BUG: Add tests demonstration current behavior of histogram based median

InsightSoftwareConsortium · Apr 27, 2021 · c6da8be · c6da8be
1 parent 6c4d6da
commit c6da8be
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Showing 3 changed files with 255 additions and 2 deletions.
diff --git a/Modules/Filtering/LabelMap/ITKKWStyleOverwrite.txt b/Modules/Filtering/LabelMap/ITKKWStyleOverwrite.txt
@@ -1,4 +1,5 @@
 test/*\.cxx Namespace Disable
 test/itkAttributePositionLabelMapFilterTest1.cxx Namespace Disable
 test/itkShapeLabelMapFilterGTest.cxx Namespace Disable
+test/itkStatisticsLabelMapFilterGTest.cxx Namespace Disable
 test/itkShapeLabelObjectAccessorsTest1.cxx SemicolonSpace Disable
diff --git a/Modules/Filtering/LabelMap/test/CMakeLists.txt b/Modules/Filtering/LabelMap/test/CMakeLists.txt
@@ -273,7 +273,7 @@ itk_add_test(NAME itkLabelImageToStatisticsLabelMapFilterTest1
       COMMAND ITKLabelMapTestDriver
     --compare DATA{${ITK_DATA_ROOT}/Input/Spots.png}
               ${ITK_TEST_OUTPUT_DIR}/Spots-labelimage-to-statisticslabel.png
-    itkLabelImageToStatisticsLabelMapFilterTest1 DATA{${ITK_DATA_ROOT}/Input/Spots.png} DATA{${ITK_DATA_ROOT}/Input/Spots.png} ${ITK_TEST_OUTPUT_DIR}/Spots-labelimage-to-statisticslabel.png 0 1 1 1 128)
+    itkLabelImageToStatisticsLabelMapFilterTest1 DATA{${ITK_DATA_ROOT}/Input/Spots.png} DATA{${ITK_DATA_ROOT}/Input/Spots.png} ${ITK_TEST_OUTPUT_DIR}/Spots-labelimage-to-statisticslabel.png 0 1 1 1 256)
 itk_add_test(NAME itkLabelMapFilterTest
       COMMAND ITKLabelMapTestDriver itkLabelMapFilterTest)
 itk_add_test(NAME itkLabelMapMaskImageFilterTest-0-0-0
@@ -598,6 +598,7 @@ itk_add_test(NAME itkStatisticsUniqueLabelMapFilterTest2
       1 100)
 
 set(ITKLabelMapGTests
-  itkShapeLabelMapFilterGTest.cxx)
+  itkShapeLabelMapFilterGTest.cxx
+  itkStatisticsLabelMapFilterGTest.cxx)
 
 CreateGoogleTestDriver(ITKLabelMap "${ITKLabelMap-Test_LIBRARIES}" "${ITKLabelMapGTests}")
diff --git a/Modules/Filtering/LabelMap/test/itkStatisticsLabelMapFilterGTest.cxx b/Modules/Filtering/LabelMap/test/itkStatisticsLabelMapFilterGTest.cxx
@@ -0,0 +1,251 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+
+#include "itkGTest.h"
+
+#include "itkImage.h"
+#include "itkLabelImageToStatisticsLabelMapFilter.h"
+#include "itkImageRegionIterator.h"
+#include <algorithm>
+
+
+namespace
+{
+
+class StatisticsLabelMapFixture : public ::testing::Test
+{
+public:
+  StatisticsLabelMapFixture() = default;
+  ~StatisticsLabelMapFixture() override = default;
+
+protected:
+  void
+  SetUp() override
+  {}
+  void
+  TearDown() override
+  {}
+
+  template <unsigned int D, typename TPixelType = unsigned short>
+  struct FixtureUtilities
+  {
+    static const unsigned int Dimension = D;
+
+    using PixelType = TPixelType;
+    using ImageType = itk::Image<PixelType, Dimension>;
+
+    using LabelPixelType = unsigned char;
+    using LabelImageType = itk::Image<LabelPixelType, Dimension>;
+
+    using LabelObjectType = itk::StatisticsLabelObject<LabelPixelType, Dimension>;
+    using StatisticsLabelMapType = itk::LabelMap<LabelObjectType>;
+
+
+    static typename ImageType::Pointer
+    CreateImage()
+    {
+      typename ImageType::Pointer image = ImageType::New();
+
+      typename ImageType::SizeType imageSize;
+      imageSize.Fill(25);
+      image->SetRegions(typename ImageType::RegionType(imageSize));
+      image->Allocate();
+      image->FillBuffer(0);
+
+      return image;
+    }
+
+    static typename ImageType::Pointer
+    CreateImageRandom(PixelType randMax = 500, unsigned int randSeed = 0)
+    {
+      typename ImageType::Pointer image = ImageType::New();
+
+      typename ImageType::SizeType imageSize;
+      imageSize.Fill(25);
+      image->SetRegions(typename ImageType::RegionType(imageSize));
+      image->Allocate();
+      image->FillBuffer(0);
+
+      srand(randSeed);
+
+      itk::ImageRegionIterator<ImageType> it(image, image->GetLargestPossibleRegion());
+      while (!it.IsAtEnd())
+      {
+        it.Set(rand() % randMax);
+        ++it;
+      }
+      return image;
+    }
+
+
+    static typename LabelImageType::Pointer
+    CreateLabelImage()
+    {
+      auto image = LabelImageType::New();
+
+      typename LabelImageType::SizeType imageSize;
+      imageSize.Fill(25);
+      image->SetRegions(typename ImageType::RegionType(imageSize));
+      image->Allocate();
+      image->FillBuffer(0);
+
+      return image;
+    }
+
+
+    static typename LabelObjectType::ConstPointer
+    ComputeLabelObject(const LabelImageType * labelImage,
+                       const ImageType *      image,
+                       const PixelType        label = 1,
+                       const size_t           numberOfBins = 0)
+    {
+
+      auto l2s = itk::LabelImageToStatisticsLabelMapFilter<LabelImageType, ImageType>::New();
+      l2s->SetInput1(labelImage);
+      l2s->SetFeatureImage(image);
+      l2s->ComputeFeretDiameterOn();
+      l2s->ComputePerimeterOn();
+      // l2s->ComputeOrientedBoundingBoxOn();
+      l2s->ComputeHistogramOn();
+      if (numberOfBins != 0)
+      {
+        l2s->SetNumberOfBins(numberOfBins);
+      }
+      l2s->Update();
+      return l2s->GetOutput()->GetLabelObject(label);
+    }
+
+    static double
+    ComputeExactMedian(const LabelObjectType * labelObject, const ImageType * image)
+    {
+      std::vector<PixelType>                       values;
+      typename LabelObjectType::ConstIndexIterator it(labelObject);
+
+      while (!it.IsAtEnd())
+      {
+        const typename ImageType::IndexType & idx = it.GetIndex();
+        values.push_back(image->GetPixel(idx));
+        ++it;
+      }
+
+      std::sort(values.begin(), values.end());
+
+      auto n1 = values.size() / 2;
+      if (values.size() % 2 == 0)
+      {
+        return 0.5 * (double(values[n1]) + double(values[n1 - 1]));
+      }
+      return values[n1];
+    }
+  };
+};
+} // namespace
+
+
+TEST_F(StatisticsLabelMapFixture, 2D_zero)
+{
+  using Utils = FixtureUtilities<2, unsigned char>;
+
+  auto image = Utils::CreateImage();
+  auto labelImage = Utils ::CreateLabelImage();
+
+  Utils::LabelPixelType label = 1;
+  labelImage->FillBuffer(label);
+
+
+  Utils::LabelObjectType::ConstPointer labelObject = Utils::ComputeLabelObject(labelImage, image, 1, 1 << 8);
+
+  EXPECT_NEAR(0.0, labelObject->GetMinimum(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetMaximum(), 1e-12);
+  EXPECT_NEAR(Utils::ComputeExactMedian(labelObject, image), labelObject->GetMedian(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetSum(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetVariance(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetStandardDeviation(), 1e-12);
+
+  if (::testing::Test::HasFailure())
+  {
+    labelObject->Print(std::cout);
+  }
+}
+
+
+TEST_F(StatisticsLabelMapFixture, 2D_ones_with_outliers)
+{
+  using Utils = FixtureUtilities<2, signed short>;
+
+  auto             image = Utils::CreateImage();
+  Utils::PixelType value = 1;
+  image->FillBuffer(value);
+
+  // Test with outliers outside the label.
+  image->SetPixel({ 0, 0 }, 32000);
+  image->SetPixel({ 0, 1 }, -32000);
+
+
+  auto                  labelImage = Utils ::CreateLabelImage();
+  Utils::LabelPixelType label = 1;
+  labelImage->FillBuffer(label);
+  labelImage->SetPixel({ 0, 0 }, 0);
+  labelImage->SetPixel({ 0, 1 }, 0);
+
+  Utils::LabelObjectType::ConstPointer labelObject = Utils::ComputeLabelObject(labelImage, image, label, 1 << 16);
+
+  EXPECT_NEAR(value, labelObject->GetMinimum(), 1e-12);
+  EXPECT_NEAR(value, labelObject->GetMaximum(), 1e-12);
+  EXPECT_NEAR(Utils::ComputeExactMedian(labelObject, image), labelObject->GetMedian(), 0.5);
+  EXPECT_NEAR(25 * 25 - 2, labelObject->GetSum(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetVariance(), 1e-12);
+  EXPECT_NEAR(0.0, labelObject->GetStandardDeviation(), 1e-12);
+
+  if (::testing::Test::HasFailure())
+  {
+    labelObject->Print(std::cout);
+  }
+}
+
+TEST_F(StatisticsLabelMapFixture, 2D_rand_with_outliers)
+{
+  using Utils = FixtureUtilities<2, signed short>;
+
+  auto image = Utils::CreateImageRandom(500, 0);
+  auto labelImage = Utils ::CreateLabelImage();
+
+  // Test with outliers outside the label.
+  image->SetPixel({ 0, 0 }, 32000);
+  image->SetPixel({ 0, 1 }, -2000);
+  // Set min/max in label
+  image->SetPixel({ 0, 2 }, 0);
+  image->SetPixel({ 0, 3 }, 500);
+
+  Utils::LabelPixelType label = 1;
+  labelImage->FillBuffer(label);
+  labelImage->SetPixel({ 0, 0 }, 0);
+  labelImage->SetPixel({ 0, 1 }, 0);
+
+
+  Utils::LabelObjectType::ConstPointer labelObject = Utils::ComputeLabelObject(labelImage, image, label, 1 << 16);
+
+  EXPECT_NEAR(0.0, labelObject->GetMinimum(), 1e-12);
+  EXPECT_NEAR(500.0, labelObject->GetMaximum(), 1e-12);
+  EXPECT_NEAR(Utils::ComputeExactMedian(labelObject, image), labelObject->GetMedian(), 0.5);
+
+  if (::testing::Test::HasFailure())
+  {
+    labelObject->Print(std::cout);
+  }
+}