@niivue/niivue 0.43.0 → 0.43.2

package/build/index.d.ts

@@ -215,11 +215,12 @@ type ImageFromUrlOptions = {
     ignoreZeroVoxels?: boolean;
     imageType?: ImageType;
     frame4D?: number;
-    colormapLabel?: string[];
+    colormapLabel?: LUT | null;
     pairedImgData?: null;
     limitFrames4D?: number;
     isManifest?: boolean;
     urlImgData?: string;
+    buffer?: ArrayBuffer;
 };
 type ImageFromFileOptions = {
     file: File | File[];
@@ -248,6 +249,14 @@ type ImageFromBase64 = {
     trustCalMinMax?: boolean;
     percentileFrac?: number;
     ignoreZeroVoxels?: boolean;
+    useQFormNotSForm?: boolean;
+    colormapNegative?: string;
+    frame4D?: number;
+    imageType?: ImageType;
+    cal_minNeg?: number;
+    cal_maxNeg?: number;
+    colorbarVisible?: boolean;
+    colormapLabel?: LUT | null;
 };
 type ImageMetadata = {
     id: string;
@@ -262,7 +271,7 @@ type ImageMetadata = {
     dt: number;
     bpv: number;
 };
-declare const NVImageFromUrlOptions: (url: string, urlImageData?: string, name?: string, colormap?: string, opacity?: number, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, alphaThreshold?: boolean, colormapLabel?: string[]) => ImageFromUrlOptions;
+declare const NVImageFromUrlOptions: (url: string, urlImageData?: string, name?: string, colormap?: string, opacity?: number, cal_min?: number, cal_max?: number, trustCalMinMax?: boolean, percentileFrac?: number, ignoreZeroVoxels?: boolean, useQFormNotSForm?: boolean, colormapNegative?: string, frame4D?: number, imageType?: ImageType, cal_minNeg?: number, cal_maxNeg?: number, colorbarVisible?: boolean, alphaThreshold?: boolean, colormapLabel?: null) => ImageFromUrlOptions;
 
 type TypedVoxelArray = Float32Array | Uint8Array | Int16Array | Float64Array | Uint16Array;
 /**
@@ -397,7 +406,7 @@ declare class NVImage {
      * factory function to load and return a new NVImage instance from a given URL
      * @returns  NVImage instance
      */
-    static loadFromUrl({ url, urlImgData, headers, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, useQFormNotSForm, colormapNegative, frame4D, isManifest, limitFrames4D, imageType, colorbarVisible }?: Partial<Omit<ImageFromUrlOptions, 'url'>> & {
+    static loadFromUrl({ url, urlImgData, headers, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, useQFormNotSForm, colormapNegative, frame4D, isManifest, limitFrames4D, imageType, colorbarVisible, buffer }?: Partial<Omit<ImageFromUrlOptions, 'url'>> & {
         url?: string | Uint8Array | ArrayBuffer;
     }): Promise<NVImage>;
     static readFileAsync(file: File, bytesToLoad?: number): Promise<ArrayBuffer>;
@@ -440,7 +449,7 @@ declare class NVImage {
      * @example
      * myImage = NVImage.loadFromBase64('SomeBase64String')
      */
-    static loadFromBase64({ base64, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels }: ImageFromBase64): NVImage;
+    static loadFromBase64({ base64, name, colormap, opacity, cal_min, cal_max, trustCalMinMax, percentileFrac, ignoreZeroVoxels, useQFormNotSForm, colormapNegative, frame4D, imageType, cal_minNeg, cal_maxNeg, colorbarVisible, colormapLabel }: ImageFromBase64): NVImage;
     /**
      * make a clone of a NVImage instance and return a new NVImage
      * @returns NVImage instance
@@ -989,26 +998,38 @@ type NVMeshLayer = {
     headers?: Record<string, string>;
     opacity: number;
     colormap: string;
-    colormapNegative: string;
-    colormapInvert: boolean;
+    colormapNegative?: string;
+    colormapInvert?: boolean;
     colormapLabel?: ColorMap | LUT;
-    useNegativeCmap: boolean;
-    global_min: number;
-    global_max: number;
+    useNegativeCmap?: boolean;
+    global_min?: number;
+    global_max?: number;
     cal_min: number;
     cal_max: number;
     cal_minNeg: number;
     cal_maxNeg: number;
-    isAdditiveBlend: boolean;
+    isAdditiveBlend?: boolean;
     frame4D: number;
     nFrame4D: number;
-    values: number[];
+    values: AnyNumberArray;
     outlineBorder?: number;
     isTransparentBelowCalMin?: boolean;
-    alphaThreshold: boolean;
+    alphaThreshold?: boolean;
     base64?: string;
     colorbarVisible?: boolean;
 };
+declare const NVMeshLayerDefaults: {
+    colormap: string;
+    opacity: number;
+    nFrame4D: number;
+    frame4D: number;
+    outlineBorder: number;
+    cal_min: number;
+    cal_max: number;
+    cal_minNeg: number;
+    cal_maxNeg: number;
+    values: number[];
+};
 declare class NVMeshFromUrlOptions {
     url: string;
     gl: WebGL2RenderingContext | null;
@@ -1031,6 +1052,7 @@ type BaseLoadParams = {
 type LoadFromUrlParams = Partial<BaseLoadParams> & {
     url: string;
     headers?: Record<string, string>;
+    buffer?: ArrayBuffer;
 };
 type LoadFromFileParams = BaseLoadParams & {
     file: Blob;
@@ -1126,7 +1148,7 @@ declare class NVMesh {
     /**
      * factory function to load and return a new NVMesh instance from a given URL
      */
-    static loadFromUrl({ url, headers, gl, name, opacity, rgba255, visible, layers }?: Partial<LoadFromUrlParams>): Promise<NVMesh>;
+    static loadFromUrl({ url, headers, gl, name, opacity, rgba255, visible, layers, buffer }?: Partial<LoadFromUrlParams>): Promise<NVMesh>;
     static readFileAsync(file: Blob): Promise<ArrayBuffer>;
     /**
      * factory function to load and return a new NVMesh instance from a file in the browser
@@ -1422,7 +1444,7 @@ declare class NVMeshLoaders {
     static readTCK(buffer: ArrayBuffer): TCK;
     static readTRK(buffer: ArrayBuffer): TRK;
     static readTxtVTK(buffer: ArrayBuffer): VTK;
-    static readLayer(name: string | undefined, buffer: ArrayBuffer, nvmesh: NVMesh, opacity?: number, colormap?: string, colormapNegative?: string, useNegativeCmap?: boolean, cal_min?: number | null, cal_max?: number | null, outlineBorder?: number): void;
+    static readLayer(name: string | undefined, buffer: ArrayBuffer, nvmesh: NVMesh, opacity?: number, colormap?: string, colormapNegative?: string, useNegativeCmap?: boolean, cal_min?: number | null, cal_max?: number | null, outlineBorder?: number): NVMeshLayer | undefined;
     static readSMP(buffer: ArrayBuffer, n_vert: number): Float32Array;
     static readSTC(buffer: ArrayBuffer, n_vert: number): Float32Array;
     static readCURV(buffer: ArrayBuffer, n_vert: number): Float32Array;
@@ -1991,6 +2013,18 @@ declare class Niivue {
      * @param url - filename
      */
     isMeshExt(url: string): boolean;
+    /**
+     * Load an image or mesh from an array buffer
+     * @param buffer - ArrayBuffer with the entire contents of a mesh or volume
+     * @param name - string of filename, extension used to infer type (NIfTI, MGH, MZ3, etc)
+     * @see {@link http://192.168.0.150:8080/features/draganddrop.html | live demo usage}
+     */
+    loadFromArrayBuffer(buffer: ArrayBuffer, name: string): Promise<void>;
+    /**
+     * Load a mesh or image from a file object
+     * @param file - File object
+     */
+    loadFromFile(file: File): Promise<void>;
     dropListener(e: DragEvent): void;
     /**
      * insert a gap between slices of a mutliplanar view.
@@ -2703,9 +2737,10 @@ declare class Niivue {
      * @param toRAS - reslice to row, column slices to right-anterior-superior not left-inferior-anterior (default false).
      * @param isLinear - reslice with linear rather than nearest-neighbor interpolation (default true).
      * @param asFloat32 - use Float32 datatype rather than Uint8 (default false).
+     * @param isRobustMinMax - clamp intensity with robust min max (~2%..98%) instead of FreeSurfer (0%..99.99%) (default false).
      * @see {@link https://niivue.github.io/niivue/features/torso.html | live demo usage}
      */
-    conform(volume: NVImage, toRAS?: boolean, isLinear?: boolean, asFloat32?: boolean): Promise<NVImage>;
+    conform(volume: NVImage, toRAS?: boolean, isLinear?: boolean, asFloat32?: boolean, isRobustMinMax?: boolean): Promise<NVImage>;
     /**
      * darken crevices and brighten corners when 3D rendering drawings.
      * @param amount - amount of ambient occlusion (default 0.4)
@@ -2882,4 +2917,4 @@ declare class Niivue {
     set gl(gl: WebGL2RenderingContext | null);
 }
 
-export { type Connectome, type ConnectomeOptions, DEFAULT_OPTIONS, DRAG_MODE, type DocumentData, type DragReleaseParams, type ExportDocumentData, INITIAL_SCENE_DATA, LabelLineTerminator, LabelTextAlignment, type LegacyConnectome, type LegacyNodes, MULTIPLANAR_TYPE, type NVConfigOptions, type NVConnectomeEdge, type NVConnectomeNode, NVController, NVDocument, NVImage, NVImageFromUrlOptions, NVLabel3D, NVLabel3DStyle, NVMesh, NVMeshFromUrlOptions, NVMeshLoaders, NVUtilities, type NiftiHeader, Niivue, type Point, SLICE_TYPE, type Scene, type Volume, cmapper, ColorTables as colortables };
+export { type Connectome, type ConnectomeOptions, DEFAULT_OPTIONS, DRAG_MODE, type DocumentData, type DragReleaseParams, type ExportDocumentData, INITIAL_SCENE_DATA, LabelLineTerminator, LabelTextAlignment, type LegacyConnectome, type LegacyNodes, MULTIPLANAR_TYPE, type NVConfigOptions, type NVConnectomeEdge, type NVConnectomeNode, NVController, NVDocument, NVImage, NVImageFromUrlOptions, NVLabel3D, NVLabel3DStyle, NVMesh, NVMeshFromUrlOptions, NVMeshLayerDefaults, NVMeshLoaders, NVUtilities, type NiftiHeader, Niivue, type Point, SLICE_TYPE, type Scene, type Volume, cmapper, ColorTables as colortables };

package/build/index.js

@@ -13,7 +13,7 @@ var __publicField = (obj, key, value) => {
 import { mat4 as mat46, vec2, vec3 as vec311, vec4 as vec48 } from "gl-matrix";
 
 // package.json
-var version = "0.43.0";
+var version = "0.43.2";
 
 // src/logger.ts
 var _Log = class _Log {
@@ -12269,6 +12269,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
   // read mesh overlay to influence vertex colors
   static readLayer(name = "", buffer, nvmesh, opacity = 0.5, colormap = "warm", colormapNegative = "winter", useNegativeCmap = false, cal_min = null, cal_max = null, outlineBorder = 0) {
     const layer = {
+      ...NVMeshLayerDefaults,
       colormapInvert: false,
       alphaThreshold: false,
       isTransparentBelowCalMin: true,
@@ -12311,9 +12312,10 @@ var NVMeshLoaders = class _NVMeshLoaders {
         cal_min: mn2,
         cal_max: mx2
       });
-      return;
+      return layer;
     }
     if (n_vert < 3) {
+      log.error("n_vert < 3 in layer");
       return;
     }
     if (ext === "MZ3") {
@@ -12357,9 +12359,10 @@ var NVMeshLoaders = class _NVMeshLoaders {
       layer.values = _NVMeshLoaders.readSTC(buffer, n_vert);
     } else {
       log.warn("Unknown layer overlay format " + name);
-      return;
+      return layer;
     }
     if (!layer.values) {
+      log.error("no values in layer");
       return;
     }
     layer.nFrame4D = layer.values.length / n_vert;
@@ -12373,11 +12376,11 @@ var NVMeshLoaders = class _NVMeshLoaders {
     }
     layer.global_min = mn;
     layer.global_max = mx;
-    layer.cal_min = cal_min;
+    layer.cal_min = cal_min || 0;
     if (!cal_min) {
       layer.cal_min = mn;
     }
-    layer.cal_max = cal_max;
+    layer.cal_max = cal_max || 0;
     if (!cal_max) {
       layer.cal_max = mx;
     }
@@ -12387,7 +12390,7 @@ var NVMeshLoaders = class _NVMeshLoaders {
     layer.colormap = colormap;
     layer.colormapNegative = colormapNegative;
     layer.useNegativeCmap = useNegativeCmap;
-    nvmesh.layers.push(layer);
+    return layer;
   }
   // readLayer()
   // read brainvoyager smp format file
@@ -14802,6 +14805,18 @@ var NVMeshLoaders = class _NVMeshLoaders {
 };
 
 // src/nvmesh.ts
+var NVMeshLayerDefaults = {
+  colormap: "gray",
+  opacity: 0,
+  nFrame4D: 0,
+  frame4D: 0,
+  outlineBorder: 0,
+  cal_min: 0,
+  cal_max: 0,
+  cal_minNeg: 0,
+  cal_maxNeg: 0,
+  values: new Array()
+};
 var NVMeshFromUrlOptions = class {
   constructor(url = "", gl = null, name = "", opacity = 1, rgba255 = new Uint8Array([255, 255, 255, 255]), visible = true, layers = [], colorbarVisible = true) {
     __publicField(this, "url");
@@ -14822,7 +14837,7 @@ var NVMeshFromUrlOptions = class {
     this.colorbarVisible = colorbarVisible;
   }
 };
-var NVMesh = class _NVMesh {
+var NVMesh2 = class _NVMesh {
   /**
    * @param pts - a 3xN array of vertex positions (X,Y,Z coordinates).
    * @param tris - a 3xN array of triangle indices (I,J,K; indexed from zero). Each triangle generated from three vertices.
@@ -14938,6 +14953,7 @@ var NVMesh = class _NVMesh {
     this.pts = pts;
     this.layers = [];
     this.type = "mesh" /* MESH */;
+    this.tris = tris;
     if (rgba255[3] < 1) {
       this.rgba255 = rgba255;
       this.fiberLength = 2;
@@ -14979,7 +14995,6 @@ var NVMesh = class _NVMesh {
       }
     }
     this.rgba255 = rgba255;
-    this.tris = tris;
     this.updateMesh(gl);
   }
   initValuesArray(va) {
@@ -15992,7 +16007,7 @@ var NVMesh = class _NVMesh {
     if ("cal_max" in layer) {
       cal_max = layer.cal_max;
     }
-    NVMeshLoaders.readLayer(
+    const newLayer = NVMeshLoaders.readLayer(
       layerName,
       buffer,
       nvmesh,
@@ -16003,6 +16018,9 @@ var NVMesh = class _NVMesh {
       cal_min,
       cal_max
     );
+    if (newLayer) {
+      nvmesh.layers.push(newLayer);
+    }
   }
   /**
    * factory function to load and return a new NVMesh instance from a given URL
@@ -16015,7 +16033,8 @@ var NVMesh = class _NVMesh {
     opacity = 1,
     rgba255 = [255, 255, 255, 255],
     visible = true,
-    layers = []
+    layers = [],
+    buffer = new ArrayBuffer(0)
   } = {}) {
     let urlParts = url.split("/");
     if (name === "") {
@@ -16035,17 +16054,22 @@ var NVMesh = class _NVMesh {
     if (!gl) {
       throw Error("gl context is null");
     }
-    const response = await fetch(url, { headers });
-    if (!response.ok) {
-      throw Error(response.statusText);
+    let buff;
+    if (buffer.byteLength > 0) {
+      buff = buffer;
+    } else {
+      const response = await fetch(url, { headers });
+      if (!response.ok) {
+        throw Error(response.statusText);
+      }
+      buff = await response.arrayBuffer();
     }
-    const buffer = await response.arrayBuffer();
-    const nvmesh = await this.readMesh(buffer, name, gl, opacity, new Uint8Array(rgba255), visible);
+    const nvmesh = await this.readMesh(buff, name, gl, opacity, new Uint8Array(rgba255), visible);
     if (!layers || layers.length < 1) {
       return nvmesh;
     }
     for (let i = 0; i < layers.length; i++) {
-      await this.loadLayer(layers[i], nvmesh);
+      await _NVMesh.loadLayer(layers[i], nvmesh);
     }
     nvmesh.updateMesh(gl);
     return nvmesh;
@@ -17952,7 +17976,7 @@ var NVIMAGE_TYPE = Object.freeze({
     return imageType;
   }
 });
-var NVImageFromUrlOptions = (url, urlImageData = "", name = "", colormap = "gray", opacity = 1, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, alphaThreshold = false, colormapLabel = []) => {
+var NVImageFromUrlOptions = (url, urlImageData = "", name = "", colormap = "gray", opacity = 1, cal_min = NaN, cal_max = NaN, trustCalMinMax = true, percentileFrac = 0.02, ignoreZeroVoxels = false, useQFormNotSForm = false, colormapNegative = "", frame4D = 0, imageType = NVIMAGE_TYPE.UNKNOWN, cal_minNeg = NaN, cal_maxNeg = NaN, colorbarVisible = true, alphaThreshold = false, colormapLabel = null) => {
   return {
     url,
     urlImageData,
@@ -20600,7 +20624,8 @@ var NVImage = class _NVImage {
     isManifest = false,
     limitFrames4D = NaN,
     imageType = NVIMAGE_TYPE.UNKNOWN,
-    colorbarVisible = true
+    colorbarVisible = true,
+    buffer = new ArrayBuffer(0)
   } = {}) {
     if (url === "") {
       throw Error("url must not be empty");
@@ -20610,12 +20635,19 @@ var NVImage = class _NVImage {
     if (url instanceof Uint8Array) {
       url = url.buffer;
     }
+    if (buffer.byteLength > 0) {
+      url = buffer;
+    }
     if (url instanceof ArrayBuffer) {
       dataBuffer = url;
-      url = "array.nii";
-      const bytes = new Uint8Array(dataBuffer);
-      if (bytes[0] === 31 && bytes[1] === 139) {
-        url = "array.nii.gz";
+      if (name !== "") {
+        url = name;
+      } else {
+        url = "array.nii";
+        const bytes = new Uint8Array(dataBuffer);
+        if (bytes[0] === 31 && bytes[1] === 139) {
+          url = "array.nii.gz";
+        }
       }
     }
     if (!isNaN(limitFrames4D)) {
@@ -21067,7 +21099,15 @@ var NVImage = class _NVImage {
     cal_max = NaN,
     trustCalMinMax = true,
     percentileFrac = 0.02,
-    ignoreZeroVoxels = false
+    ignoreZeroVoxels = false,
+    useQFormNotSForm = false,
+    colormapNegative = "",
+    frame4D = 0,
+    imageType = NVIMAGE_TYPE.UNKNOWN,
+    cal_minNeg = NaN,
+    cal_maxNeg = NaN,
+    colorbarVisible = true,
+    colormapLabel = null
   }) {
     function base64ToArrayBuffer(base642) {
       const binary_string = window.atob(base642);
@@ -21092,7 +21132,15 @@ var NVImage = class _NVImage {
         cal_max,
         trustCalMinMax,
         percentileFrac,
-        ignoreZeroVoxels
+        ignoreZeroVoxels,
+        useQFormNotSForm,
+        colormapNegative,
+        frame4D,
+        imageType,
+        cal_minNeg,
+        cal_maxNeg,
+        colorbarVisible,
+        colormapLabel
       );
     } catch (err) {
       log.debug(err);
@@ -21845,7 +21893,7 @@ var NVDocument = class _NVDocument {
           ignoreZeroVoxels: false,
           useQFormNotSForm: false,
           colormapNegative: "",
-          colormapLabel: [],
+          colormapLabel: null,
           imageType: NVIMAGE_TYPE.NII,
           frame4D: 0,
           limitFrames4D: NaN,
@@ -21890,7 +21938,7 @@ var NVDocument = class _NVDocument {
             ignoreZeroVoxels: false,
             useQFormNotSForm: false,
             colormapNegative: "",
-            colormapLabel: [],
+            colormapLabel: null,
             imageType: NVIMAGE_TYPE.NII,
             frame4D: 0,
             limitFrames4D: NaN,
@@ -21908,6 +21956,7 @@ var NVDocument = class _NVDocument {
           }
         }
         imageOptions2.colormap = volume.colormap;
+        imageOptions2.colormapLabel = volume.colormapLabel;
         imageOptions2.opacity = volume.opacity;
         imageOptions2.cal_max = volume.cal_max || NaN;
         imageOptions2.cal_min = volume.cal_min || NaN;
@@ -22019,6 +22068,10 @@ var NVDocument = class _NVDocument {
     const utf8decoder = new TextDecoder();
     const dataString = utf8decoder.decode(arrayBuffer);
     document2.data = JSON.parse(dataString);
+    if (document2.data.opts.meshThicknessOn2D === "infinity") {
+      document2.data.opts.meshThicknessOn2D = Infinity;
+    }
+    document2.scene.sceneData = { ...INITIAL_SCENE_DATA, ...document2.data.sceneData };
     _NVDocument.deserializeMeshDataObjects(document2);
     return document2;
   }
@@ -22031,7 +22084,7 @@ var NVDocument = class _NVDocument {
     if (document2.data.opts.meshThicknessOn2D === "infinity") {
       document2.data.opts.meshThicknessOn2D = Infinity;
     }
-    document2.scene.sceneData = data.sceneData;
+    document2.scene.sceneData = { ...INITIAL_SCENE_DATA, ...data.sceneData };
     _NVDocument.deserializeMeshDataObjects(document2);
     return document2;
   }
@@ -22113,7 +22166,7 @@ var defaultOptions = {
   edgeScale: 1,
   legendLineThickness: 0
 };
-var NVConnectome = class _NVConnectome extends NVMesh {
+var NVConnectome = class _NVConnectome extends NVMesh2 {
   constructor(gl, connectome) {
     super(new Float32Array([]), new Uint32Array([]), connectome.name, new Uint8Array([]), 1, true, gl, connectome);
     __publicField(this, "gl");
@@ -22935,7 +22988,7 @@ var NVController = class {
       case 9 /* MESH_FROM_URL_ADDED */:
         if (!this.niivue.getMediaByUrl(msg.meshOptions.url)) {
           msg.meshOptions.gl = this.niivue.gl;
-          NVMesh.loadFromUrl(msg.meshOptions).then((mesh) => {
+          NVMesh2.loadFromUrl(msg.meshOptions).then((mesh) => {
             this.addMesh(mesh, msg.meshOptions.url);
           }).catch((e) => {
             if (e) {
@@ -24590,6 +24643,42 @@ var Niivue = class _Niivue {
     log.debug(ext);
     return MESH_EXTENSIONS.includes(ext);
   }
+  /**
+   * Load an image or mesh from an array buffer
+   * @param buffer - ArrayBuffer with the entire contents of a mesh or volume
+   * @param name - string of filename, extension used to infer type (NIfTI, MGH, MZ3, etc)
+   * @see {@link http://192.168.0.150:8080/features/draganddrop.html | live demo usage}
+   */
+  async loadFromArrayBuffer(buffer, name) {
+    const ext = this.getFileExt(name);
+    if (MESH_EXTENSIONS.includes(ext)) {
+      await this.addMeshFromUrl({ url: name, buffer });
+      return;
+    }
+    const imageOptions = NVImageFromUrlOptions(name);
+    imageOptions.buffer = buffer;
+    imageOptions.name = name;
+    await this.addVolumeFromUrl(imageOptions);
+  }
+  /**
+   * Load a mesh or image from a file object
+   * @param file - File object
+   */
+  async loadFromFile(file) {
+    const ext = this.getFileExt(file.name);
+    if (MESH_EXTENSIONS.includes(ext)) {
+      await NVMesh2.loadFromFile({ file, gl: this.gl, name: file.name }).then((mesh) => {
+        this.addMesh(mesh);
+      });
+      return;
+    }
+    await NVImage.loadFromFile({
+      file,
+      name: file.name
+    }).then((volume) => {
+      this.addVolume(volume);
+    });
+  }
   // not included in public docs
   dropListener(e) {
     e.stopPropagation();
@@ -24668,7 +24757,7 @@ var Niivue = class _Niivue {
             if (MESH_EXTENSIONS.includes(ext)) {
               ;
               entry.file((file) => {
-                NVMesh.loadFromFile({
+                NVMesh2.loadFromFile({
                   file,
                   gl: this.gl,
                   name: file.name
@@ -25963,6 +26052,7 @@ var Niivue = class _Niivue {
     const opts = { ...DEFAULT_OPTIONS, ...document2.opts };
     this.scene.pan2Dxyzmm = document2.scene.pan2Dxyzmm ? document2.scene.pan2Dxyzmm : [0, 0, 0, 1];
     this.document.opts = opts;
+    this.setClipPlane(this.scene.clipPlaneDepthAziElev);
     log.debug("load document", document2);
     this.mediaUrlMap.clear();
     this.createEmptyDrawing();
@@ -25977,7 +26067,6 @@ var Niivue = class _Niivue {
         const image = NVImage.loadFromBase64({ base64: base642, ...imageOptions });
         if (image) {
           this.addVolume(image);
-          document2.addImageOptions(image, imageOptions);
         }
       }
     }
@@ -25995,7 +26084,7 @@ var Niivue = class _Niivue {
     for (const meshDataObject of document2.meshDataObjects ?? []) {
       const meshInit = { gl: this.gl, ...meshDataObject };
       log.debug(meshInit);
-      const meshToAdd = new NVMesh(
+      const meshToAdd = new NVMesh2(
         meshInit.pts,
         meshInit.tris,
         meshInit.name,
@@ -26017,7 +26106,9 @@ var Niivue = class _Niivue {
     if (document2.data.connectomes) {
       for (const connectomeString of document2.data.connectomes) {
         const connectome = JSON.parse(connectomeString);
-        this.loadConnectome(connectome);
+        const meshToAdd = this.loadConnectomeAsMesh(connectome);
+        meshToAdd.updateMesh(this.gl);
+        this.addMesh(meshToAdd);
       }
     }
     this.updateGLVolume();
@@ -26164,7 +26255,6 @@ var Niivue = class _Niivue {
     this.drawScene();
     this.document.previewImageDataURL = this.canvas.toDataURL();
     const json = this.document.json();
-    json.sceneData = { ...this.scene };
     return json;
   }
   /**
@@ -26175,12 +26265,12 @@ var Niivue = class _Niivue {
    * @see {@link https://niivue.github.io/niivue/features/document.3d.html | live demo usage}
    */
   async saveDocument(fileName = "untitled.nvd") {
-    this.document.opts = this.opts;
-    this.document.scene = this.scene;
     this.document.title = fileName;
     log.debug("saveDocument", this.volumes[0]);
     this.drawScene();
     this.document.previewImageDataURL = this.canvas.toDataURL();
+    this.document.volumes = this.volumes;
+    this.document.meshes = this.meshes;
     this.document.download(fileName);
   }
   /**
@@ -26241,7 +26331,7 @@ var Niivue = class _Niivue {
       this.addMesh(mesh2);
       return mesh2;
     }
-    const mesh = await NVMesh.loadFromUrl({ ...meshOptions, gl: this.gl });
+    const mesh = await NVMesh2.loadFromUrl({ ...meshOptions, gl: this.gl });
     this.mediaUrlMap.set(mesh, meshOptions.url);
     this.onMeshAddedFromUrl(meshOptions, mesh);
     this.addMesh(mesh);
@@ -26271,6 +26361,7 @@ var Niivue = class _Niivue {
     for (let i = 0; i < meshList.length; i++) {
       await this.addMeshFromUrl(meshList[i]);
     }
+    this.updateGLVolume();
     this.drawScene();
     return this;
   }
@@ -28497,6 +28588,16 @@ var Niivue = class _Niivue {
     if (volume.hdr.datatypeCode === 2 /* DT_UINT8 */) {
       return [src_min, 1];
     }
+    if (!isFinite(f_low) || !isFinite(f_high)) {
+      if (isFinite(volume.cal_min) && isFinite(volume.cal_max) && volume.cal_max > volume.cal_min) {
+        src_min = volume.cal_min;
+        src_max = volume.cal_max;
+        const scale2 = (dst_max - dst_min) / (src_max - src_min);
+        log.info(" Robust Rescale:  min: " + src_min + "  max: " + src_max + " scale: " + scale2);
+        console.log("Robust Rescale:  min: " + src_min + "  max: " + src_max + " scale: " + scale2);
+        return [src_min, scale2];
+      }
+    }
     const img = volume.img;
     const voxnum = volume.hdr.dims[1] * volume.hdr.dims[2] * volume.hdr.dims[3];
     if (volume.hdr.scl_slope !== 1 || volume.hdr.scl_inter !== 0) {
@@ -28637,9 +28738,10 @@ var Niivue = class _Niivue {
    * @param toRAS - reslice to row, column slices to right-anterior-superior not left-inferior-anterior (default false).
    * @param isLinear - reslice with linear rather than nearest-neighbor interpolation (default true).
    * @param asFloat32 - use Float32 datatype rather than Uint8 (default false).
+   * @param isRobustMinMax - clamp intensity with robust min max (~2%..98%) instead of FreeSurfer (0%..99.99%) (default false).
    * @see {@link https://niivue.github.io/niivue/features/torso.html | live demo usage}
    */
-  async conform(volume, toRAS = false, isLinear = true, asFloat32 = false) {
+  async conform(volume, toRAS = false, isLinear = true, asFloat32 = false, isRobustMinMax = false) {
     const outDim = 256;
     const outMM = 1;
     const obj = this.conformVox2Vox(volume.hdr.dims, volume.hdr.affine.flat(), outDim, outMM, toRAS);
@@ -28732,9 +28834,13 @@ var Niivue = class _Niivue {
     }
     const src_min = 0;
     const scale = 0;
+    let f_low = 0;
+    if (isRobustMinMax) {
+      f_low = NaN;
+    }
     let bytes = new Uint8Array();
     if (asFloat32) {
-      const gs = await this.getScale(volume, 0, 1);
+      const gs = await this.getScale(volume, 0, 1, f_low);
       const out_img32 = await this.scalecropFloat32(out_img, 0, 1, gs[0], gs[1]);
       bytes = await this.createNiftiArray(
         [outDim, outDim, outDim],
@@ -28744,7 +28850,7 @@ var Niivue = class _Niivue {
         new Uint8Array(out_img32.buffer)
       );
     } else {
-      const gs = await this.getScale(volume, 0, 255);
+      const gs = await this.getScale(volume, 0, 255, f_low);
       const out_img8 = await this.scalecropUint8(out_img, 0, 255, gs[0], gs[1]);
       bytes = await this.createNiftiArray(
         [outDim, outDim, outDim],
@@ -31945,8 +32051,9 @@ export {
   NVImageFromUrlOptions,
   NVLabel3D,
   NVLabel3DStyle,
-  NVMesh,
+  NVMesh2 as NVMesh,
   NVMeshFromUrlOptions,
+  NVMeshLayerDefaults,
   NVMeshLoaders,
   NVUtilities,
   Niivue,