@vitessce/vit-s 4.0.4 → 4.0.5

package/dist-tsc/VitS.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"VitS.d.ts","sourceRoot":"","sources":["../src/VitS.js"],"names":[],"mappings":"AAwCA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AACH,4BApCG;IAAsB,MAAM,EAApB,MAAM;IAGkB,SAAS,EAAjC,SAAS,GAAC,MAAM;IACF,MAAM,EAApB,MAAM;IACQ,KAAK,EAAnB,MAAM;IAEU,MAAM;IACN,cAAc;IAEd,cAAc;IAEf,cAAc,EAA7B,OAAO;IAIQ,sBAAsB,EAArC,OAAO;IAGY,GAAG,EAAtB,IAAI,GAAC,MAAM;IAGW,cAAc,EAApC,SAAS,GAAC,IAAI;IAEC,kBAAkB,EAAjC,OAAO;IAEM,SAAS,EAAtB,KAAK;IACQ,SAAS,EAAtB,KAAK;IACQ,cAAc,EAA3B,KAAK;IACQ,iBAAiB,EAA9B,KAAK;IACc,OAAO,EAA1B,IAAI,GAAC,MAAM;IACI,QAAQ,EAAvB,OAAO;IACQ,SAAS,EAAxB,OAAO;IACY,QAAQ,EAA3B,IAAI,GAAC,MAAM;CAErB,OAsSA"}
+{"version":3,"file":"VitS.d.ts","sourceRoot":"","sources":["../src/VitS.js"],"names":[],"mappings":"AAyCA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AACH,4BApCG;IAAsB,MAAM,EAApB,MAAM;IAGkB,SAAS,EAAjC,SAAS,GAAC,MAAM;IACF,MAAM,EAApB,MAAM;IACQ,KAAK,EAAnB,MAAM;IAEU,MAAM;IACN,cAAc;IAEd,cAAc;IAEf,cAAc,EAA7B,OAAO;IAIQ,sBAAsB,EAArC,OAAO;IAGY,GAAG,EAAtB,IAAI,GAAC,MAAM;IAGW,cAAc,EAApC,SAAS,GAAC,IAAI;IAEC,kBAAkB,EAAjC,OAAO;IAEM,SAAS,EAAtB,KAAK;IACQ,SAAS,EAAtB,KAAK;IACQ,cAAc,EAA3B,KAAK;IACQ,iBAAiB,EAA9B,KAAK;IACc,OAAO,EAA1B,IAAI,GAAC,MAAM;IACI,QAAQ,EAAvB,OAAO;IACQ,SAAS,EAAxB,OAAO;IACY,QAAQ,EAA3B,IAAI,GAAC,MAAM;CAErB,OA2SA"}

package/dist-tsc/VitS.js

@@ -7,6 +7,7 @@ import { transformEntriesForZipFileStore } from '@vitessce/zarr-utils';
 import { QueryCache, QueryClient, QueryClientProvider, } from '@tanstack/react-query';
 import { isEqual } from 'lodash-es';
 import { buildConfigSchema, latestConfigSchema } from '@vitessce/schemas';
+import { MatrixTooLargeError } from '@vitessce/error';
 import { log, setLogLevel, setDebugMode, DEFAULT_LOG_LEVEL, DEFAULT_DEBUG_MODE, } from '@vitessce/globals';
 import { muiTheme } from './shared-mui/styles.js';
 import { ViewConfigProvider, createViewConfigStore, AuxiliaryProvider, createAuxiliaryStore, } from './state/hooks.js';
@@ -175,7 +176,10 @@ export function VitS(props) {
         defaultOptions: {
             queries: {
                 refetchOnWindowFocus: false,
-                retry: 2,
+                // A matrix that does not fit the browser's budget will not fit on a
+                // retry either; surface that message immediately rather than after
+                // two more attempts and their backoff.
+                retry: (failureCount, error) => (failureCount < 2 && !(error instanceof MatrixTooLargeError)),
             },
         },
         // Reference: https://tkdodo.eu/blog/react-query-error-handling#the-global-callbacks

package/dist-tsc/VitS.js.map

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package/dist-tsc/data-hooks-multilevel-utils.d.ts

@@ -120,4 +120,14 @@ export function useObsSetsMultiLevel(loaders: object, dataset: string, isRequire
  * @returns {array} [data, status, errors]
  */
 export function useObsLabelsMultiLevel(loaders: object, dataset: string, isRequired: boolean, matchOnObj: object, depth: number): array;
+/**
+ * Wrapper around useDataTypeMultiLevel.
+ * @param {object} loaders
+ * @param {string} dataset
+ * @param {boolean} isRequired
+ * @param {object} matchOnObj
+ * @param {number} depth
+ * @returns {array} [data, status, errors]
+ */
+export function useObsColorsMultiLevel(loaders: object, dataset: string, isRequired: boolean, matchOnObj: object, depth: number): array;
 //# sourceMappingURL=data-hooks-multilevel-utils.d.ts.map

package/dist-tsc/data-hooks-multilevel-utils.d.ts.map

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+{"version":3,"file":"data-hooks-multilevel-utils.d.ts","sourceRoot":"","sources":["../src/data-hooks-multilevel-utils.js"],"names":[],"mappings":"AA6CA;;;;;;;;;;;;;GAaG;AACH,mEAPW,MAAM,cACN,MAAM,SACN,MAAM,WACN,MAAM,YACN,MAAM,wBAmBhB;AA8BD;;;;;;;;;;;;GAYG;AACH,gEANW,MAAM,SACN,MAAM,WACN,MAAM,YACN,MAAM,wBAiBhB;AA+BD;;;;;;;;;;;;GAYG;AACH,mDANW,MAAM,SACN,MAAM,WACN,MAAM,YACN,MAAM,wBAiBhB;AAuBD;;;;;;;;;;GAUG;AACH,oDALW,MAAM,EAAE,WACR,MAAM,+BAOhB;AAED;;;;;;GAMG;AACH,sEALW,KAAK,oBACL,KAAK,MAcf;AAED;;;;;;GAMG;AACH,sDALW,KAAK,oBACL,KAAK,MAgBf;AA+DD;;;;;;;;;GASG;AACH,uDARW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,cACN,KAAK,SACL,MAAM,SAoDhB;AAuCD;;;;;;;;GAQG;AACH,8DAPW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,SACN,MAAM,SA8ChB;AAuDD;;;;;;;;GAQG;AACH,mDAPW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,SACN,MAAM,GACJ,KAAK,CAUjB;AAED;;;;;;;;GAQG;AACH,8CAPW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,SACN,MAAM,GACJ,KAAK,CAUjB;AAED;;;;;;;;GAQG;AACH,gDAPW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,SACN,MAAM,GACJ,KAAK,CAUjB;AAED;;;;;;;;GAQG;AACH,gDAPW,MAAM,WACN,MAAM,cACN,OAAO,cACP,MAAM,SACN,MAAM,GACJ,KAAK,CAUjB"}

package/dist-tsc/data-hooks-multilevel-utils.js

@@ -444,4 +444,16 @@ export function useObsSetsMultiLevel(loaders, dataset, isRequired, matchOnObj, d
 export function useObsLabelsMultiLevel(loaders, dataset, isRequired, matchOnObj, depth) {
     return useDataTypeMultiLevel(loaders, dataset, isRequired, matchOnObj, depth, DataType.OBS_LABELS);
 }
+/**
+ * Wrapper around useDataTypeMultiLevel.
+ * @param {object} loaders
+ * @param {string} dataset
+ * @param {boolean} isRequired
+ * @param {object} matchOnObj
+ * @param {number} depth
+ * @returns {array} [data, status, errors]
+ */
+export function useObsColorsMultiLevel(loaders, dataset, isRequired, matchOnObj, depth) {
+    return useDataTypeMultiLevel(loaders, dataset, isRequired, matchOnObj, depth, DataType.OBS_COLORS);
+}
 //# sourceMappingURL=data-hooks-multilevel-utils.js.map

package/dist-tsc/data-hooks-multilevel-utils.js.map

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package/dist-tsc/data-hooks-multilevel.d.ts

@@ -70,4 +70,13 @@ export function useSegmentationMultiObsLocations(coordinationScopes: object, coo
  * @returns {array} [data, status, errors]
  */
 export function useSegmentationMultiObsSets(coordinationScopes: object, coordinationScopesBy: object, loaders: object, dataset: string): array;
+/**
+ * Wrapper around useObsColorsMultiLevel.
+ * @param {object} coordinationScopes
+ * @param {object} coordinationScopesBy
+ * @param {object} loaders
+ * @param {string} dataset
+ * @returns {array} [data, status, errors]
+ */
+export function useSegmentationMultiObsColors(coordinationScopes: object, coordinationScopesBy: object, loaders: object, dataset: string): array;
 //# sourceMappingURL=data-hooks-multilevel.d.ts.map

package/dist-tsc/data-hooks-multilevel.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"data-hooks-multilevel.d.ts","sourceRoot":"","sources":["../src/data-hooks-multilevel.js"],"names":[],"mappings":"AAgBA;;;;;;;GAOG;AACH,yEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAsDjB;AAED;;;;;;;GAOG;AACH,iEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CA8CjB;AAED;;;;;;;GAOG;AACH,gFANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAyBjB;AAED;;;;;;;GAOG;AACH,wEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAwBjB;AAED;;;;;;;GAOG;AACH,2DANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,yEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAyBjB;AAED;;;;;;;GAOG;AACH,qEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,gEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,kEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB"}

package/dist-tsc/data-hooks-multilevel.js

@@ -1,7 +1,7 @@
 import { useMemo } from 'react';
 import { CoordinationType } from '@vitessce/constants-internal';
 import { useComplexCoordination, useComplexCoordinationSecondary, } from './state/hooks.js';
-import { useFeatureSelectionMultiLevel, useObsFeatureMatrixIndicesMultiLevel, useObsLocationsMultiLevel, useObsSetsMultiLevel, useObsLabelsMultiLevel, } from './data-hooks-multilevel-utils.js';
+import { useFeatureSelectionMultiLevel, useObsFeatureMatrixIndicesMultiLevel, useObsLocationsMultiLevel, useObsSetsMultiLevel, useObsLabelsMultiLevel, useObsColorsMultiLevel, } from './data-hooks-multilevel-utils.js';
 /**
  * Wrapper around useFeatureSelectionMultiLevel.
  * @param {object} coordinationScopes
@@ -204,4 +204,24 @@ export function useSegmentationMultiObsSets(coordinationScopes, coordinationScop
     const [indicesData, indicesDataStatus, indicesDataErrors] = useObsSetsMultiLevel(loaders, dataset, false, matchOnObj, 2);
     return [indicesData, indicesDataStatus, indicesDataErrors];
 }
+/**
+ * Wrapper around useObsColorsMultiLevel.
+ * @param {object} coordinationScopes
+ * @param {object} coordinationScopesBy
+ * @param {object} loaders
+ * @param {string} dataset
+ * @returns {array} [data, status, errors]
+ */
+export function useSegmentationMultiObsColors(coordinationScopes, coordinationScopesBy, loaders, dataset) {
+    const obsTypeCoordination = useComplexCoordinationSecondary([
+        CoordinationType.OBS_TYPE,
+    ], coordinationScopes, coordinationScopesBy, CoordinationType.SEGMENTATION_LAYER, CoordinationType.SEGMENTATION_CHANNEL);
+    const matchOnObj = useMemo(() => obsTypeCoordination[0], 
+    // imageCoordination reference changes each render,
+    // use coordinationScopes and coordinationScopesBy which are
+    // indirect dependencies here.
+    [coordinationScopes, coordinationScopesBy]);
+    const [colorsData, colorsDataStatus, colorsDataErrors] = useObsColorsMultiLevel(loaders, dataset, false, matchOnObj, 2);
+    return [colorsData, colorsDataStatus, colorsDataErrors];
+}
 //# sourceMappingURL=data-hooks-multilevel.js.map

package/dist-tsc/data-hooks-multilevel.js.map

@@ -1 +1 @@
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package/dist-tsc/hooks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAqBA,oDAOC;AAED;;;;GAIG;AACH,uCAHa,KAAK,CAmBjB;AAED;;;;GAIG;AACH,mCAHa,KAAK,CAoCjB;AAED;;;;;GAKG;AACH,qCAJa,KAAK,CAqCjB;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;GAIG;AACH,8BAHW,CAAC,IAAI,GAAC,MAAM,EAAE,CAAC,EAAE,GACf,KAAK,CAYjB;AAED;;;;;;GAMG;AACH,qDAJW,GAAG,sBACD,KAAK,CA0BjB;AAED;;;;;;;;;;GAUG;AACH,+DARG;IAAuB,gBAAgB,EAA/B,MAAM;CAEd,GAAU,KAAK,CAmBjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,yDAbW,YAAY,EAAE,GAAG,IAAI,GAInB;IACZ,QAAW,EAAE,UAAU,EAAE,GAAG,IAAI,CAAC;IACjC,OAAU,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,GAAG,IAAI,CAAC;IACtC,OAAU,EAAE,MAAM,EAAE,CAAA;CACjB,CAwBH;AAED;;;;QA2BC;AAED,iEAOC;AAED,kHA4BC;AAED;;;;;;;;;;GAUG;AACH,yDALW,MAAM,oBACN,gBAAI,IAAI,iBAEN;IAAE,kBAAkB,EAAE,OAAO,CAAA;CAAE,GAAC,IAAI,CAkChD;AAED;;;;;;;GAOG;AACH,6CALW,GAAC,YACD,CAAC,OAAO,CAAC,GAEP,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CA8BlC"}
+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAsBA,oDAOC;AAED;;;;GAIG;AACH,uCAHa,KAAK,CAmBjB;AAED;;;;GAIG;AACH,mCAHa,KAAK,CAoCjB;AAED;;;;;GAKG;AACH,qCAJa,KAAK,CAqCjB;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;GAIG;AACH,8BAHW,CAAC,IAAI,GAAC,MAAM,EAAE,CAAC,EAAE,GACf,KAAK,CAYjB;AAED;;;;;;GAMG;AACH,qDAJW,GAAG,sBACD,KAAK,CA0BjB;AAED;;;;;;;;;;GAUG;AACH,+DARG;IAAuB,gBAAgB,EAA/B,MAAM;CAEd,GAAU,KAAK,CAmBjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,yDAbW,YAAY,EAAE,GAAG,IAAI,GAInB;IACZ,QAAW,EAAE,UAAU,EAAE,GAAG,IAAI,CAAC;IACjC,OAAU,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,GAAG,IAAI,CAAC;IACtC,OAAU,EAAE,MAAM,EAAE,CAAA;CACjB,CAwBH;AAMD;;;;QAyCC;AAED,iEAOC;AAED,kHA4BC;AAED;;;;;;;;;;GAUG;AACH,yDALW,MAAM,oBACN,gBAAI,IAAI,iBAEN;IAAE,kBAAkB,EAAE,OAAO,CAAA;CAAE,GAAC,IAAI,CAkChD;AAED;;;;;;;GAOG;AACH,6CALW,GAAC,YACD,CAAC,OAAO,CAAC,GAEP,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CA8BlC"}

package/dist-tsc/hooks.js

@@ -3,6 +3,7 @@ import { debounce, every } from 'lodash-es';
 import { extent } from 'd3-array';
 import { useQuery } from '@tanstack/react-query';
 import { capitalize } from '@vitessce/utils';
+import { getObsIndexMap } from '@vitessce/sets-utils';
 import { STATUS, AsyncFunctionType } from '@vitessce/constants-internal';
 import { VITESSCE_CONTAINER } from './classNames.js';
 import { useGridResize, useEmitGridResize } from './state/hooks.js';
@@ -218,6 +219,9 @@ export function useUint8FeatureSelection(expressionData) {
         return { normData, extents, missing };
     }, [expressionData]);
 }
+// Marks an instance index that equals the matrix row index, so that no
+// per-observation mapping needs to be built.
+const IDENTITY_MAPPING = 'identity';
 export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }) {
     // Get a mapping from cell ID to row index in the gene expression matrix.
     // Since the two obsIndices (instanceObsIndex = the obsIndex from obsEmbedding)
@@ -225,17 +229,31 @@ export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, exp
     // we need a way to look up an obsFeatureMatrix obsIndex index
     // given an obsEmbedding obsIndex index.
     const toMatrixIndexMap = useMemo(() => {
-        if (instanceObsIndex && matrixObsIndex) {
-            const matrixIndexMap = new Map(matrixObsIndex.map((key, i) => ([key, i])));
-            return instanceObsIndex.map(key => matrixIndexMap.get(key));
+        if (!instanceObsIndex || !matrixObsIndex) {
+            return null;
         }
-        return null;
+        if (instanceObsIndex === matrixObsIndex) {
+            // The same array (the usual case when both come from one data source)
+            // is already aligned by position.
+            return IDENTITY_MAPPING;
+        }
+        // The map is shared with other consumers of this index via getObsIndexMap.
+        const matrixIndexMap = getObsIndexMap(matrixObsIndex);
+        const mapping = new Int32Array(instanceObsIndex.length);
+        for (let i = 0; i < instanceObsIndex.length; i += 1) {
+            const rowIndex = matrixIndexMap.get(instanceObsIndex[i]);
+            mapping[i] = rowIndex === undefined ? -1 : rowIndex;
+        }
+        return mapping;
     }, [instanceObsIndex, matrixObsIndex]);
     // Set up a getter function for gene expression values, to be used
     // by the DeckGL layer to obtain values for instanced attributes.
     const getExpressionValue = useCallback((entry, { index: instanceIndex }) => {
         if (toMatrixIndexMap && expressionData && expressionData[0]) {
-            const rowIndex = toMatrixIndexMap[instanceIndex];
+            const rowIndex = toMatrixIndexMap === IDENTITY_MAPPING
+                ? instanceIndex
+                : toMatrixIndexMap[instanceIndex];
+            // An observation absent from the matrix (-1) reads as undefined, as before.
             const val = expressionData[0][rowIndex];
             return val;
         }

package/dist-tsc/hooks.js.map

@@ -1 +1 @@
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package/dist-tsc/hooks.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=hooks.test.d.ts.map

package/dist-tsc/hooks.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hooks.test.d.ts","sourceRoot":"","sources":["../src/hooks.test.jsx"],"names":[],"mappings":""}

package/dist-tsc/hooks.test.js

@@ -0,0 +1,36 @@
+import { describe, it, expect } from 'vitest';
+import { renderHook } from '@testing-library/react';
+import { useExpressionValueGetter } from './hooks.js';
+describe('useExpressionValueGetter', () => {
+    const expressionData = [new Uint8Array([10, 20, 30])];
+    it('reads by position when the instance and matrix indices are the same array', () => {
+        const obsIndex = ['a', 'b', 'c'];
+        const { result } = renderHook(() => useExpressionValueGetter({
+            instanceObsIndex: obsIndex, matrixObsIndex: obsIndex, expressionData,
+        }));
+        expect(result.current(null, { index: 0 })).toEqual(10);
+        expect(result.current(null, { index: 2 })).toEqual(30);
+    });
+    it('maps through observation IDs when the indices differ', () => {
+        const { result } = renderHook(() => useExpressionValueGetter({
+            instanceObsIndex: ['c', 'unknown', 'a'],
+            matrixObsIndex: ['a', 'b', 'c'],
+            expressionData,
+        }));
+        expect(result.current(null, { index: 0 })).toEqual(30);
+        // An observation absent from the matrix reads as undefined, as before.
+        expect(result.current(null, { index: 1 })).toEqual(undefined);
+        expect(result.current(null, { index: 2 })).toEqual(10);
+    });
+    it('returns 0 without indices or without data', () => {
+        const { result: noIndices } = renderHook(() => useExpressionValueGetter({
+            instanceObsIndex: null, matrixObsIndex: ['a'], expressionData,
+        }));
+        expect(noIndices.current(null, { index: 0 })).toEqual(0);
+        const { result: noData } = renderHook(() => useExpressionValueGetter({
+            instanceObsIndex: ['a'], matrixObsIndex: ['a'], expressionData: null,
+        }));
+        expect(noData.current(null, { index: 0 })).toEqual(0);
+    });
+});
+//# sourceMappingURL=hooks.test.js.map

package/dist-tsc/hooks.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"hooks.test.js","sourceRoot":"","sources":["../src/hooks.test.jsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,YAAY,CAAC;AAEtD,QAAQ,CAAC,0BAA0B,EAAE,GAAG,EAAE;IACxC,MAAM,cAAc,GAAG,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;IAEtD,EAAE,CAAC,2EAA2E,EAAE,GAAG,EAAE;QACnF,MAAM,QAAQ,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QACjC,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,wBAAwB,CAAC;YAC3D,gBAAgB,EAAE,QAAQ,EAAE,cAAc,EAAE,QAAQ,EAAE,cAAc;SACrE,CAAC,CAAC,CAAC;QACJ,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,sDAAsD,EAAE,GAAG,EAAE;QAC9D,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,wBAAwB,CAAC;YAC3D,gBAAgB,EAAE,CAAC,GAAG,EAAE,SAAS,EAAE,GAAG,CAAC;YACvC,cAAc,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC;YAC/B,cAAc;SACf,CAAC,CAAC,CAAC;QACJ,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QACvD,uEAAuE;QACvE,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QAC9D,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACnD,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,wBAAwB,CAAC;YACtE,gBAAgB,EAAE,IAAI,EAAE,cAAc,EAAE,CAAC,GAAG,CAAC,EAAE,cAAc;SAC9D,CAAC,CAAC,CAAC;QACJ,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QACzD,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,wBAAwB,CAAC;YACnE,gBAAgB,EAAE,CAAC,GAAG,CAAC,EAAE,cAAc,EAAE,CAAC,GAAG,CAAC,EAAE,cAAc,EAAE,IAAI;SACrE,CAAC,CAAC,CAAC;QACJ,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACxD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/dist-tsc/index.d.ts

@@ -9,7 +9,7 @@ export { createOnDrop } from "./on-drop.js";
 export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap, useColumnNameMapping } from "./hooks.js";
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes } from "./state/hooks.js";
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, useComparisonMetadata, useFeatureStatsData, useFeatureSetStatsData, useObsSetStatsData } from "./data-hooks.js";
-export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets } from "./data-hooks-multilevel.js";
+export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, useSegmentationMultiObsColors } from "./data-hooks-multilevel.js";
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles } from "./shared-plot-options/index.js";
 export { useAsyncFunction, usePageModeView } from "./contexts.js";
 export { useMemoCustomComparison, shallowDiff, shallowDiffByLayer, shallowDiffByLayerWithKeys, shallowDiffByChannel, shallowDiffByChannelWithKeys, shallowDiffByLayerCoordination, shallowDiffByLayerCoordinationWithKeys, shallowDiffByChannelCoordination, shallowDiffByChannelCoordinationWithKeys } from "./use-memo-custom-comparison.js";

package/dist-tsc/index.js

@@ -6,7 +6,7 @@ export { PopperMenu } from './shared-mui/components.js';
 export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap, useColumnNameMapping, } from './hooks.js';
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes, } from './state/hooks.js';
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, useComparisonMetadata, useFeatureStatsData, useFeatureSetStatsData, useObsSetStatsData, } from './data-hooks.js';
-export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, } from './data-hooks-multilevel.js';
+export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, useSegmentationMultiObsColors, } from './data-hooks-multilevel.js';
 export { useHasLoader, } from './data-hook-utils.js';
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options/index.js';
 export { logConfig } from './view-config-utils.js';

package/dist-tsc/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AACxD,yBAAyB;AACzB,OAAO,EACL,QAAQ,EACR,OAAO,EACP,oBAAoB,EACpB,iBAAiB,EACjB,wBAAwB,EACxB,wBAAwB,EACxB,wBAAwB,EACxB,mBAAmB,EACnB,aAAa,EACb,+BAA+B,EAC/B,mBAAmB,EACnB,eAAe,EACf,2BAA2B,EAC3B,oBAAoB,GACrB,MAAM,YAAY,CAAC;AACpB,OAAO,EACL,qBAAqB,EACrB,uBAAuB,EACvB,sBAAsB,EACtB,eAAe,EACf,sBAAsB,EACtB,+BAA+B,EAC/B,0BAA0B,EAC1B,iCAAiC,EACjC,mCAAmC,EACnC,0CAA0C,EAC1C,0BAA0B,EAC1B,2BAA2B,EAC3B,cAAc,EACd,UAAU,EACV,oBAAoB,EACpB,iBAAiB,EACjB,kBAAkB,EAClB,qBAAqB,EACrB,aAAa,EACb,gBAAgB,EAChB,iBAAiB,EACjB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,UAAU,EACV,aAAa,EACb,wBAAwB,EACxB,kBAAkB,EAClB,6CAA6C,EAC7C,0CAA0C,GAC3C,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,cAAc,EACd,YAAY,EACZ,cAAc,EACd,mBAAmB,EACnB,mBAAmB,EACnB,0BAA0B,EAC1B,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,gBAAgB,EAChB,iBAAiB,EACjB,mBAAmB,EACnB,yBAAyB,EACzB,wBAAwB,EACxB,cAAc,EAEd,eAAe,EACf,gBAAgB,EAChB,mBAAmB,EACnB,uBAAuB,EACvB,oBAAoB,EACpB,gBAAgB,EAEhB,uBAAuB,EACvB,oBAAoB,EACpB,sBAAsB,EAEtB,qBAAqB,EACrB,mBAAmB,EACnB,sBAAsB,EACtB,kBAAkB,GACnB,MAAM,iBAAiB,CAAC;AACzB,OAAO,EACL,sBAAsB,EACtB,oCAAoC,EACpC,4BAA4B,EAC5B,mCAAmC,EACnC,oCAAoC,EACpC,2CAA2C,EAC3C,gCAAgC,EAChC,2BAA2B,EAC3B,6BAA6B,GAC9B,MAAM,4BAA4B,CAAC;AACpC,OAAO,EACL,YAAY,GACb,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EACL,uBAAuB,EACvB,gBAAgB,EAChB,YAAY,EACZ,oBAAoB,GACrB,MAAM,gCAAgC,CAAC;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAC5C,OAAO,EACL,uBAAuB,EACvB,WAAW,EACX,kBAAkB,EAClB,0BAA0B,EAC1B,oBAAoB,EACpB,4BAA4B,EAC5B,8BAA8B,EAC9B,sCAAsC,EACtC,gCAAgC,EAChC,wCAAwC,GACzC,MAAM,iCAAiC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "4.0.4",
+  "version": "4.0.5",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,7 +17,7 @@
   ],
   "dependencies": {
     "@tanstack/react-query": "^5.80.2",
-    "@zarrita/storage": "0.1.4",
+    "@zarrita/storage": "0.2.0",
     "clsx": "^1.1.1",
     "d3-array": "^2.4.0",
     "fast-deep-equal": "^3.1.3",
@@ -30,18 +30,18 @@
     "react-aria": "^3.47.0",
     "react-error-boundary": "^5.0.0",
     "@placemarkio/flat-drop-files": "^1.0.2",
-    "zarrita": "0.6.1",
-    "@vitessce/styles": "4.0.4",
-    "@vitessce/abstract": "4.0.4",
-    "@vitessce/error": "4.0.4",
-    "@vitessce/schemas": "4.0.4",
-    "@vitessce/constants-internal": "4.0.4",
-    "@vitessce/utils": "4.0.4",
-    "@vitessce/zarr-utils": "4.0.4",
-    "@vitessce/sets-utils": "4.0.4",
-    "@vitessce/plugins": "4.0.4",
-    "@vitessce/config": "4.0.4",
-    "@vitessce/globals": "4.0.4"
+    "zarrita": "0.7.5",
+    "@vitessce/styles": "4.0.5",
+    "@vitessce/error": "4.0.5",
+    "@vitessce/plugins": "4.0.5",
+    "@vitessce/constants-internal": "4.0.5",
+    "@vitessce/schemas": "4.0.5",
+    "@vitessce/abstract": "4.0.5",
+    "@vitessce/sets-utils": "4.0.5",
+    "@vitessce/utils": "4.0.5",
+    "@vitessce/zarr-utils": "4.0.5",
+    "@vitessce/config": "4.0.5",
+    "@vitessce/globals": "4.0.5"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^6.6.3",
@@ -50,7 +50,7 @@
     "react-dom": "19.2.6",
     "vite": "^7.0.0",
     "vitest": "^3.1.4",
-    "@vitessce/types": "4.0.4"
+    "@vitessce/types": "4.0.5"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"

package/src/VitS.js

@@ -14,6 +14,7 @@ import {
 } from '@tanstack/react-query';
 import { isEqual } from 'lodash-es';
 import { buildConfigSchema, latestConfigSchema } from '@vitessce/schemas';
+import { MatrixTooLargeError } from '@vitessce/error';
 import {
   log,
   setLogLevel, setDebugMode,
@@ -248,7 +249,12 @@ export function VitS(props) {
     defaultOptions: {
       queries: {
         refetchOnWindowFocus: false,
-        retry: 2,
+        // A matrix that does not fit the browser's budget will not fit on a
+        // retry either; surface that message immediately rather than after
+        // two more attempts and their backoff.
+        retry: (failureCount, error) => (
+          failureCount < 2 && !(error instanceof MatrixTooLargeError)
+        ),
       },
     },
     // Reference: https://tkdodo.eu/blog/react-query-error-handling#the-global-callbacks

package/src/data-hooks-multilevel-utils.js

@@ -589,3 +589,22 @@ export function useObsLabelsMultiLevel(
     depth, DataType.OBS_LABELS,
   );
 }
+
+/**
+ * Wrapper around useDataTypeMultiLevel.
+ * @param {object} loaders
+ * @param {string} dataset
+ * @param {boolean} isRequired
+ * @param {object} matchOnObj
+ * @param {number} depth
+ * @returns {array} [data, status, errors]
+ */
+export function useObsColorsMultiLevel(
+  loaders, dataset, isRequired, matchOnObj,
+  depth,
+) {
+  return useDataTypeMultiLevel(
+    loaders, dataset, isRequired, matchOnObj,
+    depth, DataType.OBS_COLORS,
+  );
+}