genes\n and draws ONE overlay of the totals in a single color. Can be combined with\n gene_expression (the group takes the next unused palette color).\n\n Bypasses datasets/samples: hits the wsitiles route with a direct slide path\n (resolved relative to serverconfig.tpmasterdir; gated by features.wsi.allowDirectSlidePath). Minimal\n pan/zoom viewer \u2014 the same OpenLayers Zoomify setup the full viewer uses.\n*/\nimport 'ol/ol.css' // OpenLayers base styles\nimport Map from 'ol/Map.js' // the pan/zoom map widget\nimport View from 'ol/View.js' // its camera (resolutions + extent)\nimport TileLayer from 'ol/layer/Tile.js' // mosaics the slide tiles\nimport Zoomify from 'ol/source/Zoomify.js' // tile source matching wsi_tile.py's tier math\nimport VectorLayer from 'ol/layer/Vector.js' // boundary strokes / expression fills\nimport VectorSource from 'ol/source/Vector.js' // holds the polygon features\nimport Feature from 'ol/Feature.js' // one drawable geometry + style\nimport MultiPolygon from 'ol/geom/MultiPolygon.js' // many cell rings in one feature\nimport { Fill, Stroke, Style } from 'ol/style.js' // polygon styling primitives\nimport { dofetch3 } from '#common/dofetch' // fetch wrapper for meta/genecounts\nimport { sayerror } from '#dom' // inline error banner\n\nexport async function init(\n\topts: {\n\t\t/** direct slide path relative to tpmasterdir (runpp ?image_file=) */\n\t\tslide?: string\n\t\t/** alternative to slide: raw wsitiles query addressing the slide through a\n\t\t dataset (wsimage=&dslabel=&genome=&sample_id=), already URI-encoded \u2014\n\t\t lets the w2 plot reuse this viewer for spatial images without the\n\t\t allowDirectSlidePath gate */\n\t\tslideQuery?: string\n\t\t/** display name when slide is not given (e.g. the spatial image fileName) */\n\t\tlabel?: string\n\t\tcellBoundaries?: string\n\t\t/** fetch cellBoundaries (expression fills need the polygons) but don't draw their strokes */\n\t\thideCellStrokes?: boolean\n\t\tnucleusBoundaries?: string\n\t\tannotationLevel?: string | number\n\t\tgeneExpression?: string\n\t\tgeneExpressionFile?: string\n\t\tgeneGroups?: string\n\t\t/** map div size; defaults fit the full-window direct viewer */\n\t\twidth?: string\n\t\theight?: string\n\t},\n\tholder: any\n) {\n\tconst name = opts.slide ?? opts.label ?? 'slide' // display name in messages\n\tconst loading = holder.append('div').style('margin', '20px').text(`Loading ${name} \u2026`) // placeholder while meta loads\n\ttry {\n\t\t// every wsitiles request carries this query to address the slide\n\t\tconst sq = opts.slideQuery ?? `slide=${encodeURIComponent(opts.slide!)}`\n\t\tconst meta = await dofetch3(`wsitiles/meta?${sq}`) // geometry first: tiles need it\n\t\tif (!meta || meta.error || meta.status === 'error') throw meta?.error || 'failed to load slide metadata'\n\n\t\tconst [w, h] = meta.slide_dimensions // level-0 slide size in px\n\t\t// server origin for tile URLs ('' when same-origin); trailing slashes trimmed\n\t\tconst host = (sessionStorage.getItem('hostURL') || (window as any).testHost || '').replace(/\\/+$/, '')\n\n\t\t// z-planes of a 3D OME-TIFF stack (meta.planes = 1 for 2D slides);\n\t\t// start on the middle plane, matching the server's default\n\t\tconst planes: number = meta.planes || 1\n\t\tlet plane = Math.floor(planes / 2)\n\n\t\tconst makeSource = (p: number) =>\n\t\t\tnew Zoomify({\n\t\t\t\t// {z}/{x}/{y} hit wsitiles/tile; unused {TileGroup} satisfies OL's\n\t\t\t\t// requirement that a {TileGroup}/{tileIndex} placeholder be present.\n\t\t\t\t// v=<slide mtime>: regenerating the slide file in place busts the\n\t\t\t\t// browser's immutable tile cache (the server's disk cache keys on it too)\n\t\t\t\turl: `${host}/wsitiles/tile/{z}/{x}/{y}?${sq}${planes > 1 ? `&plane=${p}` : ''}&v=${\n\t\t\t\t\tmeta.version || 0\n\t\t\t\t}&_={TileGroup}`,\n\t\t\t\tsize: [w, h], // OL derives the tier count from this, same math as wsi_tile.py\n\t\t\t\tcrossOrigin: 'anonymous', // tiles come from the API origin, not the page's\n\t\t\t\tzDirection: -1 // pick the sharper tier when between two zoom levels\n\t\t\t})\n\t\tconst source = makeSource(plane) // start on the default (middle) plane\n\t\tconst grid = source.getTileGrid()! // the z/x/y grid OL computed from [w, h]\n\t\tconst extent = grid.getExtent() // slide bounds in map coordinates\n\n\t\tloading.remove() // meta arrived; the map replaces the placeholder\n\n\t\tconst slideLayer = new TileLayer({ source }) // bottom layer: the slide tiles\n\n\t\t// z-plane scroll bar ABOVE the map (the 90vh map pushes anything after\n\t\t// it below the fold); swapping the tile source refetches visible tiles\n\t\t// for the chosen plane, view position unchanged\n\t\tif (planes > 1) {\n\t\t\tconst bar = holder.append('div').style('font', '12px system-ui').style('padding', '4px 8px')\n\t\t\tbar.append('span').text('z-plane: ')\n\t\t\tconst label = () => `${plane + 1}/${planes}` // 1-based display, e.g. '3/5'\n\t\t\tconst planeText = bar.append('span').text(label())\n\t\t\tbar\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'range') // native slider, one notch per plane\n\t\t\t\t.attr('min', 0)\n\t\t\t\t.attr('max', planes - 1)\n\t\t\t\t.attr('step', 1)\n\t\t\t\t.property('value', plane) // start at the default (middle) plane\n\t\t\t\t.style('vertical-align', 'middle')\n\t\t\t\t.style('margin-left', '8px')\n\t\t\t\t.style('width', '200px')\n\t\t\t\t.on('change', function (this: HTMLInputElement) {\n\t\t\t\t\tplane = Number(this.value) // slider position = plane index\n\t\t\t\t\tplaneText.text(label()) // update the '3/5' readout\n\t\t\t\t\tslideLayer.setSource(makeSource(plane)) // refetch visible tiles for this plane\n\t\t\t\t})\n\t\t}\n\n\t\tconst mapDiv = holder\n\t\t\t.append('div')\n\t\t\t.style('width', opts.width ?? '100vw') // full-window unless the w2 plot passes a size\n\t\t\t.style('height', opts.height ?? '90vh')\n\t\tconst map = new Map({\n\t\t\ttarget: mapDiv.node(), // mount the map into the holder\n\t\t\tlayers: [slideLayer], // overlays are addLayer'd on top below\n\t\t\tview: new View({ resolutions: grid.getResolutions(), extent }) // camera locked to the pyramid\n\t\t})\n\t\tmap.getView().fit(extent) // start fully zoomed out, whole slide visible\n\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.style('font', '12px system-ui')\n\t\t\t.style('padding', '4px 8px')\n\t\t\t.text(\n\t\t\t\t`${name} \u2014 ${w}\u00D7${h}px${\n\t\t\t\t\tArray.isArray(meta.mpp) && meta.mpp.length === 2\n\t\t\t\t\t\t? `, ${meta.mpp[0].toFixed(3)}\u00D7${meta.mpp[1].toFixed(3)} \u00B5m/px`\n\t\t\t\t\t\t: ''\n\t\t\t\t}, ${meta.levels} levels`\n\t\t\t)\n\n\t\t// segmentation overlays: boundary CSVs are in \u00B5m, converted to level-0\n\t\t// pixels via the slide's mpp (defaulting to 1 = coords already in px)\n\t\tconst [mppX, mppY] = Array.isArray(meta.mpp) && meta.mpp.length === 2 ? meta.mpp : [1, 1]\n\n\t\t// annotation_level=n: show the overlays only within the n most zoomed-in\n\t\t// levels. OL picks the tile level with resolution <= the view resolution,\n\t\t// so \"within the n finest levels\" means view resolution < the (n+1)'th\n\t\t// finest grid resolution \u2014 that becomes the layer's (exclusive) maxResolution.\n\t\tconst resolutions = grid.getResolutions() // per-tier map resolutions, coarse -> fine\n\t\tconst n = Number(opts.annotationLevel) // boundaries visible in the n finest tiers\n\t\tconst maxResolution =\n\t\t\tNumber.isInteger(n) && n > 0 && n < resolutions.length ? resolutions[resolutions.length - 1 - n] : undefined\n\n\t\t// the two boundary overlays with their stroke colors (cell green, nucleus blue)\n\t\tconst overlays: Array<[string | undefined, string]> = [\n\t\t\t[opts.cellBoundaries, 'rgba(0, 200, 80, 0.9)'],\n\t\t\t[opts.nucleusBoundaries, 'rgba(0, 150, 255, 0.9)']\n\t\t]\n\t\tlet cellPolys: CellPoly[] | undefined // kept for the expression fills below\n\t\tfor (const [file, color] of overlays) {\n\t\t\tif (!file) continue // that overlay was not requested\n\t\t\ttry {\n\t\t\t\tconst polys = await fetchBoundaries(host, sq, file, mppX, mppY) // csv -> px polygons\n\t\t\t\tif (file === opts.cellBoundaries) {\n\t\t\t\t\tcellPolys = polys // expression fills reuse these rings\n\t\t\t\t\tif (opts.hideCellStrokes) continue // polygons fetched, strokes suppressed\n\t\t\t\t}\n\t\t\t\tmap.addLayer(strokeLayer(polys, color, maxResolution)) // draw on top of the slide\n\t\t\t} catch (e: any) {\n\t\t\t\tsayerror(holder, `Error loading ${file}: ${e.message || e}`) // one overlay failing kills nothing else\n\t\t\t}\n\t\t}\n\n\t\tconst geneList = (s?: string) =>\n\t\t\t(s || '')\n\t\t\t\t.split(',')\n\t\t\t\t.map(t => t.trim())\n\t\t\t\t.filter(Boolean)\n\t\tconst exprGenes = geneList(opts.geneExpression) // one overlay per gene\n\t\tconst groupGenes = geneList(opts.geneGroups) // summed into a single overlay\n\t\tif (exprGenes.length || groupGenes.length) {\n\t\t\ttry {\n\t\t\t\tif (!opts.geneExpressionFile)\n\t\t\t\t\tthrow new Error('gene_expression/gene_groups requires gene_expression_file=<h5 file>')\n\t\t\t\tif (!cellPolys) throw new Error('gene_expression/gene_groups requires cell_boundaries=<csv file>')\n\t\t\t\t// one genecounts request per gene, expr + group genes together\n\t\t\t\tconst results = await Promise.all(\n\t\t\t\t\t[...exprGenes, ...groupGenes].map(gene =>\n\t\t\t\t\t\tdofetch3(\n\t\t\t\t\t\t\t`wsitiles/genecounts?${sq}&file=${encodeURIComponent(opts.geneExpressionFile!)}&gene=${encodeURIComponent(\n\t\t\t\t\t\t\t\tgene\n\t\t\t\t\t\t\t)}`\n\t\t\t\t\t\t).catch((e: any) => ({ error: e.message || String(e) }))\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t\t// legend overlaid on the map's top-right corner \u2014 anything appended\n\t\t\t\t// below the 90vh map div lands below the fold and is never seen.\n\t\t\t\t// Created lazily so an all-errors run doesn't leave an empty box.\n\t\t\t\tlet legend: any\n\t\t\t\tconst addLegend = (rgb: string, name: string, max: number) => {\n\t\t\t\t\tif (!legend) {\n\t\t\t\t\t\tmapDiv.style('position', 'relative')\n\t\t\t\t\t\tlegend = mapDiv\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t\t\t.style('top', '8px')\n\t\t\t\t\t\t\t.style('right', '8px')\n\t\t\t\t\t\t\t.style('z-index', '10')\n\t\t\t\t\t\t\t.style('background', 'rgba(255,255,255,0.85)')\n\t\t\t\t\t\t\t.style('padding', '6px 10px')\n\t\t\t\t\t\t\t.style('border-radius', '4px')\n\t\t\t\t\t\t\t.style('font', '12px system-ui')\n\t\t\t\t\t}\n\t\t\t\t\tconst row = legend.append('div').style('margin', '2px 0')\n\t\t\t\t\trow.append('span').style('margin-right', '6px').text(name)\n\t\t\t\t\t// alpha range mirrors expressionLayer's shades (log-scaled counts)\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t.style('width', '80px')\n\t\t\t\t\t\t.style('height', '10px')\n\t\t\t\t\t\t.style('vertical-align', 'middle')\n\t\t\t\t\t\t.style('border', '1px solid #ccc')\n\t\t\t\t\t\t.style('background', `linear-gradient(to right, rgba(${rgb}, 0.15), rgba(${rgb}, 0.9))`)\n\t\t\t\t\trow.append('span').style('margin-left', '4px').text(`1\u2013${max}`)\n\t\t\t\t}\n\n\t\t\t\t// gene_expression: one layer per gene, each its own color\n\t\t\t\tlet colorIdx = 0 // next palette slot; shared with the group overlay\n\t\t\t\tfor (const [i, gene] of exprGenes.entries()) {\n\t\t\t\t\tconst r = results[i] // this gene's genecounts answer\n\t\t\t\t\tif (!r || r.error) {\n\t\t\t\t\t\tsayerror(holder, `Gene expression error (${gene}): ${r?.error || 'failed to load'}`)\n\t\t\t\t\t\tcontinue // one bad gene doesn't block the others\n\t\t\t\t\t}\n\t\t\t\t\tconst rgb = GENE_COLORS[colorIdx++ % GENE_COLORS.length] // this gene's fill color\n\t\t\t\t\tmap.addLayer(expressionLayer(cellPolys, r.cells, r.max, rgb)) // fill the expressing cells\n\t\t\t\t\taddLegend(rgb, gene, r.max) // gradient + count range in the legend\n\t\t\t\t}\n\n\t\t\t\t// gene_groups: sum each cell's counts over the group, one layer/color\n\t\t\t\tif (groupGenes.length) {\n\t\t\t\t\tconst total: { [id: string]: number } = {} // per-cell sum across the group\n\t\t\t\t\tconst found: string[] = [] // genes that actually answered\n\t\t\t\t\tfor (const [i, gene] of groupGenes.entries()) {\n\t\t\t\t\t\tconst r = results[exprGenes.length + i] // group answers follow the expr ones\n\t\t\t\t\t\tif (!r || r.error) {\n\t\t\t\t\t\t\tsayerror(holder, `Gene expression error (${gene}): ${r?.error || 'failed to load'}`)\n\t\t\t\t\t\t\tcontinue // skip the missing gene, keep summing the rest\n\t\t\t\t\t\t}\n\t\t\t\t\t\tfound.push(gene)\n\t\t\t\t\t\tfor (const id in r.cells) total[id] = (total[id] || 0) + r.cells[id] // accumulate per cell\n\t\t\t\t\t}\n\t\t\t\t\tif (found.length) {\n\t\t\t\t\t\tlet max = 0 // the summed overlay's own count ceiling\n\t\t\t\t\t\tfor (const id in total) if (total[id] > max) max = total[id]\n\t\t\t\t\t\tconst rgb = GENE_COLORS[colorIdx++ % GENE_COLORS.length] // next unused palette color\n\t\t\t\t\t\tmap.addLayer(expressionLayer(cellPolys, total, max, rgb)) // ONE overlay of the totals\n\t\t\t\t\t\taddLegend(rgb, found.join('+'), max) // e.g. 'PTPRC+EPCAM'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (e: any) {\n\t\t\t\tsayerror(holder, `Gene expression error: ${e.message || e}`)\n\t\t\t}\n\t\t}\n\t} catch (e: any) {\n\t\tloading.remove()\n\t\tsayerror(holder, `WSI error: ${e.message || e}`)\n\t}\n}\n\ntype CellPoly = { id: string; ring: number[][] }\n\n/** Fetch a boundary CSV (via wsitiles/boundaries) and parse it into one closed\n ring per cell, keyed by the unquoted cell_id (matches h5 barcodes). */\nasync function fetchBoundaries(\n\thost: string,\n\t/** wsitiles query addressing the slide (slide= or dataset params) */\n\tsq: string,\n\tfile: string,\n\tmppX: number,\n\tmppY: number\n): Promise<CellPoly[]> {\n\tconst res = await fetch(`${host}/wsitiles/boundaries?${sq}&file=${encodeURIComponent(file)}`) // raw csv text\n\tif (!res.ok) throw new Error(`${res.status} ${res.statusText}`)\n\tconst text = await res.text()\n\n\t// rows: \"cell_id\",vertex_x,vertex_y \u2014 one cell's vertices are contiguous.\n\t// OL's Zoomify extent is [0,-h,w,0]: x in px to the right, y in px negated.\n\tconst cells: CellPoly[] = [] // finished polygons\n\tlet ring: number[][] = [] // vertices of the cell being read\n\tlet curId = '' // the cell those vertices belong to\n\tfor (const line of text.split('\\n')) {\n\t\tconst [id, xs, ys] = line.split(',') // one vertex per row\n\t\tconst x = Number(xs)\n\t\tif (!xs || Number.isNaN(x)) continue // header / blank line\n\t\tif (id !== curId) {\n\t\t\t// a new cell_id starts: close out the previous cell's ring\n\t\t\tif (ring.length > 2) cells.push({ id: curId.replace(/\"/g, ''), ring })\n\t\t\tring = []\n\t\t\tcurId = id\n\t\t}\n\t\tring.push([x / mppX, -Number(ys) / mppY]) // \u00B5m -> level-0 px, y negated for OL\n\t}\n\tif (ring.length > 2) cells.push({ id: curId.replace(/\"/g, ''), ring }) // don't drop the last cell\n\treturn cells\n}\n\n/** One stroke-only vector layer holding every polygon; maxResolution (when\n set) hides the layer once the user zooms out beyond it.\n ponytail: all ~100k polygons in one MultiPolygon feature \u2014 switch to vector\n tiling if rendering within the visible zoom range ever feels sluggish. */\nfunction strokeLayer(cells: CellPoly[], color: string, maxResolution?: number): VectorLayer {\n\treturn new VectorLayer({\n\t\t// every ring wrapped into a single MultiPolygon feature\n\t\tsource: new VectorSource({ features: [new Feature(new MultiPolygon(cells.map(c => [c.ring])))] }),\n\t\tstyle: new Style({ stroke: new Stroke({ color, width: 1 }) }), // outline only, no fill\n\t\tmaxResolution // undefined = visible at every zoom\n\t})\n}\n\n// number of opacity steps for the expression fills\nconst SHADES = 8\n\n// fill colors (\"r, g, b\") cycled per gene; green/blue-ish avoided so fills\n// stay distinguishable from the cell (green) and nucleus (blue) strokes\nconst GENE_COLORS = ['255, 0, 0', '0, 90, 255', '255, 165, 0', '160, 0, 200', '0, 160, 160', '200, 160, 0']\n\n/** Fill each expressing cell with `rgb` at an opacity scaling with the cell's\n transcript count for the chosen gene; zero-count cells stay unfilled. Cells\n are bucketed into SHADES opacity steps so the layer is a handful of\n MultiPolygon features instead of one per cell. Counts are log-normalized\n (log1p(n)/log1p(max)) so a few hot cells don't push everything else into\n the faintest shade. Shown at every zoom level \u2014 annotation_level only\n gates the boundary strokes, not the expression fills. */\nfunction expressionLayer(cells: CellPoly[], counts: { [id: string]: number }, max: number, rgb: string): VectorLayer {\n\tconst buckets: number[][][][][] = Array.from({ length: SHADES }, () => []) // one polygon list per shade\n\tfor (const c of cells) {\n\t\tconst n = counts[c.id] // this cell's transcript count\n\t\tif (!n || !max) continue // zero count (or empty result): no fill\n\t\t// log-normalize the count into a shade index 0..SHADES-1\n\t\tbuckets[Math.min(SHADES - 1, Math.floor((Math.log1p(n) / Math.log1p(max)) * SHADES))].push([c.ring])\n\t}\n\tconst features: Feature[] = [] // one MultiPolygon feature per non-empty shade\n\tfor (const [i, polys] of buckets.entries()) {\n\t\tif (!polys.length) continue // no cell landed in this shade\n\t\tconst f = new Feature(new MultiPolygon(polys)) // all of this shade's cells at once\n\t\tconst alpha = 0.15 + (0.75 * (i + 1)) / SHADES // faintest 0.24 .. strongest 0.90\n\t\tf.setStyle(new Style({ fill: new Fill({ color: `rgba(${rgb}, ${alpha.toFixed(2)})` }) }))\n\t\tfeatures.push(f)\n\t}\n\treturn new VectorLayer({ source: new VectorSource({ features }) }) // fills only, no strokes\n}\n"],
-  "mappings": 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