@vitessce/vit-s 2.0.2 → 2.0.3

package/dist/hooks.js

@@ -1,215 +0,0 @@
-import { useRef, useState, useEffect, useCallback, useMemo, } from 'react';
-import debounce from 'lodash/debounce';
-import every from 'lodash/every';
-import { capitalize, fromEntries } from '@vitessce/utils';
-import { useGridResize, useEmitGridResize } from './state/hooks';
-import { VITESSCE_CONTAINER } from './classNames';
-function getWindowDimensions() {
-    const { innerWidth: width, innerHeight: height } = window;
-    return {
-        width,
-        height,
-    };
-}
-export function useVitessceContainer(ref) {
-    return useCallback(() => {
-        if (ref.current) {
-            return ref.current.closest(`.${VITESSCE_CONTAINER}`);
-        }
-        return null;
-    }, [ref]);
-}
-/**
- * Custom hook, gets the full window dimensions.
- * @returns {array} `[width, height]` where width and height
- * are numbers.
- */
-export function useWindowDimensions() {
-    const [windowDimensions, setWindowDimensions] = useState(getWindowDimensions());
-    useEffect(() => {
-        function handleResize() {
-            setWindowDimensions(getWindowDimensions());
-        }
-        const onResizeDebounced = debounce(handleResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        return () => window.removeEventListener('resize', onResizeDebounced);
-    }, []);
-    return windowDimensions;
-}
-/**
- * Custom hook, subscribes to GRID_RESIZE and window resize events.
- * @returns {array} `[width, height, containerRef]` where width and height
- * are numbers and containerRef is a React ref.
- */
-export function useGridItemSize() {
-    const containerRef = useRef();
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    const resizeCount = useGridResize();
-    const incrementResizeCount = useEmitGridResize();
-    // On window resize events, increment the grid resize count.
-    useEffect(() => {
-        function onWindowResize() {
-            incrementResizeCount();
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [incrementResizeCount]);
-    // On new grid resize counts, re-compute the component
-    // width/height.
-    useEffect(() => {
-        if (!containerRef.current)
-            return;
-        const container = containerRef.current;
-        const containerRect = container.getBoundingClientRect();
-        setHeight(containerRect.height);
-        setWidth(containerRect.width);
-    }, [resizeCount]);
-    return [width, height, containerRef];
-}
-/**
- * Custom hook, subscribes to GRID_RESIZE and window resize events.
- * @returns {array} `[width, height, deckRef]` where width and height
- * are numbers and deckRef is a React ref to be used with
- * a <DeckGL/> element (or a forwardRef to one).
- */
-export function useDeckCanvasSize() {
-    const deckRef = useRef();
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    const resizeCount = useGridResize();
-    const incrementResizeCount = useEmitGridResize();
-    // On window resize events, increment the grid resize count.
-    useEffect(() => {
-        function onWindowResize() {
-            incrementResizeCount();
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [incrementResizeCount]);
-    // On new grid resize counts, re-compute the DeckGL canvas
-    // width/height.
-    useEffect(() => {
-        if (!deckRef.current)
-            return;
-        const { canvas } = deckRef.current.deck;
-        const canvasRect = canvas.getBoundingClientRect();
-        setHeight(canvasRect.height);
-        setWidth(canvasRect.width);
-    }, [resizeCount]);
-    return [width, height, deckRef];
-}
-/**
- * This hook handles a boolean isReady value,
- * which only returns true once every item in the
- * input list has been marked as "ready".
- * @param {string[]} statusValues The items to wait on.
- * @returns {boolean} Whether the status values are all success.
- */
-export function useReady(statusValues) {
-    return useMemo(() => every(statusValues, val => val === 'success'), statusValues);
-}
-/**
- * This hook helps manage a list of URLs.
- * @param {object} loaders The loaders dependency.
- * @param {string} dataset The dataset UID dependency.
- * @returns {array} An array
- * [urls, addUrl]
- * where urls is the array of URL objects,
- * and addUrl is a function for adding a URL to the array.
- */
-export function useUrls(loaders, dataset) {
-    const [urls, setUrls] = useState([]);
-    const addUrl = useCallback((url, name) => {
-        if (url) {
-            setUrls(prev => ([...prev, { url, name }]));
-        }
-    }, [setUrls]);
-    useEffect(() => {
-        setUrls([]);
-    }, [loaders, dataset]);
-    return [urls, addUrl];
-}
-/**
- * Custom hook, subscribes to the width and height of the closest .vitessce-container
- * element and updates upon window resize events.
- * @param {Ref} ref A React ref object within the `.vitessce-container`.
- * @returns {array} `[width, height]` where width and height
- * are numbers.
- */
-export function useClosestVitessceContainerSize(ref) {
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    useEffect(() => {
-        function onWindowResize() {
-            if (ref.current) {
-                const { clientHeight: componentHeight, clientWidth: componentWidth, } = ref.current.closest(`.${VITESSCE_CONTAINER}`);
-                setWidth(componentWidth);
-                setHeight(componentHeight);
-            }
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [ref]);
-    return [width, height];
-}
-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)
-    // may be ordered differently (matrixObsIndex = the obsIndex from obsFeatureMatrix),
-    // 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));
-        }
-        return null;
-    }, [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 val = expressionData[0][rowIndex];
-            return val;
-        }
-        return 0;
-    }, [toMatrixIndexMap, expressionData]);
-    return getExpressionValue;
-}
-export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership) {
-    return useCallback((obsId) => {
-        if (obsId) {
-            const obsMembership = obsSetsMembership?.get(obsId) || [];
-            return {
-                [`${capitalize(obsType)} ID`]: obsId,
-                ...fromEntries(obsMembership.flatMap(path => path.slice(1).map((pathEl, elLevel) => ([
-                    `${path[0]}${path.length > 2 ? ` L${elLevel + 1}` : ''}`,
-                    pathEl,
-                ])))),
-                ...fromEntries(Object.entries(obsLabelsTypes).map(([scopeKey, obsLabelsType]) => ([
-                    obsLabelsType,
-                    obsLabelsData?.[scopeKey]?.obsLabels?.[
-                    // TODO: Maybe all loaders that return obsIndex should also return an obsIndexMap
-                    // with keys: obsId, values: obsIdx
-                    // which would avoid the indexOf calls.
-                    obsLabelsData?.[scopeKey]?.obsIndex?.indexOf(obsId)],
-                ])).filter(([obsLabelsType]) => Boolean(obsLabelsType))),
-            };
-        }
-        return null;
-    }, [obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership]);
-}

package/dist/joint-file-types-legacy.js

@@ -1,278 +0,0 @@
-import { FileType } from '@vitessce/constants-internal';
-import { validateOptions, emptySchema, } from './file-options-schemas';
-import { cellsJsonSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, } from './file-options-schemas-legacy';
-export function expandMoleculesJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'molecule',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LOCATIONS_MOLECULES_JSON,
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_MOLECULES_JSON,
-        },
-    ];
-}
-export function expandExpressionMatrixZarr(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR,
-        },
-    ];
-}
-export function expandRasterJson(fileDef) {
-    // Validation already happens in the RasterJsonLoader.
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.IMAGE_RASTER_JSON,
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SEGMENTATIONS_RASTER_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-            },
-        },
-    ];
-}
-export function expandRasterOmeZarr(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.IMAGE_OME_ZARR,
-        },
-    ];
-}
-export function expandCellSetsJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SETS_CELL_SETS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-            },
-        },
-    ];
-}
-export function expandCellsJson(fileDef) {
-    validateOptions(cellsJsonSchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-        },
-    };
-    delete baseFileDef.type;
-    delete baseFileDef.options;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SEGMENTATIONS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LOCATIONS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-        ...(fileDef.options?.embeddingTypes ? fileDef.options.embeddingTypes.map(et => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_EMBEDDING_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                embeddingType: et,
-            },
-        })) : []),
-        ...(fileDef.options?.obsLabelsTypes ? fileDef.options.obsLabelsTypes.map(key => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                obsLabelsType: key,
-            },
-        })) : []),
-    ];
-}
-export function expandClustersJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON,
-        },
-    ];
-}
-export function expandGenesJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_GENES_JSON,
-        },
-    ];
-}
-function getAnndataBaseFileDef(fileDef) {
-    return {
-        url: fileDef.url,
-        requestInit: fileDef.requestInit,
-        coordinationValues: {
-            ...fileDef.coordinationValues,
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-}
-export function expandAnndataCellsZarr(fileDef) {
-    validateOptions(anndataCellsZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = {} } = fileDef;
-    const embeddingTypes = options.mappings ? Object.keys(options.mappings) : [];
-    const obsLabelsTypes = options.factors ? options.factors : [];
-    return [
-        ...(options.poly ? [{
-                ...baseFileDef,
-                fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
-                options: {
-                    path: options.poly,
-                },
-                coordinationValues: {
-                    obsType: baseFileDef.coordinationValues.obsType,
-                },
-            }] : []),
-        ...(options.xy ? [{
-                ...baseFileDef,
-                fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
-                options: {
-                    path: options.xy,
-                },
-                coordinationValues: {
-                    obsType: baseFileDef.coordinationValues.obsType,
-                },
-            }] : []),
-        ...embeddingTypes.map(et => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
-            options: {
-                path: options.mappings[et].key,
-                dims: options.mappings[et].dims,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                embeddingType: et,
-            },
-        })),
-        ...obsLabelsTypes.map(olt => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
-            options: {
-                path: olt,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                obsLabelsType: olt.split('/').at(-1),
-            },
-        })),
-    ];
-}
-export function expandAnndataCellSetsZarr(fileDef) {
-    validateOptions(anndataCellSetsZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = [] } = fileDef;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SETS_ANNDATA_ZARR,
-            options: options.map(option => ({
-                name: option.groupName,
-                path: option.setName,
-                scorePath: option.scoreName,
-            })),
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-    ];
-}
-export function expandAnndataExpressionMatrixZarr(fileDef) {
-    validateOptions(anndataExpressionMatrixZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = {} } = fileDef;
-    return [
-        ...(options.geneAlias ? [{
-                ...baseFileDef,
-                fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
-                options: {
-                    path: options.geneAlias,
-                },
-                coordinationValues: {
-                    featureType: baseFileDef.coordinationValues.featureType,
-                },
-            }] : []),
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
-            options: {
-                path: options.matrix,
-                featureFilterPath: options.geneFilter,
-                initialFeatureFilterPath: options.matrixGeneFilter,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                featureType: baseFileDef.coordinationValues.featureType,
-                featureValueType: baseFileDef.coordinationValues.featureValueType,
-            },
-        },
-    ];
-}