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Ben Wilson
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Add CLIs
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‎AlignMesh/AlignMesh.cxx

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#include "AlignMeshCLP.h"
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// VTK Includes
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#include "vtkDecimatePro.h"
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#include "vtkXMLPolyDataWriter.h"
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#include "vtkXMLPolyDataReader.h"
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#include "vtkSmartPointer.h"
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#include "vtkPolyData.h"
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#include "vtkTriangleFilter.h"
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#include "vtkNew.h"
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#include "vtkCellLocator.h"
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//ITK Includes
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#include "itkMesh.h"
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#include "itkMeshFileReader.h"
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#include "itkMeshFileWriter.h"
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#include "itkLineCell.h"
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#include "itkTriangleCell.h"
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#include "itkImageFileWriter.h"
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#include "itkResampleImageFilter.h"
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#include "itkConstrainedValueAdditionImageFilter.h"
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#include "itkBSplineInterpolateImageFunction.h"
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#include "itkPluginUtilities.h"
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#include <itkDefaultDynamicMeshTraits.h>
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#include <itkMetaMeshConverter.h>
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int main (int argc, char * argv[])
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{
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PARSE_ARGS;
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try{
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typedef itk::DefaultDynamicMeshTraits<float, 3, 3, float, float> MeshTraitsType;
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typedef MeshTraitsType::PointType PointType;
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constexpr unsigned int Dimension = 3;
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using InputPixelType = float;
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using MeshType = itk::Mesh<InputPixelType, Dimension>;
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using MeshReaderType = itk::MeshFileReader<MeshType>;
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using MeshWriterType = itk::MeshFileWriter<MeshType>;
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MeshReaderType::Pointer meshReader = MeshReaderType::New();
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meshReader->SetFileName(inputVolume.c_str());
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// meshReader->Update();
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MeshType::Pointer mesh = meshReader->GetOutput();
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MeshType::PointsContainerPointer Points = mesh->GetPoints();
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int numberOfPoints = Points->Size();
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MeshReaderType::Pointer meshReader2 = MeshReaderType::New();
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meshReader2->SetFileName(inputVolumeTwo.c_str());
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// meshReader->Update();
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MeshType::Pointer mesh2 = meshReader2->GetOutput();
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MeshWriterType::Pointer writer = MeshWriterType::New();
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writer->SetInput(mesh);
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writer->SetFileName(outputVolume.c_str());
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//writer->Update();
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}
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catch (int e)
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{
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cout << "An exception occurred. Exception Nr. " << e << '\n';
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return EXIT_FAILURE;
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}
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return EXIT_SUCCESS;
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}

‎AlignMesh/AlignMesh.xml

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<?xml version="1.0" encoding="utf-8"?>
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<executable>
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<category>Surface Models.Advanced</category>
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<title>AlignMesh</title>
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<description><![CDATA[This is a CLI module that can be bundled in an extension]]></description>
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<version>0.0.1</version>
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<documentation-url>http://www.example.com/Slicer/Modules/AlignMesh</documentation-url>
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<license>Slicer</license>
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<contributor>FirstName LastName (Institution), FirstName LastName (Institution)</contributor>
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<acknowledgements>This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN</acknowledgements>
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<parameters>
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<label>IO</label>
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<description><![CDATA[Input/output parameters]]></description>
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<geometry>
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<name>inputVolume</name>
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<label>Input Volume</label>
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<channel>input</channel>
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<index>0</index>
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<description><![CDATA[Input volume]]></description>
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</geometry>
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<geometry>
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<name>inputVolumeTwo</name>
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<label>Input Volume Two </label>
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<channel>input</channel>
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<index>1</index>
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<description><![CDATA[Input volume two]]></description>
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</geometry>
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<geometry>
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<name>outputVolume</name>
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<label>Output Volume</label>
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<channel>output</channel>
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<index>2</index>
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<description><![CDATA[Output Volume]]></description>
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</geometry>
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</parameters>
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</executable>

‎AlignMesh/CMakeLists.txt

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#-----------------------------------------------------------------------------
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set(MODULE_NAME AlignMesh)
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#-----------------------------------------------------------------------------
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#
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# SlicerExecutionModel
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#
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find_package(SlicerExecutionModel REQUIRED)
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include(${SlicerExecutionModel_USE_FILE})
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#
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# ITK
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#
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set(${PROJECT_NAME}_ITK_COMPONENTS
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ITKIOImageBase
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ITKIOMeshBase
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ITKSmoothing
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ITKLabelMap
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)
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find_package(ITK 5 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED)
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set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt
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include(${ITK_USE_FILE})
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#-----------------------------------------------------------------------------
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set(MODULE_INCLUDE_DIRECTORIES
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${MRMLCore_INCLUDE_DIRS}
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${CMAKE_CURRENT_SOURCE_DIR}
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)
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set(MODULE_SRCS
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)
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set(MODULE_TARGET_LIBRARIES
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${ITK_LIBRARIES}
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${VTK_LIBRARIES}
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)
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#-----------------------------------------------------------------------------
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SEMMacroBuildCLI(
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NAME ${MODULE_NAME}
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TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
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INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES}
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ADDITIONAL_SRCS ${MODULE_SRCS}
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)
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#-----------------------------------------------------------------------------
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if(BUILD_TESTING)
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add_subdirectory(Testing)
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endif()

‎AlignMesh/Data/Baseline/AlignMeshTest.nhdr.md5

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fc6170ceeff3d8217a9dd6a1add2ec8c

‎AlignMesh/Data/Baseline/AlignMeshTest.raw.md5

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0749d4d3f07a217030f9ae33d94c4559

‎AlignMesh/Data/Input/CTHeadAxial.nhdr.md5

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6e5c289c73e14ba7a1b0f8aaf6ed249a

‎AlignMesh/Data/Input/CTHeadAxial.raw.gz.md5

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3ebd710c9cf9d75750f4569b8caf6d07

‎AlignMesh/Testing/CMakeLists.txt

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add_subdirectory(Cxx)

‎AlignMesh/Testing/Cxx/AlignMeshTest.cxx

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#if defined(_MSC_VER)
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#pragma warning ( disable : 4786 )
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#endif
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#ifdef __BORLANDC__
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#define ITK_LEAN_AND_MEAN
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#endif
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#include "itkTestMain.h"
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// STD includes
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#include <iostream>
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#ifdef WIN32
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# define MODULE_IMPORT __declspec(dllimport)
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#else
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# define MODULE_IMPORT
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#endif
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extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
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void RegisterTests()
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{
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StringToTestFunctionMap["ModuleEntryPoint"] = ModuleEntryPoint;
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}

‎AlignMesh/Testing/Cxx/CMakeLists.txt

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#-----------------------------------------------------------------------------
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set(BASELINE ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Baseline)
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set(INPUT ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Input)
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set(TEMP "${CMAKE_BINARY_DIR}/Testing/Temporary")
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set(CLP ${MODULE_NAME})
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#-----------------------------------------------------------------------------
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add_executable(${CLP}Test ${CLP}Test.cxx)
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target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})
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set_target_properties(${CLP}Test PROPERTIES LABELS ${CLP})
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#-----------------------------------------------------------------------------
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set(testname ${CLP}Test)
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ExternalData_add_test(${CLP}Data NAME ${testname} COMMAND ${SEM_LAUNCH_COMMAND} $<TARGET_FILE:${CLP}Test>
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--compare DATA{${BASELINE}/${CLP}Test.nhdr,${CLP}Test.raw}
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${TEMP}/${CLP}Test.nhdr
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ModuleEntryPoint
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--sigma 2.5 DATA{${INPUT}/CTHeadAxial.nhdr,CTHeadAxial.raw.gz} ${TEMP}/${CLP}Test.nhdr
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)
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set_property(TEST ${testname} PROPERTY LABELS ${CLP})
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#-----------------------------------------------------------------------------
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ExternalData_add_target(${CLP}Data)

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