@vitessce/all 3.1.2 → 3.1.3

package/dist/{deflate-19f2d5d6.js → deflate-e164f5b4.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{hglib-88a02387.js → hglib-27190533.js}

@@ -1,6 +1,6 @@
 import React__default from "react";
 import ReactDOM__default from "react-dom";
-import { c as commonjsGlobal, o as objectAssign, g as getDefaultExportFromCjs, e as earcut, b as getAugmentedNamespace } from "./index-b711b37e.js";
+import { c as commonjsGlobal, o as objectAssign, g as getDefaultExportFromCjs, e as earcut, b as getAugmentedNamespace } from "./index-61ee101c.js";
 function _mergeNamespaces(n, m) {
   for (var i = 0; i < m.length; i++) {
     const e = m[i];

package/dist/{index-b711b37e.js → index-61ee101c.js}

@@ -155223,16 +155223,16 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-83f54019.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-1fcadb5f.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-cb4a4ae9.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-8aa1e0b3.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-826e5bcb.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-19f2d5d6.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-193c276e.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-dae178a4.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-bf05fa7a.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-eaa82c98.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-e164f5b4.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-ad4b66a3.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-0c45509f.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-3d222f28.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -190276,6 +190276,41 @@ function coordinateTransformationsToMatrix(coordinateTransformations, axes) {
   }
   return mat;
 }
+function normalizeCoordinateTransformations(coordinateTransformations, datasets) {
+  var _a2;
+  let result = [];
+  if (Array.isArray(coordinateTransformations)) {
+    result = coordinateTransformations.map((transform3) => {
+      if (transform3.input && transform3.output) {
+        const { type: type2 } = transform3;
+        if (type2 === "translation") {
+          return {
+            type: type2,
+            translation: transform3.translation
+          };
+        }
+        if (type2 === "scale") {
+          return {
+            type: type2,
+            scale: transform3.scale
+          };
+        }
+        if (type2 === "identity") {
+          return { type: type2 };
+        }
+        console.warn(`Coordinate transformation type "${type2}" is not supported.`);
+      }
+      return transform3;
+    });
+  }
+  if (Array.isArray((_a2 = datasets == null ? void 0 : datasets[0]) == null ? void 0 : _a2.coordinateTransformations)) {
+    result = [
+      ...datasets[0].coordinateTransformations,
+      ...result
+    ];
+  }
+  return result;
+}
 var shortNumber$1 = { exports: {} };
 (function(module2, exports2) {
   (function(global2, factory2) {
@@ -198420,7 +198455,7 @@ const HIGLASS_BUNDLE_VERSION = "1.11.13";
 const HIGLASS_CSS_URL = `https://unpkg.com/${HIGLASS_PKG_NAME}@${HIGLASS_BUNDLE_VERSION}/dist/hglib.css`;
 register({ dataFetcher: ZarrMultivecDataFetcher, config: ZarrMultivecDataFetcher.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./hglib-88a02387.js").then((n3) => n3.h);
+  const { HiGlassComponent } = await import("./hglib-27190533.js").then((n3) => n3.h);
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -257383,22 +257418,21 @@ class OmeZarrLoader extends AbstractTwoStepLoader {
     const { coordinateTransformations: coordinateTransformationsFromOptions } = this.options || {};
     const loader2 = await loadOmeZarr(this.url, { fetchOptions: this.requestInit, type: "multiscales" });
     const { metadata: metadata2, data: data2 } = loader2;
-    const { omero, multiscales } = metadata2;
-    if (!omero) {
-      console.error("Path for image not valid");
+    const { omero, multiscales, channels_metadata: spatialDataChannels } = metadata2;
+    const isSpatialData = !!spatialDataChannels;
+    if (!isSpatialData && !omero) {
+      console.error("image.ome-zarr must have omero metadata in attributes.");
       return Promise.reject(payload);
     }
     if (!Array.isArray(multiscales) || multiscales.length === 0) {
       console.error("Multiscales array must exist and have at least one element");
     }
-    const { coordinateTransformations } = multiscales[0];
+    const { datasets, coordinateTransformations: coordinateTransformationsFromFile, name: imageName } = multiscales[0];
     const axes = getNgffAxes(multiscales[0].axes);
+    const normCoordinateTransformationsFromFile = normalizeCoordinateTransformations(coordinateTransformationsFromFile, datasets);
     const transformMatrixFromOptions = coordinateTransformationsToMatrix(coordinateTransformationsFromOptions, axes);
-    const transformMatrixFromFile = coordinateTransformationsToMatrix(coordinateTransformations, axes);
+    const transformMatrixFromFile = coordinateTransformationsToMatrix(normCoordinateTransformationsFromFile, axes);
     const transformMatrix = transformMatrixFromFile.multiplyLeft(transformMatrixFromOptions);
-    const { rdefs, channels: channels2, name: omeroName } = omero;
-    const t4 = rdefs.defaultT ?? 0;
-    const z2 = rdefs.defaultZ ?? 0;
     const filterSelection = (sel) => {
       if (data2.length > 0) {
         const nextSel = {};
@@ -257412,14 +257446,37 @@ class OmeZarrLoader extends AbstractTwoStepLoader {
       }
       return sel;
     };
+    let channelObjects;
+    let channelLabels = [];
+    let initialTargetT = 0;
+    let initialTargetZ = 0;
+    if (isSpatialData) {
+      const { channels: channels2 } = spatialDataChannels;
+      channelObjects = channels2.map((channel, i2) => ({
+        selection: filterSelection({ z: initialTargetZ, t: initialTargetT, c: i2 }),
+        slider: [0, 255],
+        color: [255, 255, 255]
+      }));
+      channelLabels = channels2.map((c2) => c2.label);
+    } else {
+      const { rdefs, channels: channels2 } = omero;
+      if (typeof rdefs.defaultT === "number") {
+        initialTargetT = rdefs.defaultT;
+      }
+      if (typeof rdefs.defaultZ === "number") {
+        initialTargetZ = rdefs.defaultZ;
+      }
+      channelObjects = channels2.map((channel, i2) => ({
+        selection: filterSelection({ z: initialTargetZ, t: initialTargetT, c: i2 }),
+        slider: [channel.window.start, channel.window.end],
+        color: hexToRgb(channel.color)
+      }));
+      channelLabels = channels2.map((c2) => c2.label);
+    }
     const imagesWithLoaderCreators = [
       {
-        name: omeroName || "Image",
-        channels: channels2.map((channel, i2) => ({
-          selection: filterSelection({ z: z2, t: t4, c: i2 }),
-          slider: [channel.window.start, channel.window.end],
-          color: hexToRgb(channel.color)
-        })),
+        name: imageName || "Image",
+        channels: channelObjects,
         ...transformMatrix ? {
           metadata: {
             transform: {
@@ -257427,7 +257484,7 @@ class OmeZarrLoader extends AbstractTwoStepLoader {
             }
           }
         } : {},
-        loaderCreator: async () => ({ ...loader2, channels: channels2.map((c2) => c2.label) })
+        loaderCreator: async () => ({ ...loader2, channels: channelLabels })
       }
     ];
     const [autoImageLayers, imageLayerLoaders, imageLayerMeta] = await initializeRasterLayersAndChannels(imagesWithLoaderCreators, void 0);

package/dist/index.js

@@ -1,4 +1,4 @@
-import { f, P, h, d, V, z } from "./index-b711b37e.js";
+import { f, P, h, d, V, z } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-826e5bcb.js → jpeg-eaa82c98.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-dae178a4.js → lerc-0c45509f.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-b711b37e.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-1fcadb5f.js → lzw-8aa1e0b3.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-193c276e.js → packbits-ad4b66a3.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-83f54019.js → raw-cb4a4ae9.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-bf05fa7a.js → webimage-3d222f28.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b711b37e.js";
+import { B as BaseDecoder } from "./index-61ee101c.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.1.2",
+  "version": "3.1.3",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,25 +18,25 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.1.2",
-    "@vitessce/description": "3.1.2",
-    "@vitessce/csv": "3.1.2",
-    "@vitessce/feature-list": "3.1.2",
-    "@vitessce/genomic-profiles": "3.1.2",
-    "@vitessce/heatmap": "3.1.2",
-    "@vitessce/json": "3.1.2",
-    "@vitessce/layer-controller": "3.1.2",
-    "@vitessce/obs-sets-manager": "3.1.2",
-    "@vitessce/ome-tiff": "3.1.2",
-    "@vitessce/plugins": "3.1.2",
-    "@vitessce/scatterplot-embedding": "3.1.2",
-    "@vitessce/scatterplot-gating": "3.1.2",
-    "@vitessce/schemas": "3.1.2",
-    "@vitessce/spatial": "3.1.2",
-    "@vitessce/statistical-plots": "3.1.2",
-    "@vitessce/status": "3.1.2",
-    "@vitessce/vit-s": "3.1.2",
-    "@vitessce/zarr": "3.1.2"
+    "@vitessce/constants-internal": "3.1.3",
+    "@vitessce/csv": "3.1.3",
+    "@vitessce/description": "3.1.3",
+    "@vitessce/feature-list": "3.1.3",
+    "@vitessce/genomic-profiles": "3.1.3",
+    "@vitessce/heatmap": "3.1.3",
+    "@vitessce/json": "3.1.3",
+    "@vitessce/layer-controller": "3.1.3",
+    "@vitessce/obs-sets-manager": "3.1.3",
+    "@vitessce/ome-tiff": "3.1.3",
+    "@vitessce/plugins": "3.1.3",
+    "@vitessce/scatterplot-embedding": "3.1.3",
+    "@vitessce/scatterplot-gating": "3.1.3",
+    "@vitessce/schemas": "3.1.3",
+    "@vitessce/spatial": "3.1.3",
+    "@vitessce/statistical-plots": "3.1.3",
+    "@vitessce/status": "3.1.3",
+    "@vitessce/vit-s": "3.1.3",
+    "@vitessce/zarr": "3.1.3"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",