feat(nifti): NIFTI data type enhancement (#1219)

common/reviews/api/nifti-volume-loader.api.md

@@ -43,10 +43,17 @@ declare namespace helpers {
 export { helpers }
 
 // @public (undocumented)
-function makeVolumeMetadata(niftiHeader: any, orientation: any, scalarData: any): Types.Metadata;
+function makeVolumeMetadata(niftiHeader: any, orientation: any, scalarData: any, pixelRepresentation: any): {
+    volumeMetadata: Types.Metadata;
+    dimensions: Types.Point3;
+    direction: Types.Mat3;
+};
 
 // @public (undocumented)
-function modalityScaleNifti(array: Float32Array | Int16Array | Uint8Array, niftiHeader: any): void;
+function modalityScaleNifti(niftiHeader: any, niftiImageBuffer: any): {
+    scalarData: Types.PixelDataTypedArray;
+    pixelRepresentation: number;
+};
 
 // @public (undocumented)
 export class NiftiImageVolume extends ImageVolume {

packages/core/src/RenderingEngine/helpers/createVolumeActor.ts

@@ -66,13 +66,7 @@ async function createVolumeActor(
     volumeActor.getProperty().setIndependentComponents(false);
   }
 
-  // If the volume is composed of imageIds, we can apply a default VOI based
-  // on either the metadata or the min/max of the middle slice. Example of other
-  // types of volumes which might not be composed of imageIds would be e.g., nrrd, nifti
-  // format volumes
-  if (imageVolume.imageIds?.length) {
-    await setDefaultVolumeVOI(volumeActor, imageVolume, useNativeDataType);
-  }
+  await setDefaultVolumeVOI(volumeActor, imageVolume, useNativeDataType);
 
   if (callback) {
     callback({ volumeActor, volumeId });

packages/core/src/RenderingEngine/helpers/setDefaultVolumeVOI.ts

@@ -21,6 +21,7 @@ const REQUEST_TYPE = RequestType.Prefetch;
  * Finally it sets the VOI on the volumeActor transferFunction
  * @param volumeActor - The volume actor
  * @param imageVolume - The image volume that we want to set the VOI for.
+ * @param useNativeDataType -  The image data type is native or Float32Array
  */
 async function setDefaultVolumeVOI(
   volumeActor: VolumeActor,
@@ -29,27 +30,27 @@ async function setDefaultVolumeVOI(
 ): Promise<void> {
   let voi = getVOIFromMetadata(imageVolume);
 
-  if (!voi) {
+  if (!voi && imageVolume?.imageIds?.length) {
     voi = await getVOIFromMinMax(imageVolume, useNativeDataType);
+    voi = handlePreScaledVolume(imageVolume, voi);
   }
-
-  if (!voi || voi.lower === undefined || voi.upper === undefined) {
-    throw new Error(
-      'Could not get VOI from metadata, nor from the min max of the image middle slice'
-    );
-  }
-
-  voi = handlePreScaledVolume(imageVolume, voi);
-  const { lower, upper } = voi;
-
-  if (lower === 0 && upper === 0) {
+  // if (!voi || voi.lower === undefined || voi.upper === undefined) {
+  //   throw new Error(
+  //     'Could not get VOI from metadata, nor from the min max of the image middle slice'
+  //   );
+  // }
+  if (
+    (voi?.lower === 0 && voi?.upper === 0) ||
+    voi?.lower === undefined ||
+    voi?.upper === undefined
+  ) {
     return;
   }
 
   volumeActor
     .getProperty()
     .getRGBTransferFunction(0)
-    .setMappingRange(lower, upper);
+    .setMappingRange(voi.lower, voi.upper);
 }
 
 function handlePreScaledVolume(imageVolume: IImageVolume, voi: VOIRange) {
@@ -77,35 +78,36 @@ function handlePreScaledVolume(imageVolume: IImageVolume, voi: VOIRange) {
 }
 
 /**
- * Get the VOI from the metadata of the middle slice of the image volume. It checks
- * the metadata for the VOI and if it is not found, it returns null
+ * Get the VOI from the metadata of the middle slice of the image volume or the metadata of the image volume
+ * It checks the metadata for the VOI and if it is not found, it returns null
  *
  * @param imageVolume - The image volume that we want to get the VOI from.
  * @returns VOIRange with lower and upper values
  */
 function getVOIFromMetadata(imageVolume: IImageVolume): VOIRange {
-  const { imageIds } = imageVolume;
-
-  const imageIdIndex = Math.floor(imageIds.length / 2);
-  const imageId = imageIds[imageIdIndex];
-
-  const voiLutModule = metaData.get('voiLutModule', imageId);
-
-  if (voiLutModule && voiLutModule.windowWidth && voiLutModule.windowCenter) {
-    const { windowWidth, windowCenter } = voiLutModule;
-
-    const voi = {
-      windowWidth: Array.isArray(windowWidth) ? windowWidth[0] : windowWidth,
-      windowCenter: Array.isArray(windowCenter)
-        ? windowCenter[0]
-        : windowCenter,
-    };
-
+  const { imageIds, metadata } = imageVolume;
+  let voi;
+  if (imageIds.length) {
+    const imageIdIndex = Math.floor(imageIds.length / 2);
+    const imageId = imageIds[imageIdIndex];
+    const voiLutModule = metaData.get('voiLutModule', imageId);
+    if (voiLutModule && voiLutModule.windowWidth && voiLutModule.windowCenter) {
+      const { windowWidth, windowCenter } = voiLutModule;
+      voi = {
+        windowWidth: Array.isArray(windowWidth) ? windowWidth[0] : windowWidth,
+        windowCenter: Array.isArray(windowCenter)
+          ? windowCenter[0]
+          : windowCenter,
+      };
+    }
+  } else {
+    voi = metadata?.voiLut?.[0];
+  }
+  if (voi) {
     const { lower, upper } = windowLevel.toLowHighRange(
       Number(voi.windowWidth),
       Number(voi.windowCenter)
     );
-
     return {
       lower,
       upper,
@@ -118,6 +120,7 @@ function getVOIFromMetadata(imageVolume: IImageVolume): VOIRange {
  * and max pixel values, it calculates the VOI.
  *
  * @param imageVolume - The image volume that we want to get the VOI from.
+ * @param useNativeDataType -  The image data type is native or Float32Array
  * @returns The VOIRange with lower and upper values
  */
 async function getVOIFromMinMax(
@@ -218,19 +221,15 @@ function _getImageScalarDataFromImageVolume(
   voxelsPerImage
 ) {
   const { scalarData } = imageVolume;
-  const { volumeBuffer } = scalarData;
+  const { buffer } = scalarData;
   if (scalarData.BYTES_PER_ELEMENT !== bytePerPixel) {
     byteOffset *= scalarData.BYTES_PER_ELEMENT / bytePerPixel;
   }
 
   const TypedArray = scalarData.constructor;
   const imageScalarData = new TypedArray(voxelsPerImage);
 
-  const volumeBufferView = new TypedArray(
-    volumeBuffer,
-    byteOffset,
-    voxelsPerImage
-  );
+  const volumeBufferView = new TypedArray(buffer, byteOffset, voxelsPerImage);
 
   imageScalarData.set(volumeBufferView);
 

packages/nifti-volume-loader/examples/niftiBasic/index.ts

@@ -2,15 +2,12 @@ import {
   RenderingEngine,
   Enums,
   init as csInit,
-  Types,
   volumeLoader,
   setVolumesForViewports,
 } from '@cornerstonejs/core';
 import { init as csTools3dInit } from '@cornerstonejs/tools';
 import { cornerstoneNiftiImageVolumeLoader } from '@cornerstonejs/nifti-volume-loader';
 
-import { setCtTransferFunctionForVolumeActor } from '../../../../utils/demo/helpers';
-
 // This is for debugging purposes
 console.warn(
   'Click on index.ts to open source code for this example --------->'
@@ -90,7 +87,7 @@ async function setup() {
 
   setVolumesForViewports(
     renderingEngine,
-    [{ volumeId, callback: setCtTransferFunctionForVolumeActor }],
+    [{ volumeId }],
     viewportInputArray.map((v) => v.viewportId)
   );
 

packages/nifti-volume-loader/examples/niftiWithTools/index.ts

@@ -12,10 +12,7 @@ import {
   Enums as NiftiEnums,
 } from '@cornerstonejs/nifti-volume-loader';
 
-import {
-  addDropdownToToolbar,
-  setCtTransferFunctionForVolumeActor,
-} from '../../../../utils/demo/helpers';
+import { addDropdownToToolbar } from '../../../../utils/demo/helpers';
 
 const {
   LengthTool,
@@ -276,7 +273,7 @@ async function setup() {
 
   setVolumesForViewports(
     renderingEngine,
-    [{ volumeId, callback: setCtTransferFunctionForVolumeActor }],
+    [{ volumeId }],
     viewportInputArray.map((v) => v.viewportId)
   );