ENH: Add elastix parameter "UseSamplingForGroupwiseRegistration"

Allows elastix users to specify that the image sampling is used for group-wise registration:

    (UseSamplingForGroupwiseRegistration "true")

Aims to implement a generalization to the ReducedFullSampler, pull request #52 proposed by Mathias Polfliet in 2018.

Common/GTesting/itkImageFullSamplerGTest.cxx

@@ -185,4 +185,42 @@ GTEST_TEST(ImageFullSampler, ExactlyEqualVersusSlightlyDifferentMaskImageDomain)
   EXPECT_FALSE(samplesOnExactlyEqualImageDomains.empty());
 
   EXPECT_EQ(samplesOnExactlyEqualImageDomains, samplesOnSlightlyDifferentImageDomains);
+}
+
+
+GTEST_TEST(ImageFullSampler, UseForGroupwiseRegistration)
+{
+  using PixelType = std::uint8_t;
+  static constexpr auto Dimension = 3U;
+  using ImageType = itk::Image<PixelType, Dimension>;
+  using ImageFullSamplerType = itk::ImageFullSampler<ImageType>;
+
+  std::mt19937 randomNumberEngine{};
+  const auto   imageDomain = CreateRandomImageDomain<Dimension>(randomNumberEngine);
+  const auto   image = CreateImageFilledWithSequenceOfNaturalNumbers<PixelType>(imageDomain);
+  elx::DefaultConstruct<ImageFullSamplerType> sampler{};
+
+  sampler.SetInput(image);
+  sampler.UseForGroupwiseRegistration();
+  sampler.Update();
+
+  const auto & output = DerefRawPointer(sampler.GetOutput());
+
+  const auto reducedRegion = [imageDomain] {
+    auto size = imageDomain.size;
+    size.back() = 1;
+    return itk::ImageRegion<Dimension>{ imageDomain.index, size };
+  }();
+
+  const itk::ImageRegionRange imageRegionRange(*image, reducedRegion);
+  const std::size_t           numberOfSamples{ output.size() };
+
+  ASSERT_EQ(numberOfSamples, imageRegionRange.size());
+
+  auto imageRegionIterator = imageRegionRange.cbegin();
+  for (std::size_t i{}; i < numberOfSamples; ++i)
+  {
+    EXPECT_EQ(output[i].m_ImageValue, *imageRegionIterator);
+    ++imageRegionIterator;
+  }
 }

Common/ImageSamplers/itkImageSamplerBase.h

@@ -209,6 +209,13 @@ class ITK_TEMPLATE_EXPORT ImageSamplerBase
   /** Allows disabling the use of multi-threading, by `SetUseMultiThread(false)`. */
   itkSetMacro(UseMultiThread, bool);
 
+  /** Tells that the sampler is used for groupwise registration. */
+  void
+  UseForGroupwiseRegistration()
+  {
+    m_UseForGroupwiseRegistration = true;
+  }
+
 protected:
   /** The constructor. */
   ImageSamplerBase();
@@ -264,6 +271,8 @@ class ITK_TEMPLATE_EXPORT ImageSamplerBase
 
   InputImageRegionType m_CroppedInputImageRegion{};
   InputImageRegionType m_DummyInputImageRegion{};
+
+  bool m_UseForGroupwiseRegistration{ false };
 };
 
 } // end namespace itk

Common/ImageSamplers/itkImageSamplerBase.hxx

@@ -301,6 +301,12 @@ ImageSamplerBase<TInputImage>::CropInputImageRegion()
    * InputImageRegion and the BoundingBoxRegion.
    */
   m_CroppedInputImageRegion = m_InputImageRegion;
+
+  if (m_UseForGroupwiseRegistration)
+  {
+    m_CroppedInputImageRegion.GetModifiableSize().back() = 1;
+  }
+
   if (!m_Mask.IsNull())
   {
     /** Get a handle to the input image. */

Core/ComponentBaseClasses/elxImageSamplerBase.hxx

@@ -36,6 +36,10 @@ ImageSamplerBase<TElastix>::BeforeRegistrationBase()
   const Configuration & configuration = Deref(Superclass::GetConfiguration());
   ITKBaseType &         sampler = GetSelf();
   sampler.SetUseMultiThread(configuration.RetrieveParameterValue(true, "UseMultiThreadingForSamplers", 0, false));
+  if (configuration.RetrieveParameterValue(false, "UseSamplingForGroupwiseRegistration", 0, false))
+  {
+    sampler.UseForGroupwiseRegistration();
+  }
 }
 
 /**