WIP: Create Basic CLIs

AlignMesh/AlignMesh.cxx

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

AlignMesh/AlignMesh.xml

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

AlignMesh/CMakeLists.txt

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

AlignMesh/Data/Baseline/AlignMeshTest.nhdr.md5

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+fc6170ceeff3d8217a9dd6a1add2ec8c

AlignMesh/Data/Baseline/AlignMeshTest.raw.md5

@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559

AlignMesh/Data/Input/CTHeadAxial.nhdr.md5

@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a

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

@@ -0,0 +1 @@
+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)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef __BORLANDC__
+#define ITK_LEAN_AND_MEAN
+#endif
+
+#include "itkTestMain.h"
+
+// STD includes
+#include <iostream>
+
+#ifdef WIN32
+# define MODULE_IMPORT __declspec(dllimport)
+#else
+# define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+void RegisterTests()
+{
+  StringToTestFunctionMap["ModuleEntryPoint"] = ModuleEntryPoint;
+}

AlignMesh/Testing/Cxx/CMakeLists.txt

@@ -0,0 +1,25 @@
+
+#-----------------------------------------------------------------------------
+set(BASELINE ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Baseline)
+set(INPUT ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Input)
+set(TEMP "${CMAKE_BINARY_DIR}/Testing/Temporary")
+
+set(CLP ${MODULE_NAME})
+
+#-----------------------------------------------------------------------------
+add_executable(${CLP}Test ${CLP}Test.cxx)
+target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})
+set_target_properties(${CLP}Test PROPERTIES LABELS ${CLP})
+
+#-----------------------------------------------------------------------------
+set(testname ${CLP}Test)
+ExternalData_add_test(${CLP}Data NAME ${testname} COMMAND ${SEM_LAUNCH_COMMAND} $<TARGET_FILE:${CLP}Test>
+  --compare DATA{${BASELINE}/${CLP}Test.nhdr,${CLP}Test.raw}
+  ${TEMP}/${CLP}Test.nhdr
+  ModuleEntryPoint
+  --sigma 2.5 DATA{${INPUT}/CTHeadAxial.nhdr,CTHeadAxial.raw.gz} ${TEMP}/${CLP}Test.nhdr
+  )
+set_property(TEST ${testname} PROPERTY LABELS ${CLP})
+
+#-----------------------------------------------------------------------------
+ExternalData_add_target(${CLP}Data)

AlignMeshICP/AlignMeshICP.cxx

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+#include "AlignMeshICPCLP.h"
+
+// VTK Includes
+#include "vtkXMLPolyDataWriter.h"
+#include "vtkXMLPolyDataReader.h"
+#include "vtkSmartPointer.h"
+#include "vtkPolyData.h"
+#include "vtkTriangleFilter.h"
+#include "vtkNew.h"
+#include "vtkIterativeClosestPointTransform.h"
+#include "vtkLandmarkTransform.h"
+#include "vtkTransformPolyDataFilter.h"
+#include "vtkAppendPolyData.h"
+
+
+int main (int argc, char * argv[])
+ {
+   PARSE_ARGS;
+
+   try{
+    vtkSmartPointer<vtkPolyData> source;
+    vtkSmartPointer<vtkPolyData> target;
+
+    // Read the file
+    vtkNew<vtkXMLPolyDataReader> targetReader;
+    targetReader->SetFileName(inputVolume.c_str());
+    targetReader->Update();
+    target = targetReader->GetOutput();
+
+    vtkNew<vtkXMLPolyDataReader> sourceReader;
+    sourceReader->SetFileName(inputVolumeTwo.c_str());
+    sourceReader->Update();
+    source = sourceReader->GetOutput();
+
+
+    vtkNew<vtkIterativeClosestPointTransform> icp;
+    icp->SetSource(source);
+    icp->SetTarget(target);
+    vtkSmartPointer<vtkLandmarkTransform> transform =
+      icp->GetLandmarkTransform();
+    transform->SetModeToRigidBody();
+    icp->SetMaximumNumberOfIterations(20);
+    icp->StartByMatchingCentroidsOn();
+    icp->Modified();
+    icp->Update();
+
+    vtkNew<vtkTransformPolyDataFilter> icpTransformFilter;
+    icpTransformFilter->SetInputData(source);
+    icpTransformFilter->SetTransform(icp);
+    icpTransformFilter->Update();
+
+    //Write to file
+    vtkNew<vtkXMLPolyDataWriter> writer;
+    writer->SetFileName(outputVolume.c_str());
+    writer->SetInputData(icpTransformFilter->GetOutput());
+    writer->Update();
+  }
+  catch (int e)
+   {
+     cout << "An exception occurred. Exception Nr. " << e << '\n';
+     return EXIT_FAILURE;
+   }
+
+  return EXIT_SUCCESS;
+
+ }

AlignMeshICP/AlignMeshICP.xml

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="utf-8"?>
+<executable>
+  <category>Surface Models.Advanced</category>
+  <title>AlignMeshICP</title>
+  <description><![CDATA[This is a CLI module that can be bundled in an extension]]></description>
+  <version>0.0.1</version>
+  <documentation-url>http://www.example.com/Slicer/Modules/avgMesh</documentation-url>
+  <license>Slicer</license>
+  <contributor>Ben Wilson (Kitware)</contributor>
+  <acknowledgements></acknowledgements>
+  <parameters>
+    <label>IO</label>
+    <description><![CDATA[Input/output parameters]]></description>
+    <geometry>
+      <name>inputVolume</name>
+      <label>Input Volume</label>
+      <channel>input</channel>
+      <index>0</index>
+      <description><![CDATA[Input volume]]></description>
+    </geometry>
+    <geometry>
+      <name>inputVolumeTwo</name>
+      <label>Input Volume Two </label>
+      <channel>input</channel>
+      <index>1</index>
+      <description><![CDATA[Input volume two]]></description>
+    </geometry>
+    <geometry>
+      <name>outputVolume</name>
+      <label>Output Volume</label>
+      <channel>output</channel>
+      <index>2</index>
+      <description><![CDATA[Output Volume]]></description>
+    </geometry>
+  </parameters>
+</executable>

AlignMeshICP/CMakeLists.txt

@@ -0,0 +1,47 @@
+
+#-----------------------------------------------------------------------------
+set(MODULE_NAME AlignMeshICP)
+
+#-----------------------------------------------------------------------------
+
+#
+# SlicerExecutionModel
+#
+find_package(SlicerExecutionModel REQUIRED)
+include(${SlicerExecutionModel_USE_FILE})
+
+#
+# ITK
+#
+set(${PROJECT_NAME}_ITK_COMPONENTS
+  ITKIOImageBase
+  ITKSmoothing
+  )
+find_package(ITK 5 COMPONENTS ${${PROJECT_NAME}_ITK_COMPONENTS} REQUIRED)
+set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt
+include(${ITK_USE_FILE})
+
+#-----------------------------------------------------------------------------
+set(MODULE_INCLUDE_DIRECTORIES
+  )
+
+set(MODULE_SRCS
+  )
+
+set(MODULE_TARGET_LIBRARIES
+  ${ITK_LIBRARIES}
+  ${VTK_LIBRARIES}
+  )
+
+#-----------------------------------------------------------------------------
+SEMMacroBuildCLI(
+  NAME ${MODULE_NAME}
+  TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
+  INCLUDE_DIRECTORIES ${MODULE_INCLUDE_DIRECTORIES}
+  ADDITIONAL_SRCS ${MODULE_SRCS}
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+  add_subdirectory(Testing)
+endif()

AlignMeshICP/Data/Baseline/AlignMeshICPTest.nhdr.md5

@@ -0,0 +1 @@
+fc6170ceeff3d8217a9dd6a1add2ec8c

AlignMeshICP/Data/Baseline/AlignMeshICPTest.raw.md5

@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559

AlignMeshICP/Data/Input/CTHeadAxial.nhdr.md5

@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a

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

@@ -0,0 +1 @@
+3ebd710c9cf9d75750f4569b8caf6d07

AlignMeshICP/Testing/CMakeLists.txt

@@ -0,0 +1 @@
+add_subdirectory(Cxx)