From: Dominik Spincwyk Date: Mon, 3 Feb 2014 14:44:27 +0000 (+0100) Subject: First version of PointRigidRegistration X-Git-Tag: v1.4.0~134 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=54e318c028d7dc8441a263ee71b6757e03d57ecf;hp=8b965f85c8e581f12fa9b24bc002aab2bfb7aa9b;p=clitk.git First version of PointRigidRegistration --- diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt index 144fa6f..de89527 100644 --- a/tools/CMakeLists.txt +++ b/tools/CMakeLists.txt @@ -36,6 +36,11 @@ IF (CLITK_BUILD_TOOLS) # ) 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) @@ -300,11 +305,6 @@ IF (CLITK_BUILD_TOOLS) 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 ) @@ -315,15 +315,6 @@ IF (CLITK_BUILD_TOOLS) 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) diff --git a/tools/clitkPointRigidRegistration.cxx b/tools/clitkPointRigidRegistration.cxx new file mode 100644 index 0000000..e66edd2 --- /dev/null +++ b/tools/clitkPointRigidRegistration.cxx @@ -0,0 +1,253 @@ +/*========================================================================= + 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 + * @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 + +//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 +#include + +//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 +//-------------------------------------------------------------------- diff --git a/tools/clitkPointRigidRegistration.ggo b/tools/clitkPointRigidRegistration.ggo new file mode 100644 index 0000000..311ea29 --- /dev/null +++ b/tools/clitkPointRigidRegistration.ggo @@ -0,0 +1,13 @@ +#File clitkPointRigidRegistration.ggo +package "clitkPointRigidRegistration" +version "1.0" +purpose "Finding the rigid transformation between two cartesian coordinate systems\n +based on corresponding points positions" + +option "config" - "Config file" string optional +option "verbose" v "Verbose" flag off + + + +option "input" i "Corresponding points' positions filename" string required +option "output" o "Output transformation filename" string required