@aics/vole-core 3.15.6 → 3.15.7

package/es/ContourPass.js

@@ -1,8 +1,8 @@
 import { Color, DataTexture, FloatType, RedIntegerFormat, RGBAFormat, Uniform, UnsignedIntType } from "three";
-import RenderToBuffer, { RenderPassType } from "./RenderToBuffer";
+import { clamp } from "three/src/math/MathUtils.js";
+import RenderToBuffer, { RenderPassType } from "./RenderToBuffer.js";
 /* babel-plugin-inline-import './constants/shaders/contour.frag' */
 const contourFragShader = "precision highp float;\nprecision highp int;\nprecision highp usampler2D;\nprecision highp sampler3D;\n\n/**\n * LUT mapping from the segmentation ID (raw pixel value) to the\n * global ID (index in data buffers like `featureData` and `outlierData`).\n * \n * For a given local pixel ID `localId`, the global ID is given by:\n * `localIdToGlobalId[localId - localIdOffset] - 1`.\n*/\nuniform usampler2D localIdToGlobalId;\nuniform uint localIdOffset;\nuniform bool useGlobalIdLookup;\n/* Pick buffer. Used to determine IDs. */\nuniform sampler2D pickBuffer;\n\nuniform int highlightedId;\nuniform int outlineThickness;\nuniform float outlineAlpha;\nuniform vec3 outlineColor;\nuniform float devicePixelRatio;\n\nconst uint BACKGROUND_ID = 0u;\nconst uint MISSING_DATA_ID = 0xFFFFFFFFu;\nconst int ID_OFFSET = 1;\n\nuvec4 getUintFromTex(usampler2D tex, int index) {\n  int width = textureSize(tex, 0).x;\n  ivec2 featurePos = ivec2(index % width, index / width);\n  return uvec4(texelFetch(tex, featurePos, 0));\n}\n\nuint getId(ivec2 uv) {\n  float rawId = texelFetch(pickBuffer, uv, 0).g;\n  if (rawId == 0.0) {\n    return BACKGROUND_ID;\n  }\n  int localId = int(rawId) - int(localIdOffset);\n  if (!useGlobalIdLookup) {\n    return uint(localId + ID_OFFSET);\n  }\n  uvec4 c = getUintFromTex(localIdToGlobalId, localId);\n  // Note: IDs are offset by `ID_OFFSET` (`=1`) to reserve `0` for local IDs\n  // that don't have associated data in the global lookup. `ID_OFFSET` MUST be\n  // subtracted from the ID when accessing data buffers.\n  uint globalId = c.r;\n  if (globalId == 0u) {\n    return MISSING_DATA_ID;\n  }\n  return globalId;\n}\n\nbool isEdge(ivec2 uv, int id, int thickness) {\n  float wStep = 1.0;\n  float hStep = 1.0;\n  float thicknessFloat = float(thickness);\n  // sample around the pixel to see if we are on an edge\n  int R = int(getId(uv + ivec2(thicknessFloat * wStep, 0))) - ID_OFFSET;\n  int L = int(getId(uv + ivec2(-thicknessFloat * wStep, 0))) - ID_OFFSET;\n  int T = int(getId(uv + ivec2(0, thicknessFloat * hStep))) - ID_OFFSET;\n  int B = int(getId(uv + ivec2(0, -thicknessFloat * hStep))) - ID_OFFSET;\n  // if any neighbors are not id then this is an edge\n  return id != -1 && (R != id || L != id || T != id || B != id);\n}\n\nvoid main(void) {\n  ivec2 vUv = ivec2(int(gl_FragCoord.x / devicePixelRatio), int(gl_FragCoord.y / devicePixelRatio));\n\n  uint rawId = getId(vUv);\n  int id = int(rawId) - ID_OFFSET;\n\n  if (id == highlightedId && isEdge(vUv, id, outlineThickness)) {\n    gl_FragColor = vec4(outlineColor, outlineAlpha);\n  } else {\n    gl_FragColor = vec4(0, 0, 0, 0.0);\n  }\n}";
-import { clamp } from "three/src/math/MathUtils";
 const makeDefaultUniforms = () => {
   const pickBufferTex = new DataTexture(new Float32Array([1, 0, 0, 0]), 1, 1, RGBAFormat, FloatType);
   const localIdToGlobalId = new DataTexture(new Uint32Array([0]), 1, 1, RedIntegerFormat, UnsignedIntType);

package/es/Line3d.js

@@ -1,8 +1,8 @@
 import { Group, Vector3 } from "three";
-import { LineMaterial } from "three/addons/lines/LineMaterial";
-import { MESH_NO_PICK_OCCLUSION_LAYER, OVERLAY_LAYER } from "./ThreeJsPanel";
-import { LineSegments2 } from "three/addons/lines/LineSegments2";
-import { LineSegmentsGeometry } from "three/addons/lines/LineSegmentsGeometry";
+import { LineMaterial } from "three/addons/lines/LineMaterial.js";
+import { LineSegments2 } from "three/addons/lines/LineSegments2.js";
+import { LineSegmentsGeometry } from "three/addons/lines/LineSegmentsGeometry.js";
+import { MESH_NO_PICK_OCCLUSION_LAYER, OVERLAY_LAYER } from "./ThreeJsPanel.js";
 const DEFAULT_VERTEX_BUFFER_SIZE = 1020;
 
 /**

package/es/loaders/TiffLoader.js

@@ -11,15 +11,16 @@ function prepareXML(xml) {
   return xml.trim().replace(expr, "").trim();
 }
 function getOME(xml) {
+  if (xml === undefined) {
+    return undefined;
+  }
+  const prepared = prepareXML(xml);
   const parser = new DOMParser();
   try {
-    const xmlDoc = parser.parseFromString(xml, "text/xml");
+    const xmlDoc = parser.parseFromString(prepared, "text/xml");
     return xmlDoc.getElementsByTagName("OME")[0];
   } catch (e) {
-    throw new VolumeLoadError("Could not find OME metadata in TIFF file", {
-      type: VolumeLoadErrorType.INVALID_METADATA,
-      cause: e
-    });
+    return undefined;
   }
 }
 class OMEDims {
@@ -85,6 +86,7 @@ function getOMEDims(imageEl) {
   return dims;
 }
 const getBytesPerSample = type => type === "uint8" ? 1 : type === "uint16" ? 2 : 4;
+const getPixelType = pxSize => pxSize === 1 ? "uint8" : pxSize === 2 ? "uint16" : "uint32";
 
 // Despite the class `TiffLoader` extends, this loader is not threadable, since geotiff internally uses features that
 // aren't available on workers. It uses its own specialized workers anyways.
@@ -95,17 +97,32 @@ class TiffLoader extends ThreadableVolumeLoader {
   }
   async loadOmeDims() {
     if (!this.dims) {
-      const tiff = await fromUrl(this.url, {
+      const tiff = await fromUrl(this.url[0], {
         allowFullFile: true
-      }).catch(wrapVolumeLoadError(`Could not open TIFF file at ${this.url}`, VolumeLoadErrorType.NOT_FOUND));
+      }).catch(wrapVolumeLoadError(`Could not open TIFF file at ${this.url[0]}`, VolumeLoadErrorType.NOT_FOUND));
       // DO NOT DO THIS, ITS SLOW
       // 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 tiffimgdesc = prepareXML(image.getFileDirectory().ImageDescription);
-      const omeEl = getOME(tiffimgdesc);
-      const image0El = omeEl.getElementsByTagName("Image")[0];
-      this.dims = getOMEDims(image0El);
+      const omeEl = getOME(image.getFileDirectory().ImageDescription);
+      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();
+        // 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
+        this.dims.pixeltype = getPixelType(image.getBytesPerPixel());
+        this.dims.channelnames = Array.from({
+          length: this.dims.sizec
+        }, (_, i) => "Channel" + i);
+      }
     }
     return this.dims;
   }
@@ -189,7 +206,7 @@ class TiffLoader extends ThreadableVolumeLoader {
           sizez: volumeSize.z,
           dimensionOrder: dims.dimensionorder,
           bytesPerSample: getBytesPerSample(dims.pixeltype),
-          url: this.url
+          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"

package/es/loaders/index.js

@@ -24,13 +24,14 @@ export function pathToFileType(path) {
 export async function createVolumeLoader(path, options) {
   const pathString = Array.isArray(path) ? path[0] : path;
   const fileType = options?.fileType || pathToFileType(pathString);
+  const pathArrayForTiffLoader = Array.isArray(path) ? path : [path];
   switch (fileType) {
     case VolumeFileFormat.ZARR:
       return await OMEZarrLoader.createLoader(path, options?.scene, options?.cache, options?.queue, options?.fetchOptions);
     case VolumeFileFormat.JSON:
       return new JsonImageInfoLoader(path, options?.cache);
     case VolumeFileFormat.TIFF:
-      return new TiffLoader(pathString);
+      return new TiffLoader(pathArrayForTiffLoader);
     case VolumeFileFormat.DATA:
       if (!options?.rawArrayOptions) {
         throw new Error("Must provide RawArrayOptions for RawArrayLoader");

package/es/types/ContourPass.d.ts

@@ -1,5 +1,5 @@
 import { Color, WebGLRenderer, WebGLRenderTarget } from "three";
-import { ColorizeFeature } from "./types";
+import { ColorizeFeature } from "./types.js";
 export default class ContourPass {
     private pass;
     private frameToGlobalIdLookup;

package/es/types/Line3d.d.ts

@@ -1,5 +1,5 @@
 import { Color, Euler, Group, Vector3 } from "three";
-import { IDrawableObject } from "./types";
+import { IDrawableObject } from "./types.js";
 /**
  * Simple wrapper for a 3D line segments object, with controls for vertex data,
  * color, width, and segments visible.

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

@@ -34,9 +34,9 @@ export type TiffLoadResult = {
     range: [number, number];
 };
 declare class TiffLoader extends ThreadableVolumeLoader {
-    url: string;
+    url: string[];
     dims?: OMEDims;
-    constructor(url: string);
+    constructor(url: string[]);
     private loadOmeDims;
     loadDims(_loadSpec: LoadSpec): Promise<VolumeDims[]>;
     createImageInfo(_loadSpec: LoadSpec): Promise<LoadedVolumeInfo>;

package/es/workers/VolumeLoaderContext.js

@@ -164,7 +164,9 @@ class VolumeLoaderContext {
     const pathString = Array.isArray(path) ? path[0] : path;
     const fileType = options?.fileType || pathToFileType(pathString);
     if (fileType === VolumeFileFormat.TIFF) {
-      return new TiffLoader(pathString);
+      // tiff loader accepts array of paths for separate channel sources
+      const pathArray = Array.isArray(path) ? path : [path];
+      return new TiffLoader(pathArray);
     } else if (fileType === VolumeFileFormat.DATA) {
       if (!options?.rawArrayOptions) {
         throw new Error("Failed to create loader: Must provide RawArrayOptions for RawArrayLoader");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aics/vole-core",
-  "version": "3.15.6",
+  "version": "3.15.7",
   "description": "volume renderer for 3d, 4d, or 5d imaging data with OME-Zarr support",
   "main": "es/index.js",
   "type": "module",