@vitessce/spatial-utils 2.0.3 → 3.0.0

package/dist-tsc/spatial.d.ts

@@ -0,0 +1,87 @@
+export function square(x: any, y: any, r: any): any[][];
+/**
+ * Get a representative PixelSource from a loader object returned from
+ * the Vitessce imaging loaders
+ * @param {object} loader { data: (PixelSource[]|PixelSource), metadata, channels } object
+ * @param {number=} level Level of the multiscale loader from which to get a PixelSource
+ * @returns {object} PixelSource object
+ */
+export function getSourceFromLoader(loader: object, level?: number | undefined): object;
+/**
+ * Helper method to determine whether pixel data is interleaved and rgb or not.
+ * @param {object} loader
+ * @param {array|null} channels
+ */
+export function isRgb(loader: object, channels: array | null): boolean;
+/**
+ * @param {Array.<number>} shape loader shape
+ */
+export function isInterleaved(shape: Array<number>): boolean;
+/**
+ * Initialize the channel selections for an individual layer.
+ * @param {object} loader A viv loader instance with channel names appended by Vitessce loaders
+ * of the form { data: (PixelSource[]|PixelSource), metadata: Object, channels }
+ * @returns {object[]} An array of selected channels with default
+ * domain/slider settings.
+ */
+export function initializeLayerChannels(loader: object, use3d: any): object[];
+/**
+ * Given a set of image layer loader creator functions,
+ * create loader objects for an initial layer or set of layers,
+ * which will be selected based on default values predefined in
+ * the image data file or otherwise by a heuristic
+ * (the midpoint of the layers array).
+ * @param {object[]} rasterLayers A list of layer metadata objects with
+ * shape { name, type, url, createLoader }.
+ * @param {(string[]|null)} rasterRenderLayers A list of default raster layers. Optional.
+ */
+export function initializeRasterLayersAndChannels(rasterLayers: object[], rasterRenderLayers: (string[] | null), usePhysicalSizeScaling: any): Promise<any[]>;
+export function getNgffAxes(firstMultiscalesAxes: any): {
+    type: string;
+    name: string;
+}[];
+export function getNgffAxesForTiff(dimOrder: any): any;
+/**
+ * Convert an array of coordinateTransformations objects to a 16-element
+ * plain JS array using Matrix4 linear algebra transformation functions.
+ * @param {object[]} coordinateTransformations List of objects matching the
+ * OME-NGFF v0.4 coordinateTransformations spec.
+ * @param {object[]} axes Axes in OME-NGFF v0.4 format, objects
+ * with { type, name }.
+ * @returns {Array<number>} Array of 16 numbers representing the Matrix4.
+ */
+export function coordinateTransformationsToMatrix(coordinateTransformations: object[], axes: object[]): Array<number>;
+export const GLOBAL_LABELS: string[];
+export const DEFAULT_RASTER_DOMAIN_TYPE: "Min/Max";
+export namespace DEFAULT_RASTER_LAYER_PROPS {
+    export const visible: boolean;
+    export const colormap: null;
+    export const opacity: number;
+    export { DEFAULT_RASTER_DOMAIN_TYPE as domainType };
+    export const transparentColor: number[];
+    export const renderingMode: viv.RENDERING_MODES;
+    export const use3d: boolean;
+}
+export namespace DEFAULT_MOLECULES_LAYER {
+    const opacity_1: number;
+    export { opacity_1 as opacity };
+    export const radius: number;
+    const visible_1: boolean;
+    export { visible_1 as visible };
+}
+export namespace DEFAULT_CELLS_LAYER {
+    const opacity_2: number;
+    export { opacity_2 as opacity };
+    const radius_1: number;
+    export { radius_1 as radius };
+    const visible_2: boolean;
+    export { visible_2 as visible };
+    export const stroked: boolean;
+}
+export namespace DEFAULT_NEIGHBORHOODS_LAYER {
+    const visible_3: boolean;
+    export { visible_3 as visible };
+}
+export const DEFAULT_LAYER_TYPE_ORDERING: string[];
+import { viv } from "@vitessce/gl";
+//# sourceMappingURL=spatial.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"spatial.d.ts","sourceRoot":"","sources":["../src/spatial.js"],"names":[],"mappings":"AAOA,wDAEC;AAiCD;;;;;;GAMG;AACH,4CAJW,MAAM,UACN,MAAM,eACJ,MAAM,CAMlB;AAED;;;;GAIG;AACH,8BAHW,MAAM,YACN,QAAM,IAAI,WAiBpB;AAmHD;;GAEG;AACH,qCAFW,MAAO,MAAM,CAAC,WAKxB;AAED;;;;;;GAMG;AACH,gDALW,MAAM,eAEJ,MAAM,EAAE,CAuCpB;AAED;;;;;;;;;GASG;AACH,gEAJW,MAAM,EAAE,sBAER,CAAC,MAAM,EAAE,GAAC,IAAI,CAAC,+CAuEzB;AASD;;;IAuBC;AAED,uDAQC;AAED;;;;;;;;GAQG;AACH,6EANW,MAAM,EAAE,QAER,MAAM,EAAE,GAEN,MAAM,MAAM,CAAC,CA4CzB;AAtZD,qCAAwC;AAExC,mDAAoD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAsBpD,mDAKE"}

package/dist-tsc/spatial.js

@@ -0,0 +1,375 @@
+import { isEqual } from 'lodash-es';
+import { Matrix4 } from 'math.gl';
+import { divide, compare, unit } from 'mathjs';
+import { VIEWER_PALETTE } from '@vitessce/utils';
+import { viv } from '@vitessce/gl';
+import { getMultiSelectionStats } from './layer-controller.js';
+export function square(x, y, r) {
+    return [[x, y + r], [x + r, y], [x, y - r], [x - r, y]];
+}
+export const GLOBAL_LABELS = ['z', 't'];
+export const DEFAULT_RASTER_DOMAIN_TYPE = 'Min/Max';
+export const DEFAULT_RASTER_LAYER_PROPS = {
+    visible: true,
+    colormap: null,
+    opacity: 1,
+    domainType: DEFAULT_RASTER_DOMAIN_TYPE,
+    transparentColor: [0, 0, 0],
+    renderingMode: viv.RENDERING_MODES.ADDITIVE,
+    use3d: false,
+};
+export const DEFAULT_MOLECULES_LAYER = {
+    opacity: 1, radius: 20, visible: true,
+};
+export const DEFAULT_CELLS_LAYER = {
+    opacity: 1, radius: 50, visible: true, stroked: false,
+};
+export const DEFAULT_NEIGHBORHOODS_LAYER = {
+    visible: false,
+};
+export const DEFAULT_LAYER_TYPE_ORDERING = [
+    'molecules',
+    'cells',
+    'neighborhoods',
+    'raster',
+];
+/**
+ * Get a representative PixelSource from a loader object returned from
+ * the Vitessce imaging loaders
+ * @param {object} loader { data: (PixelSource[]|PixelSource), metadata, channels } object
+ * @param {number=} level Level of the multiscale loader from which to get a PixelSource
+ * @returns {object} PixelSource object
+ */
+export function getSourceFromLoader(loader, level) {
+    const { data } = loader;
+    const source = Array.isArray(data) ? data[(level || data.length - 1)] : data;
+    return source;
+}
+/**
+ * Helper method to determine whether pixel data is interleaved and rgb or not.
+ * @param {object} loader
+ * @param {array|null} channels
+ */
+export function isRgb(loader, channels) {
+    const source = getSourceFromLoader(loader);
+    const { shape, dtype, labels } = source;
+    const channelSize = shape[(labels.includes('channel') ? labels.indexOf('channel') : labels.indexOf('c'))];
+    if (channelSize === 3 && dtype === 'Uint8') {
+        return true;
+    }
+    if (channels && channels.length === 3
+        && isEqual(channels[0].color, [255, 0, 0])
+        && isEqual(channels[1].color, [0, 255, 0])
+        && isEqual(channels[2].color, [0, 0, 255])) {
+        return true;
+    }
+    return false;
+}
+// From spatial/utils.js
+function getMetaWithTransformMatrices(imageMeta, imageLoaders) {
+    // Do not fill in transformation matrices if any of the layers specify one.
+    const sources = imageLoaders.map(loader => getSourceFromLoader(loader));
+    if (imageMeta.map(meta => meta?.metadata?.transform?.matrix
+        || meta?.metadata?.transform?.scale
+        || meta?.metadata?.transform?.translate).some(Boolean)
+        || sources.every(source => !source.meta?.physicalSizes?.x || !source.meta?.physicalSizes?.y)) {
+        return imageMeta;
+    }
+    // Get the minimum physical among all the current images.
+    const minPhysicalSize = sources.reduce((acc, source) => {
+        const hasZPhyscialSize = source.meta?.physicalSizes?.z?.size;
+        const sizes = [
+            unit(`${source.meta?.physicalSizes.x.size} ${source.meta?.physicalSizes.x.unit}`.replace('µ', 'u')),
+            unit(`${source.meta?.physicalSizes.y.size} ${source.meta?.physicalSizes.y.unit}`.replace('µ', 'u')),
+        ];
+        if (hasZPhyscialSize) {
+            sizes.push(unit(`${source.meta?.physicalSizes.z.size} ${source.meta?.physicalSizes.z.unit}`.replace('µ', 'u')));
+        }
+        acc[0] = (acc[0] === undefined || compare(sizes[0], acc[0]) === -1) ? sizes[0] : acc[0];
+        acc[1] = (acc[1] === undefined || compare(sizes[1], acc[1]) === -1) ? sizes[1] : acc[1];
+        acc[2] = (acc[2] === undefined || compare(sizes[2], acc[2]) === -1) ? sizes[2] : acc[2];
+        return acc;
+    }, []);
+    const imageMetaWithTransform = imageMeta.map((meta, j) => {
+        const source = sources[j];
+        const hasZPhyscialSize = source.meta?.physicalSizes?.z?.size;
+        const sizes = [
+            unit(`${source.meta?.physicalSizes.x.size} ${source.meta?.physicalSizes.x.unit}`.replace('µ', 'u')),
+            unit(`${source.meta?.physicalSizes.y.size} ${source.meta?.physicalSizes.y.unit}`.replace('µ', 'u')),
+        ];
+        if (hasZPhyscialSize) {
+            sizes.push(unit(`${source.meta?.physicalSizes.z.size} ${source.meta?.physicalSizes.z.unit}`.replace('µ', 'u')));
+        }
+        // Find the ratio of the sizes to get the scaling factor.
+        const scale = sizes.map((i, k) => divide(i, minPhysicalSize[k]));
+        // sizes are special objects with own equals method - see `unit` in declaration
+        if (!sizes[0].equals(sizes[1])) {
+            // Handle scaling in the Y direction for non-square pixels
+            scale[1] = divide(sizes[1], sizes[0]);
+        }
+        // Add in z dimension needed for Matrix4 scale API.
+        if (!scale[2]) {
+            scale[2] = 1;
+        }
+        // no need to store/use identity scaling
+        if (isEqual(scale, [1, 1, 1])) {
+            return meta;
+        }
+        // Make sure to scale the z direction by one.
+        const matrix = new Matrix4().scale([...scale]);
+        const newMeta = { ...meta };
+        newMeta.metadata = {
+            ...newMeta.metadata,
+            // We don't want to store matrix objects in the view config.
+            transform: { matrix: matrix.toArray() },
+        };
+        return newMeta;
+    });
+    return imageMetaWithTransform;
+}
+/**
+ * Return the midpoint of the global dimensions.
+ * @param {object} source PixelSource object from Viv
+ * @returns {object} The selection.
+ */
+function getDefaultGlobalSelection(source) {
+    const globalIndices = source.labels
+        .filter(dim => GLOBAL_LABELS.includes(dim));
+    const selection = {};
+    globalIndices.forEach((dim) => {
+        selection[dim] = Math.floor((source.shape[source.labels.indexOf(dim)] || 0) / 2);
+    });
+    return selection;
+}
+/**
+ * Create a default selection using the midpoint of the available global dimensions,
+ * and then the first four available selections from the first selectable channel.
+ * @param {object} source PixelSource object from Viv
+ * @returns {object} The selection.
+ */
+function buildDefaultSelection(source) {
+    const selection = [];
+    const globalSelection = getDefaultGlobalSelection(source);
+    // First non-global dimension with some sort of selectable values
+    const firstNonGlobalDimension = source.labels.filter(dim => !GLOBAL_LABELS.includes(dim)
+        && source.shape[source.labels.indexOf(dim)])[0];
+    for (let i = 0; i < Math.min(4, source.shape[source.labels.indexOf(firstNonGlobalDimension)]); i += 1) {
+        selection.push({
+            [firstNonGlobalDimension]: i,
+            ...globalSelection,
+        });
+    }
+    return selection;
+}
+/**
+ * @param {Array.<number>} shape loader shape
+ */
+export function isInterleaved(shape) {
+    const lastDimSize = shape[shape.length - 1];
+    return lastDimSize === 3 || lastDimSize === 4;
+}
+/**
+ * Initialize the channel selections for an individual layer.
+ * @param {object} loader A viv loader instance with channel names appended by Vitessce loaders
+ * of the form { data: (PixelSource[]|PixelSource), metadata: Object, channels }
+ * @returns {object[]} An array of selected channels with default
+ * domain/slider settings.
+ */
+export async function initializeLayerChannels(loader, use3d) {
+    const result = [];
+    const source = getSourceFromLoader(loader);
+    // Add channel automatically as the first avaialable value for each dimension.
+    let defaultSelection = buildDefaultSelection(source);
+    defaultSelection = isInterleaved(source.shape)
+        ? [{ ...defaultSelection[0], c: 0 }] : defaultSelection;
+    const stats = await getMultiSelectionStats({
+        loader: loader.data, selections: defaultSelection, use3d,
+    });
+    const domains = isRgb(loader, null)
+        ? [[0, 255], [0, 255], [0, 255]]
+        : stats.domains;
+    const colors = isRgb(loader, null)
+        ? [[255, 0, 0], [0, 255, 0], [0, 0, 255]]
+        : null;
+    const sliders = isRgb(loader, null)
+        ? [[0, 255], [0, 255], [0, 255]]
+        : stats.sliders;
+    defaultSelection.forEach((selection, i) => {
+        const domain = domains[i];
+        const slider = sliders[i];
+        const channel = {
+            selection,
+            // eslint-disable-next-line no-nested-ternary
+            color: colors ? colors[i]
+                : defaultSelection.length !== 1
+                    ? VIEWER_PALETTE[i] : [255, 255, 255],
+            visible: true,
+            slider: slider || domain,
+        };
+        result.push(channel);
+    });
+    return result;
+}
+/**
+ * Given a set of image layer loader creator functions,
+ * create loader objects for an initial layer or set of layers,
+ * which will be selected based on default values predefined in
+ * the image data file or otherwise by a heuristic
+ * (the midpoint of the layers array).
+ * @param {object[]} rasterLayers A list of layer metadata objects with
+ * shape { name, type, url, createLoader }.
+ * @param {(string[]|null)} rasterRenderLayers A list of default raster layers. Optional.
+ */
+export async function initializeRasterLayersAndChannels(rasterLayers, rasterRenderLayers, usePhysicalSizeScaling) {
+    const nextImageLoaders = [];
+    let nextImageMetaAndLayers = [];
+    const autoImageLayerDefPromises = [];
+    // Start all loader creators immediately.
+    // Reference: https://eslint.org/docs/rules/no-await-in-loop
+    const loaders = await Promise.all(rasterLayers.map(layer => layer.loaderCreator()));
+    for (let i = 0; i < rasterLayers.length; i++) {
+        const layer = rasterLayers[i];
+        const loader = loaders[i];
+        nextImageLoaders[i] = loader;
+        nextImageMetaAndLayers[i] = layer;
+    }
+    if (usePhysicalSizeScaling) {
+        nextImageMetaAndLayers = getMetaWithTransformMatrices(nextImageMetaAndLayers, nextImageLoaders);
+    }
+    // No layers were pre-defined so set up the default image layers.
+    if (!rasterRenderLayers) {
+        // Midpoint of images list as default image to show.
+        const layerIndex = Math.floor(rasterLayers.length / 2);
+        const loader = nextImageLoaders[layerIndex];
+        const autoImageLayerDefPromise = initializeLayerChannels(loader)
+            .then(channels => Promise.resolve({
+            type: nextImageMetaAndLayers[layerIndex]?.metadata?.isBitmask ? 'bitmask' : 'raster',
+            index: layerIndex,
+            ...DEFAULT_RASTER_LAYER_PROPS,
+            channels: channels.map((channel, j) => ({
+                ...channel,
+                ...(nextImageMetaAndLayers[layerIndex].channels
+                    ? nextImageMetaAndLayers[layerIndex].channels[j] : []),
+            })),
+            modelMatrix: nextImageMetaAndLayers[layerIndex]?.metadata?.transform?.matrix,
+            transparentColor: layerIndex > 0 ? [0, 0, 0] : null,
+        }));
+        autoImageLayerDefPromises.push(autoImageLayerDefPromise);
+    }
+    else {
+        // The renderLayers parameter is a list of layer names to show by default.
+        const globalIndicesOfRenderLayers = rasterRenderLayers
+            .map(imageName => rasterLayers.findIndex(image => image.name === imageName));
+        for (let i = 0; i < globalIndicesOfRenderLayers.length; i++) {
+            const layerIndex = globalIndicesOfRenderLayers[i];
+            const loader = nextImageLoaders[layerIndex];
+            const autoImageLayerDefPromise = initializeLayerChannels(loader)
+                // eslint-disable-next-line no-loop-func
+                .then(channels => Promise.resolve({
+                type: nextImageMetaAndLayers[layerIndex]?.metadata?.isBitmask ? 'bitmask' : 'raster',
+                index: layerIndex,
+                ...DEFAULT_RASTER_LAYER_PROPS,
+                channels: channels.map((channel, j) => ({
+                    ...channel,
+                    ...(nextImageMetaAndLayers[layerIndex].channels
+                        ? nextImageMetaAndLayers[layerIndex].channels[j] : []),
+                })),
+                domainType: 'Min/Max',
+                modelMatrix: nextImageMetaAndLayers[layerIndex]?.metadata?.transform?.matrix,
+                transparentColor: i > 0 ? [0, 0, 0] : null,
+            }));
+            autoImageLayerDefPromises.push(autoImageLayerDefPromise);
+        }
+    }
+    const autoImageLayerDefs = await Promise.all(autoImageLayerDefPromises);
+    return [autoImageLayerDefs, nextImageLoaders, nextImageMetaAndLayers];
+}
+function getDefaultAxisType(name) {
+    if (name === 't')
+        return 'time';
+    if (name === 'c')
+        return 'channel';
+    return 'space';
+}
+// Reference: https://github.com/hms-dbmi/vizarr/blob/ade9d5d71bbedc8c20357c5310557ff9a0c59ac5/src/utils.ts#LL114-L142C2
+export function getNgffAxes(firstMultiscalesAxes) {
+    // Returns axes in the latest v0.4+ format.
+    // defaults for v0.1 & v0.2
+    const defaultAxes = [
+        { type: 'time', name: 't' },
+        { type: 'channel', name: 'c' },
+        { type: 'space', name: 'z' },
+        { type: 'space', name: 'y' },
+        { type: 'space', name: 'x' },
+    ];
+    let axes = defaultAxes;
+    // v0.3 & v0.4+
+    if (firstMultiscalesAxes) {
+        axes = firstMultiscalesAxes.map((axis) => {
+            // axis may be string 'x' (v0.3) or object
+            if (typeof axis === 'string') {
+                return { name: axis, type: getDefaultAxisType(axis) };
+            }
+            const { name, type } = axis;
+            return { name, type: type ?? getDefaultAxisType(name) };
+        });
+    }
+    return axes;
+}
+export function getNgffAxesForTiff(dimOrder) {
+    return dimOrder
+        .toLowerCase()
+        .split('')
+        .map(name => ({
+        name,
+        type: getDefaultAxisType(name),
+    }));
+}
+/**
+ * Convert an array of coordinateTransformations objects to a 16-element
+ * plain JS array using Matrix4 linear algebra transformation functions.
+ * @param {object[]} coordinateTransformations List of objects matching the
+ * OME-NGFF v0.4 coordinateTransformations spec.
+ * @param {object[]} axes Axes in OME-NGFF v0.4 format, objects
+ * with { type, name }.
+ * @returns {Array<number>} Array of 16 numbers representing the Matrix4.
+ */
+export function coordinateTransformationsToMatrix(coordinateTransformations, axes) {
+    let mat = (new Matrix4()).identity();
+    if (coordinateTransformations && axes) {
+        // Get the indices of the objects corresponding to  X, Y, and Z from `axes`.
+        const xyzIndices = ['x', 'y', 'z'].map(name => axes.findIndex(axisObj => axisObj.type === 'space' && axisObj.name === name));
+        // Apply each transformation sequentially and in order according to the OME-NGFF v0.4 spec.
+        // Reference: https://ngff.openmicroscopy.org/0.4/#trafo-md
+        coordinateTransformations.forEach((transform) => {
+            if (transform.type === 'translation') {
+                const { translation: axisOrderedTranslation } = transform;
+                if (axisOrderedTranslation.length !== axes.length) {
+                    throw new Error('Length of translation array was expected to match length of axes.');
+                }
+                const defaultValue = 0;
+                // Get the translation values for [x, y, z].
+                const xyzTranslation = xyzIndices.map(axisIndex => (axisIndex >= 0
+                    ? axisOrderedTranslation[axisIndex]
+                    : defaultValue));
+                const nextMat = (new Matrix4()).translate(xyzTranslation);
+                mat = mat.multiplyLeft(nextMat);
+            }
+            if (transform.type === 'scale') {
+                const { scale: axisOrderedScale } = transform;
+                // Add in z dimension needed for Matrix4 scale API.
+                if (axisOrderedScale.length !== axes.length) {
+                    throw new Error('Length of scale array was expected to match length of axes.');
+                }
+                const defaultValue = 1;
+                // Get the scale values for [x, y, z].
+                const xyzScale = xyzIndices.map(axisIndex => (axisIndex >= 0
+                    ? axisOrderedScale[axisIndex]
+                    : defaultValue));
+                const nextMat = (new Matrix4()).scale(xyzScale);
+                mat = mat.multiplyLeft(nextMat);
+            }
+        });
+    }
+    return mat;
+}

package/dist-tsc/spatial.test.d.ts

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

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

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

package/dist-tsc/spatial.test.js

@@ -0,0 +1,43 @@
+import { square, coordinateTransformationsToMatrix } from './spatial.js';
+const defaultAxes = [
+    { type: 'time', name: 't' },
+    { type: 'channel', name: 'c' },
+    { type: 'space', name: 'z' },
+    { type: 'space', name: 'y' },
+    { type: 'space', name: 'x' },
+];
+describe('Spatial.js', () => {
+    describe('square()', () => {
+        it('gives the right coordinates', () => {
+            expect(square(0, 0, 50)).toEqual([[0, 50], [50, 0], [0, -50], [-50, 0]]);
+        });
+    });
+    describe('coordinateTransformationsToMatrix', () => {
+        it('returns an Array instance', () => {
+            const transformations = [
+                {
+                    type: 'translation',
+                    translation: [0, 0, 0, 1, 1],
+                },
+                {
+                    type: 'scale',
+                    scale: [1, 1, 0.5, 0.5, 0.5],
+                },
+            ];
+            expect(coordinateTransformationsToMatrix(transformations, defaultAxes)).toEqual([
+                0.5, 0, 0, 0,
+                0, 0.5, 0, 0,
+                0, 0, 0.5, 0,
+                0.5, 0.5, 0, 1,
+            ]);
+        });
+        it('returns Identity matrix when coordinateTransformations is null', () => {
+            expect(coordinateTransformationsToMatrix(null, defaultAxes)).toEqual([
+                1, 0, 0, 0,
+                0, 1, 0, 0,
+                0, 0, 1, 0,
+                0, 0, 0, 1,
+            ]);
+        });
+    });
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/spatial-utils",
-  "version": "2.0.3",
+  "version": "3.0.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -8,20 +8,29 @@
     "url": "git+https://github.com/vitessce/vitessce.git"
   },
   "license": "MIT",
-  "main": "dist/index.mjs",
+  "type": "module",
+  "main": "dist/index.js",
   "files": [
+    "src",
     "dist",
-    "src"
+    "dist-tsc"
   ],
   "dependencies": {
-    "lodash": "^4.17.21",
+    "lodash-es": "^4.17.21",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
-    "@vitessce/gl": "2.0.3",
-    "@vitessce/utils": "2.0.3"
+    "@vitessce/gl": "3.0.0",
+    "@vitessce/utils": "3.0.0"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",
     "test": "pnpm exec vitest --run -r ../../../ --dir ."
+  },
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "types": "./dist-tsc/index.d.ts",
+      "import": "./dist/index.js"
+    }
   }
 }

package/src/index.js

@@ -12,4 +12,7 @@ export {
   getSourceFromLoader,
   isInterleaved,
   isRgb,
-} from './spatial';
+  getNgffAxes,
+  getNgffAxesForTiff,
+  coordinateTransformationsToMatrix,
+} from './spatial.js';