feat(NiftiVolumeLoader): enable the nifti-volume-loader to read nifti file with datatype such as int32, float64, int8, uint16 and uint32. Because there is something wrong with function ‘createInt16SharedArray’ and ‘createUint16SharedArray’(window.crossOriginIsolated is false), Float32SharedArray is used for representing datatypes except for uint8.

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

@@ -46,7 +46,7 @@ export { helpers }
 function makeVolumeMetadata(niftiHeader: any, orientation: any, scalarData: any): Types.Metadata;
 
 // @public (undocumented)
-function modalityScaleNifti(array: Float32Array | Int16Array | Uint8Array, niftiHeader: any): void;
+function modalityScaleNifti(array: Uint8Array | Int16Array | Int32Array | Float32Array | Float64Array | Int8Array | Uint16Array | Uint32Array, niftiHeader: any): void;
 
 // @public (undocumented)
 export class NiftiImageVolume extends ImageVolume {

packages/nifti-volume-loader/src/helpers/convert.ts

@@ -18,18 +18,33 @@ const invertDataPerFrame = (dimensions, imageDataArray) => {
   } else if (imageDataArray instanceof Int16Array) {
     TypedArrayConstructor = Int16Array;
     bytesPerVoxel = 2;
+  } else if (imageDataArray instanceof Int32Array) {
+    TypedArrayConstructor = Int32Array;
+    bytesPerVoxel = 4;
   } else if (imageDataArray instanceof Float32Array) {
     TypedArrayConstructor = Float32Array;
     bytesPerVoxel = 4;
+  } else if (imageDataArray instanceof Float64Array) {
+    TypedArrayConstructor = Float64Array;
+    bytesPerVoxel = 8;
+  } else if (imageDataArray instanceof Int8Array) {
+    TypedArrayConstructor = Int8Array;
+    bytesPerVoxel = 1;
+  } else if (imageDataArray instanceof Uint16Array) {
+    TypedArrayConstructor = Uint16Array;
+    bytesPerVoxel = 2;
+  } else if (imageDataArray instanceof Uint32Array) {
+    TypedArrayConstructor = Uint32Array;
+    bytesPerVoxel = 4;
   } else {
     throw new Error(
-      'imageDataArray needs to be a Uint8Array, Int16Array or Float32Array.'
+      'imageDataArray needs to be a Uint8Array, Int16Array, Int32Array, Float32Array, Float64Array, Int8Array, Uint16Array or Uint32Array.'
     );
   }
 
   // Make a copy of the data first using the browser native fast TypedArray.set().
   const newImageDataArray = new TypedArrayConstructor(
-    imageDataArray.byteLength
+    imageDataArray.byteLength / bytesPerVoxel
   );
 
   const view = new TypedArrayConstructor(imageDataArray);

packages/nifti-volume-loader/src/helpers/fetchAndAllocateNiftiVolume.ts

@@ -71,10 +71,20 @@ 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);
+    case NIFTICONSTANTS.NIFTI_TYPE_INT32:
+      return new Int32Array(niftiImageBuffer);
+    case NIFTICONSTANTS.NIFTI_TYPE_FLOAT32:
+      return new Float32Array(niftiImageBuffer);
+    case NIFTICONSTANTS.NIFTI_TYPE_FLOAT64:
+      return new Float64Array(niftiImageBuffer);
+    case NIFTICONSTANTS.NIFTI_TYPE_INT8:
+      return new Int8Array(niftiImageBuffer);
+    case NIFTICONSTANTS.NIFTI_TYPE_UINT16:
+      return new Uint16Array(niftiImageBuffer);
+    case NIFTICONSTANTS.NIFTI_TYPE_UINT32:
+      return new Uint32Array(niftiImageBuffer);
     default:
       throw new Error(`datatypeCode ${datatypeCode} is not yet supported`);
   }
@@ -149,7 +159,6 @@ export default async function fetchAndAllocateNiftiVolume(
 
   const {
     BitsAllocated,
-    PixelRepresentation,
     PhotometricInterpretation,
     ImageOrientationPatient,
     Columns,
@@ -184,7 +193,6 @@ export default async function fetchAndAllocateNiftiVolume(
     scanAxisNormal[1],
     scanAxisNormal[2],
   ]) as Types.Mat3;
-  const signed = PixelRepresentation === 1;
 
   // Check if it fits in the cache before we allocate data
   // TODO Improve this when we have support for more types
@@ -213,22 +221,15 @@ export default async function fetchAndAllocateNiftiVolume(
 
   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]
-        );
-      }
+  switch (niftiHeader.datatypeCode) {
+    case NIFTICONSTANTS.NIFTI_TYPE_UINT8:
+      scalarData = createUint8SharedArray(
+        dimensions[0] * dimensions[1] * dimensions[2]
+      );
 
       break;
 
-    case 16:
-    case 32:
+    default:
       scalarData = createFloat32SharedArray(
         dimensions[0] * dimensions[1] * dimensions[2]
       );

packages/nifti-volume-loader/src/helpers/modalityScaleNifti.ts

@@ -8,7 +8,15 @@
  * @returns The array being scaled
  */
 export default function modalityScaleNifti(
-  array: Float32Array | Int16Array | Uint8Array,
+  array:
+    | Uint8Array
+    | Int16Array
+    | Int32Array
+    | Float32Array
+    | Float64Array
+    | Int8Array
+    | Uint16Array
+    | Uint32Array,
   niftiHeader
 ): void {
   const arrayLength = array.length;