@niivue/niivue 0.43.2 → 0.43.4

package/README.md

@@ -2,7 +2,13 @@
 
 NiiVue is web-based visualization tool for neuroimaging that can run on any operating system and any web device (phone, tablet, computer). This repository contains only the **core NiiVue package** that can be embedded into other projects. We have additional [repositories](https://github.com/niivue) that wrap NiiVue for use in jupyter notebooks, vscode, and electron applications. 
 
-[Click here to see NiiVue live demos](https://niivue.github.io/niivue/)
+# News
+
+The NiiVue iOS app is now available on iPhone and iPad.
+
+[![Apple App Store](./docs/appstore.svg)](https://apps.apple.com/gb/app/niivue/id6497066801)
+
+### [Click here to see NiiVue live demos](https://niivue.github.io/niivue/)
 
 What makes NiiVue unique is its ability to simultaneously display all the datatypes popular with neuroimaging: voxels, meshes, tractography streamlines, statistical maps and connectomes. Alternative voxel-based web tools include [ami](https://fnndsc.github.io/ami/), [BioImage Suite Web](https://bioimagesuiteweb.github.io/webapp/viewer.html), [BrainBrowser](https://brainbrowser.cbrain.mcgill.ca/volume-viewer), [nifti-drop](http://vsoch.github.io/nifti-drop), [OHIF DICOM Viewer](https://viewer.ohif.org/), [Papaya](https://www.fmrib.ox.ac.uk/ukbiobank/group_means/index.html), [VTK.js](https://kitware.github.io/paraview-glance/app/), and [slicedrop](https://slicedrop.com/).
 
@@ -26,18 +32,20 @@ The command `npm run demo` will minify the project and locally host all of the [
 # Projects and People using NiiVue
 
 - Analysis of Functional NeuroImages (AFNI) [Scientific and Statistical Computing Core](https://afni.nimh.nih.gov/) (National Institutes of Health)
-- [ChRIS Research Integration System (ChRIS)  from Boston Children's Hospital](https://chrisproject.org/) uses [NiiVue](https://app.chrisproject.org/niivue).
-- [Center for the Study of Aphasia Recovery](https://cstar.sc.edu/) (University of South Carolina)
+- [BOOSTLET.js](https://boostlet.org/) image processing plugins work with NiiVue.
+- [brainchop](https://github.com/neuroneural/brainchop) uses NiiVue for their [drag-and-drop segmentation, brain extraction and parcellation tool](https://neuroneural.github.io/brainchop/)
+- [BrainLife.io](https://brainlife.io/about/) integrates NiiVue into [ezbids](https://brainlife.io/ezbids/)
+- [CACTAS](https://github.com/mpsych/CACTAS) from [Daniel Haehn's team](https://danielhaehn.com/) is extending NiiVue drawing and segmentation capabilities
+- [ChRIS Research Integration System (ChRIS) from Boston Children's Hospital](https://chrisproject.org/) uses [NiiVue](https://app.chrisproject.org/niivue)
+- [Center for the Study of Aphasia Recovery (C-STAR)](https://cstar.sc.edu/) (University of South Carolina)
+- [Digital Brain Bank](https://elifesciences.org/articles/73153) for navigating MRI datasets
 - FMRIB's Software Library (FSL) [Wellcome Centre for Integrative Neuroimaging](https://www.win.ox.ac.uk/) (University of Oxford)
 - FreeSurfer [Laboratories for Computational Neuroimaging](https://lcn.martinos.org/) (Massachusetts General Hospital) uses NiiVue for [FreeBrowse](https://github.com/freesurfer/freebrowse)
 - [OpenNeuro.org](https://openneuro.org) uses NiiVue to visualize datasets
-- [BrainLife.io](https://brainlife.io/about/) integrates NiiVue into [ezbids](https://brainlife.io/ezbids/)
-- [nilearn](https://nilearn.github.io/stable/index.html) is extending [ipyniivue](https://github.com/niivue/ipyniivue)
 - [neurodesk](https://www.neurodesk.org/) uses NiiVue for their [QSMxT Quantitative Susceptibility Mapping toolbox](https://github.com/QSMxT/QSMxT-UI)
-- [niivue-vscode](https://github.com/niivue/niivue-vscode) is a VSCode extension for displaying images
 - [Neuroinformatics Research and Development Group](http://neuroinformatics.uw.edu/) embeds NiiVue in [tractoscope](https://github.com/nrdg/tractoscope)
-- [CACTAS](https://github.com/mpsych/CACTAS) from [Daniel Haehn's team](https://danielhaehn.com/) is extending NiiVue drawing and segmentation capabilities
-- [Digital Brain Bank](https://elifesciences.org/articles/73153) for navigating MRI datasets
+- [nilearn](https://nilearn.github.io/stable/index.html) is extending [ipyniivue](https://github.com/niivue/ipyniivue)
+- [niivue-vscode](https://github.com/niivue/niivue-vscode) is a VSCode extension for displaying images
 
 # Funding
 
@@ -48,7 +56,7 @@ The command `npm run demo` will minify the project and locally host all of the [
 
 NiiVue supports many popular brain imaging formats:
 
-- Voxel-based formats: [NIfTI](https://brainder.org/2012/09/23/the-nifti-file-format/), [NRRD](http://teem.sourceforge.net/nrrd/format.html), [MRtrix MIF](https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#mrtrix-image-formats), [AFNI HEAD/BRIK](https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html), [MGH/MGZ](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat), [ITK MHD](https://itk.org/Wiki/ITK/MetaIO/Documentation#Reading_a_Brick-of-Bytes_.28an_N-Dimensional_volume_in_a_single_file.29), [ECAT7](https://github.com/openneuropet/PET2BIDS/tree/28aae3fab22309047d36d867c624cd629c921ca6/ecat_validation/ecat_info).
+- Voxel-based formats: [NIfTI](https://brainder.org/2012/09/23/the-nifti-file-format/), [NRRD](http://teem.sourceforge.net/nrrd/format.html), [MRtrix MIF](https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#mrtrix-image-formats), [AFNI HEAD/BRIK](https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html), [MGH/MGZ](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat), [ITK MHD](https://itk.org/Wiki/ITK/MetaIO/Documentation#Reading_a_Brick-of-Bytes_.28an_N-Dimensional_volume_in_a_single_file.29), [ECAT7](https://github.com/openneuropet/PET2BIDS/tree/28aae3fab22309047d36d867c624cd629c921ca6/ecat_validation/ecat_info), [DSI-Studio SRC](https://dsi-studio.labsolver.org/doc/cli_data.html).
 - Mesh-based formats: [GIfTI](https://www.nitrc.org/projects/gifti/), [ASC](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm), [BYU/GEO/G](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm), [BrainSuite DFS](http://brainsuite.org/formats/dfs/), [ICO/TRI](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm), [PLY](<https://en.wikipedia.org/wiki/PLY_(file_format)>), [BrainNet NV](https://www.nitrc.org/projects/bnv/), [BrainVoyager SRF](https://support.brainvoyager.com/brainvoyager/automation-development/84-file-formats/344-users-guide-2-3-the-format-of-srf-files), [FreeSurfer](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm), [MZ3](https://github.com/neurolabusc/surf-ice/tree/master/mz3), [OFF](<https://en.wikipedia.org/wiki/OFF_(file_format)>), [Wavefront OBJ](https://brainder.org/tag/obj/), [STL](https://medium.com/3d-printing-stories/why-stl-format-is-bad-fea9ecf5e45), [Legacy VTK](https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf), [X3D](https://3dprint.nih.gov/).
 - Mesh overlay formats: [GIfTI](https://www.nitrc.org/projects/gifti/), [CIfTI-2](https://balsa.wustl.edu/about/fileTypes), [MZ3](https://github.com/neurolabusc/surf-ice/tree/master/mz3), [SMP](https://support.brainvoyager.com/brainvoyager/automation-development/84-file-formats/40-the-format-of-smp-files), STC, FreeSurfer (CURV/ANNOT)
 - Tractography formats: [TCK](https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#tracks-file-format-tck), [TRK](http://trackvis.org/docs/?subsect=fileformat), [TRX](https://github.com/frheault/tractography_file_format), [TSF](https://mrtrix.readthedocs.io/en/dev/getting_started/image_data.html#track-scalar-file-format-tsf), [TT](https://dsi-studio.labsolver.org/doc/cli_data.html), VTK, AFNI .niml.tract

package/build/index.d.ts

@@ -192,7 +192,9 @@ declare enum ImageType {
     V16 = 13,
     VMR = 14,
     HEAD = 15,
-    DCM_FOLDER = 16
+    DCM_FOLDER = 16,
+    SRC = 17,
+    FIB = 18
 }
 type ImageFromUrlOptions = {
     url: string;
@@ -227,7 +229,7 @@ type ImageFromFileOptions = {
     name?: string;
     colormap?: string;
     opacity?: number;
-    urlImgData?: File | null;
+    urlImgData?: File | null | FileSystemEntry;
     cal_min?: number;
     cal_max?: number;
     trustCalMinMax?: boolean;
@@ -271,7 +273,7 @@ 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?: null) => 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?: any) => ImageFromUrlOptions;
 
 type TypedVoxelArray = Float32Array | Uint8Array | Int16Array | Float64Array | Uint16Array;
 /**
@@ -323,6 +325,7 @@ declare class NVImage {
     imageType?: ImageType;
     img?: TypedVoxelArray;
     imaginary?: Float32Array;
+    v1?: Float32Array;
     fileObject?: File | File[];
     dims?: number[];
     onColormapChange: (img: NVImage) => void;
@@ -369,6 +372,8 @@ declare class NVImage {
      */
     constructor(dataBuffer?: ArrayBuffer | ArrayBuffer[] | null, name?: string, colormap?: string, opacity?: number, pairedImgData?: ArrayBuffer | null, 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, colormapLabel?: LUT | null);
     computeObliqueAngle(mtx44: mat4): number;
+    float32V1asRGBA(inImg: Float32Array): Uint8Array;
+    loadImgV1(isFlipX?: boolean, isFlipY?: boolean, isFlipZ?: boolean): boolean;
     calculateOblique(): void;
     THD_daxes_to_NIFTI(xyzDelta: number[], xyzOrigin: number[], orientSpecific: number[]): void;
     SetPixDimFromSForm(): void;
@@ -377,6 +382,8 @@ declare class NVImage {
     readV16(buffer: ArrayBuffer): ArrayBuffer;
     readVMR(buffer: ArrayBuffer): ArrayBuffer;
     readMGH(buffer: ArrayBuffer): ArrayBuffer;
+    readFIB(buffer: ArrayBuffer): [ArrayBuffer, Float32Array];
+    readSRC(buffer: ArrayBuffer): ArrayBuffer;
     readHEAD(dataBuffer: ArrayBuffer, pairedImgData: ArrayBuffer | null): ArrayBuffer;
     readMHA(buffer: ArrayBuffer, pairedImgData: ArrayBuffer | null): ArrayBuffer;
     readMIF(buffer: ArrayBuffer, pairedImgData: ArrayBuffer | null): ArrayBuffer;
@@ -588,6 +595,9 @@ type NVConfigOptions = {
     fontColor: Float32List;
     selectionBoxColor: number[];
     clipPlaneColor: number[];
+    clipThick: number;
+    clipVolumeLow: number[];
+    clipVolumeHigh: number[];
     rulerColor: number[];
     colorbarMargin: number;
     trustCalMinMax: boolean;
@@ -645,6 +655,9 @@ type SceneData = {
     clipPlaneDepthAziElev: number[];
     volScaleMultiplier: number;
     pan2Dxyzmm: vec4;
+    clipThick: number;
+    clipVolumeLow: number[];
+    clipVolumeHigh: number[];
 };
 declare const INITIAL_SCENE_DATA: {
     azimuth: number;
@@ -654,6 +667,9 @@ declare const INITIAL_SCENE_DATA: {
     clipPlaneDepthAziElev: number[];
     volScaleMultiplier: number;
     pan2Dxyzmm: vec4;
+    clipThick: number;
+    clipVolumeLow: number[];
+    clipVolumeHigh: number[];
 };
 type Scene = {
     onAzimuthElevationChange: (azimuth: number, elevation: number) => void;
@@ -681,6 +697,7 @@ type DocumentData = {
     meshesString?: string;
     sceneData?: SceneData;
     connectomes?: string[];
+    customData?: string;
 };
 type ExportDocumentData = {
     encodedImageBlobs: string[];
@@ -693,6 +710,7 @@ type ExportDocumentData = {
     meshesString: string;
     labels: NVLabel3D[];
     connectomes: string[];
+    customData: string;
 };
 /**
  * Creates and instance of NVDocument
@@ -752,6 +770,8 @@ declare class NVDocument {
      * Sets the 3D labels of the {@link Niivue} instance
      */
     set labels(labels: NVLabel3D[]);
+    get customData(): string | undefined;
+    set customData(data: string);
     /**
      * Checks if document has an image by id
      */
@@ -779,7 +799,7 @@ declare class NVDocument {
     /**
      * Downloads a JSON file with options, scene, images, meshes and drawing of {@link Niivue} instance
      */
-    download(fileName: string): void;
+    download(fileName: string, compress: boolean): Promise<void>;
     /**
      * Deserialize mesh data objects
      */
@@ -910,6 +930,22 @@ type DragReleaseParams = {
     tileIdx: number;
     axCorSag: SLICE_TYPE;
 };
+type NiiVueLocationValue = {
+    id: string;
+    mm: vec4;
+    name: string;
+    value: number;
+    vox: vec3;
+};
+type NiiVueLocation = {
+    axCorSag: number;
+    frac: vec3;
+    mm: vec4;
+    string: string;
+    values: NiiVueLocationValue[];
+    vox: vec3;
+    xy: [number, number];
+};
 
 type ValuesArray = Array<{
     id: string;
@@ -919,8 +955,7 @@ type ValuesArray = Array<{
     cal_min?: number;
     cal_max?: number;
 }>;
-type TypedNumberArray = Float64Array | Float32Array | Uint32Array | Uint16Array | Uint8Array | Int32Array | Int16Array | Int8Array;
-type AnyNumberArray = number[] | TypedNumberArray;
+type AnyNumberArray = number[] | Float64Array | Float32Array | Uint32Array | Uint16Array | Uint8Array | Int32Array | Int16Array | Int8Array;
 type DefaultMeshType = {
     positions: Float32Array;
     indices: Uint32Array;
@@ -1039,7 +1074,7 @@ declare class NVMeshFromUrlOptions {
     visible: boolean;
     layers: NVMeshLayer[];
     colorbarVisible: boolean;
-    constructor(url?: string, gl?: null, name?: string, opacity?: number, rgba255?: Uint8Array, visible?: boolean, layers?: never[], colorbarVisible?: boolean);
+    constructor(url?: string, gl?: any, name?: string, opacity?: number, rgba255?: Uint8Array, visible?: boolean, layers?: any[], colorbarVisible?: boolean);
 }
 type BaseLoadParams = {
     gl: WebGL2RenderingContext;
@@ -1089,11 +1124,13 @@ declare class NVMesh {
     rgba255: Uint8Array;
     fiberLength?: number;
     fiberLengths?: Uint32Array;
+    fiberDensity?: Float32Array;
     fiberDither: number;
     fiberColor: string;
     fiberDecimationStride: number;
     fiberSides: number;
     fiberRadius: number;
+    fiberOcclusion: number;
     f32PerVertex: number;
     fiberMask?: unknown[];
     colormap?: ColorMap | LegacyConnectome | string | null;
@@ -1133,9 +1170,10 @@ declare class NVMesh {
      * @param colorbarVisible - does this mesh display a colorbar
      * @param anatomicalStructurePrimary - region for mesh. Default is an empty string
      */
-    constructor(pts: Float32Array, tris: Uint32Array, name: string | undefined, rgba255: Uint8Array | undefined, opacity: number | undefined, visible: boolean | undefined, gl: WebGL2RenderingContext, connectome?: LegacyConnectome | string | null, dpg?: ValuesArray | null, dps?: ValuesArray | null, dpv?: ValuesArray | null, colorbarVisible?: boolean, anatomicalStructurePrimary?: string);
+    constructor(pts: Float32Array, tris: Uint32Array, name: string, rgba255: Uint8Array, opacity: number, visible: boolean, gl: WebGL2RenderingContext, connectome?: LegacyConnectome | string | null, dpg?: ValuesArray | null, dps?: ValuesArray | null, dpv?: ValuesArray | null, colorbarVisible?: boolean, anatomicalStructurePrimary?: string);
     initValuesArray(va: ValuesArray): ValuesArray;
     linesToCylinders(gl: WebGL2RenderingContext, posClrF32: Float32Array, indices: number[]): void;
+    createFiberDensityMap(): void;
     updateFibers(gl: WebGL2RenderingContext): void;
     indexNearestXYZmm(Xmm: number, Ymm: number, Zmm: number): number[];
     updateMesh(gl: WebGL2RenderingContext): void;
@@ -1398,18 +1436,23 @@ declare class NVController {
     onMeshPropertyChanged(meshIndex: number, key: string, val: unknown): void;
 }
 
+type TypedNumberArray = Float64Array | Float32Array | Uint32Array | Uint16Array | Uint8Array | Int32Array | Int16Array | Int8Array;
 /**
  * Namespace for utility functions
  * @ignore
  */
 declare class NVUtilities {
     static arrayBufferToBase64(arrayBuffer: ArrayBuffer): string;
+    static readMatV4(buffer: ArrayBuffer): Record<string, TypedNumberArray>;
     static uint8tob64(bytes: Uint8Array): string;
-    static download(content: string, fileName: string, contentType: string): void;
+    static download(content: string | ArrayBuffer, fileName: string, contentType: string): void;
     static readFileAsync(file: Blob): Promise<ArrayBuffer>;
     static blobToBase64(blob: Blob): Promise<string>;
-    static decompressBase64String(base64: string): string;
-    static compressToBase64String(string: string): string;
+    static decompressBase64String(base64: string): Promise<string>;
+    static compressToBase64String(string: string): Promise<string>;
+    static compressStringToArrayBuffer(input: string): Promise<ArrayBuffer>;
+    static isArrayBufferCompressed(buffer: ArrayBuffer): boolean;
+    static decompressArrayBuffer(buffer: ArrayBuffer): Promise<string>;
     static arraysAreEqual(a: unknown[], b: unknown[]): boolean;
     /**
      * Generate a pre-filled number array.
@@ -1444,7 +1487,7 @@ 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): NVMeshLayer | undefined;
+    static readLayer(name: string, 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;
@@ -1627,7 +1670,7 @@ declare class Niivue {
     blurShader: Shader | null;
     sobelShader: Shader | null;
     genericVAO: WebGLVertexArrayObject | null;
-    unusedVAO: null;
+    unusedVAO: any;
     crosshairs3D: NiivueObject3D | null;
     private DEFAULT_FONT_GLYPH_SHEET;
     private DEFAULT_FONT_METRICS;
@@ -1885,7 +1928,7 @@ declare class Niivue {
      * @example niivue.attachTo('gl')
      * @see {@link https://niivue.github.io/niivue/features/basic.multiplanar.html | live demo usage}
      */
-    attachTo(id: string, isAntiAlias?: null): Promise<this>;
+    attachTo(id: string, isAntiAlias?: any): Promise<this>;
     /**
      * attach the Niivue instance to a canvas element directly
      * @param canvas - the canvas element reference
@@ -1972,7 +2015,7 @@ declare class Niivue {
      */
     calculateMinMaxVoxIdx(array: number[]): number[];
     calculateNewRange({ volIdx }?: {
-        volIdx?: number | undefined;
+        volIdx?: number;
     }): void;
     generateMouseUpCallback(fracStart: vec3, fracEnd: vec3): void;
     mouseUpListener(): void;
@@ -2408,6 +2451,22 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/clipplanes.html | live demo usage}
      */
     setClipPlaneColor(color: number[]): void;
+    /**
+     * adjust thickness of the 3D clip plane
+     * @param thick - thickness of slab. Value 0..1.73 (cube opposite corner length is sqrt(3)).
+     * @example
+     * niivue.setClipPlaneThick(0.3) // thin slab
+     * @see {@link https://niivue.github.io/niivue/features/clipplanes.html | live demo usage}
+     */
+    setClipPlaneThick(thick: number): void;
+    /**
+     * set the clipping region for volume rendering
+     * @param color - the new color. expects an array of RGBA values. values can range from 0 to 1
+     * @example
+     * niivue.setClipPlaneColor([0.0, 0.0, 0.2], [1.0, 1.0, 0.7]) // remove inferior 20% and superior 30%
+     * @see {@link https://niivue.github.io/niivue/features/clipplanes.html | live demo usage}
+     */
+    setClipVolume(low: number[], high: number[]): void;
     /**
      * set proportion of volume rendering influenced by selected matcap.
      * @param gradientAmount - amount of matcap (0..1), default 0 (matte, surface normal does not influence color)
@@ -2447,7 +2506,7 @@ declare class Niivue {
    * const html = `<html><body><canvas id="gl1"></canvas><script type="module" async>
           ${javascript}</script></body></html>`;
    */
-    generateLoadDocumentJavaScript(canvasId: string, esm: string): string;
+    generateLoadDocumentJavaScript(canvasId: string, esm: string): Promise<string>;
     /**
      * generates HTML of current scene
      * @param canvasId - id of canvas NiiVue will be attached to
@@ -2458,14 +2517,14 @@ declare class Niivue {
      *       %%javascript%%</script></body></html>`;
      * nv1.generateHTML("page.html", esm);
      */
-    generateHTML(canvasId: string | undefined, esm: string): string;
+    generateHTML(canvasId: string, esm: string): Promise<string>;
     /**
      * save current scene as HTML
      * @param fileName - the name of the HTML file
      * @param canvasId - id of canvas NiiVue will be attached to
      * @param esm - bundled version of NiiVue
      */
-    saveHTML(fileName: string | undefined, canvasId: string | undefined, esm: string): void;
+    saveHTML(fileName: string, canvasId: string, esm: string): Promise<void>;
     /**
      * Converts NiiVue scene to JSON
      */
@@ -2473,11 +2532,12 @@ declare class Niivue {
     /**
      * save the entire scene (objects and settings) as a document
      * @param fileName - the name of the document storing the scene
+     * @param compress - whether the file should be compressed
      * @example
      * niivue.saveDocument("niivue.basic.nvd")
      * @see {@link https://niivue.github.io/niivue/features/document.3d.html | live demo usage}
      */
-    saveDocument(fileName?: string): Promise<void>;
+    saveDocument(fileName?: string, compress?: boolean): Promise<void>;
     /**
      * load an array of volume objects
      * @param volumeList - the array of objects to load. each object must have a resolvable "url" property at a minimum
@@ -2628,7 +2688,7 @@ declare class Niivue {
                 top: number;
             };
         })[];
-        kerning: never[];
+        kerning: any[];
     }): Promise<void>;
     loadDefaultMatCap(): Promise<WebGLTexture | null>;
     loadDefaultFont(): Promise<void>;
@@ -2688,7 +2748,7 @@ declare class Niivue {
      * @example niivue.getDescriptives(0);
      * @see {@link https://niivue.github.io/niivue/features/draw2.html | live demo usage}
      */
-    getDescriptives(layer?: number, masks?: never[], drawingIsMask?: boolean): Descriptive;
+    getDescriptives(layer?: number, masks?: any[], drawingIsMask?: boolean): Descriptive;
     refreshLayers(overlayItem: NVImage, layer: number): void;
     /**
      * query all available color maps that can be applied to volumes
@@ -2724,8 +2784,8 @@ declare class Niivue {
     largest_original_cluster_labels(bw: Uint32Array, cl: number, ls: Uint32Array): [number, Uint32Array];
     bwlabel(img: Uint32Array, dim: Uint32Array, conn?: number, binarize?: boolean, onlyLargestClusterPerClass?: boolean): [number, Uint32Array];
     createConnectedLabelImage(id: string, conn?: number, binarize?: boolean, onlyLargestClusterPerClass?: boolean): Promise<NVImage>;
-    scalecropUint8(img32: Float32Array, dst_min: number | undefined, dst_max: number | undefined, src_min: number, scale: number): Promise<Uint8Array>;
-    scalecropFloat32(img32: Float32Array, dst_min: number | undefined, dst_max: number | undefined, src_min: number, scale: number): Promise<Float32Array>;
+    scalecropUint8(img32: Float32Array, dst_min: number, dst_max: number, src_min: number, scale: number): Promise<Uint8Array>;
+    scalecropFloat32(img32: Float32Array, dst_min: number, dst_max: number, src_min: number, scale: number): Promise<Float32Array>;
     getScale(volume: NVImage, dst_min?: number, dst_max?: number, f_low?: number, f_high?: number): [number, number];
     conformVox2Vox(inDims: number[], inAffine: number[], outDim?: number, outMM?: number, toRAS?: boolean): [mat4, mat4, mat4];
     createNiftiArray(dims?: number[], pixDims?: number[], affine?: number[], datatypeCode?: NiiDataType, img?: Uint8Array): Promise<Uint8Array>;
@@ -2824,7 +2884,7 @@ declare class Niivue {
     getLegendPanelWidth(): number;
     getLegendPanelHeight(): number;
     reserveColorbarPanel(): number[];
-    drawColorbarCore(layer: number | undefined, leftTopWidthHeight: number[] | undefined, isNegativeColor: boolean | undefined, min: number | undefined, max: number | undefined, isAlphaThreshold: boolean): void;
+    drawColorbarCore(layer: number, leftTopWidthHeight: number[], isNegativeColor: boolean, min: number, max: number, isAlphaThreshold: boolean): void;
     drawColorbar(): void;
     textWidth(scale: number, str: string): number;
     textHeight(scale: number, str: string): number;
@@ -2845,7 +2905,7 @@ declare class Niivue {
      * @see {@link https://niivue.github.io/niivue/features/draw2.html | live demo usage}
      */
     setInterpolation(isNearest: boolean): void;
-    calculateMvpMatrix2D(leftTopWidthHeight: number[], mn: vec3, mx: vec3, clipTolerance: number | undefined, clipDepth: number | undefined, azimuth: number | undefined, elevation: number | undefined, isRadiolgical: boolean): MvpMatrix2D;
+    calculateMvpMatrix2D(leftTopWidthHeight: number[], mn: vec3, mx: vec3, clipTolerance: number, clipDepth: number, azimuth: number, elevation: number, isRadiolgical: boolean): MvpMatrix2D;
     swizzleVec3MM(v3: vec3, axCorSag: SLICE_TYPE): vec3;
     screenFieldOfViewVox(axCorSag?: number): vec3;
     screenFieldOfViewMM(axCorSag?: number, forceSliceMM?: boolean): vec3;
@@ -2854,7 +2914,7 @@ declare class Niivue {
     drawSliceOrientationText(leftTopWidthHeight: number[], axCorSag: SLICE_TYPE): void;
     xyMM2xyzMM(axCorSag: SLICE_TYPE, sliceFrac: number): number[];
     draw2D(leftTopWidthHeight: number[], axCorSag: SLICE_TYPE, customMM?: number): void;
-    calculateMvpMatrix(_unused: unknown, leftTopWidthHeight: number[] | undefined, azimuth: number, elevation: number): mat4[];
+    calculateMvpMatrix(_unused: unknown, leftTopWidthHeight: number[], azimuth: number, elevation: number): mat4[];
     calculateModelMatrix(azimuth: number, elevation: number): mat4;
     calculateRayDirection(azimuth: number, elevation: number): vec3;
     sceneExtentsMinMax(isSliceMM?: boolean): vec3[];
@@ -2876,7 +2936,7 @@ declare class Niivue {
     calculateScreenPoint(point: [number, number, number], mvpMatrix: mat4, leftTopWidthHeight: number[]): vec4;
     getLabelAtPoint(screenPoint: [number, number]): NVLabel3D | null;
     drawLabelLine(label: NVLabel3D, pos: vec2, mvpMatrix: mat4, leftTopWidthHeight: number[], secondPass?: boolean): void;
-    draw3DLabel(label: NVLabel3D, pos: vec2, mvpMatrix: mat4, leftTopWidthHeight: number[], bulletMargin: number | undefined, legendWidth: number, secondPass?: boolean): void;
+    draw3DLabel(label: NVLabel3D, pos: vec2, mvpMatrix: mat4, leftTopWidthHeight: number[], bulletMargin: number, legendWidth: number, secondPass?: boolean): void;
     draw3DLabels(mvpMatrix: mat4, leftTopWidthHeight: number[], secondPass?: boolean): void;
     draw3D(leftTopWidthHeight?: number[], mvpMatrix?: mat4 | null, modelMatrix?: mat4 | null, normalMatrix?: mat4 | null, azimuth?: number | null, elevation?: number): string | undefined;
     drawMesh3D(isDepthTest?: boolean, alpha?: number, m?: mat4, modelMtx?: mat4, normMtx?: mat4): void;
@@ -2917,4 +2977,4 @@ 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, NVMeshLayerDefaults, 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, type NiiVueLocation, type NiiVueLocationValue, Niivue, type Point, SLICE_TYPE, type Scene, type Volume, cmapper, ColorTables as colortables };