@vitessce/gl 2.0.0-beta.2 → 2.0.1

package/dist/index.js

@@ -14,4 +14,3 @@ export { TILE_SIZE, MAX_ROW_AGG, MIN_ROW_AGG, COLOR_BAR_SIZE, AXIS_MARGIN, DATA_
 export * as viv from './viv';
 export * as luma from './luma';
 export * as deck from './deck';
-export { GLOBAL_LABELS, DEFAULT_CELLS_LAYER, DEFAULT_MOLECULES_LAYER, DEFAULT_NEIGHBORHOODS_LAYER, DEFAULT_RASTER_DOMAIN_TYPE, DEFAULT_RASTER_LAYER_PROPS, DEFAULT_LAYER_TYPE_ORDERING, square, initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isRgb, } from './spatial';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/gl",
-  "version": "2.0.0-beta.2",
+  "version": "2.0.1",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -42,13 +42,13 @@
     "@turf/boolean-within": "^6.5.0",
     "@turf/centroid": "^6.5.0",
     "@turf/helpers": "^6.5.0",
-    "@vitessce/utils": "2.0.0-beta.2",
     "deck.gl": "8.6.7",
     "glslify": "^7.0.0",
     "lodash": "^4.17.21",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
-    "nebula.gl": "0.23.8"
+    "nebula.gl": "0.23.8",
+    "@vitessce/utils": "2.0.1"
   },
   "devDependencies": {
     "glsl-colormap": "^1.0.1"

package/dist/layer-controller.js

@@ -1,109 +0,0 @@
-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

@@ -1,281 +0,0 @@
-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

@@ -1,8 +0,0 @@
-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]]);
-        });
-    });
-});