feat(readImageLocalDICOMFileSeries): Support componentType, pixelType

src/io/readImageDICOMFileSeries.ts

@@ -16,7 +16,7 @@ const readImageDICOMFileSeries = async (
 
   let optionsToPass: ReadImageDICOMArrayBufferSeriesOptions = {}
   if (typeof options === 'object') {
-    optionsToPass = options
+    optionsToPass = { ...options }
   }
   if (typeof options === 'boolean') {
     // Backwards compatibility
@@ -25,7 +25,7 @@ const readImageDICOMFileSeries = async (
 
   const fileNames = Array.from(fileList, (file) => file.name)
   optionsToPass.fileNames = fileNames
-  return readImageDICOMArrayBufferSeries(fileContents, optionsToPass)
+  return await readImageDICOMArrayBufferSeries(fileContents, optionsToPass)
 }
 
 export default readImageDICOMFileSeries

src/io/readImageLocalDICOMFileSeries.ts

@@ -8,15 +8,19 @@ import Image from '../core/Image.js'
 import InterfaceTypes from '../core/InterfaceTypes.js'
 import runPipelineEmscripten from '../pipeline/internal/runPipelineEmscripten.js'
 import PipelineInput from '../pipeline/PipelineInput.js'
+import ReadImageDICOMFileSeriesOptions from './ReadImageDICOMFileSeriesOptions.js'
+import castImage from '../core/castImage.js'
+
+async function readImageLocalDICOMFileSeries (
+  fileNames: string[],
+  options?: ReadImageDICOMFileSeriesOptions | boolean
+): Promise<Image> {
+  let singleSortedSeries = false
+  if (typeof options === 'boolean') {
+    // Backwards compatibility
+    singleSortedSeries = options
+  }
 
-/**
- * Read an image from a series of DICOM files on the local filesystem in Node.js.
- *
- * @param: filenames Array of filepaths containing a DICOM study / series on the local filesystem.
- * @param: singleSortedSeries: it is known that the files are from a single
- * sorted series.
- */
-async function readImageLocalDICOMFileSeries (fileNames: string[], singleSortedSeries: boolean = false): Promise<Image> {
   if (fileNames.length < 1) {
     throw new Error('No fileNames provided')
   }
@@ -44,7 +48,12 @@ async function readImageLocalDICOMFileSeries (fileNames: string[], singleSortedS
   ] as PipelineInput[]
   const { outputs } = runPipelineEmscripten(seriesReaderModule, args, desiredOutputs, inputs)
 
-  return outputs[0].data as Image
+  let image = outputs[0].data as Image
+  if (typeof options === 'object' && (typeof options.componentType !== 'undefined' || typeof options.pixelType !== 'undefined')) {
+    image = castImage(image, options)
+  }
+
+  return image
 }
 
 export default readImageLocalDICOMFileSeries

test/node/io/image/DICOMSeriesTest.js

@@ -7,44 +7,18 @@ import { IntTypes, PixelTypes, getMatrixElement, readImageLocalDICOMFileSeries }
 const testSeriesDirectory = path.resolve('build-emscripten', 'ExternalData', 'test', 'Input', 'DicomImageOrientationTest')
 const testFiles = glob.sync(`${testSeriesDirectory}/*.dcm`)
 
-test('Test reading a DICOM file', async t => {
-  try {
-    const image = await readImageLocalDICOMFileSeries(testFiles)
-    t.is(image.imageType.dimension, 3, 'dimension')
-    t.is(image.imageType.componentType, IntTypes.Int16, 'componentType')
-    t.is(image.imageType.pixelType, PixelTypes.Scalar, 'pixelType')
-    t.is(image.imageType.components, 1, 'components')
-    t.is(image.origin[0], -17.3551, 'origin[0]')
-    t.is(image.origin[1], -133.9286, 'origin[1]')
-    t.is(image.origin[2], 116.7857, 'origin[2]')
-    t.is(image.spacing[0], 1.0, 'spacing[0]')
-    t.is(image.spacing[1], 1.0, 'spacing[1]')
-    t.is(image.spacing[2], 1.3000000000000007, 'spacing[2]')
-    t.is(getMatrixElement(image.direction, 3, 0, 0), 0.0, 'direction (0, 0)')
-    t.is(getMatrixElement(image.direction, 3, 0, 1), 0.0, 'direction (0, 1)')
-    t.is(getMatrixElement(image.direction, 3, 0, 2), -1.0, 'direction (0, 2)')
-    t.is(getMatrixElement(image.direction, 3, 1, 0), 1.0, 'direction (1, 0)')
-    t.is(getMatrixElement(image.direction, 3, 1, 1), 0.0, 'direction (1, 1)')
-    t.is(getMatrixElement(image.direction, 3, 1, 2), 0.0, 'direction (1, 2)')
-    t.is(getMatrixElement(image.direction, 3, 2, 0), 0.0, 'direction (2, 0)')
-    t.is(getMatrixElement(image.direction, 3, 2, 1), -1.0, 'direction (2, 1)')
-    t.is(getMatrixElement(image.direction, 3, 2, 2), 0.0, 'direction (2, 2)')
-    t.is(image.size[0], 256, 'size[0]')
-    t.is(image.size[1], 256, 'size[1]')
-    t.is(image.size[2], 3, 'size[2]')
-    t.is(image.data.length, 3 * 65536, 'data.length')
-    t.is(image.data[1000], 5, 'data[1000]')
-  } catch (err) {
-    console.error(err)
-    console.trace()
+function verifyImage (t, image, expectedComponentType, expectedPixelType) {
+  let componentType = IntTypes.Int16
+  if (expectedComponentType) {
+    componentType = expectedComponentType
+  }
+  let pixelType = PixelTypes.Scalar
+  if (expectedPixelType) {
+    pixelType = expectedPixelType
   }
-})
-
-test('Test reading a DICOM file assume sorted', async t => {
-  const image = await readImageLocalDICOMFileSeries(testFiles.sort(), true)
   t.is(image.imageType.dimension, 3, 'dimension')
-  t.is(image.imageType.componentType, IntTypes.Int16, 'componentType')
-  t.is(image.imageType.pixelType, PixelTypes.Scalar, 'pixelType')
+  t.is(image.imageType.componentType, componentType, 'componentType')
+  t.is(image.imageType.pixelType, pixelType, 'pixelType')
   t.is(image.imageType.components, 1, 'components')
   t.is(image.origin[0], -17.3551, 'origin[0]')
   t.is(image.origin[1], -133.9286, 'origin[1]')
@@ -66,4 +40,30 @@ test('Test reading a DICOM file assume sorted', async t => {
   t.is(image.size[2], 3, 'size[2]')
   t.is(image.data.length, 3 * 65536, 'data.length')
   t.is(image.data[1000], 5, 'data[1000]')
+}
+
+test('Test reading a DICOM file', async t => {
+  const image = await readImageLocalDICOMFileSeries(testFiles)
+  verifyImage(t, image)
+})
+
+test('Test reading a DICOM file, given componentType, pixelType', async t => {
+  const componentType = IntTypes.Int32
+  const pixelType = PixelTypes.Vector
+  const image = await readImageLocalDICOMFileSeries(testFiles, { componentType, pixelType })
+  verifyImage(t, image, componentType, pixelType)
+})
+
+test('Test reading a DICOM file assume sorted', async t => {
+  const singleSortedSeries = true
+  const image = await readImageLocalDICOMFileSeries(testFiles.sort(), { singleSortedSeries })
+  verifyImage(t, image)
+})
+
+test('Test reading a DICOM file assume sorted, given componentType, pixelType', async t => {
+  const singleSortedSeries = true
+  const componentType = IntTypes.Int32
+  const pixelType = PixelTypes.Vector
+  const image = await readImageLocalDICOMFileSeries(testFiles.sort(), { singleSortedSeries, componentType, pixelType })
+  verifyImage(t, image, componentType, pixelType)
 })