@aics/vole-core 4.4.0 → 4.5.0

package/es/Channel.js

@@ -157,7 +157,7 @@ export default class Channel {
     };
     this.rebuildDataTexture(this.imgData.data, w, h);
     this.loaded = true;
-    this.histogram = new Histogram(bitsArray);
+    this.histogram = new Histogram(bitsArray, rawMin, rawMax);
     this.frame = frame;
 
     // reuse old lut but auto-remap it to new data range
@@ -205,7 +205,7 @@ export default class Channel {
     this.loaded = true;
     // update from current histogram?
     this.setRawDataRange(rawMin, rawMax);
-    this.histogram = new Histogram(this.volumeData);
+    this.histogram = new Histogram(this.volumeData, rawMin, rawMax);
   }
 
   // given this.volumeData, let's unpack it into a flat textureatlas and fill up this.imgData.

package/es/Histogram.js

@@ -1,4 +1,5 @@
 import { isFloatTypeArray } from "./types.js";
+import { getDataRange } from "./utils/num_utils.js";
 const NBINS = 256;
 /**
  * Builds a histogram with 256 bins from a data array. Assume data is 8 bit single channel grayscale.
@@ -18,7 +19,7 @@ export default class Histogram {
 
   /** Index of the last bin (other than 0) with at least 1 value. */
 
-  constructor(data) {
+  constructor(data, dataMin = undefined, dataMax = undefined) {
     this.dataMinBin = 0;
     this.dataMaxBin = 0;
     this.maxBin = 0;
@@ -28,7 +29,7 @@ export default class Histogram {
     this.binSize = 0;
 
     // build up the histogram
-    const hinfo = Histogram.calculateHistogram(data, NBINS);
+    const hinfo = Histogram.calculateHistogram(data, NBINS, dataMin, dataMax);
     this.bins = hinfo.bins;
     this.min = hinfo.min;
     this.max = hinfo.max;
@@ -233,24 +234,19 @@ export default class Histogram {
     }
     return [b, e];
   }
-  static calculateHistogram(arr, numBins = 1) {
+  static calculateHistogram(arr, numBins = 1, dataMin = undefined, dataMax = undefined) {
     if (numBins < 1) {
       numBins = 1;
     }
 
-    // calculate min and max of arr
-    // TODO See convertChannel, which will also compute min and max!
-    // We could save a whole extra loop over the data, or have convertChannel compute the whole histogram.
-    // need to be careful about computing over chunks or whole ready-to-display volume
+    // ASSUMPTION: we will trust the min and max if provided.
+    let min = dataMin !== undefined ? dataMin : arr[0];
+    let max = dataMax !== undefined ? dataMax : arr[0];
 
-    let min = arr[0];
-    let max = arr[0];
-    for (let i = 1; i < arr.length; i++) {
-      if (arr[i] < min) {
-        min = arr[i];
-      } else if (arr[i] > max) {
-        max = arr[i];
-      }
+    // Find min and max in the array if the user did not provide them.
+    // Note that this is a completely separate walk through the data array which could be expensive.
+    if (dataMin === undefined || dataMax === undefined) {
+      [min, max] = getDataRange(arr);
     }
     const bins = new Uint32Array(numBins).fill(0);
 

package/es/MeshVolume.js

@@ -250,11 +250,12 @@ export default class MeshVolume {
       this.meshrep[channel] = null;
     }
   }
-  saveChannelIsosurface(channelIndex, type, namePrefix) {
+  saveChannelIsosurface(channelIndex, type, name) {
     const meshrep = this.meshrep[channelIndex];
     if (!meshrep) {
       return;
     }
+    const namePrefix = name !== undefined ? `${name}_` : "";
     if (type === "STL") {
       this.exportSTL(meshrep, namePrefix + "_" + this.volume.channelNames[channelIndex]);
     } else if (type === "GLTF") {

package/es/VectorArrows3d.js

@@ -1,7 +1,6 @@
+import BaseDrawableMeshObject from "./BaseDrawableMeshObject.js";
+import { MESH_NO_PICK_OCCLUSION_LAYER } from "./ThreeJsPanel.js";
 import { InstancedMesh, CylinderGeometry, ConeGeometry, Object3D, Vector3, MeshBasicMaterial, Color, DynamicDrawUsage, Matrix4 } from "three";
-import BaseDrawableMeshObject from "./BaseDrawableMeshObject";
-import { MESH_NO_PICK_OCCLUSION_LAYER } from "./ThreeJsPanel";
-
 // Unscaled arrowhead dimensions.
 const SHAFT_BASE_RADIUS = 0.5;
 const HEAD_BASE_RADIUS = 1.5;

package/es/loaders/JsonImageInfoLoader.js

@@ -3,6 +3,7 @@ import { ThreadableVolumeLoader } from "./IVolumeLoader.js";
 import { computeAtlasSize } from "../ImageInfo.js";
 import { isChunk } from "../VolumeCache.js";
 import { getDataRange } from "../utils/num_utils.js";
+import { remapUri } from "../utils/url_utils.js";
 
 /* eslint-disable @typescript-eslint/naming-convention */
 
@@ -70,7 +71,7 @@ class JsonImageInfoLoader extends ThreadableVolumeLoader {
     if (cachedInfo) {
       return cachedInfo;
     }
-    const response = await fetch(this.urls[time]);
+    const response = await fetch(remapUri(this.urls[time]));
     const imageInfo = await response.json();
     imageInfo.pixel_size_unit = imageInfo.pixel_size_unit || "μm";
     imageInfo.times = imageInfo.times || this.urls.length;
@@ -194,7 +195,7 @@ class JsonImageInfoLoader extends ThreadableVolumeLoader {
       if (cacheHit) {
         return;
       }
-      const response = await fetch(image.name, {
+      const response = await fetch(remapUri(image.name), {
         mode: "cors"
       });
       const blob = await response.blob();

package/es/loaders/OmeZarrLoader.js

@@ -3,6 +3,7 @@ import * as zarr from "zarrita";
 const {
   slice
 } = zarr;
+import { getDataRange } from "../utils/num_utils.js";
 import SubscribableRequestQueue from "../utils/SubscribableRequestQueue.js";
 import { ThreadableVolumeLoader } from "./IVolumeLoader.js";
 import { composeSubregion, computePackedAtlasDims, convertSubregionToPixels, pickLevelToLoad, unitNameToSymbol } from "./VolumeLoaderUtils.js";
@@ -11,23 +12,13 @@ import { getScale, getSourceChannelMeta, matchSourceScaleLevels, orderByDimensio
 import { VolumeLoadError, VolumeLoadErrorType, wrapVolumeLoadError } from "./VolumeLoadError.js";
 import wrapArray, { RelaxedFetchStore } from "./zarr_utils/wrappers.js";
 import { assertMetadataHasMultiscales, toOMEZarrMetaV4, validateOMEZarrMetadata } from "./zarr_utils/validation.js";
+import { remapUri } from "../utils/url_utils.js";
 const CHUNK_REQUEST_CANCEL_REASON = "chunk request cancelled";
 
 // returns the converted data and the original min and max values
 function convertChannel(channelData, dtype) {
   // get min and max
-  // TODO FIXME Histogram will also compute min and max!
-  let min = channelData[0];
-  let max = channelData[0];
-  for (let i = 0; i < channelData.length; i++) {
-    const val = channelData[i];
-    if (val < min) {
-      min = val;
-    }
-    if (val > max) {
-      max = val;
-    }
-  }
+  const [min, max] = getDataRange(channelData);
   if (dtype === "float64") {
     // convert to float32
     const f32 = new Float32Array(channelData.length);
@@ -91,7 +82,7 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
     if (!queue) {
       queue = new SubscribableRequestQueue(fetchOptions?.concurrencyLimit, fetchOptions?.prefetchConcurrencyLimit);
     }
-    const urlsArr = Array.isArray(urls) ? urls : [urls];
+    const urlsArr = (Array.isArray(urls) ? urls : [urls]).map(remapUri);
     const scenesArr = Array.isArray(scenes) ? scenes : [scenes];
 
     // Create one `ZarrSource` per URL
@@ -315,7 +306,7 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
       return dims;
     });
     const imgdata = {
-      name: source0.omeroMetadata?.name || "Volume",
+      name: source0.omeroMetadata?.name,
       atlasTileDims: [atlasTileDims.x, atlasTileDims.y],
       subregionSize: [pxSizeLv.x, pxSizeLv.y, pxSizeLv.z],
       subregionOffset: [0, 0, 0],
@@ -468,7 +459,6 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
       const level = this.sources[sourceIdx].scaleLevels[multiscaleLevel];
       const sliceSpec = this.orderByDimension(unorderedSpec, sourceIdx);
       const reportChunk = (coords, sub) => reportChunkBase(sourceIdx, coords, sub);
-      console.log(level);
       const result = await zarr.get(level, sliceSpec, {
         opts: {
           subscriber,

package/es/loaders/TiffLoader.js

@@ -4,6 +4,7 @@ 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";
+import { remapUri } from "../utils/url_utils.js";
 function trimNull(xml) {
   // trim trailing unicode zeros?
   return xml && xml.trim().replace(/\0/g, "").trim();
@@ -21,6 +22,7 @@ function getOME(xml) {
   }
 }
 class OMEDims {
+  name = undefined;
   sizex = 0;
   sizey = 0;
   sizez = 1;
@@ -63,14 +65,15 @@ function getAttributeOrError(el, attr) {
 function getOMEDims(imageEl) {
   const dims = new OMEDims();
   const pixelsEl = imageEl.getElementsByTagName("Pixels")[0];
+  dims.name = imageEl.getAttribute("Name") ?? "";
   dims.sizex = Number(getAttributeOrError(pixelsEl, "SizeX"));
   dims.sizey = Number(getAttributeOrError(pixelsEl, "SizeY"));
   dims.sizez = Number(pixelsEl.getAttribute("SizeZ"));
   dims.sizec = Number(pixelsEl.getAttribute("SizeC"));
   dims.sizet = Number(pixelsEl.getAttribute("SizeT"));
-  dims.unit = pixelsEl.getAttribute("PhysicalSizeXUnit") || "";
-  dims.pixeltype = pixelsEl.getAttribute("Type") || "";
-  dims.dimensionorder = pixelsEl.getAttribute("DimensionOrder") || "XYZCT";
+  dims.unit = pixelsEl.getAttribute("PhysicalSizeXUnit") ?? "";
+  dims.pixeltype = pixelsEl.getAttribute("Type") ?? "";
+  dims.dimensionorder = pixelsEl.getAttribute("DimensionOrder") ?? "XYZCT";
   dims.pixelsizex = Number(pixelsEl.getAttribute("PhysicalSizeX"));
   dims.pixelsizey = Number(pixelsEl.getAttribute("PhysicalSizeY"));
   dims.pixelsizez = Number(pixelsEl.getAttribute("PhysicalSizeZ"));
@@ -90,7 +93,7 @@ const getPixelType = pxSize => pxSize === 1 ? "uint8" : pxSize === 2 ? "uint16"
 class TiffLoader extends ThreadableVolumeLoader {
   constructor(url) {
     super();
-    this.url = url;
+    this.url = url.map(remapUri);
   }
   async loadOmeDims() {
     if (!this.dims) {
@@ -178,7 +181,7 @@ class TiffLoader extends ThreadableVolumeLoader {
     // load tiff and check metadata
     const numChannelsPerSource = this.url.length > 1 ? Array(this.url.length).fill(1) : [dims.sizec];
     const imgdata = {
-      name: "TEST",
+      name: dims.name,
       atlasTileDims: [atlasDims.x, atlasDims.y],
       subregionSize: [tilesizex, tilesizey, dims.sizez],
       subregionOffset: [0, 0, 0],
@@ -188,7 +191,7 @@ class TiffLoader extends ThreadableVolumeLoader {
       multiscaleLevelDims: [{
         shape: [dims.sizet, dims.sizec, dims.sizez, tilesizey, tilesizex],
         spacing: [1, 1, dims.pixelsizez, dims.pixelsizey * dims.sizey / tilesizey, dims.pixelsizex * dims.sizex / tilesizex],
-        spaceUnit: dims.unit || "",
+        spaceUnit: dims.unit ?? "",
         timeUnit: "",
         dataType: getDtype(dims.pixeltype)
       }],

package/es/types/BaseDrawableMeshObject.d.ts

@@ -1,5 +1,5 @@
 import { Euler, Group, Mesh, Vector3 } from "three";
-import { IDrawableObject } from "./types";
+import { IDrawableObject } from "./types.js";
 /**
  * Abstract base class for drawable 3D mesh objects.
  *

package/es/types/Histogram.d.ts

@@ -18,7 +18,7 @@ export default class Histogram {
     private dataMaxBin;
     private pixelCount;
     maxBin: number;
-    constructor(data: TypedArray<NumberType>);
+    constructor(data: TypedArray<NumberType>, dataMin?: number | undefined, dataMax?: number | undefined);
     private static findBin;
     /**
      * Returns the integer bin index for the given value. If a value is outside

package/es/types/ImageInfo.d.ts

@@ -1,7 +1,7 @@
 import { type VolumeDims } from "./VolumeDims.js";
 import { Vector3, Vector2 } from "three";
 export type ImageInfo = Readonly<{
-    name: string;
+    name: string | undefined;
     /**
      * XY dimensions of the texture atlas used by `RayMarchedAtlasVolume` and
      * `Atlas2DSlice`, in number of z-slice tiles (not pixels). Chosen by the

package/es/types/MeshVolume.d.ts

@@ -34,7 +34,7 @@ export default class MeshVolume implements IDrawableObject {
     hasIsosurface(channel: number): boolean;
     createIsosurface(channel: number, color: [number, number, number], value?: number, alpha?: number, transp?: boolean): void;
     destroyIsosurface(channel: number): void;
-    saveChannelIsosurface(channelIndex: number, type: string, namePrefix: string): void;
+    saveChannelIsosurface(channelIndex: number, type: string, name?: string): void;
     exportSTL(input: Object3D, fname: string): void;
     exportGLTF(input: Object3D, fname: string): void;
     generateIsosurfaceGeometry(channelIndex: number, isovalue: number): BufferGeometry[];

package/es/types/VectorArrows3d.d.ts

@@ -1,6 +1,6 @@
+import BaseDrawableMeshObject from "./BaseDrawableMeshObject.js";
 import { Vector3, Color } from "three";
-import { IDrawableObject } from "./types";
-import BaseDrawableMeshObject from "./BaseDrawableMeshObject";
+import { IDrawableObject } from "./types.js";
 /**
  * A drawable vector arrow field, which uses instanced meshes for performance.
  */

package/es/types/Volume.d.ts

@@ -25,7 +25,7 @@ export default class Volume {
     loadSpecRequired: Required<LoadSpec>;
     channelLoadCallback?: PerChannelCallback;
     imageMetadata: Record<string, unknown>;
-    name: string;
+    name: string | undefined;
     channels: Channel[];
     numChannels: number;
     channelNames: string[];

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

@@ -3,6 +3,7 @@ import { type ImageInfo } from "../ImageInfo.js";
 import type { VolumeDims } from "../VolumeDims.js";
 import { TypedArray, NumberType } from "../types.js";
 declare class OMEDims {
+    name: string | undefined;
     sizex: number;
     sizey: number;
     sizez: number;
@@ -34,7 +35,7 @@ export type TiffLoadResult = {
     range: [number, number];
 };
 declare class TiffLoader extends ThreadableVolumeLoader {
-    url: string[];
+    private url;
     dims?: OMEDims;
     constructor(url: string[]);
     private loadOmeDims;

package/es/types/utils/url_utils.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Remaps non-standard URIs (e.g. S3 (`s3://`), Google Cloud Storage (`gs://`), or
+ * VAST files (`/allen/aics/`)) to a standard HTTPS URL.
+ */
+export declare function remapUri(url: string): string;

package/es/utils/num_utils.js

@@ -224,8 +224,12 @@ export function getDataRange(data) {
   let min = data[0];
   let max = data[0];
   for (let i = 1; i < data.length; i++) {
-    min = Math.min(min, data[i]);
-    max = Math.max(max, data[i]);
+    const value = data[i];
+    if (value < min) {
+      min = value;
+    } else if (value > max) {
+      max = value;
+    }
   }
   return [min, max];
 }

package/es/utils/url_utils.js

@@ -0,0 +1,25 @@
+const S3_URL_PREFIX = "s3://";
+const GCS_URL_PREFIX = "gs://";
+const VAST_FILES_PREFIX = "/allen/aics/";
+const VAST_FILES_URL = "https://vast-files.int.allencell.org/";
+
+/**
+ * Remaps non-standard URIs (e.g. S3 (`s3://`), Google Cloud Storage (`gs://`), or
+ * VAST files (`/allen/aics/`)) to a standard HTTPS URL.
+ */
+export function remapUri(url) {
+  let newUrl = url.trim();
+  if (newUrl.startsWith(S3_URL_PREFIX)) {
+    // remap s3://bucket/key to https://bucket.s3.amazonaws.com/key
+    const s3Path = newUrl.slice(S3_URL_PREFIX.length);
+    const pathSegments = s3Path.split("/");
+    newUrl = `https://${pathSegments[0]}.s3.amazonaws.com/${pathSegments.slice(1).join("/")}`;
+  } else if (newUrl.startsWith(GCS_URL_PREFIX)) {
+    // remap gs://bucket/key to https://storage.googleapis.com/bucket/key
+    newUrl = newUrl.replace(GCS_URL_PREFIX, "https://storage.googleapis.com/");
+  } else if (newUrl.startsWith(VAST_FILES_PREFIX)) {
+    // remap /allen/aics/... to https://vast-files.int.allencell.org/...
+    newUrl = newUrl.replace(VAST_FILES_PREFIX, VAST_FILES_URL);
+  }
+  return newUrl;
+}

package/es/workers/FetchTiffWorker.js

@@ -1,6 +1,7 @@
 import { fromUrl } from "geotiff";
 import { serializeError } from "serialize-error";
 import { VolumeLoadError, VolumeLoadErrorType } from "../loaders/VolumeLoadError.js";
+import { getDataRange } from "../utils/num_utils.js";
 // from TIFF
 const SAMPLEFORMAT_UINT = 1;
 const SAMPLEFORMAT_INT = 2;
@@ -121,17 +122,7 @@ async function loadTiffChannel(e) {
   // all slices collected, now resample to 8 bits full data range
   const src = castToArray(buffer, bytesPerPixel, sampleFormat);
   const dtype = getDtype(sampleFormat, bytesPerPixel);
-  let chmin = src[0];
-  let chmax = src[0];
-  for (let j = 0; j < src.length; ++j) {
-    const val = src[j];
-    if (val < chmin) {
-      chmin = val;
-    }
-    if (val > chmax) {
-      chmax = val;
-    }
-  }
+  const [chmin, chmax] = getDataRange(src);
   return {
     data: src,
     channel: channelIndex,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "4.4.0",
+  "version": "4.5.0",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",