# )
SET(TOOLS_INSTALL clitkDicomInfo)
+ WRAP_GGO(clitkPointRigidRegistration_GGO_C clitkPointRigidRegistration.ggo)
+ ADD_EXECUTABLE(clitkPointRigidRegistration clitkPointRigidRegistration.cxx ${clitkPointRigidRegistration_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkPointRigidRegistration clitkCommon)
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPointRigidRegistration)
+
WRAP_GGO(clitkDicom2Image_GGO_C clitkDicom2Image.ggo)
ADD_EXECUTABLE(clitkDicom2Image clitkDicom2Image.cxx ${clitkDicom2Image_GGO_C})
TARGET_LINK_LIBRARIES(clitkDicom2Image clitkCommon)
TARGET_LINK_LIBRARIES(clitkImageUncertainty clitkCommon ${ITK_LIBRARIES})
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageUncertainty)
- WRAP_GGO(clitkNormalizeImageFilter_GGO_C clitkNormalizeImageFilter.ggo)
- ADD_EXECUTABLE(clitkNormalizeImageFilter clitkNormalizeImageFilter.cxx ${clitkNormalizeImageFilter_GGO_C})
- TARGET_LINK_LIBRARIES(clitkNormalizeImageFilter clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkNormalizeImageFilter)
-
WRAP_GGO(clitkImageGradientMagnitude_GGO_C clitkImageGradientMagnitude.ggo)
ADD_EXECUTABLE(clitkImageGradientMagnitude clitkImageGradientMagnitude.cxx ${clitkImageGradientMagnitude_GGO_C})
TARGET_LINK_LIBRARIES(clitkImageGradientMagnitude clitkCommon )
TARGET_LINK_LIBRARIES(clitkImageLaplacian clitkCommon )
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageLaplacian)
- WRAP_GGO(clitkImageIntensityWindowing_GGO_C clitkImageIntensityWindowing.ggo)
- ADD_EXECUTABLE(clitkImageIntensityWindowing clitkImageIntensityWindowing.cxx ${clitkImageIntensityWindowing_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageIntensityWindowing clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageIntensityWindowing)
-
- WRAP_GGO(clitkBlurImage_GGO_C clitkBlurImage.ggo)
- ADD_EXECUTABLE(clitkBlurImage clitkBlurImage.cxx ${clitkBlurImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkBlurImage clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBlurImage)
#=========================================================
option(CLITK_USE_ROOT "Build experimental tools using root" OFF)
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkPointRigidRegistrationGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief PointRigidRegistration an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkPointRigidRegistration_ggo.h"
+#include "clitkPointRigidRegistrationGenericFilter.h"
+
+//paste from RigidRegistration
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImage.h"
+#include "itkVector.h"
+#include "itkResampleImageFilter.h"
+#include "itkLandmarkBasedTransformInitializer.h"
+#include "itkRigid2DTransform.h"
+#include "itkVersorRigid3DTransform.h"
+#include <iostream>
+
+//paste from /home/dspinczyk/dev/clitk_superbuild_Agata/Source/clitk/common/clitkTransformUtilities.h
+#include "itkMatrix.h"
+#include "itkArray.h"
+#include "itkPoint.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
+//#define VTK_EXCLUDE_STRSTREAM_HEADERS
+#include <vtkMatrix4x4.h>
+#include <vtkSmartPointer.h>
+
+//for open file for reading
+#include "clitkIO.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
+
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkPointRigidRegistration, args_info);
+ CLITK_INIT;
+
+
+
+
+ // Iinit itk
+ // read input file
+ //open stream to reading
+ std::ifstream is;
+ clitk::openFileForReading(is, args_info.input_arg);
+
+
+
+ //pojedyncza zaczytana wartosc
+ double x = 0;
+ //clitk::skipComment(is);
+ is >> x;
+
+ //typ piksela - bo wykorzystujemy strukture itk::Image
+ typedef unsigned char PixelType;
+
+
+
+
+
+ //Ddefinicja typu obrazu: zawiera rozmiar danych, typ piksela
+ //rozmiarowosc danych
+ unsigned int Dimension_temp = (unsigned int)x;
+
+
+
+ if (Dimension_temp==2)
+ {
+ const unsigned int Dimension = 2;
+ typedef itk::Image< PixelType, Dimension > ImageType;
+ typedef float VectorComponentType;
+ typedef itk::Vector< VectorComponentType, Dimension > VectorType;
+ //Typ LandmarkBasedTransormInitializer
+ typedef itk::Rigid2DTransform< double > Rigid2DTransformType;
+ typedef itk::LandmarkBasedTransformInitializer< Rigid2DTransformType,ImageType, ImageType>
+ LandmarkBasedTransformInitializerType;
+
+ LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
+
+ // Create source and target landmarks.
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer LandmarkContainerType;
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointType LandmarkPointType;
+
+ //bufory na zaczyt wspolrzedncyh
+ LandmarkContainerType imageLandmarks;
+ LandmarkContainerType trackerLandmarks;
+
+ //bufory na pojedyncze punkty
+ LandmarkPointType imagePoint; // dane z CT
+ LandmarkPointType trackerPoint; //dane z tracking system
+
+ is >> x;
+
+
+ while (is && !is.eof()) {
+ trackerPoint[0] = x;
+ is >> trackerPoint[1];
+ //is >> trackerPoint[2];
+
+ is >> imagePoint[0];
+ is >> imagePoint[1];
+ //is >> imagePoint[2];
+
+ imageLandmarks.push_back(imagePoint );
+ trackerLandmarks.push_back(trackerPoint );
+
+
+ is >> x;
+ }
+
+ is.close();
+
+ landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
+ landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
+
+ Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
+
+ transform->SetIdentity();
+
+ // Versor rotacji i macierz translacji
+ landmarkBasedTransformInitializer->SetTransform(transform);
+ landmarkBasedTransformInitializer->InitializeTransform();
+
+ Rigid2DTransformType::MatrixType matrix = transform->GetMatrix();
+ Rigid2DTransformType::OffsetType offset = transform->GetOffset();
+
+ // Write result
+ std::ofstream out;
+ clitk::openFileForWriting(out, args_info.output_arg);
+
+ out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << offset[0] << std::endl;
+ out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << offset[1] << std::endl;
+ out << 0.0 << ' ' << 0.0 << ' ' << 1.0;
+ out.close();
+
+
+ }
+ else if (Dimension_temp==3)
+ {
+
+ std::cout << "to ja";
+ const unsigned int Dimension = 3;
+ typedef itk::Image< PixelType, Dimension > ImageType;
+ typedef float VectorComponentType;
+ typedef itk::Vector< VectorComponentType, Dimension > VectorType;
+ //Typ LandmarkBasedTransormInitializer
+ typedef itk::VersorRigid3DTransform< double > Rigid3DTransformType;
+ typedef itk::LandmarkBasedTransformInitializer< Rigid3DTransformType,ImageType, ImageType>
+ LandmarkBasedTransformInitializerType;
+
+ LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
+
+ // Create source and target landmarks.
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer LandmarkContainerType;
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointType LandmarkPointType;
+
+ //bufory na zaczyt wspolrzedncyh
+ LandmarkContainerType imageLandmarks;
+ LandmarkContainerType trackerLandmarks;
+
+ //bufory na pojedyncze punkty
+ LandmarkPointType imagePoint; // dane z CT
+ LandmarkPointType trackerPoint; //dane z tracking system
+
+ is >> x;
+
+ while (is && !is.eof()) {
+ trackerPoint[0] = x;
+ is >> trackerPoint[1];
+ is >> trackerPoint[2];
+
+ is >> imagePoint[0];
+ is >> imagePoint[1];
+ is >> imagePoint[2];
+
+ imageLandmarks.push_back(imagePoint );
+ trackerLandmarks.push_back(trackerPoint );
+
+ is >> x;
+ }
+
+ is.close();
+
+ landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
+ landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
+
+ Rigid3DTransformType::Pointer transform = Rigid3DTransformType::New();
+
+ transform->SetIdentity();
+
+ // Versor rotacji i macierz translacji
+ landmarkBasedTransformInitializer->SetTransform(transform);
+ landmarkBasedTransformInitializer->InitializeTransform();
+
+ Rigid3DTransformType::MatrixType matrix = transform->GetMatrix();
+ Rigid3DTransformType::OffsetType offset = transform->GetOffset();
+
+ // Write result
+ std::ofstream out;
+ clitk::openFileForWriting(out, args_info.output_arg);
+
+ out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << matrix[0][2] << ' '<< offset[0] << std::endl;
+ out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << matrix[1][2] << ' '<< offset[1] << std::endl;
+ out << matrix[2][0] << ' ' << matrix[2][1] << ' ' << matrix[2][2] << ' '<< offset[2] << std::endl;
+ out << 0.0 << ' ' << 0.0 << ' ' << 0.0 << ' ' << 1.0;
+ out.close();
+
+
+
+ }
+ else
+ {
+ is.close();
+ return EXIT_FAILURE;
+
+ }
+
+
+
+
+
+ return EXIT_SUCCESS;
+}// end main
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff