@aics/vole-core 4.2.0 → 4.3.1

package/es/MeshVolume.js

@@ -19,6 +19,10 @@ export default class MeshVolume {
     this.meshRoot = new Object3D(); //create an empty container
     this.meshRoot.name = "Mesh Surface Group";
 
+    // compensating for generated isosurface vertex coordinates
+    // arguably this could be set on meshPivot
+    this.meshRoot.scale.setScalar(0.5);
+
     // handle transform ordering for giving the meshroot a rotation about a pivot point
     this.meshPivot = new Group();
     this.meshPivot.name = "MeshContainerNode";

package/es/View3d.js

@@ -928,12 +928,12 @@ export class View3d {
         color: {
           type: "float"
         }
-      });
+      }).on("change", _event => this.redraw());
       folder.addInput(light, "intensity", {
         min: 0
-      });
+      }).on("change", _event => this.redraw());
       if (!light.isAmbientLight) {
-        folder.addInput(light, "position");
+        folder.addInput(light, "position").on("change", _event => this.redraw());
       }
     };
     addFolderForLight(this.spotLight, "spot light");

package/es/Volume.js

@@ -72,7 +72,7 @@ export default class Volume {
     this.setVoxelSize(this.physicalPixelSize);
     this.numChannels = this.imageInfo.numChannels;
     this.channelNames = this.imageInfo.channelNames.slice();
-    this.channelColorsDefault = this.imageInfo.channelColors ? this.imageInfo.channelColors.slice() : this.channelNames.map((name, index) => getColorByChannelIndex(index));
+    this.channelColorsDefault = this.imageInfo.channelColors ? this.imageInfo.channelColors.map((color, index) => color ?? getColorByChannelIndex(index)) : this.channelNames.map((name, index) => getColorByChannelIndex(index));
     // fill in gaps
     if (this.channelColorsDefault.length < this.imageInfo.numChannels) {
       for (let i = this.channelColorsDefault.length - 1; i < this.imageInfo.numChannels; ++i) {

package/es/VolumeDrawable.js

@@ -711,7 +711,7 @@ export default class VolumeDrawable {
 
     // remove old 3d object from scene
     if (this.renderMode === RenderMode.SLICE || this.renderMode === RenderMode.RAYMARCH) {
-      this.sceneRoot.remove(this.meshVolume.get3dObject());
+      this.childObjectsGroup.remove(this.meshVolume.get3dObject());
     }
     this.sceneRoot.remove(this.volumeRendering.get3dObject());
 
@@ -747,7 +747,7 @@ export default class VolumeDrawable {
       if (this.renderUpdateListener) {
         this.renderUpdateListener(0);
       }
-      this.sceneRoot.add(this.meshVolume.get3dObject());
+      this.childObjectsGroup.add(this.meshVolume.get3dObject());
     }
 
     // add new 3d object to scene

package/es/constants/lights.js

@@ -3,7 +3,7 @@ const spotlightSettings = Object.freeze({
   angle: 36 * MathUtils.DEG2RAD,
   castShadow: false,
   color: 0xffffff,
-  intensity: 0.4,
+  intensity: 15.0,
   position: {
     x: -4,
     y: 3.5,
@@ -12,12 +12,12 @@ const spotlightSettings = Object.freeze({
 });
 const ambientLightSettings = Object.freeze({
   color: 0xffffff,
-  intensity: 0.6
+  intensity: 1.75
 });
 const reflectedLightSettings = Object.freeze({
   castShadow: false,
   color: 0xff88aa,
-  intensity: 0.2,
+  intensity: 2.0,
   position: {
     x: 1,
     y: -5,
@@ -27,7 +27,7 @@ const reflectedLightSettings = Object.freeze({
 const fillLightSettings = Object.freeze({
   castShadow: false,
   color: 0xe8d1a9,
-  intensity: 0.15,
+  intensity: 1.5,
   position: {
     x: 2.5,
     y: 0.2,

package/es/loaders/OmeZarrLoader.js

@@ -7,7 +7,7 @@ import SubscribableRequestQueue from "../utils/SubscribableRequestQueue.js";
 import { ThreadableVolumeLoader } from "./IVolumeLoader.js";
 import { composeSubregion, computePackedAtlasDims, convertSubregionToPixels, pickLevelToLoad, unitNameToSymbol } from "./VolumeLoaderUtils.js";
 import ChunkPrefetchIterator from "./zarr_utils/ChunkPrefetchIterator.js";
-import { getScale, getSourceChannelNames, matchSourceScaleLevels, orderByDimension, orderByTCZYX, remapAxesToTCZYX } from "./zarr_utils/utils.js";
+import { getScale, getSourceChannelMeta, matchSourceScaleLevels, orderByDimension, orderByTCZYX, remapAxesToTCZYX } from "./zarr_utils/utils.js";
 import { VolumeLoadError, VolumeLoadErrorType, wrapVolumeLoadError } from "./VolumeLoadError.js";
 import wrapArray, { RelaxedFetchStore } from "./zarr_utils/wrappers.js";
 import { assertMetadataHasMultiscales, toOMEZarrMetaV4, validateOMEZarrMetadata } from "./zarr_utils/validation.js";
@@ -281,11 +281,16 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
     // Channel names is the other place where we have to check every source
     // Track which channel names we've seen so far, so that we can rename them to avoid name collisions
     const channelNamesMap = new Map();
-    const channelNames = this.sources.flatMap(src => {
-      const sourceChannelNames = getSourceChannelNames(src);
+    const channelNames = [];
+    const channelColors = [];
+    for (const src of this.sources) {
+      const {
+        names,
+        colors
+      } = getSourceChannelMeta(src);
 
       // Resolve name collisions
-      return sourceChannelNames.map(channelName => {
+      const resolvedNames = names.map(channelName => {
         const numMatchingChannels = channelNamesMap.get(channelName);
         if (numMatchingChannels !== undefined) {
           // If e.g. we've seen channel "Membrane" once before, rename this one to "Membrane (1)"
@@ -296,7 +301,9 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
           return channelName;
         }
       });
-    });
+      channelNames.push(...resolvedNames);
+      channelColors.push(...colors);
+    }
     const alldims = source0.scaleLevels.map((level, i) => {
       const dims = {
         spaceUnit: spatialUnit,
@@ -314,6 +321,7 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
       subregionOffset: [0, 0, 0],
       numChannelsPerSource,
       channelNames,
+      channelColors,
       multiscaleLevel: levelToLoad,
       multiscaleLevelDims: alldims,
       transform: {

package/es/loaders/TiffLoader.js

@@ -4,20 +4,17 @@ import { ThreadableVolumeLoader, LoadSpec } from "./IVolumeLoader.js";
 import { computePackedAtlasDims, MAX_ATLAS_EDGE } from "./VolumeLoaderUtils.js";
 import { VolumeLoadError, VolumeLoadErrorType, wrapVolumeLoadError } from "./VolumeLoadError.js";
 import { CImageInfo } from "../ImageInfo.js";
-function prepareXML(xml) {
+function trimNull(xml) {
   // trim trailing unicode zeros?
-  // eslint-disable-next-line no-control-regex
-  const expr = /[\u0000]$/g;
-  return xml.trim().replace(expr, "").trim();
+  return xml && xml.trim().replace(/\0/g, "").trim();
 }
 function getOME(xml) {
-  if (xml === undefined) {
+  if (typeof xml !== "string") {
     return undefined;
   }
-  const prepared = prepareXML(xml);
   const parser = new DOMParser();
   try {
-    const xmlDoc = parser.parseFromString(prepared, "text/xml");
+    const xmlDoc = parser.parseFromString(xml, "text/xml");
     return xmlDoc.getElementsByTagName("OME")[0];
   } catch (e) {
     return undefined;
@@ -104,20 +101,42 @@ class TiffLoader extends ThreadableVolumeLoader {
       // const imagecount = await tiff.getImageCount();
       // read the FIRST image
       const image = await tiff.getImage().catch(wrapVolumeLoadError("Failed to open TIFF image", VolumeLoadErrorType.NOT_FOUND));
-      const omeEl = getOME(image.getFileDirectory().ImageDescription);
+      const image0DescriptionRaw = image.getFileDirectory().ImageDescription;
+      // Get rid of null terminator, if it's there (`JSON.parse` doesn't know what to do with it)
+      const image0Description = trimNull(image0DescriptionRaw);
+      const omeEl = getOME(image0Description);
       if (omeEl !== undefined) {
         const image0El = omeEl.getElementsByTagName("Image")[0];
         this.dims = getOMEDims(image0El);
       } else {
         console.warn("Could not read OME-TIFF metadata from file. Doing our best with base TIFF metadata.");
         this.dims = new OMEDims();
-        this.dims.sizex = image.getWidth();
-        this.dims.sizey = image.getHeight();
+        let shape = [];
+        if (typeof image0Description === "string") {
+          try {
+            const description = JSON.parse(image0Description);
+            if (Array.isArray(description.shape)) {
+              shape = description.shape;
+            }
+            // eslint-disable-next-line no-empty
+          } catch (_e) {}
+        }
+
+        // if `ImageDescription` is valid JSON with a `shape` field, we expect it to be an array of [t?, c?, z?, y, x].
+        this.dims.sizex = shape[shape.length - 1] ?? image.getWidth();
+        this.dims.sizey = shape[shape.length - 2] ?? image.getHeight();
+        this.dims.sizez = shape[shape.length - 3] ?? (await tiff.getImageCount());
+
         // TODO this is a big hack/assumption about only loading multi-source tiffs that are not OMETIFF.
         // We really have to check each url in the array for sizec to get the total number of channels
         // See combinedNumChannels in ImageInfo below.
         // Also compare with how OMEZarrLoader does this.
-        this.dims.sizec = this.url.length > 1 ? this.url.length : 1; // if multiple urls, assume one channel per url
+        if (this.url.length > 1) {
+          // if multiple urls, assume one channel per url
+          this.dims.sizec = this.url.length;
+        } else {
+          this.dims.sizec = shape[shape.length - 4] ?? 1;
+        }
         this.dims.pixeltype = getPixelType(image.getBytesPerPixel());
         this.dims.channelnames = Array.from({
           length: this.dims.sizec

package/es/loaders/zarr_utils/utils.js

@@ -1,16 +1,51 @@
 import { VolumeLoadErrorType, VolumeLoadError } from "../VolumeLoadError.js";
+/**
+ * Attempts to parse `color` as a 24-bit (6-digit) hexadecimal color with a possible leading `#`.
+ *
+ * Six-digit hex is the only allowable color representation in the OMERO metadata spec.
+ */
+export function parseHexColor(color) {
+  if (color === undefined) {
+    return undefined;
+  }
+  const result = /^#?([a-fA-F\d]{2})([a-fA-F\d]{2})([a-fA-F\d]{2})$/i.exec(color);
+  if (result) {
+    return [parseInt(result[1], 16), parseInt(result[2], 16), parseInt(result[3], 16)];
+  } else {
+    return undefined;
+  }
+}
+
 /** Extracts channel names from a `ZarrSource`. Handles missing `omeroMetadata`. Does *not* resolve name collisions. */
-export function getSourceChannelNames(src) {
+export function getSourceChannelMeta(src) {
   if (src.omeroMetadata?.channels) {
-    return src.omeroMetadata.channels.map(({
-      label
-    }, idx) => label ?? `Channel ${idx + src.channelOffset}`);
+    const {
+      channels
+    } = src.omeroMetadata;
+    const names = [];
+    const colors = [];
+    for (let i = 0; i < channels.length; i++) {
+      const channel = channels[i];
+      names.push(channel.label ?? `Channel ${i + src.channelOffset}`);
+      colors.push(parseHexColor(channel.color));
+    }
+    return {
+      names,
+      colors
+    };
   }
   const cIdx = src.axesTCZYX[1];
   const length = cIdx < 0 ? 1 : src.scaleLevels[0].shape[cIdx];
-  return Array.from({
+  const names = Array.from({
     length
   }, (_, idx) => `Channel ${idx + src.channelOffset}`);
+  const colors = Array.from({
+    length
+  }, () => undefined);
+  return {
+    names,
+    colors
+  };
 }
 
 /** Turns `axesTCZYX` into the number of dimensions in the array */

package/es/types/ImageInfo.d.ts

@@ -17,7 +17,7 @@ export type ImageInfo = Readonly<{
     /** The names of each channel */
     channelNames: string[];
     /** Optional overrides to default channel colors, in 0-255 range, RGB order */
-    channelColors?: [number, number, number][];
+    channelColors?: ([number, number, number] | undefined)[];
     /** Dimensions of each scale level, at original size, from the first data source */
     multiscaleLevelDims: VolumeDims[];
     /** The scale level from which this image was loaded, between `0` and `numMultiscaleLevels-1` */
@@ -66,7 +66,7 @@ export declare class CImageInfo {
     /** The names of each channel */
     get channelNames(): string[];
     /** Optional overrides to default channel colors, in 0-255 range */
-    get channelColors(): [number, number, number][] | undefined;
+    get channelColors(): ([number, number, number] | undefined)[] | undefined;
     /** Size of the currently loaded subregion, in pixels */
     get subregionSize(): Vector3;
     /** Offset of the loaded subregion into the total volume, in pixels */

package/es/types/constants/lights.d.ts

@@ -3,7 +3,7 @@ declare const _default: {
         angle: number;
         castShadow: false;
         color: 16777215;
-        intensity: 0.4;
+        intensity: 15;
         position: {
             x: number;
             y: number;
@@ -12,12 +12,12 @@ declare const _default: {
     }>;
     ambientLightSettings: Readonly<{
         color: 16777215;
-        intensity: 0.6;
+        intensity: 1.75;
     }>;
     reflectedLightSettings: Readonly<{
         castShadow: false;
         color: 16746666;
-        intensity: 0.2;
+        intensity: 2;
         position: {
             x: number;
             y: number;
@@ -27,7 +27,7 @@ declare const _default: {
     fillLightSettings: Readonly<{
         castShadow: false;
         color: 15258025;
-        intensity: 0.15;
+        intensity: 1.5;
         position: {
             x: number;
             y: number;

package/es/types/loaders/zarr_utils/types.d.ts

@@ -59,7 +59,7 @@ export type OmeroTransitionalMetadata = {
     channels: {
         active?: boolean;
         coefficient?: number;
-        color: string;
+        color?: string;
         family?: string;
         inverted?: boolean;
         label?: string;

package/es/types/loaders/zarr_utils/utils.d.ts

@@ -1,6 +1,15 @@
 import type { OMEAxis, OMEDataset, OMEMultiscale, TCZYX, ZarrSource } from "./types.js";
+/**
+ * Attempts to parse `color` as a 24-bit (6-digit) hexadecimal color with a possible leading `#`.
+ *
+ * Six-digit hex is the only allowable color representation in the OMERO metadata spec.
+ */
+export declare function parseHexColor(color: string | undefined): [number, number, number] | undefined;
 /** Extracts channel names from a `ZarrSource`. Handles missing `omeroMetadata`. Does *not* resolve name collisions. */
-export declare function getSourceChannelNames(src: ZarrSource): string[];
+export declare function getSourceChannelMeta(src: ZarrSource): {
+    names: string[];
+    colors: ([number, number, number] | undefined)[];
+};
 /** Turns `axesTCZYX` into the number of dimensions in the array */
 export declare const getDimensionCount: ([t, c, z]: TCZYX<number>) => number;
 export declare function remapAxesToTCZYX(axes: OMEAxis[]): TCZYX<number>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "4.2.0",
+  "version": "4.3.1",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",