@vitessce/spatial-utils 3.6.4 → 3.6.5

package/dist/{deflate-D9ljyhNr.js → deflate-Cumj_9kB.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{index-BHjTDkex.js → index-C6jVF_qi.js}

@@ -120365,22 +120365,22 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c) => registry$2.set(c, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-BIF7paLv.js").then((m) => m.default));
-addDecoder(5, () => import("./lzw-DH_0TN8Q.js").then((m) => m.default));
+addDecoder([void 0, 1], () => import("./raw-DwHPYVQy.js").then((m) => m.default));
+addDecoder(5, () => import("./lzw-Ckpw-zOq.js").then((m) => m.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-CBCGd1ig.js").then((m) => m.default));
-addDecoder([8, 32946], () => import("./deflate-D9ljyhNr.js").then((m) => m.default));
-addDecoder(32773, () => import("./packbits-CFKxEnzI.js").then((m) => m.default));
+addDecoder(7, () => import("./jpeg-Bv9e5TsR.js").then((m) => m.default));
+addDecoder([8, 32946], () => import("./deflate-Cumj_9kB.js").then((m) => m.default));
+addDecoder(32773, () => import("./packbits-KgFJoulg.js").then((m) => m.default));
 addDecoder(
   34887,
-  () => import("./lerc-KzhcoJX_.js").then(async (m) => {
+  () => import("./lerc-CN8oy9fE.js").then(async (m) => {
     await m.zstd.init();
     return m;
   }).then((m) => m.default)
 );
-addDecoder(50001, () => import("./webimage-C0GvbHjI.js").then((m) => m.default));
+addDecoder(50001, () => import("./webimage-BeD_xi6W.js").then((m) => m.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset = 0;
@@ -138032,6 +138032,14 @@ function hexToRgb(hex) {
     parseInt(result[3].toLowerCase(), 16)
   ];
 }
+function normalizeAxes(axes) {
+  return axes.map((axisInfo) => {
+    if (typeof axisInfo === "string") {
+      return { name: axisInfo, type: "space" };
+    }
+    return axisInfo;
+  });
+}
 function normalizeCoordinateTransformations(coordinateTransformations, datasets) {
   var _a3;
   let result = [];
@@ -139625,11 +139633,12 @@ function getDomains() {
 }
 const DOMAINS = getDomains();
 export {
-  abbreviateNumber as A,
+  getBoundingCube as A,
   BaseDecoder as B,
-  filterSelection as C,
+  abbreviateNumber as C,
   DEFAULT_CELLS_LAYER as D,
-  DOMAINS as E,
+  filterSelection as E,
+  DOMAINS as F,
   GLOBAL_LABELS as G,
   ZarritaPixelSource as Z,
   DEFAULT_MOLECULES_LAYER as a,
@@ -139651,11 +139660,11 @@ export {
   getStatsForResolution as q,
   canLoadResolution as r,
   normalizeCoordinateTransformations as s,
-  loadOmeZarr as t,
-  guessTileSize as u,
-  toRgbUIString as v,
-  getSingleSelectionStats as w,
-  getMultiSelectionStats as x,
-  getPhysicalSizeScalingMatrix as y,
-  getBoundingCube as z
+  normalizeAxes as t,
+  loadOmeZarr as u,
+  guessTileSize as v,
+  toRgbUIString as w,
+  getSingleSelectionStats as x,
+  getMultiSelectionStats as y,
+  getPhysicalSizeScalingMatrix as z
 };

package/dist/index.js

@@ -1,4 +1,4 @@
-import { D, e, a, b, c, d, E, G, Z, A, r, n, C, z, x, l, m, y, w, h, q, u, o, i, f, j, k, t, s, p, v } from "./index-BHjTDkex.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, s, p, w } from "./index-C6jVF_qi.js";
 export {
   D as DEFAULT_CELLS_LAYER,
   e as DEFAULT_LAYER_TYPE_ORDERING,
@@ -6,29 +6,30 @@ export {
   b as DEFAULT_NEIGHBORHOODS_LAYER,
   c as DEFAULT_RASTER_DOMAIN_TYPE,
   d as DEFAULT_RASTER_LAYER_PROPS,
-  E as DOMAINS,
+  F as DOMAINS,
   G as GLOBAL_LABELS,
   Z as ZarritaPixelSource,
-  A as abbreviateNumber,
+  C as abbreviateNumber,
   r as canLoadResolution,
   n as coordinateTransformationsToMatrix,
-  C as filterSelection,
-  z as getBoundingCube,
-  x as getMultiSelectionStats,
+  E as filterSelection,
+  A as getBoundingCube,
+  y as getMultiSelectionStats,
   l as getNgffAxes,
   m as getNgffAxesForTiff,
-  y as getPhysicalSizeScalingMatrix,
-  w as getSingleSelectionStats,
+  z as getPhysicalSizeScalingMatrix,
+  x as getSingleSelectionStats,
   h as getSourceFromLoader,
   q as getStatsForResolution,
-  u as guessTileSize,
+  v as guessTileSize,
   o as hexToRgb,
   i as initializeLayerChannels,
   f as initializeRasterLayersAndChannels,
   j as isInterleaved,
   k as isRgb,
-  t as loadOmeZarr,
+  u as loadOmeZarr,
+  t as normalizeAxes,
   s as normalizeCoordinateTransformations,
   p as physicalSizeToMatrix,
-  v as toRgbUIString
+  w as toRgbUIString
 };

package/dist/{jpeg-CBCGd1ig.js → jpeg-Bv9e5TsR.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-KzhcoJX_.js → lerc-CN8oy9fE.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-BHjTDkex.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-C6jVF_qi.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-DH_0TN8Q.js → lzw-Ckpw-zOq.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-CFKxEnzI.js → packbits-KgFJoulg.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-BIF7paLv.js → raw-DwHPYVQy.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-C0GvbHjI.js → webimage-BeD_xi6W.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BHjTDkex.js";
+import { B as BaseDecoder } from "./index-C6jVF_qi.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/dist-tsc/index.d.ts

@@ -1,6 +1,6 @@
 export { DOMAINS } from "./constants.js";
 export { GLOBAL_LABELS, DEFAULT_CELLS_LAYER, DEFAULT_MOLECULES_LAYER, DEFAULT_NEIGHBORHOODS_LAYER, DEFAULT_RASTER_DOMAIN_TYPE, DEFAULT_RASTER_LAYER_PROPS, DEFAULT_LAYER_TYPE_ORDERING } from "@vitessce/constants-internal";
-export { initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations } from "./spatial.js";
+export { initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations, normalizeAxes } from "./spatial.js";
 export { loadOmeZarr, guessTileSize, ZarritaPixelSource } from "./load-ome-zarr.js";
 export { toRgbUIString, getSingleSelectionStats, getMultiSelectionStats, getPhysicalSizeScalingMatrix, getBoundingCube, abbreviateNumber, filterSelection } from "./layer-controller.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -1,5 +1,5 @@
 export { GLOBAL_LABELS, DEFAULT_CELLS_LAYER, DEFAULT_MOLECULES_LAYER, DEFAULT_NEIGHBORHOODS_LAYER, DEFAULT_RASTER_DOMAIN_TYPE, DEFAULT_RASTER_LAYER_PROPS, DEFAULT_LAYER_TYPE_ORDERING, } from '@vitessce/constants-internal';
-export { initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations, } from './spatial.js';
+export { initializeLayerChannels, initializeRasterLayersAndChannels, getSourceFromLoader, isInterleaved, isRgb, getNgffAxes, getNgffAxesForTiff, coordinateTransformationsToMatrix, physicalSizeToMatrix, hexToRgb, getStatsForResolution, canLoadResolution, normalizeCoordinateTransformations, normalizeAxes, } from './spatial.js';
 export { loadOmeZarr, guessTileSize, ZarritaPixelSource, } from './load-ome-zarr.js';
 export { toRgbUIString, getSingleSelectionStats, getMultiSelectionStats, getPhysicalSizeScalingMatrix, getBoundingCube, abbreviateNumber, filterSelection, } from './layer-controller.js';
 export { DOMAINS, } from './constants.js';

package/dist-tsc/spatial.d.ts

@@ -52,6 +52,7 @@ export function getNgffAxesForTiff(dimOrder: any): any;
  */
 export function coordinateTransformationsToMatrix(coordinateTransformations: object[] | undefined, axes: object[] | undefined): Matrix4;
 export function hexToRgb(hex: any): number[];
+export function normalizeAxes(axes: any): any;
 /**
  * Normalize coordinate transformations to the OME-NGFF v0.4 format,
  * despite potentially being in the new format proposed in

package/dist-tsc/spatial.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"spatial.d.ts","sourceRoot":"","sources":["../src/spatial.js"],"names":[],"mappings":"AAOA;;;;;;GAMG;AACH,4CAJW,MAAM,SACN,MAAM,GAAG,SAAS,GAChB,MAAM,CAMlB;AAoCD;;;;GAIG;AACH,8BAHW,MAAM,YACN,KAAK,GAAC,IAAI,WAiBpB;AAID,sHAmCC;AAiHD;;GAEG;AACH,qCAFW,KAAK,CAAE,MAAM,CAAC,WAKxB;AAED;;;;;;GAMG;AACH,gDALW,MAAM,eAEJ,MAAM,EAAE,CAuCpB;AAED;;;;;;;;;GASG;AACH,gEAJW,MAAM,EAAE,sBAER,CAAC,MAAM,EAAE,GAAC,IAAI,CAAC,+CAuEzB;AASD;;;IAuBC;AAED,uDAQC;AAED;;;;;;;;GAQG;AACH,6EANW,MAAM,EAAE,GAAC,SAAS,QAElB,MAAM,EAAE,GAAC,SAAS,GAEhB,OAAO,CA4CnB;AAED,6CAOC;AAED;;;;;;;;;GASG;AACH,8EANW,MAAM,EAAE,GAAC,SAAS,YAGlB,MAAM,EAAE,GACN,MAAM,EAAE,CAoDpB;AAxfM;;;;;EAYN;AAEM,yEAkBN;wBAnDuB,SAAS"}
+{"version":3,"file":"spatial.d.ts","sourceRoot":"","sources":["../src/spatial.js"],"names":[],"mappings":"AAOA;;;;;;GAMG;AACH,4CAJW,MAAM,SACN,MAAM,GAAG,SAAS,GAChB,MAAM,CAMlB;AAoCD;;;;GAIG;AACH,8BAHW,MAAM,YACN,KAAK,GAAC,IAAI,WAiBpB;AAID,sHAmCC;AAiHD;;GAEG;AACH,qCAFW,KAAK,CAAE,MAAM,CAAC,WAKxB;AAED;;;;;;GAMG;AACH,gDALW,MAAM,eAEJ,MAAM,EAAE,CAuCpB;AAED;;;;;;;;;GASG;AACH,gEAJW,MAAM,EAAE,sBAER,CAAC,MAAM,EAAE,GAAC,IAAI,CAAC,+CAuEzB;AASD;;;IAuBC;AAED,uDAQC;AAED;;;;;;;;GAQG;AACH,6EANW,MAAM,EAAE,GAAC,SAAS,QAElB,MAAM,EAAE,GAAC,SAAS,GAEhB,OAAO,CA4CnB;AAED,6CAOC;AAMD,8CASC;AAED;;;;;;;;;GASG;AACH,8EANW,MAAM,EAAE,GAAC,SAAS,YAGlB,MAAM,EAAE,GACN,MAAM,EAAE,CAoDpB;AAvgBM;;;;;EAYN;AAEM,yEAkBN;wBAnDuB,SAAS"}

package/dist-tsc/spatial.js

@@ -412,6 +412,19 @@ export function hexToRgb(hex) {
         parseInt(result[3].toLowerCase(), 16),
     ];
 }
+// TODO: is this needed?
+// In the spatialdata metadata the axis name/type/unit info are also listed in
+// coordinateTransformations[].input|output.axes[] entries.
+export function normalizeAxes(axes) {
+    // Normalize axes to OME-NGFF v0.4 format.
+    return axes.map((axisInfo) => {
+        if (typeof axisInfo === 'string') {
+            // If the axis is a string, assume it is a name and set type to 'space'.
+            return { name: axisInfo, type: 'space' };
+        }
+        return axisInfo;
+    });
+}
 /**
  * Normalize coordinate transformations to the OME-NGFF v0.4 format,
  * despite potentially being in the new format proposed in

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/spatial-utils",
-  "version": "3.6.4",
+  "version": "3.6.5",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,11 +20,11 @@
     "zarrita": "0.5.2",
     "math.gl": "^3.5.6",
     "mathjs": "^9.2.0",
-    "@vitessce/gl": "3.6.4",
-    "@vitessce/utils": "3.6.4",
-    "@vitessce/zarr-utils": "3.6.4",
-    "@vitessce/constants-internal": "3.6.4",
-    "@vitessce/globals": "3.6.4"
+    "@vitessce/gl": "3.6.5",
+    "@vitessce/utils": "3.6.5",
+    "@vitessce/zarr-utils": "3.6.5",
+    "@vitessce/constants-internal": "3.6.5",
+    "@vitessce/globals": "3.6.5"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",

package/src/index.js

@@ -21,6 +21,7 @@ export {
   getStatsForResolution,
   canLoadResolution,
   normalizeCoordinateTransformations,
+  normalizeAxes,
 } from './spatial.js';
 export {
   loadOmeZarr,

package/src/spatial.js

@@ -462,6 +462,21 @@ export function hexToRgb(hex) {
   ];
 }
 
+
+// TODO: is this needed?
+// In the spatialdata metadata the axis name/type/unit info are also listed in
+// coordinateTransformations[].input|output.axes[] entries.
+export function normalizeAxes(axes) {
+  // Normalize axes to OME-NGFF v0.4 format.
+  return axes.map((axisInfo) => {
+    if (typeof axisInfo === 'string') {
+      // If the axis is a string, assume it is a name and set type to 'space'.
+      return { name: axisInfo, type: 'space' };
+    }
+    return axisInfo;
+  });
+}
+
 /**
  * Normalize coordinate transformations to the OME-NGFF v0.4 format,
  * despite potentially being in the new format proposed in