@vitessce/all 3.9.3 → 3.9.5

package/dist/{index-Dj8mq7qw.js → index-cqprKTFO.js}

@@ -1,7 +1,7 @@
-import { G as Group, M as Matrix4, T as TrianglesDrawMode, a as TriangleFanDrawMode, b as TriangleStripDrawMode, R as REVISION, L as Loader, c as LoaderUtils, F as FileLoader, d as MeshPhysicalMaterial, V as Vector2, C as Color, S as SpotLight, P as PointLight, D as DirectionalLight, e as Vector3, I as InstancedMesh, Q as Quaternion, O as Object3D, f as TextureLoader, g as ImageBitmapLoader, B as BufferAttribute, h as InterleavedBuffer, i as LinearMipmapLinearFilter, N as NearestMipmapLinearFilter, j as LinearMipmapNearestFilter, k as NearestMipmapNearestFilter, l as LinearFilter, m as NearestFilter, n as RepeatWrapping, o as MirroredRepeatWrapping, p as ClampToEdgeWrapping, q as PointsMaterial, r as Material, s as LineBasicMaterial, t as MeshStandardMaterial, u as DoubleSide, v as MeshBasicMaterial, w as PropertyBinding, x as BufferGeometry, y as SkinnedMesh, z as Mesh, A as LineSegments, E as Line$1, H as LineLoop, J as Points, K as PerspectiveCamera, U as MathUtils, W as OrthographicCamera, X as Skeleton, Y as InterpolateDiscrete, Z as InterpolateLinear, _ as AnimationClip, $ as Bone, a0 as InterleavedBufferAttribute, a1 as Texture, a2 as VectorKeyframeTrack, a3 as QuaternionKeyframeTrack, a4 as NumberKeyframeTrack, a5 as FrontSide, a6 as Interpolant, a7 as Box3, a8 as Sphere, a9 as InstancedBufferGeometry, aa as Float32BufferAttribute, ab as InstancedInterleavedBuffer, ac as WireframeGeometry, ad as ShaderMaterial, ae as UniformsUtils, af as UniformsLib, ag as Vector4, ah as Line3, ai as SphereGeometry, aj as _extends, ak as Plane, al as Triangle, am as BackSide, an as Ray$1, ao as jsxRuntimeExports, ap as Matrix3, aq as CoordinationType, ar as Data3DTexture, as as RedFormat, at as FloatType, au as getImageSize, av as Scene } from "./index-Bhio36zT.js";
+import { G as Group, M as Matrix4, T as TrianglesDrawMode, a as TriangleFanDrawMode, b as TriangleStripDrawMode, R as REVISION, L as Loader, c as LoaderUtils, F as FileLoader, d as MeshPhysicalMaterial, V as Vector2, C as Color, S as SpotLight, P as PointLight, D as DirectionalLight, e as Vector3, I as InstancedMesh, Q as Quaternion, O as Object3D, f as TextureLoader, g as ImageBitmapLoader, B as BufferAttribute, h as InterleavedBuffer, i as LinearMipmapLinearFilter, N as NearestMipmapLinearFilter, j as LinearMipmapNearestFilter, k as NearestMipmapNearestFilter, l as LinearFilter, m as NearestFilter, n as RepeatWrapping, o as MirroredRepeatWrapping, p as ClampToEdgeWrapping, q as PointsMaterial, r as Material, s as LineBasicMaterial, t as MeshStandardMaterial, u as DoubleSide, v as MeshBasicMaterial, w as PropertyBinding, x as BufferGeometry, y as SkinnedMesh, z as Mesh, A as LineSegments, E as Line$1, H as LineLoop, J as Points, K as PerspectiveCamera, U as MathUtils, W as OrthographicCamera, X as Skeleton, Y as InterpolateDiscrete, Z as InterpolateLinear, _ as AnimationClip, $ as Bone, a0 as InterleavedBufferAttribute, a1 as Texture, a2 as VectorKeyframeTrack, a3 as QuaternionKeyframeTrack, a4 as NumberKeyframeTrack, a5 as FrontSide, a6 as Interpolant, a7 as Box3, a8 as Sphere, a9 as InstancedBufferGeometry, aa as Float32BufferAttribute, ab as InstancedInterleavedBuffer, ac as WireframeGeometry, ad as ShaderMaterial, ae as UniformsUtils, af as UniformsLib, ag as Vector4, ah as Line3, ai as SphereGeometry, aj as _extends, ak as Plane, al as Triangle, am as BackSide, an as Ray$1, ao as jsxRuntimeExports, ap as Matrix3, aq as CoordinationType, ar as Data3DTexture, as as RedFormat, at as FloatType, au as getImageSize, av as Scene } from "./index-CJ0WrLWz.js";
 import * as React from "react";
 import { useRef, useEffect, useState, forwardRef } from "react";
-import { u as useThree, a as useFrame, c as create, e as extend, b as createPortal, O as OrbitControls, C as Canvas } from "./OrbitControls-CtNyt3m6.js";
+import { u as useThree, a as useFrame, c as create, e as extend, b as createPortal, O as OrbitControls, C as Canvas } from "./OrbitControls-BdKhfTcE.js";
 const isPromise = (promise) => typeof promise === "object" && typeof promise.then === "function";
 const globalCache = [];
 function shallowEqualArrays(arrA, arrB, equal = (a, b) => a === b) {
@@ -5027,7 +5027,7 @@ const Text = /* @__PURE__ */ React.forwardRef(({
   const {
     Text: TextMeshImpl,
     preloadFont
-  } = suspend(async () => import("./troika-three-text.esm-1a1oWjdg.js"), []);
+  } = suspend(async () => import("./troika-three-text.esm-Bn837OOO.js"), []);
   const invalidate = useThree(({
     invalidate: invalidate2
   }) => invalidate2);

package/dist/{index-BEdNNnBm.js → index-vsMcaCd5.js}

@@ -1,6 +1,6 @@
-import { aw as log, ax as isEqual, ar as Data3DTexture, as as RedFormat, ay as UnsignedByteType, l as LinearFilter, az as RedIntegerFormat, aA as UnsignedIntType, m as NearestFilter, e as Vector3, V as Vector2, ag as Vector4, ae as UniformsUtils, aq as CoordinationType, aB as WebGLMultipleRenderTargets, aC as RGBAFormat, av as Scene, W as OrthographicCamera, ad as ShaderMaterial, z as Mesh, aD as PlaneGeometry, aE as useEventCallback, ao as jsxRuntimeExports, aF as GLSL3, am as BackSide } from "./index-Bhio36zT.js";
+import { aw as log, ax as isEqual, ar as Data3DTexture, as as RedFormat, ay as UnsignedByteType, l as LinearFilter, az as RedIntegerFormat, aA as UnsignedIntType, m as NearestFilter, e as Vector3, V as Vector2, ag as Vector4, ae as UniformsUtils, aq as CoordinationType, aB as WebGLMultipleRenderTargets, aC as RGBAFormat, av as Scene, W as OrthographicCamera, ad as ShaderMaterial, z as Mesh, aD as PlaneGeometry, aE as useEventCallback, ao as jsxRuntimeExports, aF as GLSL3, am as BackSide } from "./index-CJ0WrLWz.js";
 import { useRef, useState, useMemo, useEffect, Suspense } from "react";
-import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-CtNyt3m6.js";
+import { u as useThree, a as useFrame, O as OrbitControls, C as Canvas } from "./OrbitControls-BdKhfTcE.js";
 const LogLevel = {
   INFO: "info",
   WARN: "warn",
@@ -197,9 +197,17 @@ function _ptToZarr(ptx, pty, ptz, ptInfo) {
     z
   };
 }
-function _requestBufferToRequestObjects(buffer, k) {
+const DEFAULT_SIGMA_NORMALIZED = 0.25;
+function _requestBufferToRequestObjects(buffer, k, optsForWeighting) {
   const counts = /* @__PURE__ */ new Map();
-  for (let i = 0; i < buffer.length; i += 4) {
+  const { width, height, sigmaNormalized } = optsForWeighting;
+  const useWeighting = Number.isInteger(width) && Number.isInteger(height) && width > 0 && height > 0 && typeof sigmaNormalized === "number";
+  if (!useWeighting) {
+    log.warn("_requestBufferToRequestObjects: proceeding without weighting");
+  }
+  const maxPixels = Math.floor(buffer.length / 4);
+  for (let pix = 0; pix < maxPixels; pix += 1) {
+    const i = pix * 4;
     const r = buffer[i];
     const g = buffer[i + 1];
     const b = buffer[i + 2];
@@ -208,7 +216,17 @@ function _requestBufferToRequestObjects(buffer, k) {
       continue;
     }
     const packed = (r << 24 | g << 16 | b << 8 | a) >>> 0;
-    counts.set(packed, (counts.get(packed) || 0) + 1);
+    let weight = 1;
+    if (useWeighting) {
+      const x = pix % width;
+      const y = Math.floor(pix / width);
+      const dx = x - width / 2;
+      const dy = y - height / 2;
+      const nd = Math.sqrt(dx * dx / (width * width) + dy * dy / (height * height));
+      const norm = nd / sigmaNormalized;
+      weight = Math.exp(-0.5 * norm * norm);
+    }
+    counts.set(packed, (counts.get(packed) || 0) + weight);
   }
   const requests = [...counts.entries()].sort((a, b) => b[1] - a[1]).slice(0, k).map(([packed]) => ({
     x: packed >> 22 & 1023,
@@ -865,7 +883,19 @@ class VolumeDataManager {
     }
     return chunkEntry.data;
   }
-  async processRequestData(buffer) {
+  /**
+   * Process the buffer of brick requests from the shader, turning them into
+   * actual Promises for Zarr chunks on the JS side.
+   * @param {Uint8Array} buffer The bufRequest (of length width*height*4)
+   * containing the brick requests from the shader.
+   * @param {object} optsForWeighting
+   * @param {number} optsForWeighting.width The width of the render target.
+   * @param {number} optsForWeighting.height The height of the render target.
+   * @param {number} optsForWeighting.sigmaNormalized The normalized sigma value
+   * to use for weighting the brick requests based on their distance from
+   * the center of the render target.
+   */
+  async processRequestData(buffer, optsForWeighting) {
     if (this.isBusy) {
       log.debug("processRequestData: already busy, skipping");
       return;
@@ -880,7 +910,7 @@ class VolumeDataManager {
     }
     this.isBusy = true;
     this.triggerRequest = false;
-    const { requests, origRequestCount } = _requestBufferToRequestObjects(buffer, this.k);
+    const { requests, origRequestCount } = _requestBufferToRequestObjects(buffer, this.k, optsForWeighting);
     if (requests.length === 0) {
       this.noNewRequests = true;
     }
@@ -3443,7 +3473,14 @@ function handleRequests(_gl, { frameRef, dataManager, mrtRef, bufRequest, bufUsa
     ctx.bindFramebuffer(ctx.READ_FRAMEBUFFER, framebufferFor(_gl, mrtRef.current));
     ctx.readBuffer(ctx.COLOR_ATTACHMENT1);
     ctx.readPixels(0, 0, mrtRef.current.width, mrtRef.current.height, ctx.RGBA, ctx.UNSIGNED_BYTE, bufRequest.current);
-    dataManager.processRequestData(bufRequest.current);
+    dataManager.processRequestData(bufRequest.current, {
+      // If width/height are not yet available,
+      // processRequestData will proceed without weighting.
+      width: mrtRef?.current?.width,
+      height: mrtRef?.current?.height,
+      // Default sigmaNormalized = 0.25; can be tuned
+      sigmaNormalized: DEFAULT_SIGMA_NORMALIZED
+    });
   } else if (dataManager.triggerUsage === true && dataManager.noNewRequests === false) {
     ctx.bindFramebuffer(ctx.READ_FRAMEBUFFER, framebufferFor(_gl, mrtRef.current));
     ctx.readBuffer(ctx.COLOR_ATTACHMENT2);

package/dist/index.js

@@ -1,4 +1,4 @@
-import { bR, bP, bN, bQ, bO, bM, bS } from "./index-Bhio36zT.js";
+import { bR, bP, bN, bQ, bO, bM, bS } from "./index-CJ0WrLWz.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 export {
   bR as PluginAsyncFunction,

package/dist/{jpeg-Dd5hOit9.js → jpeg-BpDeSW3W.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-Bhio36zT.js";
+import { aX as BaseDecoder } from "./index-CJ0WrLWz.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-Cs8rllqp.js → lerc-ed9YjGeI.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { aG as getDefaultExportFromCjs, aX as BaseDecoder, aY as LercParameters, aZ as LercAddCompression } from "./index-Bhio36zT.js";
+import { aG as getDefaultExportFromCjs, aX as BaseDecoder, aY as LercParameters, aZ as LercAddCompression } from "./index-CJ0WrLWz.js";
 var LercDecode = { exports: {} };
 var hasRequiredLercDecode;
 function requireLercDecode() {

package/dist/{lzw-BVwtoLGt.js → lzw-7E8bYZIo.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-Bhio36zT.js";
+import { aX as BaseDecoder } from "./index-CJ0WrLWz.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-BT_ZtTHH.js → packbits-COn2hgkH.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-Bhio36zT.js";
+import { aX as BaseDecoder } from "./index-CJ0WrLWz.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-CiZtvi02.js → raw-C5vEl2Zl.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-Bhio36zT.js";
+import { aX as BaseDecoder } from "./index-CJ0WrLWz.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{troika-three-text.esm-1a1oWjdg.js → troika-three-text.esm-Bn837OOO.js}

@@ -1,4 +1,4 @@
-import { bH as MeshDistanceMaterial, bI as MeshDepthMaterial, bJ as RGBADepthPacking, ae as UniformsUtils, bK as ShaderChunk, a9 as InstancedBufferGeometry, a8 as Sphere, a7 as Box3, am as BackSide, u as DoubleSide, z as Mesh, a5 as FrontSide, v as MeshBasicMaterial, C as Color, e as Vector3, M as Matrix4, V as Vector2, ap as Matrix3, ag as Vector4, a1 as Texture, l as LinearFilter, aD as PlaneGeometry, x as BufferGeometry, aa as Float32BufferAttribute, bL as InstancedBufferAttribute } from "./index-Bhio36zT.js";
+import { bH as MeshDistanceMaterial, bI as MeshDepthMaterial, bJ as RGBADepthPacking, ae as UniformsUtils, bK as ShaderChunk, a9 as InstancedBufferGeometry, a8 as Sphere, a7 as Box3, am as BackSide, u as DoubleSide, z as Mesh, a5 as FrontSide, v as MeshBasicMaterial, C as Color, e as Vector3, M as Matrix4, V as Vector2, ap as Matrix3, ag as Vector4, a1 as Texture, l as LinearFilter, aD as PlaneGeometry, x as BufferGeometry, aa as Float32BufferAttribute, bL as InstancedBufferAttribute } from "./index-CJ0WrLWz.js";
 function workerBootstrap() {
   var modules = /* @__PURE__ */ Object.create(null);
   function registerModule(ref, callback) {

package/dist/{webimage-DINDiGit.js → webimage-f_OnujWl.js}

@@ -1,4 +1,4 @@
-import { aX as BaseDecoder } from "./index-Bhio36zT.js";
+import { aX as BaseDecoder } from "./index-CJ0WrLWz.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.9.3",
+  "version": "3.9.5",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,38 +17,38 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.9.3",
-    "@vitessce/styles": "3.9.3",
-    "@vitessce/abstract": "3.9.3",
-    "@vitessce/error": "3.9.3",
-    "@vitessce/csv": "3.9.3",
-    "@vitessce/description": "3.9.3",
-    "@vitessce/feature-list": "3.9.3",
-    "@vitessce/heatmap": "3.9.3",
-    "@vitessce/genomic-profiles": "3.9.3",
-    "@vitessce/glb": "3.9.3",
-    "@vitessce/json": "3.9.3",
-    "@vitessce/layer-controller-beta": "3.9.3",
-    "@vitessce/link-controller": "3.9.3",
-    "@vitessce/layer-controller": "3.9.3",
-    "@vitessce/ome-tiff": "3.9.3",
-    "@vitessce/plugins": "3.9.3",
-    "@vitessce/scatterplot-embedding": "3.9.3",
-    "@vitessce/scatterplot-gating": "3.9.3",
-    "@vitessce/obs-sets-manager": "3.9.3",
-    "@vitessce/schemas": "3.9.3",
-    "@vitessce/spatial": "3.9.3",
-    "@vitessce/spatial-beta": "3.9.3",
-    "@vitessce/statistical-plots": "3.9.3",
-    "@vitessce/vit-s": "3.9.3",
-    "@vitessce/zarr": "3.9.3",
-    "@vitessce/globals": "3.9.3",
-    "@vitessce/spatial-three": "3.9.3",
-    "@vitessce/status": "3.9.3",
-    "@vitessce/spatial-accelerated": "3.9.3",
-    "@vitessce/biomarker-select": "3.9.3",
-    "@vitessce/spatial-zarr": "3.9.3",
-    "@vitessce/neuroglancer": "3.9.3"
+    "@vitessce/styles": "3.9.5",
+    "@vitessce/constants-internal": "3.9.5",
+    "@vitessce/abstract": "3.9.5",
+    "@vitessce/error": "3.9.5",
+    "@vitessce/csv": "3.9.5",
+    "@vitessce/feature-list": "3.9.5",
+    "@vitessce/description": "3.9.5",
+    "@vitessce/heatmap": "3.9.5",
+    "@vitessce/genomic-profiles": "3.9.5",
+    "@vitessce/glb": "3.9.5",
+    "@vitessce/json": "3.9.5",
+    "@vitessce/layer-controller": "3.9.5",
+    "@vitessce/layer-controller-beta": "3.9.5",
+    "@vitessce/link-controller": "3.9.5",
+    "@vitessce/ome-tiff": "3.9.5",
+    "@vitessce/obs-sets-manager": "3.9.5",
+    "@vitessce/scatterplot-embedding": "3.9.5",
+    "@vitessce/scatterplot-gating": "3.9.5",
+    "@vitessce/plugins": "3.9.5",
+    "@vitessce/schemas": "3.9.5",
+    "@vitessce/spatial-beta": "3.9.5",
+    "@vitessce/statistical-plots": "3.9.5",
+    "@vitessce/vit-s": "3.9.5",
+    "@vitessce/spatial": "3.9.5",
+    "@vitessce/status": "3.9.5",
+    "@vitessce/zarr": "3.9.5",
+    "@vitessce/spatial-zarr": "3.9.5",
+    "@vitessce/globals": "3.9.5",
+    "@vitessce/spatial-accelerated": "3.9.5",
+    "@vitessce/spatial-three": "3.9.5",
+    "@vitessce/biomarker-select": "3.9.5",
+    "@vitessce/neuroglancer": "3.9.5"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",