PERF: GenerateData() should not set "WriteResultImage" (issue #370)

Both `ElastixFilter::GenerateData()` and `ElastixRegistrationMethod::GenerateData()` did overwrite a user preference by explicitly setting the "WriteResultImage" parameter. This behavior was added with commit a6e8f10 "ENH: Add ElastixFilter support for initial transform parameter file" by Kasper Marstal, 3 February 2016. Which causes a performance issue, #370 "Final image transformation takes long time", reported by orange676. With this commit these `GenerateData()` member functions longer set "WriteResultImage". When the value of this parameter is false, the elastix library will no longer generate a result image; `GetOutput()` will return an empty image. Discussed at the internal elastix sprint of 7 June 2021, with Marius, Stefan, and Viktor.
SuperElastix · Jun 7, 2021 · 2115035 · 2115035
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Showing 6 changed files with 166 additions and 9 deletions.
diff --git a/Core/ComponentBaseClasses/elxResamplerBase.h b/Core/ComponentBaseClasses/elxResamplerBase.h
@@ -38,6 +38,9 @@ namespace elastix
  *    result image is resampled and written. Choose from {"true", "false"} \n
  *    example: <tt>(WriteResultImage "false")</tt> \n
  *    The default is "true".
+ * \note When WriteResultImage is false, the executable will not write a
+ * result image, and the elastix library interface produces an empty image.
+ *
  * \parameter WriteResultImageAfterEachResolution: flag to determine if the intermediate
  *    result image is resampled and written after each resolution. Choose from {"true", "false"} \n
  *    example: <tt>(WriteResultImageAfterEachResolution "true" "false" "true")</tt> \n

diff --git a/Core/Main/GTesting/ElastixFilterGTest.cxx b/Core/Main/GTesting/ElastixFilterGTest.cxx
@@ -93,3 +93,70 @@ GTEST_TEST(ElastixFilter, Translation)
     EXPECT_EQ(std::round(std::stod(transformParameters[i])), translationOffset[i]);
   }
 }
+
+// Tests registering two images, having "WriteResultImage" set to false.
+GTEST_TEST(ElastixFilter, WriteResultImageFalse)
+{
+  constexpr auto ImageDimension = 2U;
+  using ImageType = itk::Image<float, ImageDimension>;
+  using RegionType = itk::ImageRegion<ImageDimension>;
+  using SizeType = itk::Size<ImageDimension>;
+  using IndexType = itk::Index<ImageDimension>;
+  using OffsetType = itk::Offset<ImageDimension>;
+
+  const OffsetType translationOffset{ { 1, -2 } };
+  const auto       regionSize = SizeType::Filled(2);
+  const SizeType   imageSize{ { 5, 6 } };
+  const IndexType  fixedImageRegionIndex{ { 1, 3 } };
+
+  const auto fixedImage = ImageType::New();
+  fixedImage->SetRegions(imageSize);
+  fixedImage->Allocate(true);
+  elx::CoreMainGTestUtilities::FillImageRegion(*fixedImage, fixedImageRegionIndex, regionSize);
+
+  const auto movingImage = ImageType::New();
+  movingImage->SetRegions(imageSize);
+  movingImage->Allocate(true);
+  elx::CoreMainGTestUtilities::FillImageRegion(*movingImage, fixedImageRegionIndex + translationOffset, regionSize);
+
+  const auto parameterObject = elastix::ParameterObject::New();
+  parameterObject->SetParameterMap(
+    elx::CoreMainGTestUtilities::CreateParameterMap({ { "ImageSampler", "Full" },
+                                                      { "MaximumNumberOfIterations", "2" },
+                                                      { "Metric", "AdvancedNormalizedCorrelation" },
+                                                      { "Optimizer", "AdaptiveStochasticGradientDescent" },
+                                                      { "Transform", "TranslationTransform" },
+                                                      { "WriteResultImage", "false" } }));
+
+  const auto filter = elx::ElastixFilter<ImageType, ImageType>::New();
+  ASSERT_NE(filter, nullptr);
+
+  filter->SetFixedImage(fixedImage);
+  filter->SetMovingImage(movingImage);
+  filter->SetParameterObject(parameterObject);
+  filter->Update();
+
+  // Expect an empty output image.
+  const auto * const output = filter->GetOutput();
+  ASSERT_NE(output, nullptr);
+  EXPECT_EQ(output->GetBufferedRegion().GetSize(), ImageType::SizeType());
+  EXPECT_EQ(output->GetBufferPointer(), nullptr);
+
+  const auto   transformParameterObject = filter->GetTransformParameterObject();
+  const auto & transformParameterMaps = transformParameterObject->GetParameterMap();
+
+  ASSERT_TRUE(!transformParameterMaps.empty());
+  EXPECT_EQ(transformParameterMaps.size(), 1);
+
+  const auto & transformParameterMap = transformParameterMaps.front();
+  const auto   found = transformParameterMap.find("TransformParameters");
+  ASSERT_NE(found, transformParameterMap.cend());
+
+  const auto & transformParameters = found->second;
+  ASSERT_EQ(transformParameters.size(), ImageDimension);
+
+  for (unsigned i{}; i < ImageDimension; ++i)
+  {
+    EXPECT_EQ(std::round(std::stod(transformParameters[i])), translationOffset[i]);
+  }
+}
diff --git a/Core/Main/GTesting/itkElastixRegistrationMethodGTest.cxx b/Core/Main/GTesting/itkElastixRegistrationMethodGTest.cxx
@@ -97,6 +97,74 @@ GTEST_TEST(itkElastixRegistrationMethod, Translation)
 }
 
 
+// Tests registering two images, having "WriteResultImage" set to false.
+GTEST_TEST(itkElastixRegistrationMethod, WriteResultImageFalse)
+{
+  constexpr auto ImageDimension = 2U;
+  using ImageType = itk::Image<float, ImageDimension>;
+  using RegionType = itk::ImageRegion<ImageDimension>;
+  using SizeType = itk::Size<ImageDimension>;
+  using IndexType = itk::Index<ImageDimension>;
+  using OffsetType = itk::Offset<ImageDimension>;
+
+  const OffsetType translationOffset{ { 1, -2 } };
+  const auto       regionSize = SizeType::Filled(2);
+  const SizeType   imageSize{ { 5, 6 } };
+  const IndexType  fixedImageRegionIndex{ { 1, 3 } };
+
+  const auto fixedImage = ImageType::New();
+  fixedImage->SetRegions(imageSize);
+  fixedImage->Allocate(true);
+  elx::CoreMainGTestUtilities::FillImageRegion(*fixedImage, fixedImageRegionIndex, regionSize);
+
+  const auto movingImage = ImageType::New();
+  movingImage->SetRegions(imageSize);
+  movingImage->Allocate(true);
+  elx::CoreMainGTestUtilities::FillImageRegion(*movingImage, fixedImageRegionIndex + translationOffset, regionSize);
+
+  const auto parameterObject = elastix::ParameterObject::New();
+  parameterObject->SetParameterMap(
+    elx::CoreMainGTestUtilities::CreateParameterMap({ { "ImageSampler", "Full" },
+                                                      { "MaximumNumberOfIterations", "2" },
+                                                      { "Metric", "AdvancedNormalizedCorrelation" },
+                                                      { "Optimizer", "AdaptiveStochasticGradientDescent" },
+                                                      { "Transform", "TranslationTransform" },
+                                                      { "WriteResultImage", "false" } }));
+
+  const auto filter = itk::ElastixRegistrationMethod<ImageType, ImageType>::New();
+  ASSERT_NE(filter, nullptr);
+
+  filter->SetFixedImage(fixedImage);
+  filter->SetMovingImage(movingImage);
+  filter->SetParameterObject(parameterObject);
+  filter->Update();
+
+  // Expect an empty output image.
+  const auto * const output = filter->GetOutput();
+  ASSERT_NE(output, nullptr);
+  EXPECT_EQ(output->GetBufferedRegion().GetSize(), ImageType::SizeType());
+  EXPECT_EQ(output->GetBufferPointer(), nullptr);
+
+  const auto   transformParameterObject = filter->GetTransformParameterObject();
+  const auto & transformParameterMaps = transformParameterObject->GetParameterMap();
+
+  ASSERT_TRUE(!transformParameterMaps.empty());
+  EXPECT_EQ(transformParameterMaps.size(), 1);
+
+  const auto & transformParameterMap = transformParameterMaps.front();
+  const auto   found = transformParameterMap.find("TransformParameters");
+  ASSERT_NE(found, transformParameterMap.cend());
+
+  const auto & transformParameters = found->second;
+  ASSERT_EQ(transformParameters.size(), ImageDimension);
+
+  for (unsigned i{}; i < ImageDimension; ++i)
+  {
+    EXPECT_EQ(std::round(std::stod(transformParameters[i])), translationOffset[i]);
+  }
+}
+
+
 GTEST_TEST(itkElastixRegistrationMethod, InitialTransformParameterFile)
 {
   // IndexRange is to be moved from namespace itk::Experimental

diff --git a/Core/Main/elxElastixFilter.hxx b/Core/Main/elxElastixFilter.hxx
@@ -18,7 +18,8 @@
 #ifndef elxElastixFilter_hxx
 #define elxElastixFilter_hxx
 
-#include <memory> // For unique_ptr.
+#include <algorithm> // For find.
+#include <memory>    // For unique_ptr.
 
 namespace elastix
 {
@@ -131,9 +132,6 @@ ElastixFilter<TFixedImage, TMovingImage>::GenerateData(void)
     itkExceptionMacro("Empty parameter map in parameter object.");
   }
 
-  // Elastix must always write result image to guarantee that the ITK pipeline is in a consistent state
-  parameterMapVector.back()["WriteResultImage"] = ParameterValueVectorType(1, "true");
-
   // Setup argument map
   ArgumentMapType argumentMap;
 
@@ -278,7 +276,17 @@ ElastixFilter<TFixedImage, TMovingImage>::GenerateData(void)
   }
   else
   {
-    itkExceptionMacro("Errors occured during registration: Could not read result image.");
+    const auto & parameterMap = parameterMapVector.back();
+    const auto   endOfParameterMap = parameterMap.cend();
+    const bool   writeResultImage =
+      std::find(parameterMap.cbegin(),
+                endOfParameterMap,
+                typename ParameterMapType::value_type{ "WriteResultImage", { "false" } }) == endOfParameterMap;
+
+    if (writeResultImage)
+    {
+      itkExceptionMacro("Errors occured during registration: Could not read result image.");
+    }
   }
 
   // Save parameter map

diff --git a/Core/Main/itkElastixRegistrationMethod.h b/Core/Main/itkElastixRegistrationMethod.h
@@ -171,6 +171,8 @@ class ITK_TEMPLATE_EXPORT ElastixRegistrationMethod : public itk::ImageSource<TF
   GetOutput(unsigned int idx) const;
   ResultImageType *
   GetOutput();
+
+  /* \note When "WriteResultImage" is false, the output image will be empty. */
   const ResultImageType *
   GetOutput() const;
 

diff --git a/Core/Main/itkElastixRegistrationMethod.hxx b/Core/Main/itkElastixRegistrationMethod.hxx
@@ -38,6 +38,8 @@
 #include "elxPixelType.h"
 #include "itkElastixRegistrationMethod.h"
 
+#include <algorithm> // For find.
+
 namespace itk
 {
 
@@ -150,9 +152,6 @@ ElastixRegistrationMethod<TFixedImage, TMovingImage>::GenerateData()
     itkExceptionMacro("Empty parameter map in parameter object.");
   }
 
-  // Elastix must always write result image to guarantee that the ITK pipeline is in a consistent state
-  parameterMapVector.back()["WriteResultImage"] = ParameterValueVectorType(1, "true");
-
   // Setup argument map
   ArgumentMapType argumentMap;
 
@@ -296,7 +295,17 @@ ElastixRegistrationMethod<TFixedImage, TMovingImage>::GenerateData()
   }
   else
   {
-    itkExceptionMacro("Errors occured during registration: Could not read result image.");
+    const auto & parameterMap = parameterMapVector.back();
+    const auto   endOfParameterMap = parameterMap.cend();
+    const bool   writeResultImage =
+      std::find(parameterMap.cbegin(),
+                endOfParameterMap,
+                typename ParameterMapType::value_type{ "WriteResultImage", { "false" } }) == endOfParameterMap;
+
+    if (writeResultImage)
+    {
+      itkExceptionMacro("Errors occured during registration: Could not read result image.");
+    }
   }
 
   // Save parameter map