Merge pull request #1556 from thewtex/downsample-translation

fix(downsample): shift output origin to coarse-grid pixel centers

Author: thewtex

packages/downsample/downsample-label-image.cxx

@@ -21,6 +21,7 @@
 #include "itkOutputImage.h"
 #include "itkSupportInputImageTypes.h"
 
+#include "itkContinuousIndex.h"
 #include "itkLabelImageGenericInterpolateImageFunction.h"
 #include "itkLinearInterpolateImageFunction.h"
 #include "itkResampleImageFilter.h"
@@ -56,21 +57,24 @@ class PipelineFunctor
 
     ITK_WASM_PARSE(pipeline);
 
-    const auto inputOrigin = inputImage.Get()->GetOrigin();
     const auto inputSpacing = inputImage.Get()->GetSpacing();
     const auto inputSize = inputImage.Get()->GetLargestPossibleRegion().GetSize();
+    const auto inputStartIndex = inputImage.Get()->GetLargestPossibleRegion().GetIndex();
 
-    typename ImageType::PointType   outputOrigin;
-    typename ImageType::SpacingType outputSpacing;
-    typename ImageType::SizeType    outputSize;
+    typename ImageType::PointType                outputOrigin;
+    typename ImageType::SpacingType              outputSpacing;
+    typename ImageType::SizeType                 outputSize;
+    itk::ContinuousIndex<double, ImageDimension> outputOriginIndex;
     for (unsigned int i = 0; i < ImageDimension; ++i)
     {
       const double cropRadiusValue = cropRadius.size() ? cropRadius[i] : 0.0;
 
-      outputOrigin[i] = inputOrigin[i] + cropRadiusValue * inputSpacing[i];
+      // Origin lands at the center of the first bin, matching itk::BinShrinkImageFilter
+      outputOriginIndex[i] = inputStartIndex[i] + cropRadiusValue + (shrinkFactors[i] - 1.0) / 2.0;
       outputSpacing[i] = inputSpacing[i] * shrinkFactors[i];
       outputSize[i] = std::max<itk::SizeValueType>(0, (inputSize[i] - 2 * cropRadiusValue) / shrinkFactors[i]);
     }
+    inputImage.Get()->TransformContinuousIndexToPhysicalPoint(outputOriginIndex, outputOrigin);
 
     using InterpolatorType =
       itk::LabelImageGenericInterpolateImageFunction<ImageType, itk::LinearInterpolateImageFunction>;

packages/downsample/downsample.cxx

@@ -21,6 +21,7 @@
 #include "itkOutputImage.h"
 #include "itkSupportInputImageTypes.h"
 
+#include "itkContinuousIndex.h"
 #include "itkDiscreteGaussianImageFilter.h"
 #include "itkLinearInterpolateImageFunction.h"
 #include "itkResampleImageFilter.h"
@@ -94,21 +95,24 @@ DownsampleScalarImage(itk::wasm::Pipeline & pipeline, const TImage * inputImage)
   gaussianFilter->SetSigmaArray(sigmaArray);
   gaussianFilter->SetUseImageSpacingOff();
 
-  const auto inputOrigin = inputImage->GetOrigin();
   const auto inputSpacing = inputImage->GetSpacing();
   const auto inputSize = inputImage->GetLargestPossibleRegion().GetSize();
+  const auto inputStartIndex = inputImage->GetLargestPossibleRegion().GetIndex();
 
-  typename ImageType::PointType   outputOrigin;
-  typename ImageType::SpacingType outputSpacing;
-  typename ImageType::SizeType    outputSize;
+  typename ImageType::PointType                outputOrigin;
+  typename ImageType::SpacingType              outputSpacing;
+  typename ImageType::SizeType                 outputSize;
+  itk::ContinuousIndex<double, ImageDimension> outputOriginIndex;
   for (unsigned int i = 0; i < ImageDimension; ++i)
   {
     const double cropRadiusValue = cropRadius.size() ? cropRadius[i] : 0.0;
 
-    outputOrigin[i] = inputOrigin[i] + cropRadiusValue * inputSpacing[i];
+    // Origin lands at the center of the first bin, matching itk::BinShrinkImageFilter
+    outputOriginIndex[i] = inputStartIndex[i] + cropRadiusValue + (shrinkFactors[i] - 1.0) / 2.0;
     outputSpacing[i] = inputSpacing[i] * shrinkFactors[i];
     outputSize[i] = std::max<itk::SizeValueType>(0, (inputSize[i] - 2 * cropRadiusValue) / shrinkFactors[i]);
   }
+  inputImage->TransformContinuousIndexToPhysicalPoint(outputOriginIndex, outputOrigin);
 
   using InterpolatorType = itk::LinearInterpolateImageFunction<ImageType, double>;
   auto interpolator = InterpolatorType::New();
@@ -187,21 +191,24 @@ class PipelineFunctor<itk::VectorImage<TPixel, VDimension>>
 
     auto sigmaValues = downsampleSigma(shrinkFactors);
 
-    const auto inputOrigin = inputImage.Get()->GetOrigin();
     const auto inputSpacing = inputImage.Get()->GetSpacing();
     const auto inputSize = inputImage.Get()->GetLargestPossibleRegion().GetSize();
+    const auto inputStartIndex = inputImage.Get()->GetLargestPossibleRegion().GetIndex();
 
-    typename VectorImageType::PointType   outputOrigin;
-    typename VectorImageType::SpacingType outputSpacing;
-    typename VectorImageType::SizeType    outputSize;
+    typename VectorImageType::PointType     outputOrigin;
+    typename VectorImageType::SpacingType   outputSpacing;
+    typename VectorImageType::SizeType      outputSize;
+    itk::ContinuousIndex<double, Dimension> outputOriginIndex;
     for (unsigned int i = 0; i < Dimension; ++i)
     {
       const double cropRadiusValue = cropRadius.size() ? cropRadius[i] : 0.0;
 
-      outputOrigin[i] = inputOrigin[i] + cropRadiusValue * inputSpacing[i];
+      // Origin lands at the center of the first bin, matching itk::BinShrinkImageFilter
+      outputOriginIndex[i] = inputStartIndex[i] + cropRadiusValue + (shrinkFactors[i] - 1.0) / 2.0;
       outputSpacing[i] = inputSpacing[i] * shrinkFactors[i];
       outputSize[i] = std::max<itk::SizeValueType>(0, (inputSize[i] - 2 * cropRadiusValue) / shrinkFactors[i]);
     }
+    inputImage.Get()->TransformContinuousIndexToPhysicalPoint(outputOriginIndex, outputOrigin);
 
     auto composeFilter = ComposeFilterType::New();
 

packages/downsample/package.json

@@ -1,15 +1,16 @@
 {
   "name": "@itk-wasm/downsample-build",
-  "version": "1.8.1",
+  "version": "1.9.0",
   "private": true,
   "description": "Pipelines for downsampling images.",
   "type": "module",
   "itk-wasm": {
     "emscripten-docker-image": "docker.io/itkwasm/emscripten:latest",
     "wasi-docker-image": "docker.io/itkwasm/wasi:latest",
-    "test-data-hash": "bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq",
+    "test-data-hash": "bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi",
     "test-data-urls": [
-      "https://itk.mypinata.cloud/ipfs/bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq"
+      "https://github.com/InsightSoftwareConsortium/ITK-Wasm/releases/download/test-data/downsample-test-data-2026-07-15-bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi.tar.gz",
+      "https://itk.mypinata.cloud/ipfs/bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi"
     ],
     "typescript-package-name": "@itk-wasm/downsample",
     "python-package-name": "itkwasm-downsample",
@@ -32,10 +33,10 @@
     "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 bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq https://itk.mypinata.cloud/ipfs/bafkreiesjpg3sjqkyjb77djrffdvznjjsgvudd2y44iqjrfgnd45uyyprq",
+    "test:data:download": "dam download test/data test/data.tar.gz bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi https://github.com/InsightSoftwareConsortium/ITK-Wasm/releases/download/test-data/downsample-test-data-2026-07-15-bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi.tar.gz https://itk.mypinata.cloud/ipfs/bafkreie3b4xdvf4cqykvagruaivwtb3oi55hwt4egzlhppu2o3hw2eudhi",
     "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",
+    "test:python:emscripten": "pnpm build:emscripten && pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-emscripten",
     "test:python:dispatch": "pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-dispatch",
     "test:python": "itk-wasm pnpm-script test:python",
     "test:wasi": "itk-wasm pnpm-script test:wasi -- -V"

packages/downsample/pixi.toml

@@ -104,6 +104,8 @@ description = "Download Pyodide"
 [feature.python.tasks.test-emscripten]
 cmd = '''mkdir -p dist/pyodide &&
   cp -r ../../pyodide dist/ &&
+  mkdir -p dist/pyodide/pipelines &&
+  cp ../../emscripten-build/*.js ../../emscripten-build/*.wasm.zst dist/pyodide/pipelines/ &&
   hatch build -t wheel ./dist/pyodide/ &&
   pytest --dist-dir=./dist/pyodide --rt=chrome'''
 cwd = "python/itkwasm-downsample-emscripten"

packages/downsample/python/itkwasm-downsample-emscripten/itkwasm_downsample_emscripten/_version.py

@@ -1 +1 @@
-__version__ = "1.8.1"
+__version__ = "1.9.0"

packages/downsample/python/itkwasm-downsample-emscripten/itkwasm_downsample_emscripten/js_package.py

@@ -10,6 +10,9 @@
 async def test_downsample_async(selenium, package_wheel, input_data):
     import micropip
     await micropip.install([package_wheel, 'itkwasm-image-io', 'itkwasm-compare-images'])
+    import js
+    from itkwasm_downsample_emscripten.js_package import js_package
+    js_package.config.pipelines_base_url = f"{js.location.origin}/pipelines"
     def write_input_data_to_fs(input_data, filename):
         with open(filename, 'wb') as fp:
             fp.write(input_data[filename])

packages/downsample/python/itkwasm-downsample-emscripten/test/test_downsample_async.py

@@ -10,6 +10,9 @@
 async def test_downsample_bin_shrink_async(selenium, package_wheel, input_data):
     import micropip
     await micropip.install([package_wheel, 'itkwasm-image-io', 'itkwasm-compare-images'])
+    import js
+    from itkwasm_downsample_emscripten.js_package import js_package
+    js_package.config.pipelines_base_url = f"{js.location.origin}/pipelines"
     def write_input_data_to_fs(input_data, filename):
         with open(filename, 'wb') as fp:
             fp.write(input_data[filename])

packages/downsample/python/itkwasm-downsample-emscripten/test/test_downsample_bin_shrink_async.py

@@ -10,6 +10,9 @@
 async def test_downsample_label_image_async(selenium, package_wheel, input_data):
     import micropip
     await micropip.install([package_wheel, 'itkwasm-image-io', 'itkwasm-compare-images'])
+    import js
+    from itkwasm_downsample_emscripten.js_package import js_package
+    js_package.config.pipelines_base_url = f"{js.location.origin}/pipelines"
     def write_input_data_to_fs(input_data, filename):
         with open(filename, 'wb') as fp:
             fp.write(input_data[filename])

packages/downsample/python/itkwasm-downsample-emscripten/test/test_downsample_label_image_async.py

@@ -10,6 +10,9 @@
 async def test_downsample_sigma_async(selenium, package_wheel, input_data):
     import micropip
     await micropip.install([package_wheel,])
+    import js
+    from itkwasm_downsample_emscripten.js_package import js_package
+    js_package.config.pipelines_base_url = f"{js.location.origin}/pipelines"
 
     from itkwasm_downsample_emscripten import downsample_sigma_async