@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/Wsi-S675CYTW.js

@@ -1,431 +0,0 @@
-import {
-  Map_default,
-  Tile_default,
-  View_default,
-  Zoomify_default
-} from "./chunk-WTAPOH2W.js";
-import {
-  PlotBase,
-  Tabs,
-  controlsInit,
-  renderTable
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.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/model/Model.ts
-var Model = class {
-  constructor(genome, dslabel) {
-    this.genome = genome;
-    this.dslabel = dslabel;
-  }
-  /** Every sample in the dataset that has at least one image on disk (one
-   subfolder per sample under either w2 root), with image counts. */
-  async getData() {
-    return await dofetch3("termdb/wsiBySample", {
-      body: { genome: this.genome, dslabel: this.dslabel }
-      // no sample_id = list samples
-    });
-  }
-  /** One sample's images (WsiImage | SpatialImage), enumerated from the
-   sample's subfolders in both w2 roots. */
-  async getImages(sample_id) {
-    return await dofetch3("termdb/wsiBySample", {
-      body: { genome: this.genome, dslabel: this.dslabel, sample_id }
-      // sample_id = list its images
-    });
-  }
-};
-
-// plots/w2/viewModel/ViewModel.ts
-var ViewModel = class {
-  constructor(samples, settings) {
-    this.viewData = {
-      columns: [{ label: "Sample" }, { label: "Images" }],
-      // two-column table
-      rows: samples.map((s) => [{ value: s.sampleId }, { value: String(s.count) }]),
-      // one row per sample
-      selectedSample: samples[settings.selectedSampleIndex]
-      // undefined when index is -1
-    };
-  }
-};
-
-// plots/w2/view/View.ts
-var View = class {
-  constructor(dom, viewData, images, settings, interactions, vocab) {
-    this.dom = dom;
-    this.viewData = viewData;
-    this.images = images;
-    this.settings = settings;
-    this.interactions = interactions;
-    this.vocab = vocab;
-  }
-  async render() {
-    this.renderSampleTable();
-    await this.renderViewer();
-  }
-  renderSampleTable() {
-    this.dom.table.selectAll("*").remove();
-    renderTable({
-      div: this.dom.table,
-      columns: this.viewData.columns,
-      rows: this.viewData.rows,
-      singleMode: true,
-      // radio buttons: one sample viewed at a time
-      selectedRows: this.settings.selectedSampleIndex != -1 ? [this.settings.selectedSampleIndex] : [],
-      noButtonCallback: (index) => this.interactions.selectSample(index),
-      resize: true,
-      striped: true,
-      maxHeight: "30vh",
-      header: { style: { "text-transform": "capitalize" } }
-    });
-  }
-  async renderViewer() {
-    const holder = this.dom.viewer;
-    holder.selectAll("*").remove();
-    const sample = this.viewData.selectedSample;
-    const selected = this.settings.selectedImageIndex;
-    const image = this.images[selected] ?? this.images[0];
-    if (!sample || !image) return;
-    const imageName = (f) => f.split("/").slice(-2)[0] || f;
-    new Tabs({
-      holder: holder.append("div"),
-      // tab strip sits above the map
-      tabsPosition: "horizontal",
-      tabs: this.images.map((img, i) => ({
-        label: imageName(img.fileName),
-        // e.g. 'image1'
-        active: i == (this.images[selected] ? selected : 0),
-        // highlight the shown image
-        callback: () => this.interactions.selectImage(i)
-        // dispatch -> re-render with image i
-      }))
-    }).main();
-    const params = `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${this.vocab.dslabel}&genome=${this.vocab.genome}&sample_id=${encodeURIComponent(sample.sampleId)}&imageType=${image.type}`;
-    if (image.type == "spatial") {
-      const s = this.settings;
-      const genes = s.showGeneExpression ? s.geneExpression ?? image.geneExpression : void 0;
-      const direct = await import("./wsi.direct-2WB2NGC5.js");
-      await direct.init(
-        {
-          slideQuery: params,
-          label: image.fileName,
-          // expression fills need the cell polygons even when their strokes are hidden
-          cellBoundaries: s.showCellBoundaries || genes ? image.cellBoundaries : void 0,
-          hideCellStrokes: !s.showCellBoundaries,
-          nucleusBoundaries: s.showNucleusBoundaries ? image.nucleusBoundaries : void 0,
-          geneExpressionFile: image.geneExpressionFile,
-          geneExpression: s.spatialMode == "gene_groups" ? void 0 : genes,
-          geneGroups: s.spatialMode == "gene_groups" ? genes : void 0,
-          annotationLevel: s.annotationLevel ?? image.annotationLevel,
-          width: "100%",
-          height: this.settings.viewerHeight
-        },
-        holder
-      );
-      return;
-    }
-    const meta = await dofetch3(`wsitiles/meta?${params}`);
-    if (!meta || meta.error || meta.status === "error") {
-      this.dom.error.text(`Error loading ${image.fileName}: ${meta?.error || "failed to load slide metadata"}`);
-      return;
-    }
-    const [w, h] = meta.slide_dimensions;
-    const host = (sessionStorage.getItem("hostURL") || window.testHost || "").replace(/\/+$/, "");
-    const source = new Zoomify_default({
-      // {z}/{x}/{y} hit wsitiles/tile; the unused {TileGroup} token only satisfies
-      // OpenLayers' requirement that a {TileGroup}/{tileIndex} placeholder be present.
-      // v=<slide mtime>: tiles are served immutable, so a regenerated slide must
-      // change the URL to bust the browser cache
-      url: `${host}/wsitiles/tile/{z}/{x}/{y}?${params}&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 grid = source.getTileGrid();
-    const extent = grid.getExtent();
-    const mapDiv = holder.append("div").style("width", "100%").style("height", this.settings.viewerHeight);
-    const map = new Map_default({
-      target: mapDiv.node(),
-      // mount the map into the plot's viewer div
-      layers: [new Tile_default({ source })],
-      // OL fetches+mosaics tiles as the user pans/zooms
-      view: new View_default({ resolutions: grid.getResolutions(), extent })
-      // camera locked to the pyramid
-    });
-    map.getView().fit(extent);
-  }
-};
-
-// plots/w2/interactions/WsiInteractions.ts
-var WsiInteractions = class {
-  constructor(app, id) {
-    this.app = app;
-    this.id = id;
-  }
-  /** a sample row was picked in the table; image selection resets to its first image */
-  selectSample(index) {
-    this.app.dispatch({
-      type: "plot_edit",
-      id: this.id,
-      config: { settings: { wsi: { selectedSampleIndex: index, selectedImageIndex: 0 } } }
-    });
-  }
-  /** an image tab was picked for the selected sample */
-  selectImage(index) {
-    this.app.dispatch({
-      type: "plot_edit",
-      id: this.id,
-      config: { settings: { wsi: { selectedImageIndex: index } } }
-    });
-  }
-};
-
-// plots/w2/Wsi.ts
-var Wsi = class _Wsi extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    /** gene names available in the current image's expression h5, cached per file */
-    this.geneNames = [];
-    this.type = _Wsi.type;
-    const holder = opts.holder.classed("sjpp-wsi-main", true);
-    const div = holder.append("div").style("padding", "5px");
-    this.dom = {
-      div,
-      // burger menu for spatial viewer settings; hidden until a spatial image is shown
-      controls: div.append("div").attr("id", "sjpp-wsi-controls").style("display", "none"),
-      error: div.append("div").attr("id", "sjpp-wsi-error").style("opacity", 0.75),
-      table: div.append("div").attr("id", "sjpp-wsi-table"),
-      viewer: div.append("div").attr("id", "sjpp-wsi-viewer")
-    };
-    if (opts.header)
-      this.dom.header = opts.header.text("WHOLE SLIDE IMAGES").style("font-size", "0.7em").style("opacity", 0.6);
-  }
-  static {
-    this.type = "wsi";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      vocab: appState.vocab,
-      config
-    };
-  }
-  async init() {
-    this.interactions = new WsiInteractions(this.app, this.id);
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.childType != this.type && config.chartType != this.type) return;
-    if (!this.interactions) throw "Interactions not initialized [wsi main()]";
-    const settings = config.settings.wsi;
-    this.dom.error.text("");
-    const model = new Model(this.state.vocab.genome, this.state.vocab.dslabel);
-    const data = await model.getData();
-    if (!data || data.error || !data.samples?.length) {
-      this.dom.table.selectAll("*").remove();
-      this.dom.viewer.selectAll("*").remove();
-      this.dom.error.style("padding", "20px").text(data?.error || "No samples with whole-slide images.");
-      return;
-    }
-    const viewModel = new ViewModel(data.samples, settings);
-    const selectedSample = viewModel.viewData.selectedSample;
-    const images = selectedSample ? (await model.getImages(selectedSample.sampleId)).images ?? [] : [];
-    const image = images[settings.selectedImageIndex] ?? images[0];
-    const isSpatial = image?.type == "spatial";
-    this.dom.header?.text(isSpatial ? "SPATIAL VIEWER" : "WHOLE SLIDE IMAGES");
-    if (isSpatial) {
-      const spImage = image;
-      const genes = await this.fetchGeneNames(spImage, selectedSample.sampleId);
-      if (settings.geneExpression == null) {
-        const configured = (spImage.geneExpression || "").split(",").map((s) => s.trim()).filter((g) => genes.includes(g));
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config: {
-            settings: {
-              wsi: {
-                geneExpression: configured.join(",") || genes[0] || "",
-                annotationLevel: settings.annotationLevel ?? spImage.annotationLevel
-              }
-            }
-          }
-        });
-        return;
-      }
-      if (!this.components.controls) await this.setControls();
-      this.addGeneDatalist();
-    }
-    this.dom.controls.style("display", isSpatial ? "inline-block" : "none");
-    await new View(this.dom, viewModel.viewData, images, settings, this.interactions, this.state.vocab).render();
-  }
-  /** Discover the genes present in the image's cell_feature_matrix h5 via
-   wsitiles/genenames (same slide-scoped access checks as genecounts).
-   Returns [] when the image has no expression file or the request fails. */
-  async fetchGeneNames(image, sampleId) {
-    if (!image.geneExpressionFile) return [];
-    if (this.geneNamesFile == image.geneExpressionFile) return this.geneNames;
-    const v = this.state.vocab;
-    const params = `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&file=${encodeURIComponent(
-      image.geneExpressionFile
-    )}`;
-    const r = await dofetch3(`wsitiles/genenames?${params}`).catch(() => null);
-    this.geneNames = Array.isArray(r?.genes) ? r.genes : [];
-    this.geneNamesFile = image.geneExpressionFile;
-    return this.geneNames;
-  }
-  /** Attach the discovered gene names to the Genes text input as a native
-   datalist, so typing autocompletes to genes that exist in the data.
-   (Autocomplete applies to the whole field, i.e. the first gene of a
-   comma-separated list — later genes are typed without suggestions.) */
-  addGeneDatalist() {
-    if (!this.geneNames.length) return;
-    const input = this.dom.controls.select("input[type=text]").node();
-    if (!input) return;
-    const id = `sjpp-wsi-genes-${this.id}`;
-    document.getElementById(id)?.remove();
-    const dl = document.createElement("datalist");
-    dl.id = id;
-    for (const g of this.geneNames) {
-      const opt = document.createElement("option");
-      opt.value = g;
-      dl.appendChild(opt);
-    }
-    input.after(dl);
-    input.setAttribute("list", id);
-  }
-  /** Burger menu with the spatial overlay settings; fields are pre-seeded
-   with defaults discovered from the data by main() before this runs. */
-  async setControls() {
-    this.components.controls = await controlsInit({
-      app: this.app,
-      id: this.id,
-      holder: this.dom.controls,
-      inputs: [
-        {
-          label: "Nucleus boundaries",
-          title: "Show or hide the nucleus segmentation overlay",
-          type: "checkbox",
-          chartType: "wsi",
-          settingsKey: "showNucleusBoundaries",
-          boxLabel: "show"
-        },
-        {
-          label: "Cell boundaries",
-          title: "Show or hide the cell segmentation overlay",
-          type: "checkbox",
-          chartType: "wsi",
-          settingsKey: "showCellBoundaries",
-          boxLabel: "show"
-        },
-        {
-          label: "Gene expression",
-          title: "Show or hide the gene expression overlay",
-          type: "checkbox",
-          chartType: "wsi",
-          settingsKey: "showGeneExpression",
-          boxLabel: "show"
-        },
-        {
-          label: "Genes",
-          title: "Comma-separated gene names to overlay",
-          type: "text",
-          chartType: "wsi",
-          settingsKey: "geneExpression",
-          placeholder: "gene1,gene2,\u2026"
-        },
-        {
-          label: "Overlay mode",
-          title: "Color each gene separately (gene_expression), or sum all genes into one overlay (gene_groups)",
-          type: "radio",
-          chartType: "wsi",
-          settingsKey: "spatialMode",
-          options: [
-            { label: "Per gene", value: "gene_expression" },
-            { label: "Gene group", value: "gene_groups" }
-          ]
-        },
-        {
-          label: "Annotation level",
-          title: "Show boundaries only within the n most zoomed-in levels; 0 = always show",
-          type: "number",
-          chartType: "wsi",
-          settingsKey: "annotationLevel",
-          min: 0,
-          step: 1
-        }
-      ]
-    });
-  }
-};
-var wsiInit = getCompInit(Wsi);
-var componentInit = wsiInit;
-function getDefaultWsiSettings(overrides = {}) {
-  const defaults = {
-    selectedSampleIndex: 0,
-    // first sample selected on launch
-    selectedImageIndex: 0,
-    // the sample's first image displayed by default
-    viewerHeight: "70vh",
-    // spatial overlay settings; null = fall back to the dataset's values
-    showCellBoundaries: true,
-    showNucleusBoundaries: true,
-    showGeneExpression: true,
-    geneExpression: null,
-    annotationLevel: null,
-    spatialMode: "gene_expression"
-  };
-  return Object.assign(defaults, overrides);
-}
-async function getPlotConfig(opts, _app) {
-  const config = {
-    chartType: "wsi",
-    settings: {
-      wsi: getDefaultWsiSettings(opts.overrides)
-    },
-    hidePlotFilter: true
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getDefaultWsiSettings,
-  getPlotConfig,
-  wsiInit
-};
-//# sourceMappingURL=Wsi-S675CYTW.js.map

package/dist/Wsi-S675CYTW.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/w2/model/Model.ts", "../plots/w2/viewModel/ViewModel.ts", "../plots/w2/view/View.ts", "../plots/w2/interactions/WsiInteractions.ts", "../plots/w2/Wsi.ts"],
-  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport type { WsiBySampleResponse } from '#types'\n\n/** Server data access for the w2 plot. Both calls hit termdb/wsiBySample,\n which lists straight from the ds.queries.w2 roots (folder/wsiFolder) on disk. */\nexport class Model {\n\tconstructor(readonly genome: string, readonly dslabel: string) {}\n\n\t/** Every sample in the dataset that has at least one image on disk (one\n\t subfolder per sample under either w2 root), with image counts. */\n\tasync getData(): Promise<WsiBySampleResponse> {\n\t\treturn await dofetch3('termdb/wsiBySample', {\n\t\t\tbody: { genome: this.genome, dslabel: this.dslabel } // no sample_id = list samples\n\t\t})\n\t}\n\n\t/** One sample's images (WsiImage | SpatialImage), enumerated from the\n\t sample's subfolders in both w2 roots. */\n\tasync getImages(sample_id: string): Promise<WsiBySampleResponse> {\n\t\treturn await dofetch3('termdb/wsiBySample', {\n\t\t\tbody: { genome: this.genome, dslabel: this.dslabel, sample_id } // sample_id = list its images\n\t\t})\n\t}\n}\n", "import type { WsiSampleSummary } from '#types'\nimport type { TableColumn, TableRow } from '#dom'\nimport type Settings from '../Settings.ts'\n\nexport type ViewData = {\n\t/** sample table skeleton for renderTable() */\n\tcolumns: TableColumn[]\n\trows: TableRow[]\n\t/** the sample whose image is shown in the viewer; undefined when none selected */\n\tselectedSample?: WsiSampleSummary\n}\n\n/** Shapes the server data for rendering: one table row per sample that has\n whole-slide images on disk, plus the currently selected sample. */\nexport class ViewModel {\n\tviewData: ViewData\n\n\tconstructor(samples: WsiSampleSummary[], settings: Settings) {\n\t\tthis.viewData = {\n\t\t\tcolumns: [{ label: 'Sample' }, { label: 'Images' }], // two-column table\n\t\t\trows: samples.map(s => [{ value: s.sampleId }, { value: String(s.count) }]), // one row per sample\n\t\t\tselectedSample: samples[settings.selectedSampleIndex] // undefined when index is -1\n\t\t}\n\t}\n}\n", "import { renderTable, Tabs } from '#dom' // sample table + per-image tab strip\nimport { dofetch3 } from '#common/dofetch' // fetch wrapper for the meta request\nimport 'ol/ol.css' // OpenLayers base styles (zoom buttons etc.)\nimport OlMap from 'ol/Map.js' // the pan/zoom map widget\nimport OlView from 'ol/View.js' // its camera (resolutions + extent)\nimport TileLayer from 'ol/layer/Tile.js' // layer that mosaics the fetched tiles\nimport Zoomify from 'ol/source/Zoomify.js' // tile source matching wsi_tile.py's tier math\nimport type { SpatialImage, WsiImage } from '#types'\nimport type Settings from '../Settings.ts'\nimport type { ViewData } from '../viewModel/ViewModel.ts'\nimport type { WsiInteractions } from '../interactions/WsiInteractions.ts'\n\n/** Renders the sample table and, when a sample is selected, tabs for its\n images (one per image folder on disk, shown when there are several) and an\n OpenLayers pan/zoom viewer for the selected image via the openslide-backed\n wsitiles route (no tile server sidecar, no auth). */\nexport class View {\n\tconstructor(\n\t\treadonly dom: { table: any; viewer: any; error: any },\n\t\treadonly viewData: ViewData,\n\t\t/** the selected sample's images from termdb/wsiBySample */\n\t\treadonly images: (WsiImage | SpatialImage)[],\n\t\treadonly settings: Settings,\n\t\treadonly interactions: WsiInteractions,\n\t\treadonly vocab: { genome: string; dslabel: string }\n\t) {}\n\n\tasync render() {\n\t\tthis.renderSampleTable() // the pick-a-sample table\n\t\tawait this.renderViewer() // tabs + map for the selected sample/image\n\t}\n\n\tprivate renderSampleTable() {\n\t\tthis.dom.table.selectAll('*').remove() // full re-render on every state change\n\t\trenderTable({\n\t\t\tdiv: this.dom.table,\n\t\t\tcolumns: this.viewData.columns,\n\t\t\trows: this.viewData.rows,\n\t\t\tsingleMode: true, // radio buttons: one sample viewed at a time\n\t\t\tselectedRows: this.settings.selectedSampleIndex != -1 ? [this.settings.selectedSampleIndex] : [],\n\t\t\tnoButtonCallback: index => this.interactions.selectSample(index),\n\t\t\tresize: true,\n\t\t\tstriped: true,\n\t\t\tmaxHeight: '30vh',\n\t\t\theader: { style: { 'text-transform': 'capitalize' } }\n\t\t})\n\t}\n\n\tprivate async renderViewer() {\n\t\tconst holder = this.dom.viewer\n\t\tholder.selectAll('*').remove() // discard the previous map/tabs\n\n\t\tconst sample = this.viewData.selectedSample // row picked in the table\n\t\tconst selected = this.settings.selectedImageIndex // tab picked by the user\n\t\tconst image = this.images[selected] ?? this.images[0] // fall back to the first image\n\t\tif (!sample || !image) return // nothing to show\n\n\t\t// a tab per image (labelled by its folder name on disk), mirroring the\n\t\t// singleCell chart's per-sample tabs; always shown so the user sees how\n\t\t// many images the sample has, and picking one re-renders the viewer\n\t\t// fileName is <imageName>/<file> in both roots\n\t\tconst imageName = (f: string) => f.split('/').slice(-2)[0] || f // the image's folder name\n\t\tnew Tabs({\n\t\t\tholder: holder.append('div'), // tab strip sits above the map\n\t\t\ttabsPosition: 'horizontal',\n\t\t\ttabs: this.images.map((img, i) => ({\n\t\t\t\tlabel: imageName(img.fileName), // e.g. 'image1'\n\t\t\t\tactive: i == (this.images[selected] ? selected : 0), // highlight the shown image\n\t\t\t\tcallback: () => this.interactions.selectImage(i) // dispatch -> re-render with image i\n\t\t\t}))\n\t\t}).main() // render the tabs now\n\n\t\t// query params match the wsitiles route (server/src/routes/wsitiles.ts);\n\t\t// the server resolves the file inside the sample's subfolder of the w2\n\t\t// root matching imageType (folder for spatial, wsiFolder for wsi), so\n\t\t// same-named paths in both roots can't select the wrong slide\n\t\tconst params = `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${this.vocab.dslabel}&genome=${\n\t\t\tthis.vocab.genome\n\t\t}&sample_id=${encodeURIComponent(sample.sampleId)}&imageType=${image.type}`\n\n\t\tif (image.type == 'spatial') {\n\t\t\t// spatial (Xenium) image: reuse the direct viewer, which draws the\n\t\t\t// boundary/expression overlays, addressing the slide via the dataset.\n\t\t\t// Burger-menu settings override the dataset's values (null = not edited yet)\n\t\t\tconst s = this.settings\n\t\t\t// gene list to overlay: checkbox off = none; field never edited = dataset default\n\t\t\tconst genes = s.showGeneExpression ? s.geneExpression ?? image.geneExpression : undefined\n\t\t\tconst direct = await import('../wsi.direct') // lazy-load the overlay viewer\n\t\t\tawait direct.init(\n\t\t\t\t{\n\t\t\t\t\tslideQuery: params,\n\t\t\t\t\tlabel: image.fileName,\n\t\t\t\t\t// expression fills need the cell polygons even when their strokes are hidden\n\t\t\t\t\tcellBoundaries: s.showCellBoundaries || genes ? image.cellBoundaries : undefined,\n\t\t\t\t\thideCellStrokes: !s.showCellBoundaries,\n\t\t\t\t\tnucleusBoundaries: s.showNucleusBoundaries ? image.nucleusBoundaries : undefined,\n\t\t\t\t\tgeneExpressionFile: image.geneExpressionFile,\n\t\t\t\t\tgeneExpression: s.spatialMode == 'gene_groups' ? undefined : genes,\n\t\t\t\t\tgeneGroups: s.spatialMode == 'gene_groups' ? genes : undefined,\n\t\t\t\t\tannotationLevel: s.annotationLevel ?? image.annotationLevel,\n\t\t\t\t\twidth: '100%',\n\t\t\t\t\theight: this.settings.viewerHeight\n\t\t\t\t},\n\t\t\t\tholder\n\t\t\t)\n\t\t\treturn\n\t\t}\n\n\t\t// slide dimensions are needed before tiles can be requested\n\t\tconst meta = await dofetch3(`wsitiles/meta?${params}`)\n\t\tif (!meta || meta.error || meta.status === 'error') {\n\t\t\tthis.dom.error.text(`Error loading ${image.fileName}: ${meta?.error || 'failed to load slide metadata'}`)\n\t\t\treturn\n\t\t}\n\n\t\tconst [w, h] = meta.slide_dimensions // level-0 slide size in px\n\t\t// server origin for tile URLs ('' when same-origin); trailing slashes trimmed\n\t\tconst host = (sessionStorage.getItem('hostURL') || (window as any).testHost || '').replace(/\\/+$/, '')\n\n\t\tconst source = new Zoomify({\n\t\t\t// {z}/{x}/{y} hit wsitiles/tile; the unused {TileGroup} token only satisfies\n\t\t\t// OpenLayers' requirement that a {TileGroup}/{tileIndex} placeholder be present.\n\t\t\t// v=<slide mtime>: tiles are served immutable, so a regenerated slide must\n\t\t\t// change the URL to bust the browser cache\n\t\t\turl: `${host}/wsitiles/tile/{z}/{x}/{y}?${params}&v=${meta.version || 0}&_={TileGroup}`,\n\t\t\tsize: [w, h], // OL derives the tier count from this, same math as wsi_tile.py\n\t\t\tcrossOrigin: 'anonymous', // tiles come from the API origin, not the page's\n\t\t\tzDirection: -1 // pick the sharper tier when between two zoom levels\n\t\t})\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\tconst mapDiv = holder.append('div').style('width', '100%').style('height', this.settings.viewerHeight)\n\t\tconst map = new OlMap({\n\t\t\ttarget: mapDiv.node(), // mount the map into the plot's viewer div\n\t\t\tlayers: [new TileLayer({ source })], // OL fetches+mosaics tiles as the user pans/zooms\n\t\t\tview: new OlView({ 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\t}\n}\n", "/** User interactions for the wsi plot; each one dispatches a plot_edit so the\n change flows through app state and main() re-renders. */\nexport class WsiInteractions {\n\tconstructor(readonly app: any, readonly id: string) {}\n\n\t/** a sample row was picked in the table; image selection resets to its first image */\n\tselectSample(index: number) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { settings: { wsi: { selectedSampleIndex: index, selectedImageIndex: 0 } } }\n\t\t})\n\t}\n\n\t/** an image tab was picked for the selected sample */\n\tselectImage(index: number) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { settings: { wsi: { selectedImageIndex: index } } }\n\t\t})\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport type { BasePlotConfig, MassState } from '#mass/types/mass'\nimport type { SpatialImage } from '#types'\nimport { dofetch3 } from '#common/dofetch' // gene-name discovery from the expression h5\nimport { controlsInit } from '../controls'\nimport type Settings from './Settings.ts'\nimport { Model } from './model/Model'\nimport { ViewModel } from './viewModel/ViewModel'\nimport { View } from './view/View'\nimport { WsiInteractions } from './interactions/WsiInteractions'\n\n/** Mass plot listing every sample in the dataset that has whole-slide images\n (the wsisamples route performs the per-sample check), with a pan/zoom viewer\n for the selected sample's slide. Architecture mirrors plots/corrVolcano:\n Model (server data) -> ViewModel (view data) -> View (render), with\n interactions dispatching state edits. */\ntype WsiDom = {\n\tdiv: any\n\tcontrols: any\n\terror: any\n\ttable: any\n\tviewer: any\n\theader?: any\n}\n\nclass Wsi extends PlotBase implements RxComponent {\n\tstatic type = 'wsi'\n\n\ttype: string\n\tdom: WsiDom\n\tinteractions?: WsiInteractions\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = Wsi.type\n\t\tconst holder = opts.holder.classed('sjpp-wsi-main', true)\n\t\tconst div = holder.append('div').style('padding', '5px')\n\t\tthis.dom = {\n\t\t\tdiv,\n\t\t\t// burger menu for spatial viewer settings; hidden until a spatial image is shown\n\t\t\tcontrols: div.append('div').attr('id', 'sjpp-wsi-controls').style('display', 'none'),\n\t\t\terror: div.append('div').attr('id', 'sjpp-wsi-error').style('opacity', 0.75),\n\t\t\ttable: div.append('div').attr('id', 'sjpp-wsi-table'),\n\t\t\tviewer: div.append('div').attr('id', 'sjpp-wsi-viewer')\n\t\t}\n\t\tif (opts.header)\n\t\t\tthis.dom.header = opts.header.text('WHOLE SLIDE IMAGES').style('font-size', '0.7em').style('opacity', 0.6)\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\tvocab: appState.vocab,\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.interactions = new WsiInteractions(this.app, this.id)\n\t}\n\n\tasync main() {\n\t\tconst config = structuredClone(this.state.config) // this plot's slice of app state\n\t\tif (config.childType != this.type && config.chartType != this.type) return // not for this plot\n\t\tif (!this.interactions) throw 'Interactions not initialized [wsi main()]'\n\n\t\tconst settings: Settings = config.settings.wsi // selection + overlay settings\n\t\tthis.dom.error.text('') // clear any previous error banner\n\n\t\t// which samples have whole-slide images on disk?\n\t\tconst model = new Model(this.state.vocab.genome, this.state.vocab.dslabel)\n\t\tconst data = await model.getData() // termdb/wsiBySample sample listing\n\t\tif (!data || data.error || !data.samples?.length) {\n\t\t\tthis.dom.table.selectAll('*').remove() // nothing to show; clear the ui\n\t\t\tthis.dom.viewer.selectAll('*').remove()\n\t\t\tthis.dom.error.style('padding', '20px').text(data?.error || 'No samples with whole-slide images.')\n\t\t\treturn\n\t\t}\n\n\t\t// shape for rendering\n\t\tconst viewModel = new ViewModel(data.samples, settings)\n\n\t\t// the selected sample's images from termdb/wsiBySample; on launch the\n\t\t// first sample is selected by default so its first image displays\n\t\tconst selectedSample = viewModel.viewData.selectedSample\n\t\tconst images = selectedSample ? (await model.getImages(selectedSample.sampleId)).images ?? [] : []\n\n\t\t// spatial image: rename the sandbox header and show the burger menu\n\t\tconst image = images[settings.selectedImageIndex] ?? images[0] // the image being viewed\n\t\tconst isSpatial = image?.type == 'spatial' // drives header text + burger visibility\n\t\tthis.dom.header?.text(isSpatial ? 'SPATIAL VIEWER' : 'WHOLE SLIDE IMAGES')\n\t\tif (isSpatial) {\n\t\t\tconst spImage = image as SpatialImage\n\t\t\t// gene names discovered from the expression h5 itself, so the burger\n\t\t\t// menu offers/validates genes that actually exist in the data\n\t\t\tconst genes = await this.fetchGeneNames(spImage, selectedSample!.sampleId)\n\t\t\t// seed the burger menu's gene/level fields once (null = never edited)\n\t\t\t// so the shown values match the overlay and can be edited or cleared;\n\t\t\t// re-renders once with the seeded state\n\t\t\tif (settings.geneExpression == null) {\n\t\t\t\t// the dataset's configured default is only an override: keep the\n\t\t\t\t// genes of it that exist in the file, else fall back to the file's\n\t\t\t\t// first gene, so the default is never a gene the data lacks\n\t\t\t\tconst configured = (spImage.geneExpression || '')\n\t\t\t\t\t.split(',')\n\t\t\t\t\t.map(s => s.trim())\n\t\t\t\t\t.filter(g => genes.includes(g))\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\twsi: {\n\t\t\t\t\t\t\t\tgeneExpression: configured.join(',') || genes[0] || '',\n\t\t\t\t\t\t\t\tannotationLevel: settings.annotationLevel ?? spImage.annotationLevel\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!this.components.controls) await this.setControls()\n\t\t\tthis.addGeneDatalist() // autocomplete on the Genes field from the discovered names\n\t\t}\n\t\tthis.dom.controls.style('display', isSpatial ? 'inline-block' : 'none')\n\n\t\tawait new View(this.dom, viewModel.viewData, images, settings, this.interactions, this.state.vocab).render()\n\t}\n\n\t/** gene names available in the current image's expression h5, cached per file */\n\tprivate geneNames: string[] = []\n\tprivate geneNamesFile?: string\n\n\t/** Discover the genes present in the image's cell_feature_matrix h5 via\n\t wsitiles/genenames (same slide-scoped access checks as genecounts).\n\t Returns [] when the image has no expression file or the request fails. */\n\tprivate async fetchGeneNames(image: SpatialImage, sampleId: string): Promise<string[]> {\n\t\tif (!image.geneExpressionFile) return []\n\t\tif (this.geneNamesFile == image.geneExpressionFile) return this.geneNames // cached\n\t\tconst v = this.state.vocab\n\t\tconst params =\n\t\t\t`wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}` +\n\t\t\t`&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&file=${encodeURIComponent(\n\t\t\t\timage.geneExpressionFile\n\t\t\t)}`\n\t\tconst r = await dofetch3(`wsitiles/genenames?${params}`).catch(() => null)\n\t\tthis.geneNames = Array.isArray(r?.genes) ? r.genes : [] // failure = no discovery, config still works\n\t\tthis.geneNamesFile = image.geneExpressionFile\n\t\treturn this.geneNames\n\t}\n\n\t/** Attach the discovered gene names to the Genes text input as a native\n\t datalist, so typing autocompletes to genes that exist in the data.\n\t (Autocomplete applies to the whole field, i.e. the first gene of a\n\t comma-separated list \u2014 later genes are typed without suggestions.) */\n\tprivate addGeneDatalist() {\n\t\tif (!this.geneNames.length) return\n\t\tconst input = this.dom.controls.select('input[type=text]').node() as HTMLInputElement | null\n\t\tif (!input) return // controls not rendered (shouldn't happen)\n\t\tconst id = `sjpp-wsi-genes-${this.id}`\n\t\tdocument.getElementById(id)?.remove() // rebuild when the image (and its genes) changed\n\t\tconst dl = document.createElement('datalist')\n\t\tdl.id = id\n\t\tfor (const g of this.geneNames) {\n\t\t\tconst opt = document.createElement('option')\n\t\t\topt.value = g\n\t\t\tdl.appendChild(opt)\n\t\t}\n\t\tinput.after(dl)\n\t\tinput.setAttribute('list', id) // link the input to its suggestions\n\t}\n\n\t/** Burger menu with the spatial overlay settings; fields are pre-seeded\n\t with defaults discovered from the data by main() before this runs. */\n\tprivate async setControls() {\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.controls,\n\t\t\tinputs: [\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Nucleus boundaries',\n\t\t\t\t\ttitle: 'Show or hide the nucleus segmentation overlay',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'showNucleusBoundaries',\n\t\t\t\t\tboxLabel: 'show'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Cell boundaries',\n\t\t\t\t\ttitle: 'Show or hide the cell segmentation overlay',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'showCellBoundaries',\n\t\t\t\t\tboxLabel: 'show'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Gene expression',\n\t\t\t\t\ttitle: 'Show or hide the gene expression overlay',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'showGeneExpression',\n\t\t\t\t\tboxLabel: 'show'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Genes',\n\t\t\t\t\ttitle: 'Comma-separated gene names to overlay',\n\t\t\t\t\ttype: 'text',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'geneExpression',\n\t\t\t\t\tplaceholder: 'gene1,gene2,\u2026'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Overlay mode',\n\t\t\t\t\ttitle: 'Color each gene separately (gene_expression), or sum all genes into one overlay (gene_groups)',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'spatialMode',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Per gene', value: 'gene_expression' },\n\t\t\t\t\t\t{ label: 'Gene group', value: 'gene_groups' }\n\t\t\t\t\t]\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Annotation level',\n\t\t\t\t\ttitle: 'Show boundaries only within the n most zoomed-in levels; 0 = always show',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'annotationLevel',\n\t\t\t\t\tmin: 0,\n\t\t\t\t\tstep: 1\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n}\n\nexport const wsiInit = getCompInit(Wsi)\nexport const componentInit = wsiInit\n\nexport function getDefaultWsiSettings(overrides = {}): Settings {\n\tconst defaults: Settings = {\n\t\tselectedSampleIndex: 0, // first sample selected on launch\n\t\tselectedImageIndex: 0, // the sample's first image displayed by default\n\t\tviewerHeight: '70vh',\n\t\t// spatial overlay settings; null = fall back to the dataset's values\n\t\tshowCellBoundaries: true,\n\t\tshowNucleusBoundaries: true,\n\t\tshowGeneExpression: true,\n\t\tgeneExpression: null,\n\t\tannotationLevel: null,\n\t\tspatialMode: 'gene_expression'\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts: any, _app: any) {\n\tconst config = {\n\t\tchartType: 'wsi',\n\t\tsettings: {\n\t\t\twsi: getDefaultWsiSettings(opts.overrides)\n\t\t},\n\t\thidePlotFilter: true\n\t}\n\treturn copyMerge(config, opts)\n}\n"],
-  "mappings": 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package/dist/adSandbox-ZJQ5ZW2T.js

@@ -1,33 +0,0 @@
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-import "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.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";
-export {
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