@vitessce/spatial-utils 3.3.1 → 3.3.3

package/dist/{deflate-d62c010f.js → deflate-f0db96f7.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {

package/dist/{index-27c044ac.js → index-20c94d37.js}

@@ -22,11 +22,7 @@ var __privateSet = (obj, member, value, setter2) => {
   setter2 ? setter2.call(obj, value) : member.set(obj, value);
   return value;
 };
-var __privateMethod = (obj, member, method) => {
-  __accessCheck(obj, member, "access private method");
-  return method;
-};
-var _bytes, _encoder, _encode_buffer, _strides, _TypedArray, _BYTES_PER_ELEMENT, _shape, _endian, _shape2, _strides2, _metadata, _metadata2, _a2, _b, _overrides, _use_suffix_request, _merge_init, merge_init_fn;
+var _bytes, _encoder, _encode_buffer, _strides, _TypedArray, _BYTES_PER_ELEMENT, _shape, _endian, _shape2, _strides2, _metadata, _metadata2, _a2, _b;
 import "react";
 function _mergeNamespaces(n3, m) {
   for (var i2 = 0; i2 < m.length; i2++) {
@@ -50,9 +46,9 @@ function _mergeNamespaces(n3, m) {
 var freeGlobal$1 = typeof global == "object" && global && global.Object === Object && global;
 const freeGlobal$2 = freeGlobal$1;
 var freeSelf$1 = typeof self == "object" && self && self.Object === Object && self;
-var root$2 = freeGlobal$2 || freeSelf$1 || Function("return this")();
-const root$3 = root$2;
-var Symbol$1 = root$3.Symbol;
+var root$1 = freeGlobal$2 || freeSelf$1 || Function("return this")();
+const root$2 = root$1;
+var Symbol$1 = root$2.Symbol;
 const Symbol$2 = Symbol$1;
 var objectProto$f = Object.prototype;
 var hasOwnProperty$e = objectProto$f.hasOwnProperty;
@@ -155,7 +151,7 @@ function isFunction$3(value) {
   var tag2 = baseGetTag(value);
   return tag2 == funcTag$2 || tag2 == genTag$1 || tag2 == asyncTag || tag2 == proxyTag;
 }
-var coreJsData = root$3["__core-js_shared__"];
+var coreJsData = root$2["__core-js_shared__"];
 const coreJsData$1 = coreJsData;
 var maskSrcKey = function() {
   var uid2 = /[^.]+$/.exec(coreJsData$1 && coreJsData$1.keys && coreJsData$1.keys.IE_PROTO || "");
@@ -201,7 +197,7 @@ function getNative(object2, key) {
   var value = getValue$1(object2, key);
   return baseIsNative(value) ? value : void 0;
 }
-var WeakMap$1 = getNative(root$3, "WeakMap");
+var WeakMap$1 = getNative(root$2, "WeakMap");
 const WeakMap$2 = WeakMap$1;
 var objectCreate = Object.create;
 var baseCreate = function() {
@@ -343,7 +339,7 @@ function stubFalse() {
 var freeExports$2 = typeof exports == "object" && exports && !exports.nodeType && exports;
 var freeModule$2 = freeExports$2 && typeof module == "object" && module && !module.nodeType && module;
 var moduleExports$2 = freeModule$2 && freeModule$2.exports === freeExports$2;
-var Buffer$3 = moduleExports$2 ? root$3.Buffer : void 0;
+var Buffer$3 = moduleExports$2 ? root$2.Buffer : void 0;
 var nativeIsBuffer = Buffer$3 ? Buffer$3.isBuffer : void 0;
 var isBuffer$3 = nativeIsBuffer || stubFalse;
 const isBuffer$4 = isBuffer$3;
@@ -550,7 +546,7 @@ ListCache.prototype["delete"] = listCacheDelete;
 ListCache.prototype.get = listCacheGet;
 ListCache.prototype.has = listCacheHas;
 ListCache.prototype.set = listCacheSet;
-var Map$1 = getNative(root$3, "Map");
+var Map$1 = getNative(root$2, "Map");
 const Map$2 = Map$1;
 function mapCacheClear() {
   this.size = 0;
@@ -656,7 +652,7 @@ function baseAssignIn(object2, source) {
 var freeExports = typeof exports == "object" && exports && !exports.nodeType && exports;
 var freeModule = freeExports && typeof module == "object" && module && !module.nodeType && module;
 var moduleExports = freeModule && freeModule.exports === freeExports;
-var Buffer$2 = moduleExports ? root$3.Buffer : void 0, allocUnsafe = Buffer$2 ? Buffer$2.allocUnsafe : void 0;
+var Buffer$2 = moduleExports ? root$2.Buffer : void 0, allocUnsafe = Buffer$2 ? Buffer$2.allocUnsafe : void 0;
 function cloneBuffer(buffer2, isDeep) {
   if (isDeep) {
     return buffer2.slice();
@@ -717,11 +713,11 @@ function getAllKeys(object2) {
 function getAllKeysIn(object2) {
   return baseGetAllKeys(object2, keysIn, getSymbolsIn$1);
 }
-var DataView$1 = getNative(root$3, "DataView");
+var DataView$1 = getNative(root$2, "DataView");
 const DataView$2 = DataView$1;
-var Promise$1 = getNative(root$3, "Promise");
+var Promise$1 = getNative(root$2, "Promise");
 const Promise$2 = Promise$1;
-var Set$1 = getNative(root$3, "Set");
+var Set$1 = getNative(root$2, "Set");
 const Set$2 = Set$1;
 var mapTag$4 = "[object Map]", objectTag$2 = "[object Object]", promiseTag = "[object Promise]", setTag$4 = "[object Set]", weakMapTag$1 = "[object WeakMap]";
 var dataViewTag$3 = "[object DataView]";
@@ -758,7 +754,7 @@ function initCloneArray(array) {
   }
   return result;
 }
-var Uint8Array$1 = root$3.Uint8Array;
+var Uint8Array$1 = root$2.Uint8Array;
 const Uint8Array$2 = Uint8Array$1;
 function cloneArrayBuffer(arrayBuffer2) {
   var result = new arrayBuffer2.constructor(arrayBuffer2.byteLength);
@@ -9254,7 +9250,7 @@ function clone$6(obj) {
   Decimal2.log = log$5;
   Decimal2.log10 = log10;
   Decimal2.log2 = log2$1;
-  Decimal2.max = max;
+  Decimal2.max = max$1;
   Decimal2.min = min;
   Decimal2.mod = mod$2;
   Decimal2.mul = mul;
@@ -9325,7 +9321,7 @@ function log2$1(x2) {
 function log10(x2) {
   return new this(x2).log(10);
 }
-function max() {
+function max$1() {
   return maxOrMin(this, arguments, "lt");
 }
 function min() {
@@ -28572,7 +28568,9 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_JSON: "obsSegmentations.json",
   OBS_SETS_CSV: "obsSets.csv",
   OBS_SETS_JSON: "obsSets.json",
+  // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
+  OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_SETS_ANNDATA_ZARR: "obsSets.anndata.zarr",
@@ -29025,30 +29023,39 @@ const omeCoordinateTransformations = z.array(z.union([
     scale: z.array(z.number())
   })
 ]));
-z.object({
+const imageOmeTiffSchema = z.object({
   offsetsUrl: z.string().optional(),
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
+imageOmeTiffSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
 const imageOmeZarrSchema = z.object({
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
 imageOmeZarrSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
+const imageSpatialdataSchema = imageOmeZarrSchema.extend({
   path: z.string()
 });
-z.object({
+const obsSegmentationsSpatialdataSchema = z.object({
+  // TODO: should this also extend the imageOmeZarrSchema?
+  // TODO: should this be renamed labelsSpatialdataSchema?
+  // TODO: support obsTypesFromChannelNames?
   path: z.string()
 });
 z.object({
   path: z.string()
 });
-z.object({
+const obsSpotsSpatialdataSchema = z.object({
   path: z.string(),
   tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected.")
 });
-annDataObsFeatureMatrix.extend({
+const obsFeatureMatrixSpatialdataSchema = annDataObsFeatureMatrix.extend({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional()
 });
-z.object({
+const obsSetsSpatialdataSchema = z.object({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
   tablePath: z.string().optional().describe("The path to a table which contains the index for the set values."),
   obsSets: annDataObsSets
@@ -29111,6 +29118,19 @@ z.object({
     z.array(annDataConvenienceObsEmbeddingItem)
   ])
 }).partial();
+z.object({
+  // TODO: should `image` be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  image: imageSpatialdataSchema,
+  // TODO: should this be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  labels: obsSegmentationsSpatialdataSchema,
+  obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
+  obsSpots: obsSpotsSpatialdataSchema,
+  // TODO: obsPoints
+  // TODO: obsLocations
+  obsSets: obsSetsSpatialdataSchema
+}).partial();
 z.object({
   obsLabelsTypes: z.array(z.string()).optional(),
   embeddingTypes: z.array(z.string()).optional()
@@ -35464,10 +35484,10 @@ var json2csv_umd = { exports: {} };
         value: function promise() {
           var _this = this;
           var returnCSV = arguments.length > 0 && arguments[0] !== void 0 ? arguments[0] : true;
-          return new Promise(function(resolve2, reject) {
+          return new Promise(function(resolve, reject) {
             if (!returnCSV) {
               _this.processor.on("finish", function() {
-                return resolve2();
+                return resolve();
               }).on("error", function(err2) {
                 return reject(err2);
               });
@@ -35477,7 +35497,7 @@ var json2csv_umd = { exports: {} };
             _this.processor.on("data", function(chunk) {
               return csvBuffer.push(chunk.toString());
             }).on("finish", function() {
-              return resolve2(fastJoin$3(csvBuffer, ""));
+              return resolve(fastJoin$3(csvBuffer, ""));
             }).on("error", function(err2) {
               return reject(err2);
             });
@@ -35726,8 +35746,8 @@ class WorkerJob {
     });
     this.name = jobName;
     this.workerThread = workerThread;
-    this.result = new Promise((resolve2, reject) => {
-      this._resolve = resolve2;
+    this.result = new Promise((resolve, reject) => {
+      this._resolve = resolve;
       this._reject = reject;
     });
   }
@@ -36624,8 +36644,8 @@ class RequestScheduler {
       priority: 0,
       getPriority
     };
-    const promise = new Promise((resolve2) => {
-      request.resolve = resolve2;
+    const promise = new Promise((resolve) => {
+      request.resolve = resolve;
       return request;
     });
     this.requestQueue.push(request);
@@ -36636,7 +36656,7 @@ class RequestScheduler {
   _issueRequest(request) {
     const {
       handle,
-      resolve: resolve2
+      resolve
     } = request;
     let isDone = false;
     const done = () => {
@@ -36648,7 +36668,7 @@ class RequestScheduler {
       }
     };
     this.activeRequestCount++;
-    return resolve2 ? resolve2({
+    return resolve ? resolve({
       done
     }) : Promise.resolve({
       done
@@ -36850,11 +36870,11 @@ async function getInitialDataUrl(resource) {
   }
   if (resource instanceof Blob) {
     const blobSlice = resource.slice(0, 5);
-    return await new Promise((resolve2) => {
+    return await new Promise((resolve) => {
       const reader = new FileReader();
       reader.onload = (event) => {
         var _event$target;
-        return resolve2(event === null || event === void 0 ? void 0 : (_event$target = event.target) === null || _event$target === void 0 ? void 0 : _event$target.result);
+        return resolve(event === null || event === void 0 ? void 0 : (_event$target = event.target) === null || _event$target === void 0 ? void 0 : _event$target.result);
       };
       reader.readAsDataURL(blobSlice);
     });
@@ -38221,9 +38241,9 @@ async function loadToImage(url, options) {
     await image2.decode();
     return image2;
   }
-  return await new Promise((resolve2, reject) => {
+  return await new Promise((resolve, reject) => {
     try {
-      image2.onload = () => resolve2(image2);
+      image2.onload = () => resolve(image2);
       image2.onerror = (err2) => reject(new Error("Could not load image ".concat(url, ": ").concat(err2)));
     } catch (error2) {
       reject(error2);
@@ -41526,10 +41546,10 @@ let pathPrefix = "";
 function loadImage$1(url, opts2) {
   assert$7(typeof url === "string");
   url = pathPrefix + url;
-  return new Promise((resolve2, reject) => {
+  return new Promise((resolve, reject) => {
     try {
       const image2 = new Image();
-      image2.onload = () => resolve2(image2);
+      image2.onload = () => resolve(image2);
       image2.onerror = () => reject(new Error("Could not load image ".concat(url, ".")));
       image2.crossOrigin = opts2 && opts2.crossOrigin || "anonymous";
       image2.src = url;
@@ -44037,10 +44057,10 @@ class Query extends Resource$1 {
       return this._pollingPromise;
     }
     let counter2 = 0;
-    this._pollingPromise = new Promise((resolve2, reject) => {
+    this._pollingPromise = new Promise((resolve, reject) => {
       const poll = () => {
         if (this.isResultAvailable()) {
-          resolve2(this.getResult());
+          resolve(this.getResult());
           this._pollingPromise = null;
         } else if (counter2++ > limit) {
           reject("Timed out");
@@ -45234,8 +45254,8 @@ class AnimationLoop {
   waitForRender() {
     this.setNeedsRedraw("waitForRender");
     if (!this._nextFramePromise) {
-      this._nextFramePromise = new Promise((resolve2) => {
-        this._resolveNextFrame = resolve2;
+      this._nextFramePromise = new Promise((resolve) => {
+        this._resolveNextFrame = resolve;
       });
     }
     return this._nextFramePromise;
@@ -45282,13 +45302,13 @@ class AnimationLoop {
   }
   _getPageLoadPromise() {
     if (!this._pageLoadPromise) {
-      this._pageLoadPromise = isPage ? new Promise((resolve2, reject) => {
+      this._pageLoadPromise = isPage ? new Promise((resolve, reject) => {
         if (isPage && document.readyState === "complete") {
-          resolve2(document);
+          resolve(document);
           return;
         }
         window.addEventListener("load", () => {
-          resolve2(document);
+          resolve(document);
         });
       }) : Promise.resolve({});
     }
@@ -85681,14 +85701,14 @@ function initializeBasisTrascoderModule(BasisModule, wasmBinary) {
   if (wasmBinary) {
     options.wasmBinary = wasmBinary;
   }
-  return new Promise((resolve2) => {
+  return new Promise((resolve) => {
     BasisModule(options).then((module2) => {
       const {
         BasisFile,
         initializeBasis
       } = module2;
       initializeBasis();
-      resolve2({
+      resolve({
         BasisFile
       });
     });
@@ -85715,7 +85735,7 @@ function initializeBasisEncoderModule(BasisEncoderModule, wasmBinary) {
   if (wasmBinary) {
     options.wasmBinary = wasmBinary;
   }
-  return new Promise((resolve2) => {
+  return new Promise((resolve) => {
     BasisEncoderModule(options).then((module2) => {
       const {
         BasisFile,
@@ -85724,7 +85744,7 @@ function initializeBasisEncoderModule(BasisEncoderModule, wasmBinary) {
         BasisEncoder
       } = module2;
       initializeBasis();
-      resolve2({
+      resolve({
         BasisFile,
         KTX2File,
         BasisEncoder
@@ -87578,10 +87598,10 @@ function initializeDracoDecoder(DracoDecoderModule, wasmBinary) {
   if (wasmBinary) {
     options.wasmBinary = wasmBinary;
   }
-  return new Promise((resolve2) => {
+  return new Promise((resolve) => {
     DracoDecoderModule({
       ...options,
-      onModuleLoaded: (draco) => resolve2({
+      onModuleLoaded: (draco) => resolve({
         draco
       })
     });
@@ -88795,7 +88815,7 @@ async function waitForGLTFAssets(gltfObjects) {
 }
 async function waitWhileCondition(condition) {
   while (condition()) {
-    await new Promise((resolve2) => requestAnimationFrame(resolve2));
+    await new Promise((resolve) => requestAnimationFrame(resolve));
   }
 }
 const vs$6 = "#version 300 es\n\n// Instance attributes\nin vec3 instancePositions;\nin vec3 instancePositions64Low;\nin vec4 instanceColors;\nin vec3 instancePickingColors;\nin mat3 instanceModelMatrix;\nin vec3 instanceTranslation;\n\n// Uniforms\nuniform float sizeScale;\nuniform float sizeMinPixels;\nuniform float sizeMaxPixels;\nuniform mat4 sceneModelMatrix;\nuniform bool composeModelMatrix;\n\n// Attributes\nin vec4 POSITION;\n\n#ifdef HAS_UV\n  in vec2 TEXCOORD_0;\n#endif\n\n#ifdef MODULE_PBR\n  #ifdef HAS_NORMALS\n    in vec4 NORMAL;\n  #endif\n#endif\n\n// Varying\nout vec4 vColor;\n\n// MODULE_PBR contains all the varying definitions needed\n#ifndef MODULE_PBR\n  #ifdef HAS_UV\n    out vec2 vTEXCOORD_0;\n  #endif\n#endif\n\n// Main\nvoid main(void) {\n  #if defined(HAS_UV) && !defined(MODULE_PBR)\n    vTEXCOORD_0 = TEXCOORD_0;\n    geometry.uv = vTEXCOORD_0;\n  #endif\n\n  geometry.worldPosition = instancePositions;\n  geometry.pickingColor = instancePickingColors;\n\n  vec3 normal = vec3(0.0, 0.0, 1.0);\n  #ifdef MODULE_PBR\n    #ifdef HAS_NORMALS\n      normal = instanceModelMatrix * (sceneModelMatrix * vec4(NORMAL.xyz, 0.0)).xyz;\n    #endif\n  #endif\n\n  float originalSize = project_size_to_pixel(sizeScale);\n  float clampedSize = clamp(originalSize, sizeMinPixels, sizeMaxPixels);\n\n  vec3 pos = (instanceModelMatrix * (sceneModelMatrix * POSITION).xyz) * sizeScale * (clampedSize / originalSize) + instanceTranslation;\n  if(composeModelMatrix) {\n    DECKGL_FILTER_SIZE(pos, geometry);\n    // using instancePositions as world coordinates\n    // when using globe mode, this branch does not re-orient the model to align with the surface of the earth\n    // call project_normal before setting position to avoid rotation\n    geometry.normal = project_normal(normal);\n    gl_Position = project_position_to_clipspace(pos + instancePositions, instancePositions64Low, vec3(0.0), geometry.position);\n  }\n  else {\n    pos = project_size(pos);\n    DECKGL_FILTER_SIZE(pos, geometry);\n    gl_Position = project_position_to_clipspace(instancePositions, instancePositions64Low, pos, geometry.position);\n    geometry.normal = project_normal(normal);\n  }\n  DECKGL_FILTER_GL_POSITION(gl_Position, geometry);\n\n  #ifdef MODULE_PBR\n    // set PBR data\n    pbr_vPosition = geometry.position.xyz;\n    #ifdef HAS_NORMALS\n      pbr_vNormal = geometry.normal;\n    #endif\n\n    #ifdef HAS_UV\n      pbr_vUV = TEXCOORD_0;\n    #else\n      pbr_vUV = vec2(0., 0.);\n    #endif\n    geometry.uv = pbr_vUV;\n  #endif\n\n  vColor = instanceColors;\n  DECKGL_FILTER_COLOR(vColor, geometry);\n}\n";
@@ -91220,12 +91240,12 @@ class Tileset3D {
       this.lastUpdatedVieports = viewports;
     }
     if (!this.updatePromise) {
-      this.updatePromise = new Promise((resolve2) => {
+      this.updatePromise = new Promise((resolve) => {
         setTimeout(() => {
           if (this.lastUpdatedVieports) {
             this.doUpdate(this.lastUpdatedVieports);
           }
-          resolve2(this._frameNumber);
+          resolve(this._frameNumber);
           this.updatePromise = null;
         }, this.options.debounceTime);
       });
@@ -116237,7 +116257,7 @@ function unwrapListeners(arr) {
   return ret;
 }
 function once2(emitter, name2) {
-  return new Promise(function(resolve2, reject) {
+  return new Promise(function(resolve, reject) {
     function errorListener(err2) {
       emitter.removeListener(name2, resolver);
       reject(err2);
@@ -116246,7 +116266,7 @@ function once2(emitter, name2) {
       if (typeof emitter.removeListener === "function") {
         emitter.removeListener("error", errorListener);
       }
-      resolve2([].slice.call(arguments));
+      resolve([].slice.call(arguments));
     }
     eventTargetAgnosticAddListener(emitter, name2, resolver, { once: true });
     if (name2 !== "error") {
@@ -124849,12 +124869,12 @@ var reIsOctal = /^0o[0-7]+$/i;
 var freeParseInt = parseInt;
 var freeGlobal = typeof commonjsGlobal == "object" && commonjsGlobal && commonjsGlobal.Object === Object && commonjsGlobal;
 var freeSelf = typeof self == "object" && self && self.Object === Object && self;
-var root$1 = freeGlobal || freeSelf || Function("return this")();
+var root = freeGlobal || freeSelf || Function("return this")();
 var objectProto = Object.prototype;
 var objectToString = objectProto.toString;
 var nativeMax = Math.max, nativeMin = Math.min;
 var now = function() {
-  return root$1.Date.now();
+  return root.Date.now();
 };
 function debounce(func, wait, options) {
   var lastArgs, lastThis, maxWait, result, timerId, lastCallTime, lastInvokeTime = 0, leading = false, maxing = false, trailing = true;
@@ -133567,16 +133587,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c) => registry$2.set(c, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-7e5381d5.js").then((m) => m.default));
-addDecoder(5, () => import("./lzw-a22317ac.js").then((m) => m.default));
+addDecoder([void 0, 1], () => import("./raw-e5bd3ae5.js").then((m) => m.default));
+addDecoder(5, () => import("./lzw-e7880394.js").then((m) => m.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-780f2a29.js").then((m) => m.default));
-addDecoder([8, 32946], () => import("./deflate-d62c010f.js").then((m) => m.default));
-addDecoder(32773, () => import("./packbits-757ef203.js").then((m) => m.default));
-addDecoder(34887, () => import("./lerc-11712e42.js").then((m) => m.default));
-addDecoder(50001, () => import("./webimage-ec283d98.js").then((m) => m.default));
+addDecoder(7, () => import("./jpeg-a983c5fa.js").then((m) => m.default));
+addDecoder([8, 32946], () => import("./deflate-f0db96f7.js").then((m) => m.default));
+addDecoder(32773, () => import("./packbits-17057e1d.js").then((m) => m.default));
+addDecoder(34887, () => import("./lerc-302d4191.js").then((m) => m.default));
+addDecoder(50001, () => import("./webimage-c3b216cf.js").then((m) => m.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset = 0;
@@ -135263,11 +135283,11 @@ var pFinally = (promise, onFinally) => {
   onFinally = onFinally || (() => {
   });
   return promise.then(
-    (val) => new Promise((resolve2) => {
-      resolve2(onFinally());
+    (val) => new Promise((resolve) => {
+      resolve(onFinally());
     }).then(() => val),
-    (err2) => new Promise((resolve2) => {
-      resolve2(onFinally());
+    (err2) => new Promise((resolve) => {
+      resolve(onFinally());
     }).then(() => {
       throw err2;
     })
@@ -135279,18 +135299,18 @@ class TimeoutError extends Error {
     this.name = "TimeoutError";
   }
 }
-const pTimeout = (promise, milliseconds, fallback) => new Promise((resolve2, reject) => {
+const pTimeout = (promise, milliseconds, fallback) => new Promise((resolve, reject) => {
   if (typeof milliseconds !== "number" || milliseconds < 0) {
     throw new TypeError("Expected `milliseconds` to be a positive number");
   }
   if (milliseconds === Infinity) {
-    resolve2(promise);
+    resolve(promise);
     return;
   }
   const timer = setTimeout(() => {
     if (typeof fallback === "function") {
       try {
-        resolve2(fallback());
+        resolve(fallback());
       } catch (error2) {
         reject(error2);
       }
@@ -135305,7 +135325,7 @@ const pTimeout = (promise, milliseconds, fallback) => new Promise((resolve2, rej
   }, milliseconds);
   pFinally(
     // eslint-disable-next-line promise/prefer-await-to-then
-    promise.then(resolve2, reject),
+    promise.then(resolve, reject),
     () => {
       clearTimeout(timer);
     }
@@ -144882,22 +144902,40 @@ function extent(values, valueof) {
   }
   return [min2, max2];
 }
+function max(values, valueof) {
+  let max2;
+  if (valueof === void 0) {
+    for (const value of values) {
+      if (value != null && (max2 < value || max2 === void 0 && value >= value)) {
+        max2 = value;
+      }
+    }
+  } else {
+    let index2 = -1;
+    for (let value of values) {
+      if ((value = valueof(value, ++index2, values)) != null && (max2 < value || max2 === void 0 && value >= value)) {
+        max2 = value;
+      }
+    }
+  }
+  return max2;
+}
 function normalize(arr) {
   const [min2, max2] = extent(arr);
   const ratio = 255 / (max2 - min2);
   const data = new Uint8Array(arr.map((i2) => Math.floor((i2 - min2) * ratio)));
   return data;
 }
-function multiSetsToTextureData(multiFeatureValues, setColorValues, channelIsSetColorMode, texSize) {
+function multiSetsToTextureData(multiFeatureValues, multiMatrixObsIndex, setColorValues, channelIsSetColorMode, texSize) {
   let totalValuesLength = 0;
   let totalColorsLength = 0;
   channelIsSetColorMode.forEach((isSetColorMode, channelIndex) => {
-    var _a3, _b2, _c, _d, _e;
+    var _a3, _b2, _c, _d;
     if (isSetColorMode) {
-      totalValuesLength += ((_b2 = (_a3 = setColorValues[channelIndex]) == null ? void 0 : _a3.obsIndex) == null ? void 0 : _b2.length) || 0;
-      totalColorsLength += (((_d = (_c = setColorValues[channelIndex]) == null ? void 0 : _c.setColors) == null ? void 0 : _d.length) || 0) * 3;
+      totalColorsLength += (((_b2 = (_a3 = setColorValues[channelIndex]) == null ? void 0 : _a3.setColors) == null ? void 0 : _b2.length) || 0) * 3;
+      totalValuesLength += ((_c = setColorValues[channelIndex]) == null ? void 0 : _c.obsIndex) ? max(setColorValues[channelIndex].obsIndex.map((d) => parseInt(d))) : 0;
     } else {
-      totalValuesLength += ((_e = multiFeatureValues[channelIndex]) == null ? void 0 : _e.length) || 0;
+      totalValuesLength += multiMatrixObsIndex[channelIndex] ? max(multiMatrixObsIndex[channelIndex].map((d) => parseInt(d))) : ((_d = multiFeatureValues[channelIndex]) == null ? void 0 : _d.length) || 0;
     }
   });
   const valueTexHeight = Math.max(2, Math.ceil(totalValuesLength / texSize));
@@ -144915,12 +144953,20 @@ function multiSetsToTextureData(multiFeatureValues, setColorValues, channelIsSet
   let indexOffset = 0;
   let colorOffset = 0;
   channelIsSetColorMode.forEach((isSetColorMode, channelIndex) => {
+    const matrixObsIndex = multiMatrixObsIndex[channelIndex];
+    const bitmaskValueIsIndex = matrixObsIndex === null;
     if (isSetColorMode) {
       const { setColorIndices, setColors, obsIndex } = setColorValues[channelIndex] || {};
       if (setColorIndices && setColors && obsIndex) {
         for (let i2 = 0; i2 < obsIndex.length; i2++) {
-          const colorIndex = setColorIndices.get(String(i2 + 1));
-          totalData[indexOffset + i2] = colorIndex === void 0 ? 0 : colorIndex + 1;
+          let obsId = String(i2 + 1);
+          let obsI = i2;
+          if (!bitmaskValueIsIndex) {
+            obsId = obsIndex[i2];
+            obsI = parseInt(obsId) - 1;
+          }
+          const colorIndex = setColorIndices.get(obsId);
+          totalData[indexOffset + obsI] = colorIndex === void 0 ? 0 : colorIndex + 1;
         }
         for (let i2 = 0; i2 < setColors.length; i2++) {
           const { color: [r2, g2, b] } = setColors[i2];
@@ -144935,7 +144981,16 @@ function multiSetsToTextureData(multiFeatureValues, setColorValues, channelIsSet
       colorOffset += (setColors == null ? void 0 : setColors.length) || 0;
     } else {
       const featureArr = multiFeatureValues[channelIndex];
-      totalData.set(normalize(featureArr), indexOffset);
+      const normalizedFeatureArr = normalize(featureArr);
+      if (!bitmaskValueIsIndex && matrixObsIndex) {
+        for (let i2 = 0; i2 < matrixObsIndex.length; i2++) {
+          const obsId = matrixObsIndex[i2];
+          const obsI = parseInt(obsId) - 1;
+          totalData[indexOffset + obsI] = normalizedFeatureArr[i2];
+        }
+      } else {
+        totalData.set(normalizedFeatureArr, indexOffset);
+      }
       indicesOffsets.push(indexOffset);
       indexOffset += featureArr.length;
       colorsOffsets.push(colorOffset);
@@ -144962,6 +145017,17 @@ function padWithDefault(arr, defaultValue2, padWidth) {
 function getColor(arr) {
   return arr ? arr.map((v) => v / 255) : [0, 0, 0];
 }
+function isEqualShallow(prevArr, nextArr) {
+  if (prevArr === nextArr) {
+    return true;
+  }
+  if (Array.isArray(prevArr) && Array.isArray(nextArr)) {
+    if (prevArr.length === nextArr.length) {
+      return !prevArr.some((v, i2) => v !== nextArr[i2] && (!Array.isArray(v) && !Array.isArray(nextArr[i2]) || (v.length > 0 || nextArr[i2].length > 0)));
+    }
+  }
+  return prevArr === nextArr;
+}
 const defaultProps = {
   channelStrokeWidths: { type: "array", value: null, compare: true },
   channelsFilled: { type: "array", value: null, compare: true },
@@ -144971,6 +145037,7 @@ const defaultProps = {
   colormap: { type: "string", value: GLSL_COLORMAP_DEFAULT, compare: true },
   expressionData: { type: "object", value: null, compare: true },
   multiFeatureValues: { type: "array", value: null, compare: true },
+  multiMatrixObsIndex: { type: "array", value: null, compare: true },
   setColorValues: { type: "array", value: null, compare: true },
   channelFeatureValueColormaps: { type: "array", value: null, compare: true },
   channelFeatureValueColormapRanges: { type: "array", value: null, compare: true },
@@ -145017,9 +145084,9 @@ class BitmaskLayer2 extends XRLayer {
   }
   updateState({ props: props2, oldProps, changeFlags }) {
     super.updateState({ props: props2, oldProps, changeFlags });
-    if (props2.multiFeatureValues !== oldProps.multiFeatureValues || props2.setColorValues !== oldProps.setColorValues || props2.channelIsSetColorMode !== oldProps.channelIsSetColorMode) {
-      const { multiFeatureValues, setColorValues, channelIsSetColorMode } = this.props;
-      const [valueTex, colorTex, valueTexOffsets, colorTexOffsets, valueTexHeight, colorTexHeight] = this.multiSetsToTexture(multiFeatureValues, setColorValues, channelIsSetColorMode);
+    if (!isEqualShallow(props2.multiFeatureValues, oldProps.multiFeatureValues) || !isEqualShallow(props2.multiMatrixObsIndex, oldProps.multiMatrixObsIndex) || !isEqualShallow(props2.setColorValues, oldProps.setColorValues) || !isEqualShallow(props2.channelIsSetColorMode, oldProps.channelIsSetColorMode)) {
+      const { multiFeatureValues, multiMatrixObsIndex, setColorValues, channelIsSetColorMode } = this.props;
+      const [valueTex, colorTex, valueTexOffsets, colorTexOffsets, valueTexHeight, colorTexHeight] = this.multiSetsToTexture(multiFeatureValues, multiMatrixObsIndex, setColorValues, channelIsSetColorMode);
       this.setState({
         valueTex,
         colorTex,
@@ -145171,9 +145238,9 @@ class BitmaskLayer2 extends XRLayer {
       type: GL$1.FLOAT
     });
   }
-  multiSetsToTexture(multiFeatureValues, setColorValues, channelIsSetColorMode) {
+  multiSetsToTexture(multiFeatureValues, multiMatrixObsIndex, setColorValues, channelIsSetColorMode) {
     const isWebGL2On = isWebGL2$1(this.context.gl);
-    const [totalData, valueTexHeight, indicesOffsets, totalColors, colorTexHeight, colorsOffsets] = multiSetsToTextureData(multiFeatureValues, setColorValues, channelIsSetColorMode, MULTI_FEATURE_TEX_SIZE);
+    const [totalData, valueTexHeight, indicesOffsets, totalColors, colorTexHeight, colorsOffsets] = multiSetsToTextureData(multiFeatureValues, multiMatrixObsIndex, setColorValues, channelIsSetColorMode, MULTI_FEATURE_TEX_SIZE);
     return [
       // Color indices texture
       new Texture2D(this.context.gl, {
@@ -146396,9 +146463,6 @@ class Location {
     return new Location(this.store, new URL(path, root2).pathname);
   }
 }
-function root(store) {
-  return new Location(store ?? /* @__PURE__ */ new Map());
-}
 class Group extends Location {
   constructor(store, path, metadata) {
     super(store, path);
@@ -147016,92 +147080,6 @@ function set_from_chunk_binary(dest, src2, bytes_per_element2, projections) {
     }, bytes_per_element2, projs);
   }
 }
-function fetch_range(url, offset, length2, opts2 = {}) {
-  if (offset !== void 0 && length2 !== void 0) {
-    opts2 = {
-      ...opts2,
-      headers: {
-        ...opts2.headers,
-        Range: `bytes=${offset}-${offset + length2 - 1}`
-      }
-    };
-  }
-  return fetch(url, opts2);
-}
-function resolve(root2, path) {
-  const base = typeof root2 === "string" ? new URL(root2) : root2;
-  if (!base.pathname.endsWith("/")) {
-    base.pathname += "/";
-  }
-  const resolved = new URL(path.slice(1), base);
-  resolved.search = base.search;
-  return resolved;
-}
-async function handle_response(response) {
-  if (response.status === 404 || response.status === 403) {
-    return void 0;
-  }
-  if (response.status == 200 || response.status == 206) {
-    return new Uint8Array(await response.arrayBuffer());
-  }
-  throw new Error(`Unexpected response status ${response.status} ${response.statusText}`);
-}
-async function fetch_suffix(url, suffix_length, init, use_suffix_request) {
-  if (use_suffix_request) {
-    return fetch(url, {
-      ...init,
-      headers: { ...init.headers, Range: `bytes=-${suffix_length}` }
-    });
-  }
-  let response = await fetch(url, { ...init, method: "HEAD" });
-  if (!response.ok) {
-    return response;
-  }
-  let content_length = response.headers.get("Content-Length");
-  let length2 = Number(content_length);
-  return fetch_range(url, length2 - suffix_length, length2, init);
-}
-class FetchStore {
-  constructor(url, options = {}) {
-    __privateAdd(this, _merge_init);
-    __publicField(this, "url");
-    __privateAdd(this, _overrides, void 0);
-    __privateAdd(this, _use_suffix_request, void 0);
-    this.url = url;
-    __privateSet(this, _overrides, options.overrides ?? {});
-    __privateSet(this, _use_suffix_request, options.useSuffixRequest ?? false);
-  }
-  async get(key, options = {}) {
-    let href = resolve(this.url, key).href;
-    let response = await fetch(href, __privateMethod(this, _merge_init, merge_init_fn).call(this, options));
-    return handle_response(response);
-  }
-  async getRange(key, range2, options = {}) {
-    let url = resolve(this.url, key);
-    let init = __privateMethod(this, _merge_init, merge_init_fn).call(this, options);
-    let response;
-    if ("suffixLength" in range2) {
-      response = await fetch_suffix(url, range2.suffixLength, init, __privateGet(this, _use_suffix_request));
-    } else {
-      response = await fetch_range(url, range2.offset, range2.length, init);
-    }
-    return handle_response(response);
-  }
-}
-_overrides = new WeakMap();
-_use_suffix_request = new WeakMap();
-_merge_init = new WeakSet();
-merge_init_fn = function(overrides) {
-  return {
-    ...__privateGet(this, _overrides),
-    ...overrides,
-    headers: {
-      ...__privateGet(this, _overrides).headers,
-      ...overrides.headers
-    }
-  };
-};
-const FetchStore$1 = FetchStore;
 function getV2DataType(dtype) {
   const mapping = {
     int8: "|i1",
@@ -147141,10 +147119,6 @@ function createZarrArrayAdapter(arr) {
     }
   });
 }
-function zarrOpenRoot(url, requestInit2) {
-  const store = new FetchStore$1(url, { overrides: requestInit2 });
-  return root(store);
-}
 function prevPowerOf2(x2) {
   return 2 ** Math.floor(Math.log2(x2));
 }
@@ -147189,8 +147163,7 @@ class ZarritaPixelSource extends ZarrPixelSource {
     this._readChunks = false;
   }
 }
-async function loadOmeZarr(url, requestInit2) {
-  const root2 = await zarrOpenRoot(url, requestInit2);
+async function loadOmeZarr(root2) {
   const { data, rootAttrs, labels } = await loadMultiscales(root2);
   const tileSize = guessTileSize(data[0]);
   const pyramid = data.map((arr) => new ZarritaPixelSource(

package/dist/index.js

@@ -1,4 +1,4 @@
-import { D, e, a, b, c, d, F, G, Z, C, r, n, E, A, y, l, m, z, x, h, q, v, o, i, f, j, k, u, t, p, s, w } from "./index-27c044ac.js";
+import { D, e, a, b, c, d, F, G, Z, C, r, n, E, A, y, l, m, z, x, h, q, v, o, i, f, j, k, u, t, p, s, w } from "./index-20c94d37.js";
 import "react";
 export {
   D as DEFAULT_CELLS_LAYER,

package/dist/{jpeg-780f2a29.js → jpeg-a983c5fa.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 const dctZigZag = new Int32Array([
   0,

package/dist/{lerc-11712e42.js → lerc-302d4191.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-27c044ac.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 const LercParameters = {
   Version: 0,

package/dist/{lzw-a22317ac.js → lzw-e7880394.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;

package/dist/{packbits-757ef203.js → packbits-17057e1d.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {

package/dist/{raw-7e5381d5.js → raw-e5bd3ae5.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {

package/dist/{webimage-ec283d98.js → webimage-c3b216cf.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-27c044ac.js";
+import { B as BaseDecoder } from "./index-20c94d37.js";
 import "react";
 class WebImageDecoder extends BaseDecoder {
   constructor() {

package/dist-tsc/load-ome-zarr.d.ts

@@ -1,5 +1,5 @@
 export function guessTileSize(arr: any): number;
-export function loadOmeZarr(url: any, requestInit: any): Promise<{
+export function loadOmeZarr(root: any): Promise<{
     data: ZarritaPixelSource[];
     metadata: import("zarrita").Attributes;
 }>;

package/dist-tsc/load-ome-zarr.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"load-ome-zarr.d.ts","sourceRoot":"","sources":["../src/load-ome-zarr.js"],"names":[],"mappings":"AAkBA,gDAMC;AAiDD;;;GAcC;AA9BD;IACE,kDASC;IADC,qBAAwB;CAE3B"}
+{"version":3,"file":"load-ome-zarr.d.ts","sourceRoot":"","sources":["../src/load-ome-zarr.js"],"names":[],"mappings":"AAkBA,gDAMC;AAiDD;;;GAaC;AA7BD;IACE,kDASC;IADC,qBAAwB;CAE3B"}

package/dist-tsc/load-ome-zarr.js

@@ -1,6 +1,6 @@
 import { viv } from '@vitessce/gl';
 import { open as zarrOpen } from 'zarrita';
-import { zarrOpenRoot, createZarrArrayAdapter } from '@vitessce/zarr-utils';
+import { createZarrArrayAdapter } from '@vitessce/zarr-utils';
 function prevPowerOf2(x) {
     return 2 ** Math.floor(Math.log2(x));
 }
@@ -62,8 +62,7 @@ export class ZarritaPixelSource extends viv.ZarrPixelSource {
 }
 // We use our own loadOmeZarr function (instead of viv.loadOmeZarr)
 // to bypass usage of zarr.js which is used in Viv's version.
-export async function loadOmeZarr(url, requestInit) {
-    const root = await zarrOpenRoot(url, requestInit);
+export async function loadOmeZarr(root) {
     const { data, rootAttrs, labels } = await loadMultiscales(root);
     const tileSize = guessTileSize(data[0]);
     const pyramid = data

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/spatial-utils",
-  "version": "3.3.1",
+  "version": "3.3.3",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,9 +20,9 @@
     "zarrita": "0.4.0-next.4",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
-    "@vitessce/gl": "3.3.1",
-    "@vitessce/zarr-utils": "3.3.1",
-    "@vitessce/utils": "3.3.1"
+    "@vitessce/gl": "3.3.3",
+    "@vitessce/utils": "3.3.3",
+    "@vitessce/zarr-utils": "3.3.3"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",

package/src/load-ome-zarr.js

@@ -1,6 +1,6 @@
 import { viv } from '@vitessce/gl';
 import { open as zarrOpen } from 'zarrita';
-import { zarrOpenRoot, createZarrArrayAdapter } from '@vitessce/zarr-utils';
+import { createZarrArrayAdapter } from '@vitessce/zarr-utils';
 
 function prevPowerOf2(x) {
   return 2 ** Math.floor(Math.log2(x));
@@ -71,8 +71,7 @@ export class ZarritaPixelSource extends viv.ZarrPixelSource {
 
 // We use our own loadOmeZarr function (instead of viv.loadOmeZarr)
 // to bypass usage of zarr.js which is used in Viv's version.
-export async function loadOmeZarr(url, requestInit) {
-  const root = await zarrOpenRoot(url, requestInit);
+export async function loadOmeZarr(root) {
   const { data, rootAttrs, labels } = await loadMultiscales(root);
   const tileSize = guessTileSize(data[0]);
   const pyramid = data