feat(CSPS): add preliminary support for CSPS

Add preliminary support for Color SoftCopy Presentation State (CSPS).
Referenced image is read as-is without any color transformations.
ICC color profile associated with the presentation state is provided
separately as a property value (base64 string) in the output JSON.

include/itkPipeline.h

@@ -63,6 +63,8 @@
 
 // Parse options while allowing extra flags, not exiting with help flags, and clearning parse state after finished.
 // Use this to parse some positionals or options before all options have been added.
+// WARNING: It is best to only add the pre-parse options and read them through ITK_WASM_PRE_PARSE before adding other options,
+// as you may face issues(EXCEPTIONS) generating bindings (bindgen), if you add "required" options/flags before the PRE_PARSE.
 #define ITK_WASM_PRE_PARSE(pipeline) \
     try { \
         (pipeline).set_help_flag(); \

packages/dicom/apply-presentation-state-to-image.cxx

@@ -93,6 +93,7 @@
 #include "dcmtk/dcmdata/cmdlnarg.h"
 #include "dcmtk/ofstd/ofcmdln.h"
 #include "dcmtk/ofstd/ofconapp.h"
+#include "dcmtk/ofstd/ofvector.h"
 #include "dcmtk/dcmdata/dcuid.h"      /* for dcmtk version name */
 
 #include "cpp-base64/base64.h"
@@ -145,6 +146,15 @@ static void dumpPresentationState(STD_NAMESPACE ostream &out, DVPresentationStat
     doc.AddMember("CurrentVOIDescription", Value(StringRef(ps.getCurrentVOIDescription())), alloc);
   }
 
+  // ICC color Profile
+  const OFVector<Uint8> iccProfile = ps.getICCProfile();
+  if (!iccProfile.empty())
+  {
+    // Encode the binary color profile data as a base64 string
+    std::string iccProfileAsString(iccProfile.begin(), iccProfile.end());
+    doc.AddMember("ICCProfile", Value(base64_encode(iccProfileAsString, false).c_str(), alloc), alloc);
+  }
+
   doc.AddMember("Flip", Value(ps.getFlip()), alloc);
   int rotation = 0;
   switch (ps.getRotation())
@@ -468,10 +478,59 @@ static void dumpPresentationState(STD_NAMESPACE ostream &out, DVPresentationStat
   out << buffer.GetString();
 }
 
+constexpr unsigned int Dimension = 2;
+using GrayPixelType = uint8_t;
+using GrayImageType = itk::Image<GrayPixelType, Dimension>;
+using OutputGrayImageType = itk::wasm::OutputImage<GrayImageType>;
+
+using ColorPixelType = itk::RGBPixel<uint8_t>;
+using ColorImageType = itk::Image<ColorPixelType, Dimension>;
+using OutputColorImageType = itk::wasm::OutputImage<ColorImageType>;
+
+template<typename OutputImageType, typename PixelType, unsigned int Dim>
+int GenerateOutputImage(OutputImageType& outputImage, const unsigned long width, const unsigned long height, const std::array<double, 2>& pixelSpacing, const void* pixelData)
+{
+  using ImportFilterType = itk::ImportImageFilter<PixelType, Dim>;
+  auto importFilter = itk::ImportImageFilter<PixelType, Dim>::New();
+  typename ImportFilterType::SizeType size;
+  size[0] = width;
+  size[1] = height;
+
+  typename itk::ImportImageFilter<PixelType, Dim>::IndexType start;
+  start.Fill(0);
+
+  typename itk::ImportImageFilter<PixelType, Dim>::RegionType region;
+  region.SetIndex(start);
+  region.SetSize(size);
+  importFilter->SetRegion(region);
+
+  const itk::SpacePrecisionType origin[Dim] = { 0.0, 0.0 };
+  importFilter->SetOrigin(origin);
+  const itk::SpacePrecisionType spacing[Dim] = { pixelSpacing[0], pixelSpacing[1] };
+  importFilter->SetSpacing(spacing);
+  const unsigned int numberOfPixels = size[0] * size[1];
+  // ColorImageType::Internal
+  importFilter->SetImportPointer((PixelType*)pixelData, numberOfPixels, false);
+  importFilter->Update();
+
+  // set as output image
+  outputImage.Set(importFilter->GetOutput());
+  return EXIT_SUCCESS;
+}
+
+template int GenerateOutputImage<OutputGrayImageType,  GrayPixelType,  2U>(OutputGrayImageType&,  const unsigned long, const unsigned long, const std::array<double, 2>&, const void*);
+template int GenerateOutputImage<OutputColorImageType, ColorPixelType, 2U>(OutputColorImageType&, const unsigned long, const unsigned long, const std::array<double, 2>&, const void*);
 
 int main(int argc, char *argv[])
 {
-  itk::wasm::Pipeline pipeline("apply-presentation-state-to-image", "Apply a presentation state to a given DICOM image and render output as pgm bitmap or dicom file.", argc, argv);
+  itk::wasm::Pipeline pipeline("apply-presentation-state-to-image", "Apply a presentation state to a given DICOM image and render output as bitmap, or dicom file.", argc, argv);
+
+  // Expecting color output
+  bool colorOutput{false};
+  pipeline.add_flag("--color-output", colorOutput, "output image as RGB (default: false)");
+
+  // pre-parse command line to determine if we need color or gray output image
+  ITK_WASM_PRE_PARSE(pipeline);
 
   // Inputs
   std::string imageIn;
@@ -485,14 +544,6 @@ int main(int argc, char *argv[])
   itk::wasm::OutputTextStream pstateOutStream;
   pipeline.add_option("presentation-state-out-stream", pstateOutStream, "Output overlay information")->type_name("OUTPUT_JSON");
 
-  // Processed output image
-  constexpr unsigned int Dimension = 2;
-  using PixelType = unsigned char;
-  using ImageType = itk::Image<PixelType, Dimension>;
-  using OutputImageType = itk::wasm::OutputImage<ImageType>;
-  OutputImageType outputImage;
-  pipeline.add_option("output-image", outputImage, "Output image")->type_name("OUTPUT_IMAGE");
-
   // Parameters
   std::string configFile;
   pipeline.add_option("--config-file", configFile, "filename: string. Process using settings from configuration file");
@@ -506,6 +557,18 @@ int main(int argc, char *argv[])
   bool noBitmapOutput{false};
   pipeline.add_flag("--no-bitmap-output", noBitmapOutput, "Do not get resulting image as bitmap output stream.");
 
+  // Define output image and bind to CLI option
+  OutputGrayImageType outputGrayImage;
+  OutputColorImageType outputColorImage;
+  if (colorOutput)
+  {
+    pipeline.add_option("output-image", outputColorImage, "Output image")->type_name("OUTPUT_IMAGE");
+  }
+  else
+  {
+    pipeline.add_option("output-image", outputGrayImage, "Output image")->type_name("OUTPUT_IMAGE");
+  }
+
   // DICOM output is currently not supported.
   // bool outputFormatPGM{true};
   // pipeline.add_flag("--pgm", outputFormatPGM, "save image as PGM (default)");
@@ -585,30 +648,14 @@ int main(int argc, char *argv[])
         }
         else
         {
-          using ImportFilterType = itk::ImportImageFilter<PixelType, Dimension>;
-          auto importFilter = ImportFilterType::New();
-          ImportFilterType::SizeType size;
-          size[0] = width;
-          size[1] = height;
-
-          ImportFilterType::IndexType start;
-          start.Fill(0);
-
-          ImportFilterType::RegionType region;
-          region.SetIndex(start);
-          region.SetSize(size);
-          importFilter->SetRegion(region);
-
-          const itk::SpacePrecisionType origin[Dimension] = { 0.0, 0.0 };
-          importFilter->SetOrigin(origin);
-          const itk::SpacePrecisionType spacing[Dimension] = { pixelSpacing[0], pixelSpacing[1] };
-          importFilter->SetSpacing(spacing);
-          const unsigned int numberOfPixels = size[0] * size[1];
-          importFilter->SetImportPointer((PixelType*)pixelData, numberOfPixels, false);
-          importFilter->Update();
-
-          // set as output image
-          outputImage.Set(importFilter->GetOutput());
+          if (colorOutput)
+          {
+            return GenerateOutputImage<OutputColorImageType, ColorPixelType, 2U>(outputColorImage, width, height, pixelSpacing, pixelData);
+          }
+          else
+          {
+            return GenerateOutputImage<OutputGrayImageType, GrayPixelType, 2U>(outputGrayImage, width, height, pixelSpacing, pixelData);
+          }
         }
       }
       else

packages/dicom/typescript/package.json

@@ -37,7 +37,7 @@
   "author": "",
   "license": "Apache-2.0",
   "dependencies": {
-    "itk-wasm": "^1.0.0-b.101"
+    "itk-wasm": "../../.."
   },
   "devDependencies": {
     "@rollup/plugin-commonjs": "^24.0.0",

packages/dicom/typescript/src/apply-presentation-state-to-image-node.ts

@@ -17,7 +17,7 @@ import ApplyPresentationStateToImageNodeResult from './apply-presentation-state-
 import path from 'path'
 
 /**
- * Apply a presentation state to a given DICOM image and render output as pgm bitmap or dicom file.
+ * Apply a presentation state to a given DICOM image and render output as bitmap, or dicom file.
  *
  * @param {BinaryFile} imageIn - Input DICOM file
  * @param {BinaryFile} presentationStateFile - Process using presentation state file
@@ -48,6 +48,9 @@ async function applyPresentationStateToImageNode(
   args.push('1')
   // Options
   args.push('--memory-io')
+  if (typeof options.colorOutput !== "undefined") {
+    args.push('--color-output')
+  }
   if (typeof options.configFile !== "undefined") {
     args.push('--config-file', options.configFile.toString())
   }

packages/dicom/typescript/src/apply-presentation-state-to-image-options.ts

@@ -1,4 +1,7 @@
 interface ApplyPresentationStateToImageOptions {
+  /** output image as RGB (default: false) */
+  colorOutput?: boolean
+
   /** filename: string. Process using settings from configuration file */
   configFile?: string
 

packages/dicom/typescript/src/apply-presentation-state-to-image.ts

@@ -20,7 +20,7 @@ import { getPipelinesBaseUrl } from './pipelines-base-url.js'
 import { getPipelineWorkerUrl } from './pipeline-worker-url.js'
 
 /**
- * Apply a presentation state to a given DICOM image and render output as pgm bitmap or dicom file.
+ * Apply a presentation state to a given DICOM image and render output as bitmap, or dicom file.
  *
  * @param {BinaryFile} imageIn - Input DICOM file
  * @param {BinaryFile} presentationStateFile - Process using presentation state file
@@ -52,6 +52,9 @@ async function applyPresentationStateToImage(
   args.push('1')
   // Options
   args.push('--memory-io')
+  if (typeof options.colorOutput !== "undefined") {
+    args.push('--color-output')
+  }
   if (typeof options.configFile !== "undefined") {
     args.push('--config-file', options.configFile.toString())
   }

packages/dicom/typescript/test/node.js

@@ -11,10 +11,13 @@ import {
     return (a.length === b.length && a.every((val, idx) => val === b[idx]))
   }
 
+const testPathPrefix = '../test/data/input/';
+const baselinePathPrefix = '../test/data/baseline/';
+
 test('structuredReportToText', async t => {
 
   const fileName = '88.33-comprehensive-SR.dcm'
-  const testFilePath = `../test/data/input/${fileName}`
+  const testFilePath = testPathPrefix + fileName
 
   const dicomFileBuffer = fs.readFileSync(testFilePath)
   const dicomFile = new Uint8Array(dicomFileBuffer)
@@ -31,7 +34,7 @@ test('structuredReportToText', async t => {
 test('structuredReportToHtml', async t => {
 
   const fileName = '88.33-comprehensive-SR.dcm'
-  const testFilePath = `../test/data/input/${fileName}`
+  const testFilePath = testPathPrefix + fileName
 
   const dicomFileBuffer = fs.readFileSync(testFilePath)
   const dicomFile = new Uint8Array(dicomFileBuffer)
@@ -57,7 +60,7 @@ test('structuredReportToHtml', async t => {
 test('read Radiation Dose SR', async t => {
 
   const fileName = '88.67-radiation-dose-SR.dcm'
-  const testFilePath = `../test/data/input/${fileName}`
+  const testFilePath = testPathPrefix + fileName
 
   const dicomFileBuffer = fs.readFileSync(testFilePath)
   const dicomFile = new Uint8Array(dicomFileBuffer)
@@ -71,7 +74,7 @@ test('read Radiation Dose SR', async t => {
 test('readDicomEncapsulatedPdfNode', async t => {
 
   const fileName = '104.1-SR-printed-to-pdf.dcm'
-  const testFilePath = `../test/data/input/${fileName}`
+  const testFilePath = testPathPrefix + fileName
   const dicomFileBuffer = fs.readFileSync(testFilePath)
   const dicomFile = new Uint8Array(dicomFileBuffer)
   const { pdfBinaryOutput: outputBinaryStream } = await readDicomEncapsulatedPdfNode({ data: dicomFile, path: fileName })
@@ -82,7 +85,7 @@ test('readDicomEncapsulatedPdfNode', async t => {
 test('read Key Object Selection SR', async t => {
 
   const fileName = '88.59-KeyObjectSelection-SR.dcm'
-  const testFilePath = `../test/data/input/${fileName}`
+  const testFilePath = testPathPrefix + fileName
   const dicomFileBuffer = fs.readFileSync(testFilePath)
   const dicomFile = new Uint8Array(dicomFileBuffer)
 
@@ -98,7 +101,7 @@ test('read Key Object Selection SR', async t => {
   t.assert(outputText.includes(`<link rel="stylesheet" type="text/css" href="https://css-host/dir/subdir/my-first-style.css">`))
 
   const cssfileName = 'test-style.css'
-  const testCssFilePath = `../test/data/input/${cssfileName}`
+  const testCssFilePath = testPathPrefix + cssfileName
   const cssFileBuffer = fs.readFileSync(testCssFilePath)
 
   const { outputText: outputWithCSSFile } = await structuredReportToHtmlNode(
@@ -116,17 +119,21 @@ test('Apply presentation state to dicom image.', async t => {
 
   // Read the input image file
   const inputFile = 'gsps-pstate-test-input-image.dcm'
-  const inputFilePath = `../test/data/input/${inputFile}`
+  const inputFilePath = testPathPrefix + inputFile
   const dicomFileBuffer = fs.readFileSync(inputFilePath)
   const inputImage = new Uint8Array(dicomFileBuffer)
 
   // Read the presentation state file (that references the above image internally using its SOPInstanceUID).
   const pstateFile = 'gsps-pstate-test-input-pstate.dcm'
-  const pstateFilePath = `../test/data/input/${pstateFile}`
+  const pstateFilePath = testPathPrefix + pstateFile
   const pstateFileBuffer = fs.readFileSync(pstateFilePath)
   const inputPState = new Uint8Array(pstateFileBuffer)
 
-  const { presentationStateOutStream: pstateJsonOut, outputImage } = await applyPresentationStateToImageNode({ data: inputImage, path: inputFile }, { data: inputPState, path: pstateFile })
+  const { presentationStateOutStream: pstateJsonOut, outputImage } = await applyPresentationStateToImageNode(
+    { data: inputImage, path: inputFile },
+    { data: inputPState, path: pstateFile }
+  )
+
 
   t.assert(pstateJsonOut != null)
   t.assert(outputImage != null)
@@ -142,21 +149,73 @@ test('Apply presentation state to dicom image.', async t => {
   t.assert(arrayEquals(outputImage.size, [512, 512]))
 
   const baselineJsonFile = 'gsps-pstate-baseline.json'
-  const baselineJsonFilePath = `../test/data/baseline/${baselineJsonFile}`
+  const baselineJsonFilePath = baselinePathPrefix + baselineJsonFile
   const baselineJsonFileBuffer = fs.readFileSync(baselineJsonFilePath)
   // the slice operation removes the last EOF char from the baseline file.
   const baselineJsonString = baselineJsonFileBuffer.toString().slice(0, -1)
   const baselineJsonObject = JSON.parse(baselineJsonString)
+
   t.assert(baselineJsonObject.PresentationLabel === pstateJsonOut.PresentationLabel)
   t.assert(baselineJsonObject.PresentationSizeMode === pstateJsonOut.PresentationSizeMode)
   t.assert(baselineJsonObject.toString() === pstateJsonOut.toString())
 
   const baselineImage = 'gsps-pstate-image-baseline.pgm'
-  const baselineImageFilePath = `../test/data/baseline/${baselineImage}`
+  const baselineImageFilePath = baselinePathPrefix + baselineImage
   const baselineImageFileBuffer = fs.readFileSync(baselineImageFilePath)
   // slice to get only the pixel buffer from the baseline image (pgm file)
   const baselinePixels = baselineImageFileBuffer.slice(15)
   t.assert(baselinePixels.length === outputImage.data.length)
   t.assert(Buffer.compare(baselinePixels, outputImage.data) === 0)
 
 })
+
+test('Apply color presentation state (CSPS) to a color dicom image.', async t => {
+
+  // Read the input image file
+  const inputFile = 'csps-input-image.dcm'
+  const inputFilePath = testPathPrefix + inputFile
+  const dicomFileBuffer = fs.readFileSync(inputFilePath)
+  const inputImage = new Uint8Array(dicomFileBuffer)
+
+  // Read the presentation state file (that references the above image internally using its SOPInstanceUID).
+  const pstateFile = 'csps-input-pstate.dcm'
+  const pstateFilePath = testPathPrefix + pstateFile
+  const pstateFileBuffer = fs.readFileSync(pstateFilePath)
+  const inputPState = new Uint8Array(pstateFileBuffer)
+
+  const { presentationStateOutStream: pstateJsonOut, outputImage } = await applyPresentationStateToImageNode(
+    { data: inputImage, path: inputFile }, { data: inputPState, path: pstateFile },
+    { frame: 1, colorOutput: true }
+  )
+
+  t.assert(pstateJsonOut != null)
+  t.assert(outputImage != null)
+  t.assert(outputImage.imageType.dimension === 2)
+  t.assert(outputImage.imageType.componentType === 'uint8')
+  t.assert(outputImage.imageType.pixelType === 'RGB')
+  t.assert(outputImage.imageType.components === 3)
+
+  t.assert(arrayEquals(outputImage.origin, [0, 0]))
+  t.assert(arrayEquals(outputImage.spacing, [0.683, 0.683]))
+  t.assert(arrayEquals(outputImage.direction, [1, 0, 0, 1]))
+  t.assert(arrayEquals(outputImage.size, [768, 1024]))
+
+  const baselineJsonFile = 'csps-pstate-baseline.json'
+  const baselineJsonFilePath = baselinePathPrefix + baselineJsonFile
+  const baselineJsonFileBuffer = fs.readFileSync(baselineJsonFilePath)
+  // the slice operation removes the last EOF char from the baseline file.
+  const baselineJsonString = baselineJsonFileBuffer.toString().slice(0, -1)
+  const baselineJsonObject = JSON.parse(baselineJsonString)
+
+  t.assert(baselineJsonObject.PresentationLabel === pstateJsonOut.PresentationLabel)
+  t.assert(baselineJsonObject.PresentationSizeMode === pstateJsonOut.PresentationSizeMode)
+  t.assert(baselineJsonObject.toString() === pstateJsonOut.toString())
+
+  const baselineImage = 'csps-output-image-baseline.bmp'
+  const baselineImageFilePath = baselinePathPrefix + baselineImage
+  const baselineImageFileBuffer = fs.readFileSync(baselineImageFilePath)
+  // Slice to get only the pixel buffer from the baseline image (BMP file has 54 bytes of header data before pixel buffer begins).
+  const baselinePixels = baselineImageFileBuffer.slice(54)
+  t.assert(baselinePixels.length === outputImage.data.length)
+  t.assert(Buffer.compare(baselinePixels, outputImage.data) === 0)
+})