@vitessce/gl 2.0.1 → 2.0.3-beta.0

package/dist/layer-controller.js

@@ -0,0 +1,109 @@
+import { Matrix4 } from 'math.gl';
+import { getChannelStats } from './viv';
+async function getSingleSelectionStats2D({ loader, selection }) {
+    const data = Array.isArray(loader) ? loader[loader.length - 1] : loader;
+    const raster = await data.getRaster({ selection });
+    const selectionStats = getChannelStats(raster.data);
+    const { domain, contrastLimits: slider } = selectionStats;
+    return { domain, slider };
+}
+async function getSingleSelectionStats3D({ loader, selection }) {
+    const lowResSource = loader[loader.length - 1];
+    const { shape, labels } = lowResSource;
+    // eslint-disable-next-line no-bitwise
+    const sizeZ = shape[labels.indexOf('z')] >> (loader.length - 1);
+    const raster0 = await lowResSource.getRaster({
+        selection: { ...selection, z: 0 },
+    });
+    const rasterMid = await lowResSource.getRaster({
+        selection: { ...selection, z: Math.floor(sizeZ / 2) },
+    });
+    const rasterTop = await lowResSource.getRaster({
+        selection: { ...selection, z: Math.max(0, sizeZ - 1) },
+    });
+    const stats0 = getChannelStats(raster0.data);
+    const statsMid = getChannelStats(rasterMid.data);
+    const statsTop = getChannelStats(rasterTop.data);
+    return {
+        domain: [
+            Math.min(stats0.domain[0], statsMid.domain[0], statsTop.domain[0]),
+            Math.max(stats0.domain[1], statsMid.domain[1], statsTop.domain[1]),
+        ],
+        slider: [
+            Math.min(stats0.contrastLimits[0], statsMid.contrastLimits[0], statsTop.contrastLimits[0]),
+            Math.max(stats0.contrastLimits[1], statsMid.contrastLimits[1], statsTop.contrastLimits[1]),
+        ],
+    };
+}
+/**
+ * Get bounding cube for a given loader i.e [[0, width], [0, height], [0, depth]]
+ * @param {Object} loader PixelSource|PixelSource[]
+ * @param {[]} selection Selection for stats.
+ * @param {boolean} use3d Whether or not to get 3d stats.
+ * @returns {Object} { domains, sliders }
+ */
+export const getSingleSelectionStats = async ({ loader, selection, use3d }) => {
+    const getStats = use3d
+        ? getSingleSelectionStats3D
+        : getSingleSelectionStats2D;
+    return getStats({ loader, selection });
+};
+export const getMultiSelectionStats = async ({ loader, selections, use3d }) => {
+    const stats = await Promise.all(selections.map(selection => getSingleSelectionStats({ loader, selection, use3d })));
+    const domains = stats.map(stat => stat.domain);
+    const sliders = stats.map(stat => stat.slider);
+    return { domains, sliders };
+};
+/**
+ * Get physical size scaling Matrix4
+ * @param {Object} loader PixelSource
+ * @returns {Object} matrix
+ */
+export function getPhysicalSizeScalingMatrix(loader) {
+    const { x, y, z } = loader?.meta?.physicalSizes ?? {};
+    if (x?.size && y?.size && z?.size) {
+        const min = Math.min(z.size, x.size, y.size);
+        const ratio = [x.size / min, y.size / min, z.size / min];
+        return new Matrix4().scale(ratio);
+    }
+    return new Matrix4().identity();
+}
+/**
+ * Get bounding cube for a given loader
+ * @param {Object} loader PixelSource|PixelSource[]
+ * @returns {Array} [0, width], [0, height], [0, depth]]
+ */
+export function getBoundingCube(loader) {
+    const source = Array.isArray(loader) ? loader[0] : loader;
+    const { shape, labels } = source;
+    const physicalSizeScalingMatrix = getPhysicalSizeScalingMatrix(source);
+    const xSlice = [0, physicalSizeScalingMatrix[0] * shape[labels.indexOf('x')]];
+    const ySlice = [0, physicalSizeScalingMatrix[5] * shape[labels.indexOf('y')]];
+    const zSlice = [
+        0,
+        physicalSizeScalingMatrix[10] * shape[labels.indexOf('z')],
+    ];
+    return [xSlice, ySlice, zSlice];
+}
+export function abbreviateNumber(value) {
+    // Return an abbreviated representation of value, in 5 characters or less.
+    const maxLength = 5;
+    let maxNaiveDigits = maxLength;
+    /* eslint-disable no-plusplus */
+    if (!Number.isInteger(value)) {
+        --maxNaiveDigits;
+    } // Wasted on "."
+    if (value < 1) {
+        --maxNaiveDigits;
+    } // Wasted on "0."
+    /* eslint-disable no-plusplus */
+    const naive = Intl.NumberFormat('en-US', {
+        maximumSignificantDigits: maxNaiveDigits,
+        useGrouping: false,
+    }).format(value);
+    if (naive.length <= maxLength)
+        return naive;
+    // "e+9" consumes 3 characters, so if we even had two significant digits,
+    // it would take take us to six characters, including the decimal point.
+    return value.toExponential(0);
+}

package/dist/spatial.js

@@ -0,0 +1,281 @@
+import isEqual from 'lodash/isEqual';
+import { Matrix4 } from 'math.gl';
+import { divide, compare, unit } from 'mathjs';
+import { VIEWER_PALETTE } from '@vitessce/utils';
+import { getMultiSelectionStats } from './layer-controller';
+import { RENDERING_MODES } from './viv';
+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: 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]));
+        // 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];
+}

package/dist/spatial.test.js

@@ -0,0 +1,8 @@
+import { square } from './spatial';
+describe('Spatial.js', () => {
+    describe('square()', () => {
+        it('gives the right coordinates', () => {
+            expect(square(0, 0, 50)).toEqual([[0, 50], [50, 0], [0, -50], [-50, 0]]);
+        });
+    });
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/gl",
-  "version": "2.0.1",
+  "version": "2.0.3-beta.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -13,25 +13,25 @@
     "dist"
   ],
   "dependencies": {
-    "@deck.gl/aggregation-layers": "8.6.7",
-    "@deck.gl/core": "8.6.7",
-    "@deck.gl/extensions": "8.6.7",
-    "@deck.gl/geo-layers": "8.6.7",
-    "@deck.gl/layers": "8.6.7",
-    "@deck.gl/mesh-layers": "8.6.7",
-    "@deck.gl/react": "8.6.7",
-    "@hms-dbmi/viv": "~0.12.6",
+    "@deck.gl/aggregation-layers": "~8.8.6",
+    "@deck.gl/core": "~8.8.6",
+    "@deck.gl/extensions": "~8.8.6",
+    "@deck.gl/geo-layers": "~8.8.6",
+    "@deck.gl/layers": "~8.8.6",
+    "@deck.gl/mesh-layers": "~8.8.6",
+    "@deck.gl/react": "~8.8.6",
+    "@hms-dbmi/viv": "~0.13.3",
     "@loaders.gl/3d-tiles": "^3.0.0",
     "@loaders.gl/core": "^3.0.0",
     "@loaders.gl/images": "^3.0.0",
     "@loaders.gl/loader-utils": "^3.0.0",
-    "@luma.gl/constants": "8.5.10",
-    "@luma.gl/core": "8.5.10",
-    "@luma.gl/engine": "8.5.10",
-    "@luma.gl/experimental": "8.5.10",
-    "@luma.gl/gltools": "8.5.10",
-    "@luma.gl/shadertools": "8.5.10",
-    "@luma.gl/webgl": "8.5.10",
+    "@luma.gl/constants": "~8.5.16",
+    "@luma.gl/core": "~8.5.16",
+    "@luma.gl/engine": "~8.5.16",
+    "@luma.gl/experimental": "~8.5.16",
+    "@luma.gl/gltools": "~8.5.16",
+    "@luma.gl/shadertools": "~8.5.16",
+    "@luma.gl/webgl": "~8.5.16",
     "@math.gl/core": "^3.5.6",
     "@nebula.gl/edit-modes": "0.23.8",
     "@nebula.gl/layers": "0.23.8",
@@ -42,13 +42,13 @@
     "@turf/boolean-within": "^6.5.0",
     "@turf/centroid": "^6.5.0",
     "@turf/helpers": "^6.5.0",
-    "deck.gl": "8.6.7",
+    "deck.gl": "~8.8.6",
     "glslify": "^7.0.0",
     "lodash": "^4.17.21",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
     "nebula.gl": "0.23.8",
-    "@vitessce/utils": "2.0.1"
+    "@vitessce/utils": "2.0.3-beta.0"
   },
   "devDependencies": {
     "glsl-colormap": "^1.0.1"