@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/Wsi-PB77PVAA.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' // fetch wrapper for the termdb route\nimport type { WsiBySampleResponse } from '#types' // the route's response shape\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) {} // both requests address the dataset\n\n\t/** Every sample in the dataset that has at least one PLAIN slide on disk\n\t (a wsiFolder subfolder with a slide), with plain-slide counts. Spatial-only\n\t samples are not listed \u2014 spatial images are viewed through the sc app,\n\t which fetches them per sample via getImages(). */\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). imageType restricts the\n\t enumeration to that root ('wsi' = wsiFolder, 'spatial' = folder) so the\n\t other tree is never read; omitted = both kinds. */\n\tasync getImages(sample_id: string, imageType?: 'spatial' | 'wsi'): Promise<WsiBySampleResponse> {\n\t\treturn await dofetch3('termdb/wsiBySample', {\n\t\t\tbody: { genome: this.genome, dslabel: this.dslabel, sample_id, imageType } // sample_id = list its images\n\t\t})\n\t}\n}\n", "import type { WsiSampleSummary } from '#types' // per-sample listing from wsiBySample\nimport type { TableColumn, TableRow } from '#dom' // renderTable's row/column shapes\nimport type Settings from '../Settings.ts' // plot settings (selected sample index)\n\n/** what View.render() consumes */\nexport type ViewData = {\n\t/** sample table skeleton for renderTable() */\n\tcolumns: TableColumn[]\n\t/** one row per sample with images */\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 // built once in the constructor, read by View\n\n\tconstructor(samples: WsiSampleSummary[], settings: Settings) {\n\t\t// table skeleton + current selection, derived from server data and 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' // the two image kinds wsiBySample returns\nimport type Settings from '../Settings.ts' // burger-menu + selection settings\nimport type { ViewData } from '../viewModel/ViewModel.ts' // shaped sample table data\nimport type { WsiInteractions } from '../interactions/WsiInteractions.ts' // state-edit dispatchers\nimport { addScaleBar } from '../scaleBar' // bottom-right \u00B5m scale bar, every image (spatial or plain)\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\t/** the plot's table/viewer/error divs (created by Wsi's constructor) */\n\t\treadonly dom: { table: any; viewer: any; error: any },\n\t\t/** shaped sample table rows + current selection */\n\t\treadonly viewData: ViewData,\n\t\t/** the selected sample's images from termdb/wsiBySample */\n\t\treadonly images: (WsiImage | SpatialImage)[],\n\t\t/** burger-menu + selection settings */\n\t\treadonly settings: Settings,\n\t\t/** dispatchers for sample/image selection */\n\t\treadonly interactions: WsiInteractions,\n\t\t/** addresses the dataset in wsitiles queries */\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, // mount point\n\t\t\tcolumns: this.viewData.columns, // Sample | Images\n\t\t\trows: this.viewData.rows, // one row per sample with images\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), // row click = select sample\n\t\t\tresize: true, // user-resizable table\n\t\t\tstriped: true, // alternating row shading\n\t\t\tmaxHeight: '30vh', // table scrolls; the viewer keeps the space below\n\t\t\theader: { style: { 'text-transform': 'capitalize' } } // 'sample' -> 'Sample'\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// genes always load so the hover tooltip reports their counts; the\n\t\t\t// 'Gene expression' checkbox only controls the fill overlay\n\t\t\tconst genes = s.geneExpression ?? image.geneExpression\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, // addresses the slide through the dataset (no direct-path gate)\n\t\t\t\t\t// lets the neighborhood-enrichment panel offer a similar-region\n\t\t\t\t\t// search against the dataset's other spatial samples\n\t\t\t\t\tgenome: this.vocab.genome,\n\t\t\t\t\tdslabel: this.vocab.dslabel,\n\t\t\t\t\tsampleId: sample.sampleId,\n\t\t\t\t\tlabel: image.fileName, // display name in the info line\n\t\t\t\t\tspatialData: image.spatialData, // the consolidated h5ad, source of every overlay\n\t\t\t\t\thideCellStrokes: !s.showCellBoundaries, // polygons without their green outlines\n\t\t\t\t\thideNucleusStrokes: !s.showNucleusBoundaries, // skip the nucleus overlay entirely\n\t\t\t\t\tshowCellTypes: s.showCellTypes, // fill cells by their cell_type annotation\n\t\t\t\t\tcellTypeFilter: s.cellTypeFilter ?? undefined, // 'Types shown' dropdowns; []/null = all\n\t\t\t\t\tgeneExpression: s.spatialMode == 'gene_groups' ? undefined : genes, // one overlay per gene\n\t\t\t\t\tgeneGroups: s.spatialMode == 'gene_groups' ? genes : undefined, // or one summed overlay\n\t\t\t\t\thideExpressionFills: !s.showGeneExpression, // checkbox off = hover counts only, no fills\n\t\t\t\t\tannotationLevel: s.annotationLevel ?? image.annotationLevel, // burger overrides dataset\n\t\t\t\t\tcellCountLimit: s.cellCountLimit ?? undefined, // null = wsi.direct.ts's own default\n\t\t\t\t\twidth: '100%', // fill the sandbox\n\t\t\t\t\theight: this.settings.viewerHeight // e.g. 70vh\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\t// surface the failure in the plot's error div; no viewer without geometry\n\t\t\tthis.dom.error.text(`Error loading ${image.fileName}: ${meta?.error || 'failed to load slide metadata'}`)\n\t\t\treturn\n\t\t}\n\n\t\tconst [w, h] = meta.slide_dimensions // level-0 slide size in px\n\t\t// server origin for tile URLs ('' when same-origin); trailing slashes trimmed\n\t\tlet host = sessionStorage.getItem('hostURL') || (window as any).testHost || ''\n\t\twhile (host.endsWith('/')) host = host.slice(0, -1)\n\n\t\tconst source = new Zoomify({\n\t\t\t// {z}/{x}/{y} hit wsitiles/tile; the unused {TileGroup} token only satisfies\n\t\t\t// OpenLayers' requirement that a {TileGroup}/{tileIndex} placeholder be present.\n\t\t\t// v=<slide mtime>: tiles are served immutable, so a regenerated slide must\n\t\t\t// change the URL to bust the browser cache\n\t\t\turl: `${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\taddScaleBar(map, Array.isArray(meta.mpp) && meta.mpp.length === 2 ? meta.mpp[0] : undefined)\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) {} // rx app + this plot's id, for dispatching\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' // rx plumbing\nimport { PlotBase } from '../PlotBase' // shared mass-plot base class\nimport type { BasePlotConfig, MassState } from '#mass/types/mass' // app state shapes\nimport type { SpatialImage } from '#types' // spatial image entry from wsiBySample\nimport { dofetch3 } from '#common/dofetch' // gene-name/cell-type discovery requests\nimport { controlsInit } from '../controls' // burger-menu builder\nimport type Settings from './Settings.ts' // this plot's settings shape\nimport { Model } from './model/Model' // server data access\nimport { ViewModel } from './viewModel/ViewModel' // shapes data for rendering\nimport { View } from './view/View' // renders table + viewer\nimport { WsiInteractions } from './interactions/WsiInteractions' // state-edit dispatchers\n\n/** Mass plot listing every sample in the dataset that has plain whole-slide\n images, with a pan/zoom viewer for the selected sample's slide. Spatial\n images are excluded here \u2014 they are viewed through the single-cell app's\n Spatial button, which spawns this same plot in fixed-sample mode\n (config.sample.sID). Architecture mirrors plots/corrVolcano:\n Model (server data) -> ViewModel (view data) -> View (render), with\n interactions dispatching state edits. */\ntype WsiDom = {\n\tdiv: any // the plot's outer container\n\tcontrols: any // burger menu holder (spatial only)\n\terror: any // inline error banner\n\ttable: any // pick-a-sample table\n\tviewer: any // tabs + map\n\theader?: any // sandbox header, renamed per image kind\n}\n\nclass Wsi extends PlotBase implements RxComponent {\n\tstatic type = 'wsi' // rx chart type name\n\n\ttype: string // instance copy of the chart type\n\tdom: WsiDom // the divs built in the constructor\n\tinteractions?: WsiInteractions // created in init()\n\t/** showCellTypes of the previous render, to tell which exclusive fill\n\t checkbox was just toggled when both end up checked */\n\tprivate prevShowCellTypes = false\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api) // PlotBase wires app/id/opts\n\t\tthis.type = Wsi.type // rx uses this to route state updates\n\t\tconst holder = opts.holder.classed('sjpp-wsi-main', true) // sandbox mount point\n\t\tconst div = holder.append('div').style('padding', '5px') // the plot's own container\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), // inline errors\n\t\t\ttable: div.append('div').attr('id', 'sjpp-wsi-table'), // sample table mount\n\t\t\tviewer: div.append('div').attr('id', 'sjpp-wsi-viewer') // tabs + map mount\n\t\t}\n\t\tif (opts.header)\n\t\t\t// sandbox title; main() renames it to SPATIAL VIEWER for spatial images\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\t/** the app-state slice this plot reacts to */\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id) // this plot's config\n\t\tif (!config) {\n\t\t\t// the plot was registered wrong; fail loudly\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, // genome + dslabel for server requests\n\t\t\tconfig // the plot's own settings\n\t\t}\n\t}\n\n\t/** rx lifecycle: one-time setup before the first main() */\n\tasync init() {\n\t\tthis.interactions = new WsiInteractions(this.app, this.id) // dispatchers used by the view\n\t}\n\n\t/** rx lifecycle: re-renders the whole plot on every relevant state change */\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\n\t\t// the cell-type and gene-expression FILLS are mutually exclusive\n\t\t// (unreadable on top of each other): when both boxes end up checked, the\n\t\t// one just toggled wins and the other is unchecked. Unchecked 'Gene\n\t\t// expression' only hides the fills \u2014 hover counts stay (View.ts).\n\t\tif (settings.showCellTypes && settings.showGeneExpression) {\n\t\t\t// whichever was already on before this edit is the one to turn off\n\t\t\tconst off = this.prevShowCellTypes ? 'showCellTypes' : 'showGeneExpression'\n\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { settings: { wsi: { [off]: false } } } })\n\t\t\treturn\n\t\t}\n\t\tthis.prevShowCellTypes = settings.showCellTypes\n\n\t\tthis.dom.error.text('') // clear any previous error banner\n\n\t\t// fixed sample: one already-chosen sample, no sample picker. Which image\n\t\t// kind it shows is the spawner's choice: the sc app's Spatial button\n\t\t// spawns the default 'spatial'; the omnisearch \"Whole Slide Images\"\n\t\t// action passes config.imageType 'wsi' for the sample's plain slides\n\t\tconst fixedSample = config.sample?.sID\n\t\tconst fixedKind: 'spatial' | 'wsi' = config.imageType == 'wsi' ? 'wsi' : 'spatial'\n\t\tconst model = new Model(this.state.vocab.genome, this.state.vocab.dslabel)\n\t\tlet samples\n\t\tif (fixedSample) {\n\t\t\tthis.dom.table.style('display', 'none') // the sample is already chosen\n\t\t\tsettings.selectedSampleIndex = 0 // fixed mode always selects its sole pinned sample\n\t\t\tsamples = [{ sampleId: fixedSample, count: 1 }] // count unused (table hidden)\n\t\t} else {\n\t\t\t// which samples have whole-slide images on disk?\n\t\t\tconst data = await model.getData() // termdb/wsiBySample sample listing\n\t\t\tif (!data || data.error || !data.samples?.length) {\n\t\t\t\tthis.dom.table.selectAll('*').remove() // nothing to show; clear the ui\n\t\t\t\tthis.dom.viewer.selectAll('*').remove() // and any stale viewer\n\t\t\t\tthis.dom.error.style('padding', '20px').text(data?.error || 'No samples with whole-slide images.') // say why\n\t\t\t\treturn\n\t\t\t}\n\t\t\tsamples = data.samples\n\t\t}\n\n\t\t// shape for rendering\n\t\tconst viewModel = new ViewModel(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\t// spatial images are viewed only through the sc app's Spatial button\n\t\t// (fixed-sample mode); the standalone plot shows plain slides only.\n\t\t// The route enumerates just the requested root, so neither mode's\n\t\t// cost or failures depend on the other tree\n\t\tconst imageData = selectedSample\n\t\t\t? await model.getImages(selectedSample.sampleId, fixedSample ? fixedKind : 'wsi')\n\t\t\t: undefined\n\t\tif (imageData?.error) throw new Error(imageData.error)\n\t\tconst images = imageData?.images ?? []\n\t\tif (fixedSample && !images.length) {\n\t\t\tthis.dom.viewer.selectAll('*').remove()\n\t\t\tthis.dom.error\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.text(`No ${fixedKind == 'spatial' ? 'spatial image' : 'whole-slide image'} for sample ${fixedSample}.`)\n\t\t\treturn\n\t\t}\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 // narrowed: spatial images carry companion paths\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// cell types discovered by the meta request, for the type-filter dropdowns\n\t\t\tconst cellTypes = await this.fetchCellTypes(spImage, selectedSample!.sampleId)\n\t\t\t// switching images can leave cellTypeFilter naming types the new\n\t\t\t// image lacks: the dropdowns would show 'All types' while the viewer\n\t\t\t// filters every cell out. Persist the cleaned selection instead\n\t\t\t// (only when discovery succeeded \u2014 [] may just mean the request failed)\n\t\t\tif (settings.cellTypeFilter?.length && cellTypes.length) {\n\t\t\t\tconst cleaned = settings.cellTypeFilter.filter(t => cellTypes.includes(t)) // types this image has\n\t\t\t\tif (cleaned.length != settings.cellTypeFilter.length) {\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { settings: { wsi: { cellTypeFilter: cleaned } } }\n\t\t\t\t\t})\n\t\t\t\t\treturn // re-renders with the reconciled filter\n\t\t\t\t}\n\t\t\t}\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 || '') // dataset's comma-separated default genes\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)) // keep only genes the h5 actually has\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t// one-time seeding edit; triggers a re-render with the seeded values\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\t// dataset default (w2.cellTypes); the burger checkbox overrides\n\t\t\t\t\t\t\t\t// after. Fills are mutually exclusive, so cell types on means\n\t\t\t\t\t\t\t\t// expression fills off (hover counts stay either way)\n\t\t\t\t\t\t\t\tshowCellTypes: spImage.cellTypes ?? settings.showCellTypes,\n\t\t\t\t\t\t\t\tshowGeneExpression: spImage.cellTypes ? false : settings.showGeneExpression\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() // build the burger menu once\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') // burger only for spatial\n\n\t\tawait new View(this.dom, viewModel.viewData, images, settings, this.interactions, this.state.vocab).render() // draw\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 // the h5 the cache was built from\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\tconst src = image.spatialData // the consolidated h5ad holds the expression matrix\n\t\tif (!src) return [] // no expression source, nothing to discover\n\t\tif (this.geneNamesFile == src) return this.geneNames // cached\n\t\tconst v = this.state.vocab // genome + dslabel for the request\n\t\tconst params = // standard wsitiles slide addressing + the expression file\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(src)}`\n\t\tconst r = await dofetch3(`wsitiles/genenames?${params}`).catch(() => null)\n\t\tthis.geneNames = Array.isArray(r?.genes) ? r.genes : [] // failure = no discovery, config still works\n\t\tthis.geneNamesFile = src // remember which file the cache is for\n\t\treturn this.geneNames\n\t}\n\n\t/** cell types available in the current image's annotations CSV, cached per file */\n\tprivate cellTypeNames: string[] = []\n\tprivate cellTypesFile?: string // the CSV the cache was built from\n\n\t/** Discover the distinct cell_type values of the image's per-cell\n\t annotations CSV via the meta request (?cellAnnotations= makes\n\t wsitiles/meta scan it). Returns [] when the image has no annotations\n\t file or the request fails. */\n\tprivate async fetchCellTypes(image: SpatialImage, sampleId: string): Promise<string[]> {\n\t\tconst src = image.spatialData // the consolidated h5ad holds the annotations\n\t\tif (!src) {\n\t\t\t// this image has no annotations: clear the cache so stale types\n\t\t\t// from a previously shown image don't populate the dropdowns\n\t\t\tthis.cellTypeNames = []\n\t\t\tthis.cellTypesFile = undefined\n\t\t\treturn this.cellTypeNames\n\t\t}\n\t\tif (this.cellTypesFile == src) return this.cellTypeNames // cached\n\t\tconst v = this.state.vocab // genome + dslabel for the request\n\t\tconst params = // standard wsitiles slide addressing + the annotations source to scan\n\t\t\t`wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}` +\n\t\t\t`&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&cellAnnotations=${encodeURIComponent(src)}`\n\t\tconst r = await dofetch3(`wsitiles/meta?${params}`).catch(() => null)\n\t\tthis.cellTypeNames = Array.isArray(r?.cellTypes) ? r.cellTypes : [] // failure = no dropdowns, overlay still works\n\t\tthis.cellTypesFile = src // remember which file the cache is for\n\t\treturn this.cellTypeNames\n\t}\n\n\t/** Attach the discovered gene names to the Genes text input as a native\n\t datalist, so typing autocompletes to genes that exist in the data.\n\t (Autocomplete applies to the whole field, i.e. the first gene of a\n\t comma-separated list \u2014 later genes are typed without suggestions.) */\n\tprivate addGeneDatalist() {\n\t\tif (!this.geneNames.length) return // nothing discovered, no suggestions\n\t\tconst input = this.dom.controls.select('input[type=text]').node() as HTMLInputElement | null // the Genes field\n\t\tif (!input) return // controls not rendered (shouldn't happen)\n\t\tconst id = `sjpp-wsi-genes-${this.id}` // per-plot-instance datalist id\n\t\tdocument.getElementById(id)?.remove() // rebuild when the image (and its genes) changed\n\t\tconst dl = document.createElement('datalist') // native autocomplete source\n\t\tdl.id = id // the id the input's list attribute points to\n\t\tfor (const g of this.geneNames) {\n\t\t\tconst opt = document.createElement('option') // one suggestion per gene\n\t\t\topt.value = g // the text autocomplete inserts\n\t\t\tdl.appendChild(opt)\n\t\t}\n\t\tinput.after(dl) // datalist must be in the DOM to work\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, // rx app the inputs dispatch through\n\t\t\tid: this.id, // this plot's id in app state\n\t\t\tholder: this.dom.controls, // the burger-menu div\n\t\t\tinputs: [\n\t\t\t\t{\n\t\t\t\t\t// checkbox: toggle the blue nucleus outlines\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\t// checkbox: toggle the green cell outlines\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\t// checkbox: toggle the categorical cell-type fills (mutually\n\t\t\t\t\t// exclusive with the gene expression fills, enforced in main())\n\t\t\t\t\tlabel: 'Cell types',\n\t\t\t\t\ttitle: 'Fill cells by their cell_type from the annotations CSV (when present)',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'wsi',\n\t\t\t\t\tsettingsKey: 'showCellTypes',\n\t\t\t\t\tboxLabel: 'show'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t// chained dropdowns: one per selected type, plus an add-dropdown of\n\t\t\t\t\t// the remaining types that appears once the previous is picked.\n\t\t\t\t\t// No selection = all types. Hidden when the overlay is off or the\n\t\t\t\t\t// image's CSV has no cell_type column.\n\t\t\t\t\tlabel: 'Types shown',\n\t\t\t\t\ttitle: 'Fill only the selected cell types; no selection = all types',\n\t\t\t\t\ttype: 'custom',\n\t\t\t\t\tsettingsKey: 'cellTypeFilter',\n\t\t\t\t\tinit: (self: any) => ({\n\t\t\t\t\t\tmain: (plot: any) => {\n\t\t\t\t\t\t\tconst td = self.dom.inputTd // the row's input cell\n\t\t\t\t\t\t\ttd.selectAll('*').remove() // rebuild the dropdowns on every state change\n\t\t\t\t\t\t\tconst types = this.cellTypeNames // discovered by fetchCellTypes for the shown image\n\t\t\t\t\t\t\tconst s: Settings = plot.settings.wsi // current settings from state\n\t\t\t\t\t\t\tif (!s.showCellTypes || !types.length) {\n\t\t\t\t\t\t\t\tself.dom.row.style('display', 'none') // overlay off / no annotation column\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tself.dom.row.style('display', 'table-row') // show the row\n\t\t\t\t\t\t\t// defensive only: main() reconciles cellTypeFilter to this\n\t\t\t\t\t\t\t// image's types before rendering, so this filter is a no-op\n\t\t\t\t\t\t\t// unless a render sneaks in mid-reconciliation\n\t\t\t\t\t\t\tconst selected = (s.cellTypeFilter || []).filter(t => types.includes(t))\n\t\t\t\t\t\t\tconst dispatch = (list: string[]) =>\n\t\t\t\t\t\t\t\t// write the new selection back to state; re-render redraws the\n\t\t\t\t\t\t\t\t// dropdowns. Stored as a LIST: type names are free text and may\n\t\t\t\t\t\t\t\t// contain commas, so a joined string would corrupt them\n\t\t\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\t\t\tconfig: { settings: { wsi: { cellTypeFilter: list } } }\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tconst addSelect = () =>\n\t\t\t\t\t\t\t\ttd\n\t\t\t\t\t\t\t\t\t.append('select')\n\t\t\t\t\t\t\t\t\t.attr('aria-label', 'Cell type filter')\n\t\t\t\t\t\t\t\t\t.style('display', 'block')\n\t\t\t\t\t\t\t\t\t.style('margin', '2px 0')\n\t\t\t\t\t\t\t\t\t.style('max-width', '180px')\n\t\t\t\t\t\t\t// one dropdown per chosen type: change replaces it, blank removes it\n\t\t\t\t\t\t\tfor (const [i, t] of selected.entries()) {\n\t\t\t\t\t\t\t\tconst sel = addSelect().on('change', function (this: HTMLSelectElement) {\n\t\t\t\t\t\t\t\t\tconst next = selected.slice() // edit a copy of the selection\n\t\t\t\t\t\t\t\t\tif (this.value) next[i] = this.value // picked a type = replace this slot\n\t\t\t\t\t\t\t\t\telse next.splice(i, 1) // picked the blank option = remove this slot\n\t\t\t\t\t\t\t\t\tdispatch(next)\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\tsel.append('option').attr('value', '').text('\u00D7 remove') // the blank remove option\n\t\t\t\t\t\t\t\t// offer this slot's own type plus every type no other slot holds\n\t\t\t\t\t\t\t\tfor (const ty of types)\n\t\t\t\t\t\t\t\t\tif (ty == t || !selected.includes(ty))\n\t\t\t\t\t\t\t\t\t\tsel\n\t\t\t\t\t\t\t\t\t\t\t.append('option')\n\t\t\t\t\t\t\t\t\t\t\t.attr('value', ty)\n\t\t\t\t\t\t\t\t\t\t\t.property('selected', ty == t) // current choice pre-selected\n\t\t\t\t\t\t\t\t\t\t\t.text(ty)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t// the next dropdown, offering the not-yet-selected types\n\t\t\t\t\t\t\tconst remaining = types.filter(ty => !selected.includes(ty))\n\t\t\t\t\t\t\tif (remaining.length) {\n\t\t\t\t\t\t\t\tconst add = addSelect().on('change', function (this: HTMLSelectElement) {\n\t\t\t\t\t\t\t\t\tif (this.value) dispatch([...selected, this.value]) // append the picked type\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\tadd\n\t\t\t\t\t\t\t\t\t.append('option')\n\t\t\t\t\t\t\t\t\t.attr('value', '') // placeholder, selecting it changes nothing\n\t\t\t\t\t\t\t\t\t.text(selected.length ? 'Add type\u2026' : 'All types')\n\t\t\t\t\t\t\t\tfor (const ty of remaining) add.append('option').attr('value', ty).text(ty) // the candidates\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\t{\n\t\t\t\t\t// checkbox: toggle the expression FILLS only \u2014 hover counts stay\n\t\t\t\t\t// either way (View.ts always loads the genes)\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\t// text field: which genes to load, with datalist autocomplete\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\t// radio: per-gene overlays vs one summed gene-group overlay\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\t// number: how many zoomed-in levels show the boundary strokes\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) // the rx component factory\nexport const componentInit = wsiInit // alias the plot loader expects\n\n/** the plot's default settings, with optional per-dataset overrides */\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', // map height in the sandbox\n\t\t// spatial overlay settings; null = fall back to the dataset's values\n\t\tshowCellBoundaries: true, // green cell outlines on\n\t\tshowNucleusBoundaries: true, // blue nucleus outlines on\n\t\tshowGeneExpression: true, // expression fills on (seeding may flip this off)\n\t\tshowCellTypes: false, // opt-in: fills all annotated cells, visually heavy\n\t\tcellTypeFilter: null, // null/[] = fill every annotated type\n\n\t\tgeneExpression: null, // null = seed from the data on first spatial render\n\t\tannotationLevel: null, // null = dataset default\n\t\tcellCountLimit: null, // null = wsi.direct.ts's own default\n\t\tspatialMode: 'gene_expression' // per-gene overlays by default\n\t}\n\treturn Object.assign(defaults, overrides) // dataset overrides win\n}\n\n/** initial plot config when the chart is launched */\nexport async function getPlotConfig(opts: any, _app: any) {\n\tconst config = {\n\t\tchartType: 'wsi', // routes state updates to this component\n\t\tsettings: {\n\t\t\twsi: getDefaultWsiSettings(opts.overrides) // defaults + dataset overrides\n\t\t},\n\t\thidePlotFilter: true // the mass filter UI doesn't apply to slides\n\t}\n\treturn copyMerge(config, opts) // launch-time opts win over defaults\n}\n"],
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-  "names": []
-}

package/dist/aboutSunburst-5Z24ODIN.js

@@ -1,93 +0,0 @@
-import {
-  SunburstChart,
-  getPlotConfig
-} from "./chunk-XSBGICK5.js";
-import {
-  LINK,
-  TEXT_DARK
-} from "./chunk-7UK7CU4F.js";
-import "./chunk-OOVVKQSD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-QRZRAMHA.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-KLJM7HE5.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-HGC4EON3.js";
-import "./chunk-QFQJO7LD.js";
-import "./chunk-2N345NXD.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/sunburst/aboutSunburst.ts
-var AboutSunburst = class {
-  constructor(holder, app, onOpen) {
-    this.app = app;
-    this.onOpen = onOpen;
-    const div = holder.append("div").attr("data-testid", "sjpp-about-sunburst").style("white-space", "normal");
-    this.chart = new SunburstChart({
-      holder: div,
-      app,
-      // the Rings box and the stats close to the chart, 12px from it on both sides
-      gap: 6,
-      // a plot of the selection is shown in the plots tab, as the About tab's launch items are
-      beforeLaunch: () => app.dispatch({ type: "tab_set", activeTab: 1 })
-    });
-  }
-  /** draw the counts of the app state's filter, unless they are shown already */
-  async update(appState) {
-    const termfilter = appState.termfilter;
-    const sig = JSON.stringify(termfilter);
-    if (sig == this.filterShown) return;
-    this.filterShown = sig;
-    this.ringsLoaded ??= getPlotConfig({}, this.app).then((config) => {
-      this.twLst = config.twLst;
-      this.renderRings();
-      return config.twLst;
-    });
-    let twLst;
-    try {
-      twLst = await this.ringsLoaded;
-    } catch (e) {
-      this.ringsLoaded = void 0;
-      this.filterShown = void 0;
-      this.chart.dom.errdiv.style("display", "").text(e?.message || String(e));
-      return;
-    }
-    const drawn = await this.chart.update({
-      genome: appState.vocab.genome,
-      dslabel: appState.vocab.dslabel,
-      twLst,
-      termfilter,
-      colors: appState.termdbConfig?.sunburst?.colors
-    });
-    if (drawn === false && this.filterShown == sig) this.filterShown = void 0;
-  }
-  /** one line per ring with its term name, then the link to the full chart */
-  renderRings() {
-    for (const [i, tw] of this.twLst.entries()) {
-      this.chart.ringLine(i).append("div").style("font-size", ".9em").style("color", TEXT_DARK).style("overflow", "hidden").style("white-space", "nowrap").style("text-overflow", "ellipsis").attr("title", tw.term.name).text(tw.term.name);
-    }
-    this.chart.dom.rings.body.append("div").attr("data-testid", "sjpp-about-sunburst-open").attr("role", "button").style("margin-top", "10px").style("font-size", ".85em").style("color", LINK).style("cursor", "pointer").text("Edit rings in the full chart \u203A").attr("tabindex", 0).on("click", this.onOpen).on("keydown", (event) => {
-      if (event.key == "Enter" || event.key == " ") {
-        event.preventDefault();
-        this.onOpen();
-      }
-    });
-    this.chart.markShownRings();
-  }
-};
-export {
-  AboutSunburst
-};
-//# sourceMappingURL=aboutSunburst-5Z24ODIN.js.map

package/dist/adSandbox-AFORHU3V.js

@@ -1,29 +0,0 @@
-import {
-  openSandbox
-} from "./chunk-G5BQJGRA.js";
-import "./chunk-OOVVKQSD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-QRZRAMHA.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-KLJM7HE5.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-HGC4EON3.js";
-import "./chunk-QFQJO7LD.js";
-import "./chunk-2N345NXD.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  openSandbox
-};
-//# sourceMappingURL=adSandbox-AFORHU3V.js.map