@aics/vole-core 4.1.0 → 4.2.0

package/es/ImageInfo.js

@@ -6,7 +6,7 @@ export function defaultImageInfo() {
     atlasTileDims: [1, 1],
     subregionSize: [1, 1, 1],
     subregionOffset: [0, 0, 0],
-    combinedNumChannels: 1,
+    numChannelsPerSource: [1],
     channelNames: ["0"],
     channelColors: [[255, 255, 255]],
     multiscaleLevel: 0,
@@ -34,7 +34,12 @@ export class CImageInfo {
 
   /** Number of channels in the image */
   get numChannels() {
-    return this.imageInfo.combinedNumChannels;
+    return this.imageInfo.numChannelsPerSource.reduce((a, b) => a + b, 0);
+  }
+
+  /** Number of channels per source, ordered by source index */
+  get numChannelsPerSource() {
+    return this.imageInfo.numChannelsPerSource;
   }
 
   /** XYZ size of the *original* (not downsampled) volume, in pixels */

package/es/VolumeDrawable.js

@@ -45,7 +45,9 @@ export default class VolumeDrawable {
     this.viewMode = Axis.NONE; // 3D mode
 
     this.channelColors = this.volume.channelColorsDefault.slice();
-    this.channelOptions = new Array(this.volume.imageInfo.numChannels).fill({});
+    this.channelOptions = Array.from({
+      length: this.volume.imageInfo.numChannels
+    }, () => ({}));
     this.fusion = this.channelColors.map((col, index) => {
       let rgbColor;
       // take copy of original channel color

package/es/loaders/JsonImageInfoLoader.js

@@ -29,7 +29,7 @@ const convertImageInfo = json => {
     atlasTileDims: [json.cols, json.rows],
     subregionSize: [json.tile_width, json.tile_height, json.tiles],
     subregionOffset: [0, 0, 0],
-    combinedNumChannels: json.channels,
+    numChannelsPerSource: json.images.map(image => image.channels.length),
     channelNames: json.channel_names,
     channelColors: json.channel_colors,
     multiscaleLevel: 0,

package/es/loaders/OmeZarrLoader.js

@@ -247,12 +247,14 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
     const levelToLoad = pickLevelToLoad(loadSpec, this.getLevelShapesZYX());
     const shapeLv = source0.scaleLevels[levelToLoad].shape;
     const [spatialUnit, timeUnit] = this.getUnitSymbols();
+    const numChannelsPerSource = [];
+    for (let i = 0; i < this.sources.length; i++) {
+      const source = this.sources[i];
+      const cIndex = source.axesTCZYX[1];
+      const sourceChannelCount = cIndex > -1 ? source.scaleLevels[levelToLoad].shape[cIndex] : 1;
+      numChannelsPerSource.push(sourceChannelCount);
+    }
 
-    // Now we care about other sources: # of channels is the `channelOffset` of the last source plus its # of channels
-    const sourceLast = this.sources[this.sources.length - 1];
-    const cLast = sourceLast.axesTCZYX[1];
-    const lastHasC = cLast > -1;
-    const numChannels = sourceLast.channelOffset + (lastHasC ? sourceLast.scaleLevels[levelToLoad].shape[cLast] : 1);
     // we need to make sure that the corresponding matched shapes
     // use the min size of T
     let times = 1;
@@ -310,7 +312,7 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
       atlasTileDims: [atlasTileDims.x, atlasTileDims.y],
       subregionSize: [pxSizeLv.x, pxSizeLv.y, pxSizeLv.z],
       subregionOffset: [0, 0, 0],
-      combinedNumChannels: numChannels,
+      numChannelsPerSource,
       channelNames,
       multiscaleLevel: levelToLoad,
       multiscaleLevelDims: alldims,
@@ -423,9 +425,10 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
     const updatedImageInfo = this.updateImageInfoForLoad(imageInfo, loadSpec);
     onUpdateMetadata(updatedImageInfo);
     const {
-      combinedNumChannels,
+      numChannelsPerSource,
       multiscaleLevel
     } = updatedImageInfo;
+    const combinedNumChannels = numChannelsPerSource.reduce((a, b) => a + b, 0);
     const channelIndexes = loadSpec.channels ?? Array.from({
       length: combinedNumChannels
     }, (_, i) => i);

package/es/loaders/OpenCellLoader.js

@@ -24,7 +24,7 @@ class OpenCellLoader extends ThreadableVolumeLoader {
       atlasTileDims: [27, 1],
       subregionSize: [600, 600, 27],
       subregionOffset: [0, 0, 0],
-      combinedNumChannels: numChannels,
+      numChannelsPerSource: [numChannels],
       channelNames: chnames,
       multiscaleLevel: 0,
       multiscaleLevelDims: [{

package/es/loaders/RawArrayLoader.js

@@ -37,7 +37,7 @@ const convertImageInfo = (json, dtype) => {
     atlasTileDims: [atlasTileDims.x, atlasTileDims.y],
     subregionSize: [json.sizeX, json.sizeY, json.sizeZ],
     subregionOffset: [0, 0, 0],
-    combinedNumChannels: json.sizeC,
+    numChannelsPerSource: [json.sizeC],
     channelNames: json.channelNames,
     channelColors: undefined,
     multiscaleLevel: 0,
@@ -92,7 +92,8 @@ class RawArrayLoader extends ThreadableVolumeLoader {
       multiscaleLevel: 0
     };
     onUpdateMetadata(undefined, adjustedLoadSpec);
-    for (let chindex = 0; chindex < imageInfo.combinedNumChannels; ++chindex) {
+    const totalChannels = imageInfo.numChannelsPerSource.reduce((a, b) => a + b, 0);
+    for (let chindex = 0; chindex < totalChannels; ++chindex) {
       if (requestedChannels && requestedChannels.length > 0 && !requestedChannels.includes(chindex)) {
         continue;
       }

package/es/loaders/TiffLoader.js

@@ -157,13 +157,13 @@ class TiffLoader extends ThreadableVolumeLoader {
     const tilesizey = Math.floor(targetSize / atlasDims.y);
 
     // load tiff and check metadata
-
+    const numChannelsPerSource = this.url.length > 1 ? Array(this.url.length).fill(1) : [dims.sizec];
     const imgdata = {
       name: "TEST",
       atlasTileDims: [atlasDims.x, atlasDims.y],
       subregionSize: [tilesizex, tilesizey, dims.sizez],
       subregionOffset: [0, 0, 0],
-      combinedNumChannels: dims.sizec,
+      numChannelsPerSource,
       channelNames: dims.channelnames,
       multiscaleLevel: 0,
       multiscaleLevelDims: [{
@@ -194,41 +194,44 @@ class TiffLoader extends ThreadableVolumeLoader {
     const volumeSize = cimageinfo.volumeSize;
     const channelProms = [];
     // do each channel on a worker?
-    for (let channel = 0; channel < imageInfo.combinedNumChannels; ++channel) {
-      const thisChannelProm = new Promise((resolve, reject) => {
-        const params = {
-          channel: channel,
-          // these are target xy sizes for the in-memory volume data
-          // they may or may not be the same size as original xy sizes
-          tilesizex: volumeSize.x,
-          tilesizey: volumeSize.y,
-          sizec: imageInfo.combinedNumChannels,
-          sizez: volumeSize.z,
-          dimensionOrder: dims.dimensionorder,
-          bytesPerSample: getBytesPerSample(dims.pixeltype),
-          url: this.url.length > 1 ? this.url[channel] : this.url[0] // if multiple urls, use the channel index to select the right one
-        };
-        const worker = new Worker(new URL("../workers/FetchTiffWorker", import.meta.url), {
-          type: "module"
+    for (let source = 0; source < imageInfo.numChannelsPerSource.length; ++source) {
+      const numChannels = imageInfo.numChannelsPerSource[source];
+      for (let channel = 0; channel < numChannels; ++channel) {
+        const thisChannelProm = new Promise((resolve, reject) => {
+          const params = {
+            channel: channel,
+            // these are target xy sizes for the in-memory volume data
+            // they may or may not be the same size as original xy sizes
+            tilesizex: volumeSize.x,
+            tilesizey: volumeSize.y,
+            sizec: numChannels,
+            sizez: volumeSize.z,
+            dimensionOrder: dims.dimensionorder,
+            bytesPerSample: getBytesPerSample(dims.pixeltype),
+            url: this.url[source]
+          };
+          const worker = new Worker(new URL("../workers/FetchTiffWorker", import.meta.url), {
+            type: "module"
+          });
+          worker.onmessage = e => {
+            if (e.data.isError) {
+              reject(deserializeError(e.data.error));
+              return;
+            }
+            const {
+              data,
+              dtype,
+              channel,
+              range
+            } = e.data;
+            onData([channel], [dtype], [data], [range]);
+            worker.terminate();
+            resolve();
+          };
+          worker.postMessage(params);
         });
-        worker.onmessage = e => {
-          if (e.data.isError) {
-            reject(deserializeError(e.data.error));
-            return;
-          }
-          const {
-            data,
-            dtype,
-            channel,
-            range
-          } = e.data;
-          onData([channel], [dtype], [data], [range]);
-          worker.terminate();
-          resolve();
-        };
-        worker.postMessage(params);
-      });
-      channelProms.push(thisChannelProm);
+        channelProms.push(thisChannelProm);
+      }
     }
 
     // waiting for all channels to load allows errors to propagate to the caller via this promise

package/es/loaders/VolumeLoaderUtils.js

@@ -211,7 +211,8 @@ export function buildDefaultMetadata(rawImageInfo) {
   };
   metadata["Multiresolution levels"] = rawImageInfo.multiscaleLevelDims;
   // TODO decide???? combined or not?
-  metadata["Channels"] = rawImageInfo.combinedNumChannels; //imageInfo.numChannels;
+  const totalChannels = imageInfo.numChannelsPerSource.reduce((a, b) => a + b, 0);
+  metadata["Channels"] = totalChannels;
   metadata["Time series frames"] = imageInfo.times || 1;
   // don't add User data if it's empty
   if (rawImageInfo.userData && !isEmpty(rawImageInfo.userData)) {

package/es/types/ImageInfo.d.ts

@@ -3,20 +3,17 @@ import { Vector3, Vector2 } from "three";
 export type ImageInfo = Readonly<{
     name: string;
     /**
-     * XY dimensions of the texture atlas used by `RayMarchedAtlasVolume` and `Atlas2DSlice`, in number of z-slice
-     * tiles (not pixels). Chosen by the loader to lay out the 3D volume in the squarest possible 2D texture atlas.
+     * XY dimensions of the texture atlas used by `RayMarchedAtlasVolume` and
+     * `Atlas2DSlice`, in number of z-slice tiles (not pixels). Chosen by the
+     * loader to lay out the 3D volume in the squarest possible 2D texture atlas.
      */
     atlasTileDims: [number, number];
     /** Size of the currently loaded subregion, in pixels, in XYZ order */
     subregionSize: [number, number, number];
     /** Offset of the loaded subregion into the total volume, in pixels, in XYZ order */
     subregionOffset: [number, number, number];
-    /** Number of channels in the image, accounting for convergence of multiple sources.
-     * Because of multiple sources, which is not accounted for in ImageInfo,
-     * that this could be different than the number of channels in the multiscaleLevelDims.
-     * NOTE Currently there is one ImageInfo per Volume, not per source.
-     */
-    combinedNumChannels: number;
+    /** The number of channels in each source, in source order. */
+    numChannelsPerSource: number[];
     /** The names of each channel */
     channelNames: string[];
     /** Optional overrides to default channel colors, in 0-255 range, RGB order */
@@ -26,9 +23,9 @@ export type ImageInfo = Readonly<{
     /** The scale level from which this image was loaded, between `0` and `numMultiscaleLevels-1` */
     multiscaleLevel: number;
     /**
-     * An *optional* transform which may be supplied by image metadata. It is *not* applied by
-     * default, but may be read and fed to `View3d` methods: `setVolumeTransform`,
-     * `setVolumeRotation`, `setVolumeScale`.
+     * An *optional* transform which may be supplied by image metadata. It is
+     * *not* applied by default, but may be read and fed to `View3d` methods:
+     * `setVolumeTransform`, `setVolumeRotation`, `setVolumeScale`.
      */
     transform: {
         /** Translation of the volume from the center of space, in volume voxels in XYZ order */
@@ -48,6 +45,8 @@ export declare class CImageInfo {
     get currentLevelDims(): VolumeDims;
     /** Number of channels in the image */
     get numChannels(): number;
+    /** Number of channels per source, ordered by source index */
+    get numChannelsPerSource(): number[];
     /** XYZ size of the *original* (not downsampled) volume, in pixels */
     get originalSize(): Vector3;
     /** Size of the volume, in pixels */

package/es/types/types.d.ts

@@ -96,28 +96,26 @@ export interface FuseChannel {
 }
 /** If `FuseChannel.rgbColor` is this value, it is disabled from fusion. */
 export declare const FUSE_DISABLED_RGB_COLOR = 0;
-/**
- * Provide options to control the visual appearance of a Volume
- * @typedef {Object} VolumeChannelDisplayOptions
- * @property {boolean} enabled array of boolean per channel
- * @property {Array.<number>} color array of rgb per channel
- * @property {Array.<number>} specularColor array of rgb per channel
- * @property {Array.<number>} emissiveColor array of rgb per channel
- * @property {number} glossiness array of float per channel
- * @property {boolean} isosurfaceEnabled array of boolean per channel
- * @property {number} isovalue array of number per channel
- * @property {number} isosurfaceOpacity array of number per channel
- * @example let options = {
-   };
- */
 export interface VolumeChannelDisplayOptions {
+    /** Whether the channel's volume data should be rendered for this channel. */
     enabled?: boolean;
+    /** RGB color array, with values in the range of [0, 255]. */
     color?: [number, number, number];
+    /** RGB color array for specular (highlight) color, with values in the range of [0, 255]. */
     specularColor?: [number, number, number];
+    /** RGB color array for emissive (glow) color, with values in the range of [0, 255]. */
     emissiveColor?: [number, number, number];
+    /** Exponent factor controlling the glossiness ("shininess") of the material. 0 is default. */
     glossiness?: number;
+    /** Whether the isosurface mesh should be rendered for this channel. */
     isosurfaceEnabled?: boolean;
+    /**
+     * Isovalue used to calculate the isosurface mesh, in a [0, 255] range.
+     * Isosurface is found at the set of all boundaries between voxels whose
+     * intensities span across this isovalue.
+     */
     isovalue?: number;
+    /** Opacity of the isosurface, in a [0, 1] range. */
     isosurfaceOpacity?: number;
 }
 export declare enum RenderMode {

package/es/types.js

@@ -18,22 +18,6 @@ export function isFloatTypeArray(array) {
 }
 /** If `FuseChannel.rgbColor` is this value, it is disabled from fusion. */
 export const FUSE_DISABLED_RGB_COLOR = 0;
-
-/**
- * Provide options to control the visual appearance of a Volume
- * @typedef {Object} VolumeChannelDisplayOptions
- * @property {boolean} enabled array of boolean per channel
- * @property {Array.<number>} color array of rgb per channel
- * @property {Array.<number>} specularColor array of rgb per channel
- * @property {Array.<number>} emissiveColor array of rgb per channel
- * @property {number} glossiness array of float per channel
- * @property {boolean} isosurfaceEnabled array of boolean per channel
- * @property {number} isovalue array of number per channel
- * @property {number} isosurfaceOpacity array of number per channel
- * @example let options = {
-   };
- */
-
 export let RenderMode = /*#__PURE__*/function (RenderMode) {
   RenderMode[RenderMode["RAYMARCH"] = 0] = "RAYMARCH";
   RenderMode[RenderMode["PATHTRACE"] = 1] = "PATHTRACE";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "4.1.0",
+  "version": "4.2.0",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",