@vitessce/all 4.0.0-test.0 → 4.0.0-test.2

package/dist/{index-DxpZAn2M.js → index-CNZN2FGp.js}

@@ -3,7 +3,7 @@ import React__default, { useRef, useState, useEffect, Suspense, forwardRef } fro
 import { Canvas } from "@react-three/fiber";
 import { Center, Text, Line, Bvh, OrbitControls } from "@react-three/drei";
 import { Matrix3, Matrix4, Vector3, Vector2, UniformsUtils, Data3DTexture, RedFormat, FloatType, LinearFilter, FrontSide, Scene, Group, MeshPhysicalMaterial, MeshBasicMaterial, MeshStandardMaterial, BackSide } from "three";
-import { C as CoordinationType, g as getImageSize } from "./index-5W6nu-ix.js";
+import { C as CoordinationType, g as getImageSize } from "./index-BYPSbKAg.js";
 function MeasureLine({ currentLine, scale }) {
   const textRef = useRef(null);
   return jsxs("group", { children: [jsx(Center, { bottom: true, right: true, position: [currentLine.midPoint.x, currentLine.midPoint.y, currentLine.midPoint.z], rotation: [0, 0, 0], children: jsx(Text, { color: "gray", scale: 0.05, ref: textRef, children: `${(currentLine.startPoint.distanceTo(currentLine.endPoint) * scale).toFixed(2)} µm` }) }), jsx(Line, {
@@ -16,19 +16,45 @@ function MeasureLine({ currentLine, scale }) {
 }
 class Volume {
   spacing = [1, 1, 1];
+  // Offset of the volume in the RAS coordinate system
   offset = [0, 0, 0];
+  // The IJK to RAS matrix
   matrix = new Matrix3().identity();
+  // The list of all the slices associated to this volume
   sliceList = [];
+  /**
+   * The voxels with values under this
+   * threshold won't appear in the slices.
+   * If changed, geometryNeedsUpdate is automatically set to true on all
+   * the slices associated to this volume
+   */
   lowerThresholdValue = -Infinity;
+  /**
+   * The voxels with values over this
+   * threshold won't appear in the slices.
+   * If changed, geometryNeedsUpdate is automatically set to true on all
+   * the slices associated to this volume
+   */
   upperThresholdValue = Infinity;
+  // Width of the volume in the IJK coordinate system
   xLength = 1;
+  // Height of the volume in the IJK coordinate system
   yLength = 1;
+  // Depth of the volume in the IJK coordinate system
   zLength = 1;
+  // Data of the volume
   data;
   RASDimensions;
   inverseMatrix;
   min;
   max;
+  /**
+   * @param {number} xLength Width of the volume
+   * @param {number} yLength Length of the volume
+   * @param {number} zLength Depth of the volume
+   * @param {string} type The type of data (uint8, uint16, ...)
+   * @param {ArrayBuffer} arrayBuffer The buffer with volume data
+   */
   constructor(xLength, yLength, zLength, type, arrayBuffer) {
     if (xLength !== void 0) {
       this.xLength = Number(xLength) || 1;
@@ -128,18 +154,33 @@ class Volume {
       slice.geometryNeedsUpdate = true;
     });
   }
+  /**
+   * Shortcut for data[access(i,j,k)]
+   */
   getData(i, j, k) {
     return this.data[k * this.xLength * this.yLength + j * this.xLength + i];
   }
+  /**
+   * Compute the index in the data
+   * array corresponding to the given coordinates in IJK system
+   */
   access(i, j, k) {
     return k * this.xLength * this.yLength + j * this.xLength + i;
   }
+  /**
+   * Retrieve the IJK coordinates of the voxel
+   * corresponding of the given index in the data
+   */
   reverseAccess(index2) {
     const z = Math.floor(index2 / (this.yLength * this.xLength));
     const y = Math.floor((index2 - z * this.yLength * this.xLength) / this.xLength);
     const x = index2 - z * this.yLength * this.xLength - y * this.xLength;
     return [x, y, z];
   }
+  /**
+   * Apply a function to all the voxels, be careful,
+   * the value will be replaced
+   */
   // eslint-disable-next-line max-len
   map(functionToMap, contextParam) {
     const { length } = this.data;
@@ -149,6 +190,13 @@ class Volume {
     }
     return this;
   }
+  /**
+   * Compute the orientation
+   * of the slice and returns all the information relative to the
+   * geometry such as sliceAccess,
+   * the plane matrix (orientation and position in RAS coordinate)
+   * and the dimensions of the plane in both coordinate system.
+   */
   extractPerpendicularPlane(axis, RASIndex) {
     const planeMatrix = new Matrix4().identity();
     const volume = this;
@@ -227,6 +275,11 @@ class Volume {
       planeHeight
     };
   }
+  /**
+   * Compute the minimum
+   * and the maximum of the data in the volume
+   * @returns {Array} [min,max]
+   */
   computeMinMax() {
     let min = Infinity;
     let max = -Infinity;
@@ -832,7 +885,11 @@ function getData3DTexture(volume) {
 }
 function getPhysicalSizeScalingMatrix(loader) {
   const { x, y, z } = loader?.meta?.physicalSizes ?? {};
-  return [{ size: x ?? 1 }, { size: y ?? 1 }, { size: z ?? 1 }];
+  return [
+    x ?? { size: 1 },
+    y ?? { size: 1 },
+    z ?? { size: 1 }
+  ];
 }
 function minMaxVolume(volume) {
   const [min, max] = volume.computeMinMax();
@@ -870,10 +927,10 @@ function stringifyLineData(lineData) {
   return `${lineData.startPoint.x},${lineData.startPoint.y},${lineData.startPoint.z};${lineData.endPoint.x},${lineData.endPoint.y},${lineData.endPoint.z}`;
 }
 function isValidGeometrySize(size) {
-  if (!Array.isArray(size) || size.length !== 6) {
+  if (!Array.isArray(size) || size.length !== 3) {
     return false;
   }
-  return size.every((s) => typeof s === "number" || s === void 0);
+  return size.every((s) => typeof s === "number" && Number.isFinite(s));
 }
 function GeometryAndMesh(props) {
   const { segmentationGroup, segmentationSettings, segmentationSceneScale, renderingSettings, materialRef, highlightEntity, setObsHighlight } = props;
@@ -887,7 +944,7 @@ function GeometryAndMesh(props) {
     setObsHighlight(e.object.name);
   }, onPointerOut: () => setObsHighlight(null) }) })] }) : null, renderingSettings.uniforms && renderingSettings.shader && renderingSettings.meshScale && renderingSettings.geometrySize ? jsx("group", { children: jsxs("mesh", { scale: renderingSettings.meshScale, ref: materialRef, children: [jsx("boxGeometry", { args: renderingSettings.geometrySize }), jsx("shaderMaterial", { customProgramCacheKey: () => "1", side: FrontSide, uniforms: renderingSettings.uniforms, needsUpdate: true, transparent: true, vertexShader: renderingSettings.shader.vertexShader, fragmentShader: renderingSettings.shader.fragmentShader })] }) }) : null] }), jsx("group", { name: "lines", children: lines.map((object) => jsx(MeasureLine, { currentLine: object, scale: 1 }, stringifyLineData(object))) })] });
 }
-const LazyGeometryAndMeshXR = React__default.lazy(() => import("./GeometryAndMeshXR-Bewsp5O-.js").catch(() => ({ default: GeometryAndMesh })));
+const LazyGeometryAndMeshXR = React__default.lazy(() => import("./GeometryAndMeshXR-KXexgmZr.js").catch(() => ({ default: GeometryAndMesh })));
 const LazyXRSceneComponents = React__default.lazy(() => import("./XRSceneComponents-DnZLSAJz.js").catch(() => ({ default: () => null })));
 function SpatialThree(props) {
   const materialRef = useRef(null);

package/dist/{index-DXuQcXKb.js → index-CoIDzRuL.js}

@@ -4,7 +4,7 @@ import { useThree, useFrame, Canvas } from "@react-three/fiber";
 import { OrbitControls } from "@react-three/drei";
 import * as THREE from "three";
 import { Data3DTexture, RedFormat, UnsignedByteType, LinearFilter, RedIntegerFormat, UnsignedIntType, NearestFilter, Vector3, Vector2, Vector4, UniformsUtils, WebGLMultipleRenderTargets } from "three";
-import { l as log, i as isEqual, C as CoordinationType, u as useEventCallback } from "./index-5W6nu-ix.js";
+import { l as log, i as isEqual, C as CoordinationType, u as useEventCallback } from "./index-BYPSbKAg.js";
 const LogLevel = {
   INFO: "info",
   WARN: "warn",
@@ -232,7 +232,8 @@ function _requestBufferToRequestObjects(buffer, k, optsForWeighting) {
     }
     counts.set(packed, (counts.get(packed) || 0) + weight);
   }
-  const requests = [...counts.entries()].sort((a, b) => b[1] - a[1]).slice(0, k).map(([packed]) => ({
+  const sorted = Array.from(counts.entries()).toSorted((a, b) => b[1] - a[1]);
+  const requests = sorted.slice(0, k).map(([packed]) => ({
     x: packed >> 22 & 1023,
     y: packed >> 12 & 1023,
     z: packed & 4095
@@ -900,6 +901,10 @@ class VolumeDataManager {
    * the center of the render target.
    */
   async processRequestData(buffer, optsForWeighting) {
+    if (this.initStatus !== INIT_STATUS.COMPLETE) {
+      log.debug("processRequestData: not yet initialized, skipping");
+      return;
+    }
     if (this.isBusy) {
       log.debug("processRequestData: already busy, skipping");
       return;
@@ -3584,6 +3589,7 @@ function VolumeView(props) {
     geometrySize: [1, 1, 1]
   });
   const is3D = spatialRenderingMode === "3D";
+  const [dmInitComplete, setDmInitComplete] = useState(false);
   const screenSceneRef = useRef(null);
   const screenCameraRef = useRef(null);
   const screenQuadRef = useRef(null);
@@ -3656,6 +3662,7 @@ function VolumeView(props) {
     const initializeDataManager = async () => {
       if (dataManager.initStatus === INIT_STATUS.COMPLETE) {
         log.debug("dataManager already initialized, skipping");
+        setDmInitComplete(true);
         return;
       }
       dataManager.initImages(images, imageLayerScopes);
@@ -3668,6 +3675,7 @@ function VolumeView(props) {
       renderManager.setZarrUniforms(dataManager.zarrStore, dataManager.PT);
       renderManager.setChannelMapping(dataManager.channels.colorMappings);
       log.debug("rm.uniforms", renderManager.uniforms);
+      setDmInitComplete(true);
       invalidate();
     };
     initializeDataManager();
@@ -3677,7 +3685,7 @@ function VolumeView(props) {
   }, [dataManager, renderManager, images, imageLayerScopes]);
   useEffect(() => {
     const on3D = spatialRenderingMode === "3D";
-    if (on3D && dataManager && renderManager) {
+    if (on3D && dataManager && renderManager && dmInitComplete) {
       logWithColor("useEffect spatialRenderingMode");
       const propsForRenderManager = {
         images,
@@ -3711,7 +3719,7 @@ function VolumeView(props) {
         }
       }
     }
-  }, [dataManager, renderManager, images, imageLayerScopes, imageLayerCoordination, imageChannelScopesByLayer, imageChannelCoordination, spatialRenderingMode]);
+  }, [dataManager, renderManager, images, imageLayerScopes, imageLayerCoordination, imageChannelScopesByLayer, imageChannelCoordination, spatialRenderingMode, dmInitComplete]);
   const RENDER_PRIORITY = 1;
   useFrame((state, delta, xrFrame) => {
     if (!mrtRef.current || !dataManager || !renderManager) {
@@ -3762,6 +3770,8 @@ function VolumeView(props) {
     }, 300);
   });
   useEffect(() => {
+    if (!dmInitComplete)
+      return;
     logWithColor("useEffect firstImageLayerChannelCoordination");
     setIsInteracting(true);
     log.debug("something about channels changed");
@@ -3771,7 +3781,7 @@ function VolumeView(props) {
     interactionTimeoutRef.current = setTimeout(() => {
       setIsInteracting(false);
     }, 300);
-  }, [dataManager, firstImageLayerChannelCoordination, renderManager, setIsInteracting]);
+  }, [dataManager, firstImageLayerChannelCoordination, renderManager, setIsInteracting, dmInitComplete]);
   const stopLoading = useEventCallback(() => {
     if (dataManager) {
       dataManager.stopLoading();

package/dist/index.js

@@ -1,4 +1,4 @@
-import { a5, a3, a1, a4, a2, a0, a6 } from "./index-5W6nu-ix.js";
+import { a5, a3, a1, a4, a2, a0, a6 } from "./index-BYPSbKAg.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 export {
   a5 as PluginAsyncFunction,

package/dist/{jpeg-fpomMAyh.js → jpeg-Bo_KSlUd.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-5W6nu-ix.js";
+import { B as BaseDecoder } from "./index-BYPSbKAg.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-5t7sN-sd.js → lerc-CXalC3Iu.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { a as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, b as LercAddCompression } from "./index-5W6nu-ix.js";
+import { a as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, b as LercAddCompression } from "./index-BYPSbKAg.js";
 var LercDecode = { exports: {} };
 var hasRequiredLercDecode;
 function requireLercDecode() {

package/dist/{lzw-CC_Aw25a.js → lzw-COIaKN_E.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-5W6nu-ix.js";
+import { B as BaseDecoder } from "./index-BYPSbKAg.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-VBSAsHuN.js → packbits-Cg6ncl2O.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-5W6nu-ix.js";
+import { B as BaseDecoder } from "./index-BYPSbKAg.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-DK74vK-V.js → raw-4Cprab4h.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-5W6nu-ix.js";
+import { B as BaseDecoder } from "./index-BYPSbKAg.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-BdYU0dUW.js → webimage-DsCsw_bd.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-5W6nu-ix.js";
+import { B as BaseDecoder } from "./index-BYPSbKAg.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/dist-tsc/base-plugins.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AAWA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACtB,mBAAmB,EACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EAsDF,MAAM,mBAAmB,CAAC;AAqL3B,eAAO,MAAM,aAAa,kBA+BzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA6EzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;yBAqGpB,CAAC;gCAEa,CAAC;;;yBAA8E,CAAC;gCAEhG,CAAC;;;;;;;;;;;;;;;;iBAsBK,CAAC;;;;iBAG6D,CAAC;;;;;;;YAMzC,CAAC;;;YAC5B,CAAC;;;;;;;YAOK,CAAC;;;YAEO,CAAC;;;;;;;YAQsB,CAAC;;;YAAmE,CAAC;;;;;;;;;;;;;;YAUpF,CAAC;;;YAGb,CAAC;;;;;;;;YAalB,CAAC;;;;YAII,CAAC;;;;;;;;;;;;;;;;;;;;;;;;yBAmBD,CAAC;gCAAuD,CAAA;;;;;;;;iBAGhD,CAAC;;;;YACF,CAAC;;;;YACS,CAAC;;;;YACS,CAAC;;;;;;;YAEvB,CAAC;;;;YACC,CAAC;;;;;;;;;;;;;;;;;;;;yBAIqD,CAAC;gCACjC,CAAC;;;;;;;;iBAE1B,CAAC;;;;YAA8F,CAAC;;;;YAC7B,CAAC;;;;YACO,CAAC;;;;;;;YAE5C,CAAC;;;;YAC9B,CAAC;;;;;;;;;;;wBA8DowD,CAAC;;;wBAA6E,CAAC;;;;;;;;iBAAwR,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;iBAA+X,CAAC;wBAA8C,CAAC;0BAAgD,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;0BAAgD,CAAC;wBAA8C,CAAC;;;;;;;;;;yBAAkZ,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;yBAA8E,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;;;;;iBAAgR,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;;;qBAAygB,CAAC;;;;qBAA2J,CAAC;;;;;;qBAAsN,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;qBAA0K,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;;YAAoP,CAAC;;;YAAmE,CAAC;;;;;;;;YAAuR,CAAC;;;;YAAkG,CAAC;;;;;;;;;;;;;;;;;;;;;;wBAAmoB,CAAC;;;;iBAAyG,CAAC;wBAA8C,CAAC;;;;iBAAkG,CAAC;wBAA8C,CAAC;0BAAgD,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;YAAgG,CAAC;;;;YAAmG,CAAC;;;;;;;;;;;;wBAA6R,CAAC;;;;iBAAyG,CAAC;wBAA8C,CAAC;;;;iBAAkG,CAAC;wBAA8C,CAAC;0BAAgD,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;YAAgG,CAAC;;;;YAAmG,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAzjBn9S,CAAC;;;;;qBAG2B,CAAC;qBACpB,CAAC;;;;;;;;;qBAGsB,CAAC;6BACD,CAAC;;sBAClC,CAAC;;;;;qBAMQ,CAAC;qBAEL,CAAC;;;;;;;;;qBAWX,CAAC;6BAEM,CAAC;;;;;;;;;;;;;kBAuBQ,CAAC;mBAEjB,CAAA;gBAGY,CAAC;gBACK,CAAC;uBAElB,CAAC;iBACc,CAAC;oBAEb,CAAC;oBACS,CAAC;qBAEP,CAAC;;kBAEL,CAAC;mBACc,CAAC;gBAEb,CAAC;gBACM,CAAC;uBAIpB,CAAF;iBACqB,CAAC;oBACI,CAAC;oBAItB,CAAC;qBAEiB,CAAC;;;;;;gBAMV,CAAC;sBACD,CAAC;;;;;qBAOV,CAAC;qBAEJ,CAAD;;;;;;;;;qBAagB,CAAC;6BAGN,CAAC;;mBAEA,CAAC;kBACZ,CAAC;mBAED,CAAA;gBAEU,CAAC;gBAER,CAAC;uBAED,CAAC;iBAEF,CAAC;oBACa,CAAC;oBACgB,CAAC;qBAGlC,CAAA;;;;;;gBAMF,CAAC;sBAA0B,CAAC;;;;;qBAMF,CAAC;qBAA4C,CAAC;;;;;;;;;qBAIhC,CAAC;6BAAoD,CAAC;;mBAE5C,CAAC;kBAAsB,CAAC;mBAC3C,CAAC;gBACN,CAAC;gBAAsC,CAAC;uBAA6C,CAAC;iBAAuC,CAAC;oBAC9I,CAAC;oBACT,CAAC;qBACqB,CAAA;;;;;;;;;gBAIS,CAAC;sBAA2B,CAAA;;;;;qBAII,CAAC;qBAA4C,CAAC;;;;;;;;;qBAQ9C,CAAC;6BAClB,CAAC;;mBACf,CAAC;kBAC7B,CAAC;mBAAyC,CAAC;gBACF,CAAC;gBACxB,CAAC;uBACR,CAAC;iBAAuC,CAAC;oBACpB,CAAC;oBAC5B,CAAC;qBAA2C,CAAC;;;;;;;;;;;gBAInB,CAAC;sBAA0B,CAAC;;;;;qBAI/D,CAAD;qBAA4C,CAAC;;;;;;;;;qBAIhB,CAAC;6BACzB,CAAC;;mBACJ,CAAC;kBAAsB,CAAC;mBACtB,CAAC;gBACF,CAAC;gBAAsC,CAAC;uBAC/B,CAAC;iBAAuC,CAAC;oBACxC,CAAC;oBAA0C,CAAC;qBACjD,CAAC;;;;;;;;;;;;;;OAoGT,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;aApXtB,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cACQ,CAAC;eACW,CAAC;;;;;;;;;;;;;;;;;;;aAqBe,CAAC;cACjB,CAAC;eACzB,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;aArEW,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cACQ,CAAC;eACW,CAAC;;;;;;;;;;;;;;;;;;;aAqBe,CAAC;cACjB,CAAC;eACzB,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kzBA+iBA,CAAC;AAEF,eAAO,MAAM,kBAAkB,uBAK9B,CAAC"}

package/dist-tsc/base-plugins.js

@@ -311,6 +311,7 @@ export const baseCoordinationTypes = [
     new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, [255, 255, 255], z.array(z.number()).length(3).nullable()),
     new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_FILLED, true, z.boolean()),
     new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_STROKE_WIDTH, 1.0, z.number()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_POINT_STROKE_WIDTH, 0.0, z.number()),
     new PluginCoordinationType(CoordinationType.SPATIAL_LOD_FACTOR, 1.0, z.number()),
     // Reference: https://www.awaresystems.be/imaging/tiff/tifftags/photometricinterpretation.html
     new PluginCoordinationType(CoordinationType.PHOTOMETRIC_INTERPRETATION, null, z.enum(['BlackIsZero', 'RGB']).nullable()),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "4.0.0-test.0",
+  "version": "4.0.0-test.2",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,42 +17,43 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "4.0.0-test.0",
-    "@vitessce/error": "4.0.0-test.0",
-    "@vitessce/csv": "4.0.0-test.0",
-    "@vitessce/styles": "4.0.0-test.0",
-    "@vitessce/genomic-profiles": "4.0.0-test.0",
-    "@vitessce/description": "4.0.0-test.0",
-    "@vitessce/abstract": "4.0.0-test.0",
-    "@vitessce/heatmap": "4.0.0-test.0",
-    "@vitessce/feature-list": "4.0.0-test.0",
-    "@vitessce/glb": "4.0.0-test.0",
-    "@vitessce/json": "4.0.0-test.0",
-    "@vitessce/layer-controller-beta": "4.0.0-test.0",
-    "@vitessce/link-controller": "4.0.0-test.0",
-    "@vitessce/ome-tiff": "4.0.0-test.0",
-    "@vitessce/plugins": "4.0.0-test.0",
-    "@vitessce/layer-controller": "4.0.0-test.0",
-    "@vitessce/obs-sets-manager": "4.0.0-test.0",
-    "@vitessce/spatial-beta": "4.0.0-test.0",
-    "@vitessce/statistical-plots": "4.0.0-test.0",
-    "@vitessce/scatterplot-embedding": "4.0.0-test.0",
-    "@vitessce/schemas": "4.0.0-test.0",
-    "@vitessce/scatterplot-gating": "4.0.0-test.0",
-    "@vitessce/vit-s": "4.0.0-test.0",
-    "@vitessce/globals": "4.0.0-test.0",
-    "@vitessce/spatial": "4.0.0-test.0",
-    "@vitessce/status": "4.0.0-test.0",
-    "@vitessce/spatial-zarr": "4.0.0-test.0",
-    "@vitessce/zarr": "4.0.0-test.0",
-    "@vitessce/spatial-three": "4.0.0-test.0",
-    "@vitessce/spatial-accelerated": "4.0.0-test.0",
-    "@vitessce/neuroglancer": "4.0.0-test.0",
-    "@vitessce/biomarker-select": "4.0.0-test.0"
+    "@vitessce/constants-internal": "4.0.0-test.2",
+    "@vitessce/styles": "4.0.0-test.2",
+    "@vitessce/genomic-profiles": "4.0.0-test.2",
+    "@vitessce/error": "4.0.0-test.2",
+    "@vitessce/abstract": "4.0.0-test.2",
+    "@vitessce/heatmap": "4.0.0-test.2",
+    "@vitessce/description": "4.0.0-test.2",
+    "@vitessce/glb": "4.0.0-test.2",
+    "@vitessce/feature-list": "4.0.0-test.2",
+    "@vitessce/csv": "4.0.0-test.2",
+    "@vitessce/layer-controller": "4.0.0-test.2",
+    "@vitessce/json": "4.0.0-test.2",
+    "@vitessce/link-controller": "4.0.0-test.2",
+    "@vitessce/layer-controller-beta": "4.0.0-test.2",
+    "@vitessce/obs-sets-manager": "4.0.0-test.2",
+    "@vitessce/scatterplot-embedding": "4.0.0-test.2",
+    "@vitessce/spatial-beta": "4.0.0-test.2",
+    "@vitessce/statistical-plots": "4.0.0-test.2",
+    "@vitessce/status": "4.0.0-test.2",
+    "@vitessce/vit-s": "4.0.0-test.2",
+    "@vitessce/spatial": "4.0.0-test.2",
+    "@vitessce/globals": "4.0.0-test.2",
+    "@vitessce/spatial-accelerated": "4.0.0-test.2",
+    "@vitessce/ome-tiff": "4.0.0-test.2",
+    "@vitessce/schemas": "4.0.0-test.2",
+    "@vitessce/plugins": "4.0.0-test.2",
+    "@vitessce/biomarker-select": "4.0.0-test.2",
+    "@vitessce/zarr": "4.0.0-test.2",
+    "@vitessce/scatterplot-gating": "4.0.0-test.2",
+    "@vitessce/spatial-zarr": "4.0.0-test.2",
+    "@vitessce/spatial-three": "4.0.0-test.2",
+    "@vitessce/neuroglancer": "4.0.0-test.2"
   },
   "devDependencies": {
     "@types/react": "^19.0.0",
     "react": "19.1.0",
+    "react-dom": "19.1.0",
     "vitest": "^3.1.4"
   },
   "peerDependencies": {

package/src/base-plugins.ts

@@ -594,6 +594,7 @@ export const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, [255, 255, 255], z.array(z.number()).length(3).nullable()),
   new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_FILLED, true, z.boolean()),
   new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_STROKE_WIDTH, 1.0, z.number()),
+  new PluginCoordinationType(CoordinationType.SPATIAL_POINT_STROKE_WIDTH, 0.0, z.number()),
   new PluginCoordinationType(CoordinationType.SPATIAL_LOD_FACTOR, 1.0, z.number()),
   // Reference: https://www.awaresystems.be/imaging/tiff/tifftags/photometricinterpretation.html
   new PluginCoordinationType(CoordinationType.PHOTOMETRIC_INTERPRETATION, null, z.enum(['BlackIsZero', 'RGB']).nullable()),