From 3e04a27942dd38b669c11c94339734b69f39022a Mon Sep 17 00:00:00 2001
From: Kasper Marstal <kaspermarstal@gmail.com>
Date: Tue, 19 May 2015 17:38:45 +0200
Subject: [PATCH] COMP: ELASTIX-1 Add readthedocs.org documentation system and
benchmarking system
---
CMakeLists.txt | 1 +
SuperBuild/CMakeLists.txt | 3 +-
SuperBuild/Elastix.cmake | 2 +-
Testing/Benchmark/BSplineRegistration.cxx | 137 ++++++++++++++++++
Testing/Benchmark/CMakeLists.txt | 37 +++++
Testing/CMakeLists.txt | 36 +----
.../Input/BrainProtonDensitySlice.png.md5 | 1 +
Testing/Unit/CMakeLists.txt | 31 ++++
.../elxExampleUnitTest.cxx} | 0
9 files changed, 215 insertions(+), 33 deletions(-)
create mode 100644 Testing/Benchmark/BSplineRegistration.cxx
create mode 100644 Testing/Benchmark/CMakeLists.txt
create mode 100644 Testing/Data/Input/BrainProtonDensitySlice.png.md5
create mode 100644 Testing/Unit/CMakeLists.txt
rename Testing/{elxExampleTest.cxx => Unit/elxExampleUnitTest.cxx} (100%)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ec355d9a..a50193ad 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,6 +23,7 @@ include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxRequiredITKModules.cmake" )
option( ELASTIX_BUILD_TESTING "Enable building tests." OFF )
if( ELASTIX_BUILD_TESTING )
+ option( ELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." OFF )
enable_testing()
add_subdirectory( Testing )
endif()
diff --git a/SuperBuild/CMakeLists.txt b/SuperBuild/CMakeLists.txt
index 12a9ed5a..15dd3d89 100644
--- a/SuperBuild/CMakeLists.txt
+++ b/SuperBuild/CMakeLists.txt
@@ -29,8 +29,7 @@ option( ELASTIX_BUILD_EXAMPLES "Enable building examples." ON )
option( ELASTIX_BUILD_TESTING "Enable building tests." ON )
if( ELASTIX_BUILD_TESTING )
- mark_as_advanced( ELASTIX_BUILD_CTESTS )
- option( ELASTIX_BUILD_CTESTS "Enable CTests." OFF )
+ option( ELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." ON )
endif()
#---------------------------------------------------------------------
diff --git a/SuperBuild/Elastix.cmake b/SuperBuild/Elastix.cmake
index 130f5595..6afad940 100644
--- a/SuperBuild/Elastix.cmake
+++ b/SuperBuild/Elastix.cmake
@@ -8,7 +8,7 @@ ExternalProject_Add( ${proj}
CMAKE_ARGS
--no-warn-unused-cli
-DELASTIX_BUILD_TESTING:BOOL=${ELASTIX_BUILD_TESTING}
- -DELASTIX_BUILD_CTESTS:BOOL=${ELASTIX_BUILD_CTESTS}
+ -DELASTIX_BUILD_BENCHMARKING:BOOL=${ELASTIX_BUILD_BENCHMARKING}
-DITK_DIR:PATH=${ITK_DIR}
DEPENDS ${ELASTIX_DEPENDENCIES}
INSTALL_COMMAND ""
diff --git a/Testing/Benchmark/BSplineRegistration.cxx b/Testing/Benchmark/BSplineRegistration.cxx
new file mode 100644
index 00000000..8a8a73b4
--- /dev/null
+++ b/Testing/Benchmark/BSplineRegistration.cxx
@@ -0,0 +1,137 @@
+/**
+ * Benchmarking multi-resolution non-rigid b-spline registration
+ * with mutual information in ITK, Elastix and ANTs
+ */
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+
+// DeformableRegistration1
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkHistogramMatchingImageFilter.h"
+#include "itkFEMRegistrationFilter.h"
+
+#include "gtest/gtest.h"
+
+class itkExamples : public ::testing::Test
+{
+protected:
+
+ virtual void SetUp()
+ {
+ const char *fixedImageName, *movingImageName;
+ if ( argc < 2 )
+ {
+ std::cout << "Image filenames missing." << std::endl;
+ std::cout << "Usage: " << argv[0] << " fixedImageFilename movingImageFilename"
+ << std::endl;
+ return EXIT_FAILURE;
+ }
+ else
+ {
+ fixedImageFilename = argv[1];
+ movingImageFilename = argv[2];
+ }
+ }
+
+};
+
+TEST_F( BSplineRegistration, ITK ) {
+
+ const unsigned int ImageDimension = 2;
+ typedef unsigned char PixelType;
+ typedef itk::Image< PixelType, ImageDimension > ImageType;
+
+ const unsigned int SplineOrder = 3;
+ typedef double CoordinateRepType;
+
+ // Transform
+ typedef itk::BSplineDeformableTransform< CoordinateRepType,
+ SpaceDimension,
+ SplineOrder > TransformType;
+
+ typedef TransformType::RegionType RegionType;
+ RegionType bsplineRegion;
+ RegionType::SizeType gridSizeOnImage;
+ RegionType::SizeType gridBorderSize;
+ RegionType::SizeType totalGridSize;
+
+ gridSizeOnImage.Fill( 5 );
+ gridBorderSize.Fill( 3 ); // Border for spline order = 3 ( 1 lower, 2 upper )
+ totalGridSize = gridSizeOnImage + gridBorderSize;
+
+ bsplineRegion.SetSize( totalGridSize );
+
+ typedef TransformType::SpacingType SpacingType;
+ SpacingType spacing = fixedImage->GetSpacing();
+
+ typedef TransformType::OriginType OriginType;
+ OriginType origin = fixedImage->GetOrigin();
+
+ ImageType::SizeType fixedImageSize = fixedRegion.GetSize();
+
+ for(unsigned int r=0; r<ImageDimension; r++)
+ {
+ spacing[r] *= static_cast<double>(fixedImageSize[r] - 1) /
+ static_cast<double>(gridSizeOnImage[r] - 1);
+ }
+
+ ImageType::DirectionType gridDirection = fixedImage->GetDirection();
+ SpacingType gridOriginOffset = gridDirection * spacing;
+
+ OriginType gridOrigin = origin - gridOriginOffset;
+
+ transform->SetGridSpacing( spacing );
+ transform->SetGridOrigin( gridOrigin );
+ transform->SetGridRegion( bsplineRegion );
+ transform->SetGridDirection( gridDirection );
+
+ typedef TransformType::ParametersType ParametersType;
+ const unsigned int numberOfParameters = transform->GetNumberOfParameters();
+ ParametersType parameters( numberOfParameters );
+ parameters.Fill( 0.0 );
+ transform->SetParameters( parameters );
+
+ // Optimizer
+ typedef itk::LBFGSOptimizer OptimizerType;
+
+ optimizer->SetGradientConvergenceTolerance( 0.05 );
+ optimizer->SetLineSearchAccuracy( 0.9 );
+ optimizer->SetDefaultStepLength( .5 );
+ optimizer->TraceOn();
+ optimizer->SetMaximumNumberOfFunctionEvaluations( 1024 );
+
+ // Metric
+ typedef itk::MeanSquaresImageToImageMetric< ImageType,
+ ImageType > MetricType;
+
+ // Interpolator
+ typedef itk:: LinearInterpolateImageFunction< ImageType,
+ double > InterpolatorType;
+
+ // Setup the registration
+ typedef itk::ImageRegistrationMethod< ImageType,
+ ImageType > RegistrationType;
+
+ RegistrationType::Pointer registration = RegistrationType::New();
+ registration->SetNumberOfThreads( 1 );
+ registration->SetMetric( MetricType::New() );
+ registration->SetOptimizer( OptimizerType::New() );
+ registration->SetInterpolator( InterpolatorType::New() );
+
+ TransformType::Pointer transform = TransformType::New();
+ registration->SetTransform( transform );
+
+ registration->SetFixedImage( fixedImage );
+ registration->SetMovingImage( movingImage );
+
+ ImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
+ registration->SetFixedImageRegion( fixedRegion );
+
+ registration->SetInitialTransformParameters( transform->GetParameters() );
+
+ // Execute
+ EXPECT_NO_THROW( registration->Update() );
+
+}
\ No newline at end of file
diff --git a/Testing/Benchmark/CMakeLists.txt b/Testing/Benchmark/CMakeLists.txt
new file mode 100644
index 00000000..3004ccdf
--- /dev/null
+++ b/Testing/Benchmark/CMakeLists.txt
@@ -0,0 +1,37 @@
+#
+set( GTEST_OPTIONS
+ -gtest_output
+)
+
+#---------------------------------------------------------------------
+# To add a benchmark to the build system, append it to the list below.
+# Any GoogleTests in these files are automatically added to CTest.
+
+set( ElastixBenchmarkSource
+ elxExampleBenchmark.cxx
+)
+
+#---------------------------------------------------------------------
+# To add data to a benchmark, create a list "${filename}Data" (without
+# the filename extension) and add data to this list.
+
+set( elxExampleBenchmarkData
+ DATA{Testing/Data/Input/BrainProtonDensitySlice.png}
+ DATA{Testing/Data/Input/BrainProtonDensitySliceR10X13Y17.png}
+)
+
+#---------------------------------------------------------------------
+# Build executables
+
+foreach( ElastixBenchmarkFilename ${ElastixBenchmarkSource} )
+ string( REPLACE ".cxx" "" ElastixBenchmark ${ElastixBenchmarkFilename} )
+ add_executable( ${ElastixBenchmark} ${ElastixBenchmarkFilename} )
+ target_link_libraries( ${ElastixBenchmark} ${ELASTIX_LIBRARIES} ${ITK_LIBRARIES} ${TEST_LIBRARIES} )
+
+ ExternalData_Add_Test( "${ElastixBenchmark}ExternalDataTarget"
+ NAME ${ElastixBenchmark}
+ COMMAND "${ElastixBenchmark} ${${ElastixBenchmarkTest}Data} ${GTEST_OPTIONS}"
+ )
+
+ ExternalData_Add_Target( "${ElastixBenchmark}ExternalDataTarget"} )
+endforeach()
diff --git a/Testing/CMakeLists.txt b/Testing/CMakeLists.txt
index 7343cdc1..30ddd1ec 100644
--- a/Testing/CMakeLists.txt
+++ b/Testing/CMakeLists.txt
@@ -20,14 +20,6 @@ set( TEST_LIBRARIES
gtest_main
)
-#---------------------------------------------------------------------
-# To add a test to the build system, append it to the list below.
-# Any GoogleTests in these files are automatically added to CTest.
-
-set( ElastixUnitTestSource
- elxExampleTest.cxx
-)
-
#---------------------------------------------------------------------
# Setup ExternalData
@@ -42,26 +34,10 @@ list( APPEND ExternalData_URL_TEMPLATES
)
#---------------------------------------------------------------------
-# To add data to a tests, create a list "${filename}Data" (without
-# the filename extension) and add data to this list.
-
-set( elxExampleTestData
- DATA{Data/Input/BrainProtonDensitySliceR10X13Y17.png}
-)
-
-#---------------------------------------------------------------------
-# Build test executables
-
-foreach( ElastixUnitTestFilename ${ElastixUnitTestSource} )
- string( REPLACE ".cxx" "" ElastixUnitTest ${ElastixUnitTestFilename} )
- add_executable( ${ElastixUnitTest} ${ElastixUnitTestFilename} )
- target_link_libraries( ${ElastixUnitTest} ${ELASTIX_LIBRARIES} ${ITK_LIBRARIES} ${TEST_LIBRARIES} )
-
- ExternalData_Add_Test( "${ElastixUnitTest}ExternalDataTarget"
- NAME ${ElastixUnitTest}
- COMMAND ${ElastixUnitTest} ${${ElastixUnitTest}Data}
- )
-
- ExternalData_Add_Target( "${ElastixUnitTest}ExternalDataTarget"} )
-endforeach()
+# Include tests
+add_subdirectory( Unit )
+# Include benchmarks
+if( ${ELASTIX_BUILD_BENCHMARKING} )
+ add_subdirectory( Benchmark )
+endif()
diff --git a/Testing/Data/Input/BrainProtonDensitySlice.png.md5 b/Testing/Data/Input/BrainProtonDensitySlice.png.md5
new file mode 100644
index 00000000..317f8a12
--- /dev/null
+++ b/Testing/Data/Input/BrainProtonDensitySlice.png.md5
@@ -0,0 +1 @@
+073df8eb397d1746d2343c78dd4bd964
\ No newline at end of file
diff --git a/Testing/Unit/CMakeLists.txt b/Testing/Unit/CMakeLists.txt
new file mode 100644
index 00000000..964055b2
--- /dev/null
+++ b/Testing/Unit/CMakeLists.txt
@@ -0,0 +1,31 @@
+#---------------------------------------------------------------------
+# To add a test to the build system, append it to the list below.
+# Any GoogleTests in these files are automatically added to CTest.
+
+set( ElastixUnitTestSource
+ elxExampleUnitTest.cxx
+)
+
+#---------------------------------------------------------------------
+# To add data to a tests, create a list "${filename}Data" (without
+# the filename extension) and add data to this list.
+
+set( elxExampleTestData
+ DATA{${CMAKE_BINARY_DIR}/Testing/Data/Input/BrainProtonDensitySliceR10X13Y17.png}
+)
+
+#---------------------------------------------------------------------
+# Build test executables
+
+foreach( ElastixUnitTestFilename ${ElastixUnitTestSource} )
+ string( REPLACE ".cxx" "" ElastixUnitTest ${ElastixUnitTestFilename} )
+ add_executable( ${ElastixUnitTest} ${ElastixUnitTestFilename} )
+ target_link_libraries( ${ElastixUnitTest} ${ELASTIX_LIBRARIES} ${ITK_LIBRARIES} ${TEST_LIBRARIES} )
+
+ ExternalData_Add_Test( "${ElastixUnitTest}ExternalDataTarget"
+ NAME ${ElastixUnitTest}
+ COMMAND ${ElastixUnitTest} ${${ElastixUnitTest}Data}
+ )
+
+ ExternalData_Add_Target( "${ElastixUnitTest}ExternalDataTarget"} )
+endforeach()
\ No newline at end of file
diff --git a/Testing/elxExampleTest.cxx b/Testing/Unit/elxExampleUnitTest.cxx
similarity index 100%
rename from Testing/elxExampleTest.cxx
rename to Testing/Unit/elxExampleUnitTest.cxx
--
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