Merge pull request #844 from jadh4v/ENH-handle-CSPS-using-DCMTK

feat(CSPS): add preliminary support for CSPS

.github/workflows/python-wasm.yml

@@ -143,6 +143,7 @@ jobs:
         if: ${{ matrix.python-minor-version < 10 }}
         working-directory: ./packages/dicom/python/itkwasm-dicom-wasi
         run: |
+          python -m pip install pillow
           python -m pip install -e .
           pytest
       - name: Test dicom-emscripten chrome

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(); \

package.json

@@ -25,8 +25,8 @@
   "scripts": {
     "commit": "git cz",
     "bindgen": "node ./src/itk-wasm-cli.js bindgen ./dist/dicom/src ./dist/dicom/public/pipelines/*.wasm",
-    "build": "npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs && npm run build:emscripten:packages",
-    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeig4g7wosycckndpiouphtwowakccbkmunsvvgrg5bvjoz63p4s6hi https://w3s.link/ipfs/bafkreicrqj3nps6xep75zafmevtseitj6md2dgbce22jgizefuouc5vfca",
+    "build": "npm run build:testData && npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs && npm run build:emscripten:packages",
+    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeic2ckitzhl5b476fgfewt7ilel3mkzi5x66o6gga5s7n34g2t36xm https://w3s.link/ipfs/bafkreibxuanogkwccski66azxafdpjjj3sbua6g3pqdvwwwe72h3d6agoi",
     "build:debug": "npm run build:emscripten -- --debug && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack -- --mode development",
     "build:tsc": "tsc --pretty",
     "build:tscWorkersModuleLoader": "tsc --types --lib es2017,webworker --rootDir ./src/ --outDir ./dist/ --moduleResolution node --target es2017 --module es2020 --strict --forceConsistentCasingInFileNames --declaration ./src/core/internal/loadEmscriptenModuleWebWorker.ts",
@@ -36,11 +36,11 @@
     "build:webpack": "webpack --mode production --progress --color && webpack --mode development --progress --color",
     "build:emscripten": "node ./src/build-emscripten.js",
     "build:emscripten:compress-stringify": "node ./src/itk-wasm-cli.js -s packages/compress-stringify -b emscripten-build build ",
-    "build:bindgen:typescript:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b emscripten-build bindgen --package-version 0.4.5 --package-name @itk-wasm/compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
-    "build:bindgen:python:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b wasi-build bindgen --language python --package-name itkwasm-compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --package-version 0.4.5 --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:typescript:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b emscripten-build bindgen --package-version 0.5.0 --package-name @itk-wasm/compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:python:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b wasi-build bindgen --language python --package-name itkwasm-compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --package-version 0.5.0 --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:dicom": "node ./src/itk-wasm-cli.js -s packages/dicom -b emscripten-build build ",
-    "build:bindgen:typescript:dicom": "./src/itk-wasm-cli.js -s packages/dicom -b emscripten-build bindgen --package-version 2.0.3 --package-name @itk-wasm/dicom --package-description \"Read files and images related to DICOM file format.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
-    "build:bindgen:python:dicom": "./src/itk-wasm-cli.js -s packages/dicom -b wasi-build bindgen --package-version 2.0.3 --language python --package-name itkwasm-dicom --package-description \"Read files and images related to DICOM file format.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:typescript:dicom": "./src/itk-wasm-cli.js -s packages/dicom -b emscripten-build bindgen --package-version 2.1.0 --package-name @itk-wasm/dicom --package-description \"Read files and images related to DICOM file format.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:python:dicom": "./src/itk-wasm-cli.js -s packages/dicom -b wasi-build bindgen --package-version 2.1.0 --language python --package-name itkwasm-dicom --package-description \"Read files and images related to DICOM file format.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:packages": "npm run build:emscripten:compress-stringify && npm run build:bindgen:typescript:compress-stringify && npm run build:emscripten:dicom && npm run build:bindgen:typescript:dicom",
     "build:wasi": "node ./src/build-wasi.js && npm run build:wasi:packages",
     "build:wasi:compress-stringify": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/compress-stringify -b wasi-build build",

packages/compress-stringify/python/itkwasm-compress-stringify-emscripten/itkwasm_compress_stringify_emscripten/_version.py

@@ -1 +1 @@
-__version__ = "0.4.5"
+__version__ = "0.5.0"

packages/compress-stringify/python/itkwasm-compress-stringify-wasi/.gitignore

@@ -0,0 +1 @@
+dist/

packages/compress-stringify/python/itkwasm-compress-stringify-wasi/itkwasm_compress_stringify_wasi/_version.py

@@ -1 +1 @@
-__version__ = "0.4.5"
+__version__ = "0.5.0"

packages/compress-stringify/python/itkwasm-compress-stringify/.gitignore

@@ -0,0 +1 @@
+dist/

packages/compress-stringify/python/itkwasm-compress-stringify/itkwasm_compress_stringify/_version.py

@@ -1 +1 @@
-__version__ = "0.4.5"
+__version__ = "0.5.0"

packages/compress-stringify/python/itkwasm-compress-stringify/itkwasm_compress_stringify/compress_stringify.py

@@ -1,7 +1,7 @@
 # Generated file. Do not edit.
 
 import os
-from typing import Dict, Tuple, Optional
+from typing import Dict, Tuple, Optional, List
 
 from itkwasm import (
     environment_dispatch,

packages/compress-stringify/python/itkwasm-compress-stringify/itkwasm_compress_stringify/compress_stringify_async.py

@@ -1,7 +1,7 @@
 # Generated file. Do not edit.
 
 import os
-from typing import Dict, Tuple, Optional
+from typing import Dict, Tuple, Optional, List
 
 from itkwasm import (
     environment_dispatch,

packages/compress-stringify/python/itkwasm-compress-stringify/itkwasm_compress_stringify/parse_string_decompress.py

@@ -1,7 +1,7 @@
 # Generated file. Do not edit.
 
 import os
-from typing import Dict, Tuple, Optional
+from typing import Dict, Tuple, Optional, List
 
 from itkwasm import (
     environment_dispatch,

packages/compress-stringify/python/itkwasm-compress-stringify/itkwasm_compress_stringify/parse_string_decompress_async.py

@@ -1,7 +1,7 @@
 # Generated file. Do not edit.
 
 import os
-from typing import Dict, Tuple, Optional
+from typing import Dict, Tuple, Optional, List
 
 from itkwasm import (
     environment_dispatch,

packages/compress-stringify/typescript/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@itk-wasm/compress-stringify",
-  "version": "0.4.5",
+  "version": "0.5.0",
   "description": "Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.",
   "type": "module",
   "module": "./dist/bundles/compress-stringify.js",
@@ -38,7 +38,7 @@
   "author": "",
   "license": "Apache-2.0",
   "dependencies": {
-    "itk-wasm": "^1.0.0-b.79"
+    "itk-wasm": "^1.0.0-b.111"
   },
   "devDependencies": {
     "@rollup/plugin-commonjs": "^24.0.0",

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/python/itkwasm-dicom-emscripten/itkwasm_dicom_emscripten/_version.py

@@ -1 +1 @@
-__version__ = "2.0.3"
+__version__ = "2.1.0"

packages/dicom/python/itkwasm-dicom-emscripten/itkwasm_dicom_emscripten/apply_presentation_state_to_image_async.py

@@ -20,19 +20,23 @@
 async def apply_presentation_state_to_image_async(
     image_in: os.PathLike,
     presentation_state_file: os.PathLike,
+    color_output: bool = False,
     config_file: str = "",
     frame: int = 1,
     no_presentation_state_output: bool = False,
     no_bitmap_output: bool = False,
 ) -> Tuple[Dict, Image]:
-    """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 image_in: Input DICOM file
     :type  image_in: os.PathLike
 
     :param presentation_state_file: Process using presentation state file
     :type  presentation_state_file: os.PathLike
 
+    :param color_output: output image as RGB (default: false)
+    :type  color_output: bool
+
     :param config_file: filename: string. Process using settings from configuration file
     :type  config_file: str
 
@@ -55,6 +59,8 @@ async def apply_presentation_state_to_image_async(
     web_worker = js_resources.web_worker
 
     kwargs = {}
+    if color_output:
+        kwargs["colorOutput"] = to_js(color_output)
     if config_file:
         kwargs["configFile"] = to_js(config_file)
     if frame:

packages/dicom/python/itkwasm-dicom-emscripten/test/fixtures.py

@@ -17,8 +17,12 @@ def input_data():
     from pathlib import Path
     input_base_path = Path('..', '..', 'test', 'data')
     test_files = [
+        Path('input') / 'csps-input-image.dcm',
+        Path('input') / 'csps-input-pstate.dcm',
         Path('input') / 'gsps-pstate-test-input-image.dcm',
         Path('input') / 'gsps-pstate-test-input-pstate.dcm',
+        Path('baseline') / 'csps-pstate-baseline.json',
+        Path('baseline') / 'csps-output-image-baseline.bmp',
         Path('baseline') / 'gsps-pstate-baseline.json',
         Path('baseline') / 'gsps-pstate-image-baseline.pgm',
         Path('input') / '104.1-SR-printed-to-pdf.dcm',

packages/dicom/python/itkwasm-dicom-emscripten/test/test_apply_presentation_state_to_image_async.py

@@ -47,11 +47,74 @@ def write_input_data_to_fs(input_data, filename):
         # the slice operation removes the last EOF char from the baseline file.
         buffer = fp.read()[:-1]
     baseline_json_object = json.loads(buffer)
-    assert baseline_json_object['PresentationLabel'] == p_state_json_out['PresentationLabel']
-    assert baseline_json_object['PresentationSizeMode'] == p_state_json_out['PresentationSizeMode']
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
 
     baseline_image = 'gsps-pstate-image-baseline.pgm'
     baseline_buffer = input_data[baseline_image]
     # slice to get only the pixel buffer from the baseline image (pgm file)
     baseline_pixels = baseline_buffer[15:]
-    assert np.array_equal(np.frombuffer(baseline_pixels, dtype=np.uint8), output_image.data.ravel())
+    assert np.array_equal(np.frombuffer(baseline_pixels, dtype=np.uint8), output_image.data.ravel())
+
+@run_in_pyodide(packages=['micropip','pillow'])
+async def test_apply_color_presentation_state_to_dicom_image(selenium, package_wheel, input_data):
+    import json
+
+    import micropip
+    await micropip.install(package_wheel)
+    def write_input_data_to_fs(input_data, filename):
+        with open(filename, 'wb') as fp:
+            fp.write(input_data[filename])
+
+    from itkwasm_dicom_emscripten import apply_presentation_state_to_image_async
+    import numpy as np
+
+    input_file = 'csps-input-image.dcm'
+    write_input_data_to_fs(input_data, input_file)
+
+    p_state_file = 'csps-input-pstate.dcm'
+    write_input_data_to_fs(input_data, p_state_file)
+
+    from itkwasm.pyodide import to_js
+    p_state_json_out, output_image = await apply_presentation_state_to_image_async(input_file, p_state_file, color_output=True)
+
+    assert p_state_json_out != None
+    assert output_image != None
+
+    assert output_image.imageType.dimension == 2
+    assert output_image.imageType.componentType == 'uint8'
+    assert output_image.imageType.pixelType == 'RGB'
+    assert output_image.imageType.components == 3
+
+    assert np.array_equal(output_image.origin, [0, 0])
+    assert np.array_equal(output_image.spacing, [0.683, 0.683])
+    assert np.array_equal(output_image.direction, [[1, 0], [0, 1]])
+    assert np.array_equal(output_image.size, [768, 1024])
+
+    baseline_json_file = 'csps-pstate-baseline.json'
+    write_input_data_to_fs(input_data, baseline_json_file)
+    with open(baseline_json_file, 'r') as fp:
+        # the slice operation removes the last EOF char from the baseline file.
+        buffer = fp.read()[:-1]
+    baseline_json_object = json.loads(buffer)
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
+
+    baseline_image = 'csps-output-image-baseline.bmp'
+    write_input_data_to_fs(input_data, baseline_image)
+
+    from PIL import Image
+    im = Image.open(baseline_image)
+
+    baseline_pixels = np.array(im).flatten()
+    output_pixels = output_image.data.ravel().flatten()
+
+    assert np.array_equal(output_pixels, baseline_pixels)