Add resample pipeline to @itk-wasm/downsample (transform + selectable interpolator)

packages/core/typescript/itk-wasm/src/bindgen/python/wasi/wasi-function-module.js

@@ -239,7 +239,7 @@ from itkwasm import (
           ? `    if ${snake}:\n`
           : `    if ${snake} is not None:\n`
         if (parameter.type.startsWith('TEXT:{')) {
-          const choices = parameter.type.split('{')[1].split('}')[0].split(', ')
+          const choices = parameter.type.split('{')[1].split('}')[0].split(',')
           args += `        if ${snake} not in (${choices.map((c) => `'${c}'`).join(',')}):\n`
           args += `            raise ValueError(f'${snake} must be one of ${choices.join(', ')}')\n`
         }

packages/downsample/CMakeLists.txt

@@ -14,6 +14,8 @@ else()
   set(io_components
     ITKImageIO
     ITKTransformIO
+    ITKIOTransformInsightLegacy
+    ITKIOTransformHDF5
     )
 endif()
 
@@ -22,6 +24,7 @@ find_package(ITK REQUIRED
    WebAssemblyInterface
    ITKSmoothing
    ITKImageGrid
+   ITKImageFunction
    ITKTransform
    GenericLabelInterpolator
    ${io_components}
@@ -35,6 +38,7 @@ set(pipelines
   downsample-bin-shrink
   downsample-label-image
   resample-bounding-box
+  resample-to-reference
   )
 
 # resample-bounding-box-generate-inputs fabricates the self-contained inputs (fixed image, moving image,
@@ -163,3 +167,67 @@ if(NOT EMSCRIPTEN)
     COMMAND resample-bounding-box-test
       )
 endif()
+
+# Interpolator coverage: one self-contained test per interpolator, using
+# cthead1.png as both the moving image and the reference geometry (identity
+# transform), so every interpolator selection is exercised. Needs no new data.
+# The linear case doubles as the pipeline smoke test.
+add_test(NAME resample-to-reference-linear
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_linear.png
+    --interpolator linear
+    )
+
+add_test(NAME resample-to-reference-nearest-neighbor
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_nearest_neighbor.png
+    --interpolator nearest_neighbor
+    )
+
+add_test(NAME resample-to-reference-b-spline
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_b_spline.png
+    --interpolator b_spline
+    )
+
+add_test(NAME resample-to-reference-windowed-sinc
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_windowed_sinc.png
+    --interpolator windowed_sinc
+    )
+
+add_test(NAME resample-to-reference-gaussian
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_gaussian.png
+    --interpolator gaussian
+    )
+
+# Label-image interpolator on the existing multi-label test image.
+add_test(NAME resample-to-reference-label-image
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/2th_cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/2th_cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/2th_cthead1_resampled_label_image.png
+    --interpolator label_image
+    )
+
+# Background value: exercise the --default-value flag on the filesystem/CLI path (the memory-IO
+# pixel-value assertions live in the Node and Python suites). Identity resample onto the same grid.
+add_test(NAME resample-to-reference-default-value
+  COMMAND resample-to-reference
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/cthead1.png
+    ${CMAKE_CURRENT_BINARY_DIR}/cthead1_resampled_default_value.png
+    --interpolator linear
+    --default-value 128
+    )

packages/downsample/downsample.cxx

@@ -29,6 +29,39 @@
 
 #include "downsampleSigma.h"
 
+// Groups the CLI options shared by the scalar and vector downsample paths so both declare exactly one
+// option surface -- identical names, order, type_names, and help text. The option-target members must
+// outlive ITK_WASM_PARSE (CLI11 binds them by reference), so the caller owns this struct on its own stack
+// and passes it to addDownsampleOptions() before parsing.
+template <typename TImage>
+struct DownsampleOptions
+{
+  std::vector<unsigned int>      shrinkFactors{ 2, 2 };
+  std::vector<unsigned int>      cropRadius;
+  itk::wasm::OutputImage<TImage> downsampledImage;
+};
+
+// Declares the shared downsample option surface into `pipeline`, binding each option to the corresponding
+// member of `options`. The `input` option is declared separately by each functor (the scalar path adds it
+// before pre-parse dispatch), so it is not part of this shared surface.
+template <typename TImage>
+void
+addDownsampleOptions(itk::wasm::Pipeline & pipeline, DownsampleOptions<TImage> & options)
+{
+  constexpr unsigned int ImageDimension = TImage::ImageDimension;
+
+  pipeline.add_option("-s,--shrink-factors", options.shrinkFactors, "Shrink factors")
+    ->required()
+    ->type_size(ImageDimension);
+
+  pipeline.add_option("-r,--crop-radius", options.cropRadius, "Optional crop radius in pixel units.")
+    ->type_size(ImageDimension);
+
+  pipeline.add_option("downsampled", options.downsampledImage, "Output downsampled image")
+    ->required()
+    ->type_name("OUTPUT_IMAGE");
+}
+
 // Scalar image processing
 template <typename TImage>
 int
@@ -39,21 +72,15 @@ DownsampleScalarImage(itk::wasm::Pipeline & pipeline, const TImage * inputImage)
 
   pipeline.get_option("input")->required()->type_name("INPUT_IMAGE");
 
-  std::vector<unsigned int> shrinkFactors{ 2, 2 };
-  pipeline.add_option("-s,--shrink-factors", shrinkFactors, "Shrink factors")->required()->type_size(ImageDimension);
-
-  std::vector<unsigned int> cropRadius;
-  pipeline.add_option("-r,--crop-radius", cropRadius, "Optional crop radius in pixel units.")
-    ->type_size(ImageDimension);
-
-  using OutputImageType = itk::wasm::OutputImage<ImageType>;
-  OutputImageType downsampledImage;
-  pipeline.add_option("downsampled", downsampledImage, "Output downsampled image")
-    ->required()
-    ->type_name("OUTPUT_IMAGE");
+  DownsampleOptions<ImageType> options;
+  addDownsampleOptions(pipeline, options);
 
   ITK_WASM_PARSE(pipeline);
 
+  const std::vector<unsigned int> & shrinkFactors = options.shrinkFactors;
+  const std::vector<unsigned int> & cropRadius = options.cropRadius;
+  auto &                            downsampledImage = options.downsampledImage;
+
   auto sigmaValues = downsampleSigma(shrinkFactors);
 
   using GaussianFilterType = itk::DiscreteGaussianImageFilter<ImageType, ImageType>;
@@ -142,20 +169,15 @@ class PipelineFunctor<itk::VectorImage<TPixel, VDimension>>
     InputImageType inputImage;
     pipeline.add_option("input", inputImage, "Input image")->required()->type_name("INPUT_IMAGE");
 
-    std::vector<unsigned int> shrinkFactors{ 2, 2 };
-    pipeline.add_option("-s,--shrink-factors", shrinkFactors, "Shrink factors")->required()->type_size(Dimension);
-
-    std::vector<unsigned int> cropRadius;
-    pipeline.add_option("-r,--crop-radius", cropRadius, "Optional crop radius in pixel units.")->type_size(Dimension);
-
-    using OutputImageType = itk::wasm::OutputImage<VectorImageType>;
-    OutputImageType downsampledImage;
-    pipeline.add_option("downsampled", downsampledImage, "Output downsampled image")
-      ->required()
-      ->type_name("OUTPUT_IMAGE");
+    DownsampleOptions<VectorImageType> options;
+    addDownsampleOptions(pipeline, options);
 
     ITK_WASM_PARSE(pipeline);
 
+    const std::vector<unsigned int> & shrinkFactors = options.shrinkFactors;
+    const std::vector<unsigned int> & cropRadius = options.cropRadius;
+    auto &                            downsampledImage = options.downsampledImage;
+
     // Get number of components
     const unsigned int numberOfComponents = inputImage.Get()->GetNumberOfComponentsPerPixel();
 

packages/downsample/package.json

@@ -7,9 +7,9 @@
   "itk-wasm": {
     "emscripten-docker-image": "docker.io/itkwasm/emscripten:latest",
     "wasi-docker-image": "docker.io/itkwasm/wasi:latest",
-    "test-data-hash": "bafkreigtrr3oeqaunbyhrpuvvhc5hfmpbddc4u52jvonsvr2m2xe5ni3jq",
+    "test-data-hash": "bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq",
     "test-data-urls": [
-      "https://itk.mypinata.cloud/ipfs/bafkreigtrr3oeqaunbyhrpuvvhc5hfmpbddc4u52jvonsvr2m2xe5ni3jq"
+      "https://itk.mypinata.cloud/ipfs/bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq"
     ],
     "typescript-package-name": "@itk-wasm/downsample",
     "python-package-name": "itkwasm-downsample",
@@ -32,7 +32,7 @@
     "build:gen:typescript": "itk-wasm pnpm-script build:gen:typescript",
     "build:gen:python": "pnpm build:wasi && pnpm bindgen:python",
     "test": "pnpm test:data:download && pnpm build:gen:python && pnpm test:python",
-    "test:data:download": "dam download test/data test/data.tar.gz bafkreigtrr3oeqaunbyhrpuvvhc5hfmpbddc4u52jvonsvr2m2xe5ni3jq https://itk.mypinata.cloud/ipfs/bafkreigtrr3oeqaunbyhrpuvvhc5hfmpbddc4u52jvonsvr2m2xe5ni3jq",
+    "test:data:download": "dam download test/data test/data.tar.gz bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq https://itk.mypinata.cloud/ipfs/bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq",
     "test:data:pack": "dam pack test/data test/data.tar.gz",
     "test:python:wasi": "pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-wasi",
     "test:python:emscripten": "pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-emscripten",