@cornerstonejs/nifti-volume-loader 1.14.1

package/LICENSE

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+MIT License
+
+Copyright (c) 2019 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @cornerstonejs/nifti-volume-loader
+
+Nifti volume loader for the cornerstone3D framework.

package/dist/esm/NiftiImageVolume.d.ts

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+import { ImageVolume } from '@cornerstonejs/core';
+import type { Types } from '@cornerstonejs/core';
+declare type LoadStatus = {
+    loaded: boolean;
+    loading: boolean;
+    callbacks: Array<(...args: unknown[]) => void>;
+};
+declare type NiftiImageProperties = {
+    loadStatus: LoadStatus;
+    controller: AbortController;
+};
+export default class NiftiImageVolume extends ImageVolume {
+    loadStatus: LoadStatus;
+    controller: AbortController;
+    constructor(imageVolumeProperties: Types.IVolume, streamingProperties: NiftiImageProperties);
+    cancelLoading: () => void;
+    clearLoadCallbacks(): void;
+    load: (callback: (...args: unknown[]) => void, priority?: number) => void;
+    decache(): void;
+}
+export {};

package/dist/esm/NiftiImageVolume.js

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+import { ImageVolume, cache } from '@cornerstonejs/core';
+export default class NiftiImageVolume extends ImageVolume {
+    constructor(imageVolumeProperties, streamingProperties) {
+        super(imageVolumeProperties);
+        this.cancelLoading = () => {
+            const { loadStatus } = this;
+            if (!loadStatus || !loadStatus.loading) {
+                return;
+            }
+            loadStatus.loading = false;
+            this.clearLoadCallbacks();
+            this.controller.abort();
+        };
+        this.load = (callback, priority = 5) => {
+        };
+        this.loadStatus = streamingProperties.loadStatus;
+        this.controller = streamingProperties.controller;
+    }
+    clearLoadCallbacks() {
+        this.loadStatus.callbacks = [];
+    }
+    decache() {
+        cache.removeVolumeLoadObject(this.volumeId);
+    }
+}
+//# sourceMappingURL=NiftiImageVolume.js.map

package/dist/esm/NiftiImageVolume.js.map

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package/dist/esm/constants/index.d.ts

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+import NIFTI_LOADER_SCHEME from './niftiLoaderScheme';
+export { NIFTI_LOADER_SCHEME };

package/dist/esm/constants/index.js

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+import NIFTI_LOADER_SCHEME from './niftiLoaderScheme';
+export { NIFTI_LOADER_SCHEME };
+//# sourceMappingURL=index.js.map

package/dist/esm/constants/index.js.map

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package/dist/esm/constants/niftiLoaderScheme.d.ts

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+declare const niftiLoaderScheme = "nifti";
+export default niftiLoaderScheme;

package/dist/esm/constants/niftiLoaderScheme.js

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+const niftiLoaderScheme = 'nifti';
+export default niftiLoaderScheme;
+//# sourceMappingURL=niftiLoaderScheme.js.map

package/dist/esm/constants/niftiLoaderScheme.js.map

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+{"version":3,"file":"niftiLoaderScheme.js","sourceRoot":"","sources":["../../../src/constants/niftiLoaderScheme.ts"],"names":[],"mappings":"AAAA,MAAM,iBAAiB,GAAG,OAAO,CAAC;AAElC,eAAe,iBAAiB,CAAC"}

package/dist/esm/cornerstoneNiftiImageLoader.d.ts

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+import NiftiImageVolume from './NiftiImageVolume';
+interface IVolumeLoader {
+    promise: Promise<NiftiImageVolume>;
+    cancel: () => void;
+}
+export default function cornerstoneNiftiImageVolumeLoader(volumeId: string): IVolumeLoader;
+export {};

package/dist/esm/cornerstoneNiftiImageLoader.js

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+import { fetchAndAllocateNiftiVolume } from './helpers';
+export default function cornerstoneNiftiImageVolumeLoader(volumeId) {
+    const niftiVolumePromise = fetchAndAllocateNiftiVolume(volumeId);
+    return {
+        promise: niftiVolumePromise,
+        cancel: () => {
+        },
+    };
+}
+//# sourceMappingURL=cornerstoneNiftiImageLoader.js.map

package/dist/esm/cornerstoneNiftiImageLoader.js.map

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package/dist/esm/enums/Events.d.ts

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+declare enum Events {
+    NIFTI_VOLUME_LOADED = "CORNERSTONE_NIFTI_VOLUME_LOADED",
+    NIFTI_VOLUME_PROGRESS = "CORNERSTONE_NIFTI_VOLUME_PROGRESS"
+}
+export default Events;

package/dist/esm/enums/Events.js

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+var Events;
+(function (Events) {
+    Events["NIFTI_VOLUME_LOADED"] = "CORNERSTONE_NIFTI_VOLUME_LOADED";
+    Events["NIFTI_VOLUME_PROGRESS"] = "CORNERSTONE_NIFTI_VOLUME_PROGRESS";
+})(Events || (Events = {}));
+export default Events;
+//# sourceMappingURL=Events.js.map

package/dist/esm/enums/Events.js.map

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package/dist/esm/enums/index.d.ts

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+import Events from './Events';
+export { Events };

package/dist/esm/enums/index.js

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+import Events from './Events';
+export { Events };
+//# sourceMappingURL=index.js.map

package/dist/esm/enums/index.js.map

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package/dist/esm/helpers/affineUtilities.d.ts

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+import type { Types } from '@cornerstonejs/core';
+declare function generateAffineMatrix(origin: Types.Point3, orientation: Types.Mat3, spacing: Types.Point3): Types.AffineMatrix;
+declare function parseAffineMatrix(affine: any): {
+    origin: Types.Point3;
+    orientation: Types.Mat3;
+    spacing: Types.Point3;
+};
+export { generateAffineMatrix, parseAffineMatrix };

package/dist/esm/helpers/affineUtilities.js

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+function generateAffineMatrix(origin, orientation, spacing) {
+    const Ox = origin[0];
+    const Oy = origin[1];
+    const Oz = origin[2];
+    const S1 = spacing[0];
+    const S2 = spacing[1];
+    const S3 = spacing[2];
+    const D11 = orientation[0];
+    const D12 = orientation[1];
+    const D13 = orientation[2];
+    const D21 = orientation[3];
+    const D22 = orientation[4];
+    const D23 = orientation[5];
+    const D31 = orientation[6];
+    const D32 = orientation[7];
+    const D33 = orientation[8];
+    return [
+        [D11 * S1, D12 * S2, D13 * S3, Ox],
+        [D21 * S1, D22 * S2, D23 * S3, Oy],
+        [D31 * S1, D32 * S2, D33 * S3, Oz],
+        [0, 0, 0, 1],
+    ];
+}
+function parseAffineMatrix(affine) {
+    const origin = [affine[0][3], affine[1][3], affine[2][3]];
+    const spacing = [
+        Math.sqrt(affine[0][0] ** 2 + affine[1][0] ** 2 + affine[2][0] ** 2),
+        Math.sqrt(affine[0][1] ** 2 + affine[1][1] ** 2 + affine[2][1] ** 2),
+        Math.sqrt(affine[0][2] ** 2 + affine[1][2] ** 2 + affine[2][2] ** 2),
+    ];
+    const orientation = [
+        affine[0][0] / spacing[0],
+        affine[0][1] / spacing[1],
+        affine[0][2] / spacing[2],
+        affine[1][0] / spacing[0],
+        affine[1][1] / spacing[1],
+        affine[1][2] / spacing[2],
+        affine[2][0] / spacing[0],
+        affine[2][1] / spacing[1],
+        affine[2][2] / spacing[2],
+    ];
+    return { origin, orientation, spacing };
+}
+export { generateAffineMatrix, parseAffineMatrix };
+//# sourceMappingURL=affineUtilities.js.map

package/dist/esm/helpers/affineUtilities.js.map

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package/dist/esm/helpers/convert.d.ts

@@ -0,0 +1,19 @@
+import type { Types } from '@cornerstonejs/core';
+declare const invertDataPerFrame: (dimensions: any, imageDataArray: any) => any;
+declare function rasToLps(niftiHeader: any): {
+    origin: Types.Point3;
+    orientation: number[];
+    spacing: Types.Point3;
+};
+declare function lpsToRas(header: any): {
+    orientation: any[];
+    origin: any[];
+    dataType: any;
+    dimensions: any;
+    spacing: any;
+    slope: any;
+    inter: any;
+    max: any;
+    min: any;
+};
+export { lpsToRas, rasToLps, invertDataPerFrame };

package/dist/esm/helpers/convert.js

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+import { parseAffineMatrix } from './affineUtilities';
+const invertDataPerFrame = (dimensions, imageDataArray) => {
+    let TypedArrayConstructor;
+    let bytesPerVoxel;
+    if (imageDataArray instanceof Uint8Array ||
+        imageDataArray instanceof ArrayBuffer ||
+        imageDataArray instanceof SharedArrayBuffer) {
+        TypedArrayConstructor = Uint8Array;
+        bytesPerVoxel = 1;
+    }
+    else if (imageDataArray instanceof Int16Array) {
+        TypedArrayConstructor = Int16Array;
+        bytesPerVoxel = 2;
+    }
+    else if (imageDataArray instanceof Float32Array) {
+        TypedArrayConstructor = Float32Array;
+        bytesPerVoxel = 4;
+    }
+    else {
+        throw new Error('imageDataArray needs to be a Uint8Array, Int16Array or Float32Array.');
+    }
+    const newImageDataArray = new TypedArrayConstructor(imageDataArray.byteLength);
+    const view = new TypedArrayConstructor(imageDataArray);
+    newImageDataArray.set(view);
+    const numFrames = dimensions[2];
+    const frameLength = dimensions[0] * dimensions[1];
+    const buffer = newImageDataArray.buffer;
+    for (let frame = 0; frame < numFrames; frame++) {
+        const byteOffset = frameLength * frame * bytesPerVoxel;
+        const frameView = new TypedArrayConstructor(buffer, byteOffset, frameLength);
+        frameView.reverse();
+    }
+    return newImageDataArray;
+};
+function rasToLps(niftiHeader) {
+    const { affine } = niftiHeader;
+    const { orientation, origin, spacing } = parseAffineMatrix(affine);
+    const newOrigin = [-origin[0], -origin[1], origin[2]];
+    const newOrientation = [
+        -orientation[0],
+        -orientation[3],
+        orientation[6],
+        -orientation[1],
+        -orientation[4],
+        orientation[7],
+        -orientation[2],
+        -orientation[5],
+        orientation[8],
+    ];
+    return {
+        origin: newOrigin,
+        orientation: newOrientation,
+        spacing,
+    };
+}
+function lpsToRas(header) {
+    const { origin, orientation, spacing, dimensions, dataType } = header;
+    const newOrigin = [-origin[0], -origin[1], origin[2]];
+    const newOrientation = [
+        -orientation[0],
+        -orientation[3],
+        orientation[6],
+        -orientation[1],
+        -orientation[4],
+        orientation[7],
+        -orientation[2],
+        -orientation[5],
+        orientation[8],
+    ];
+    return {
+        orientation: newOrientation,
+        origin: [newOrigin[0], newOrigin[1], newOrigin[2]],
+        dataType,
+        dimensions,
+        spacing,
+        slope: header.slope,
+        inter: header.inter,
+        max: header.max,
+        min: header.min,
+    };
+}
+export { lpsToRas, rasToLps, invertDataPerFrame };
+//# sourceMappingURL=convert.js.map

package/dist/esm/helpers/convert.js.map

@@ -0,0 +1 @@
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package/dist/esm/helpers/fetchAndAllocateNiftiVolume.d.ts

@@ -0,0 +1,4 @@
+import NiftiImageVolume from '../NiftiImageVolume';
+export declare const urlsMap: Map<any, any>;
+export declare const getTypedNiftiArray: (datatypeCode: any, niftiImageBuffer: any) => Float32Array | Int16Array | Uint8Array;
+export default function fetchAndAllocateNiftiVolume(volumeId: string): Promise<NiftiImageVolume>;

package/dist/esm/helpers/fetchAndAllocateNiftiVolume.js

@@ -0,0 +1,163 @@
+import * as NiftiReader from 'nifti-reader-js';
+import { cache, utilities, Enums, eventTarget, triggerEvent, } from '@cornerstonejs/core';
+import { vec3 } from 'gl-matrix';
+import makeVolumeMetadata from './makeVolumeMetadata';
+import NiftiImageVolume from '../NiftiImageVolume';
+import * as NIFTICONSTANTS from './niftiConstants';
+import { invertDataPerFrame, rasToLps } from './convert';
+import modalityScaleNifti from './modalityScaleNifti';
+import Events from '../enums/Events';
+import { NIFTI_LOADER_SCHEME } from '../constants';
+const { createUint8SharedArray, createFloat32SharedArray } = utilities;
+export const urlsMap = new Map();
+function fetchArrayBuffer(url, onProgress, signal, onload) {
+    return new Promise((resolve, reject) => {
+        const xhr = new XMLHttpRequest();
+        xhr.open('GET', url, true);
+        xhr.responseType = 'arraybuffer';
+        const onLoadHandler = function (e) {
+            if (onload && typeof onload === 'function') {
+                onload();
+            }
+            if (signal) {
+                signal.removeEventListener('abort', onAbortHandler);
+            }
+            resolve(xhr.response);
+        };
+        const onAbortHandler = () => {
+            xhr.abort();
+            xhr.removeEventListener('load', onLoadHandler);
+            reject(new Error('Request aborted'));
+        };
+        xhr.addEventListener('load', onLoadHandler);
+        if (onProgress && typeof onProgress === 'function') {
+            xhr.onprogress = function (e) {
+                onProgress(e.loaded, e.total);
+            };
+        }
+        if (signal && signal.aborted) {
+            xhr.abort();
+            reject(new Error('Request aborted'));
+        }
+        else if (signal) {
+            signal.addEventListener('abort', onAbortHandler);
+        }
+        xhr.send();
+    });
+}
+export const getTypedNiftiArray = (datatypeCode, niftiImageBuffer) => {
+    switch (datatypeCode) {
+        case NIFTICONSTANTS.NIFTI_TYPE_UINT8:
+            return new Uint8Array(niftiImageBuffer);
+        case NIFTICONSTANTS.NIFTI_TYPE_FLOAT32:
+            return new Float32Array(niftiImageBuffer);
+        case NIFTICONSTANTS.NIFTI_TYPE_INT16:
+            return new Int16Array(niftiImageBuffer);
+        default:
+            throw new Error(`datatypeCode ${datatypeCode} is not yet supported`);
+    }
+};
+export default async function fetchAndAllocateNiftiVolume(volumeId) {
+    const niftiURL = volumeId.substring(NIFTI_LOADER_SCHEME.length + 1);
+    const progress = (loaded, total) => {
+        const data = { volumeId, loaded, total };
+        triggerEvent(eventTarget, Events.NIFTI_VOLUME_PROGRESS, {
+            data,
+        });
+    };
+    const onLoad = () => {
+        const data = { volumeId };
+        triggerEvent(eventTarget, Events.NIFTI_VOLUME_LOADED, {
+            data,
+        });
+    };
+    const controller = new AbortController();
+    const signal = controller.signal;
+    urlsMap.set(niftiURL, { controller, loading: true });
+    let niftiBuffer = (await fetchArrayBuffer(niftiURL, progress, signal, onLoad));
+    urlsMap.delete(niftiURL);
+    let niftiHeader = null;
+    let niftiImage = null;
+    if (NiftiReader.isCompressed(niftiBuffer)) {
+        niftiBuffer = NiftiReader.decompress(niftiBuffer);
+    }
+    if (NiftiReader.isNIFTI(niftiBuffer)) {
+        niftiHeader = NiftiReader.readHeader(niftiBuffer);
+        niftiImage = NiftiReader.readImage(niftiHeader, niftiBuffer);
+    }
+    const typedNiftiArray = getTypedNiftiArray(niftiHeader.datatypeCode, niftiImage);
+    const { orientation, origin, spacing } = rasToLps(niftiHeader);
+    invertDataPerFrame(niftiHeader.dims.slice(1, 4), typedNiftiArray);
+    modalityScaleNifti(typedNiftiArray, niftiHeader);
+    const volumeMetadata = makeVolumeMetadata(niftiHeader, orientation, typedNiftiArray);
+    const scanAxisNormal = vec3.create();
+    vec3.set(scanAxisNormal, orientation[6], orientation[7], orientation[8]);
+    const { BitsAllocated, PixelRepresentation, PhotometricInterpretation, ImageOrientationPatient, Columns, Rows, } = volumeMetadata;
+    const rowCosineVec = vec3.fromValues(ImageOrientationPatient[0], ImageOrientationPatient[1], ImageOrientationPatient[2]);
+    const colCosineVec = vec3.fromValues(ImageOrientationPatient[3], ImageOrientationPatient[4], ImageOrientationPatient[5]);
+    const { dims } = niftiHeader;
+    const numFrames = dims[3];
+    const dimensions = [Columns, Rows, numFrames];
+    const direction = new Float32Array([
+        rowCosineVec[0],
+        rowCosineVec[1],
+        rowCosineVec[2],
+        colCosineVec[0],
+        colCosineVec[1],
+        colCosineVec[2],
+        scanAxisNormal[0],
+        scanAxisNormal[1],
+        scanAxisNormal[2],
+    ]);
+    const signed = PixelRepresentation === 1;
+    let bytesPerVoxel = 1;
+    if (BitsAllocated === 16 || BitsAllocated === 32) {
+        bytesPerVoxel = 4;
+    }
+    const sizeInBytesPerComponent = bytesPerVoxel * dimensions[0] * dimensions[1] * dimensions[2];
+    let numComponents = 1;
+    if (PhotometricInterpretation === 'RGB') {
+        numComponents = 3;
+    }
+    const sizeInBytes = sizeInBytesPerComponent * numComponents;
+    const isCacheable = cache.isCacheable(sizeInBytes);
+    if (!isCacheable) {
+        throw new Error(Enums.Events.CACHE_SIZE_EXCEEDED);
+    }
+    cache.decacheIfNecessaryUntilBytesAvailable(sizeInBytes);
+    let scalarData;
+    switch (BitsAllocated) {
+        case 8:
+            if (signed) {
+                throw new Error('8 Bit signed images are not yet supported by this plugin.');
+            }
+            else {
+                scalarData = createUint8SharedArray(dimensions[0] * dimensions[1] * dimensions[2]);
+            }
+            break;
+        case 16:
+        case 32:
+            scalarData = createFloat32SharedArray(dimensions[0] * dimensions[1] * dimensions[2]);
+            break;
+    }
+    scalarData.set(typedNiftiArray);
+    const niftiImageVolume = new NiftiImageVolume({
+        volumeId,
+        metadata: volumeMetadata,
+        dimensions,
+        spacing,
+        origin,
+        direction,
+        scalarData,
+        sizeInBytes,
+    }, {
+        loadStatus: {
+            loaded: false,
+            loading: false,
+            callbacks: [],
+        },
+        controller,
+    });
+    return niftiImageVolume;
+}
+//# sourceMappingURL=fetchAndAllocateNiftiVolume.js.map

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package/dist/esm/helpers/index.d.ts

@@ -0,0 +1,4 @@
+import makeVolumeMetadata from './makeVolumeMetadata';
+import modalityScaleNifti from './modalityScaleNifti';
+import fetchAndAllocateNiftiVolume from './fetchAndAllocateNiftiVolume';
+export { modalityScaleNifti, makeVolumeMetadata, fetchAndAllocateNiftiVolume };

package/dist/esm/helpers/index.js

@@ -0,0 +1,5 @@
+import makeVolumeMetadata from './makeVolumeMetadata';
+import modalityScaleNifti from './modalityScaleNifti';
+import fetchAndAllocateNiftiVolume from './fetchAndAllocateNiftiVolume';
+export { modalityScaleNifti, makeVolumeMetadata, fetchAndAllocateNiftiVolume };
+//# sourceMappingURL=index.js.map

package/dist/esm/helpers/index.js.map

@@ -0,0 +1 @@
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package/dist/esm/helpers/makeVolumeMetadata.d.ts

@@ -0,0 +1,2 @@
+import { Types } from '@cornerstonejs/core';
+export default function makeVolumeMetadata(niftiHeader: any, orientation: any, scalarData: any): Types.Metadata;

package/dist/esm/helpers/makeVolumeMetadata.js

@@ -0,0 +1,51 @@
+import { vec3 } from 'gl-matrix';
+export default function makeVolumeMetadata(niftiHeader, orientation, scalarData) {
+    const { numBitsPerVoxel, littleEndian, pixDims, dims } = niftiHeader;
+    const rowCosines = vec3.create();
+    const columnCosines = vec3.create();
+    vec3.set(rowCosines, orientation[0], orientation[1], orientation[2]);
+    vec3.set(columnCosines, orientation[3], orientation[4], orientation[5]);
+    let min = Infinity;
+    let max = -Infinity;
+    const xDim = dims[1];
+    const yDim = dims[2];
+    const zDim = dims[3];
+    const frameLength = xDim * yDim;
+    const middleFrameIndex = Math.floor(zDim / 2);
+    const offset = frameLength * middleFrameIndex;
+    for (let voxelIndex = offset; voxelIndex < offset + frameLength; voxelIndex++) {
+        const voxelValue = scalarData[voxelIndex];
+        if (voxelValue > max) {
+            max = voxelValue;
+        }
+        if (voxelValue < min) {
+            min = voxelValue;
+        }
+    }
+    const windowCenter = (max + min) / 2;
+    const windowWidth = max - min;
+    return {
+        BitsAllocated: numBitsPerVoxel,
+        BitsStored: numBitsPerVoxel,
+        SamplesPerPixel: 1,
+        HighBit: littleEndian ? numBitsPerVoxel - 1 : 1,
+        PhotometricInterpretation: 'MONOCHROME2',
+        PixelRepresentation: 1,
+        ImageOrientationPatient: [
+            rowCosines[0],
+            rowCosines[1],
+            rowCosines[2],
+            columnCosines[0],
+            columnCosines[1],
+            columnCosines[2],
+        ],
+        PixelSpacing: [pixDims[1], pixDims[2]],
+        Columns: xDim,
+        Rows: yDim,
+        voiLut: [{ windowCenter, windowWidth }],
+        FrameOfReferenceUID: '1.2.3',
+        Modality: 'MR',
+        VOILUTFunction: 'LINEAR',
+    };
+}
+//# sourceMappingURL=makeVolumeMetadata.js.map

package/dist/esm/helpers/makeVolumeMetadata.js.map

@@ -0,0 +1 @@
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package/dist/esm/helpers/modalityScaleNifti.d.ts

@@ -0,0 +1 @@
+export default function modalityScaleNifti(array: Float32Array | Int16Array | Uint8Array, niftiHeader: any): void;

package/dist/esm/helpers/modalityScaleNifti.js

@@ -0,0 +1,11 @@
+export default function modalityScaleNifti(array, niftiHeader) {
+    const arrayLength = array.length;
+    const { scl_slope, scl_inter } = niftiHeader;
+    if (!scl_slope || scl_slope === 0 || Number.isNaN(scl_slope)) {
+        return;
+    }
+    for (let i = 0; i < arrayLength; i++) {
+        array[i] = array[i] * scl_slope + scl_inter;
+    }
+}
+//# sourceMappingURL=modalityScaleNifti.js.map

package/dist/esm/helpers/modalityScaleNifti.js.map

@@ -0,0 +1 @@
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