tools/clitkPointRigidRegistration.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 /* =================================================
  20  * @file   clitkPointRigidRegistrationGenericFilter.txx
  21  * @author xxx <xxx@creatis.insa-lyon.fr>
  22  * @date   29 June 2029
  23  *
  24  * @brief PointRigidRegistration an image
  25  *
  26  ===================================================*/
  27
  28 // clitk
  29 #include "clitkPointRigidRegistration_ggo.h"
  30 #include "clitkPointRigidRegistrationGenericFilter.h"
  31
  32 //paste from RigidRegistration
  33 #include "itkImageFileReader.h"
  34 #include "itkImageFileWriter.h"
  35 #include "itkImage.h"
  36 #include "itkVector.h"
  37 #include "itkResampleImageFilter.h"
  38 #include "itkLandmarkBasedTransformInitializer.h"
  39 #include "itkRigid2DTransform.h"
  40 #include "itkVersorRigid3DTransform.h"
  41 #include <iostream>
  42
  43 //paste from /home/dspinczyk/dev/clitk_superbuild_Agata/Source/clitk/common/clitkTransformUtilities.h
  44 #include "itkMatrix.h"
  45 #include "itkArray.h"
  46 #include "itkPoint.h"
  47 #include "clitkImageCommon.h"
  48 #include "clitkCommon.h"
  49 //#define VTK_EXCLUDE_STRSTREAM_HEADERS
  50 #include <vtkMatrix4x4.h>
  51 #include <vtkSmartPointer.h>
  52
  53 //for open file for reading
  54 #include "clitkIO.h"
  55 #include "clitkImageCommon.h"
  56 #include "clitkCommon.h"
  57
  58
  59 //--------------------------------------------------------------------
  60 int main(int argc, char * argv[])
  61 {
  62
  63   // Init command line
  64   GGO(clitkPointRigidRegistration, args_info);
  65   CLITK_INIT;
  66
  67
  68
  69
  70   // Iinit itk
  71   // read input file
  72   //open stream to reading
  73   std::ifstream is;
  74   clitk::openFileForReading(is, args_info.input_arg);
  75
  76
  77
  78   //pojedyncza zaczytana wartosc
  79   double x = 0;
  80   //clitk::skipComment(is);
  81   is >> x;
  82
  83   //typ piksela - bo wykorzystujemy strukture itk::Image
  84   typedef   unsigned char  PixelType;
  85
  86
  87
  88
  89
  90     //Ddefinicja typu obrazu: zawiera rozmiar danych, typ piksela
  91     //rozmiarowosc danych
  92     unsigned int Dimension_temp = (unsigned int)x;
  93
  94
  95
  96         if (Dimension_temp==2)
  97         {
  98             const     unsigned int   Dimension = 2;
  99             typedef   itk::Image< PixelType, Dimension > ImageType;
 100             typedef   float          VectorComponentType;
 101             typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
 102             //Typ LandmarkBasedTransormInitializer
 103             typedef itk::Rigid2DTransform< double > Rigid2DTransformType;
 104             typedef itk::LandmarkBasedTransformInitializer< Rigid2DTransformType,ImageType, ImageType>
 105                 LandmarkBasedTransformInitializerType;
 106
 107             LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
 108
 109             //  Create source and target landmarks.
 110             typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer     LandmarkContainerType;
 111             typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;
 112
 113             //bufory na zaczyt wspolrzedncyh
 114             LandmarkContainerType imageLandmarks;
 115             LandmarkContainerType trackerLandmarks;
 116
 117             //bufory na pojedyncze punkty
 118             LandmarkPointType imagePoint; // dane z CT
 119             LandmarkPointType trackerPoint; //dane z tracking system
 120
 121             is >> x;
 122
 123
 124             while (is && !is.eof()) {
 125                 trackerPoint[0] = x;
 126                 is >> trackerPoint[1];
 127                 //is >> trackerPoint[2];
 128
 129                 is >> imagePoint[0];
 130                 is >> imagePoint[1];
 131                 //is >> imagePoint[2];
 132
 133                 imageLandmarks.push_back(imagePoint );
 134                 trackerLandmarks.push_back(trackerPoint );
 135
 136
 137               is >> x;
 138             }
 139
 140             is.close();
 141
 142             landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
 143             landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
 144
 145             Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
 146
 147             transform->SetIdentity();
 148
 149             // Versor rotacji i macierz translacji
 150             landmarkBasedTransformInitializer->SetTransform(transform);
 151             landmarkBasedTransformInitializer->InitializeTransform();
 152
 153             Rigid2DTransformType::MatrixType matrix = transform->GetMatrix();
 154             Rigid2DTransformType::OffsetType offset = transform->GetOffset();
 155
 156             // Write result
 157               std::ofstream out;
 158               clitk::openFileForWriting(out, args_info.output_arg);
 159
 160               out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << offset[0] << std::endl;
 161               out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << offset[1] << std::endl;
 162               out << 0.0  << ' ' << 0.0 << ' ' << 1.0;
 163               out.close();
 164
 165
 166         }
 167         else if (Dimension_temp==3)
 168         {
 169
 170             std::cout << "to ja";
 171             const     unsigned int   Dimension = 3;
 172             typedef   itk::Image< PixelType, Dimension > ImageType;
 173             typedef   float          VectorComponentType;
 174             typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
 175             //Typ LandmarkBasedTransormInitializer
 176             typedef itk::VersorRigid3DTransform< double > Rigid3DTransformType;
 177             typedef itk::LandmarkBasedTransformInitializer< Rigid3DTransformType,ImageType, ImageType>
 178                 LandmarkBasedTransformInitializerType;
 179
 180             LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
 181
 182             //  Create source and target landmarks.
 183             typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer     LandmarkContainerType;
 184             typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;
 185
 186             //bufory na zaczyt wspolrzedncyh
 187             LandmarkContainerType imageLandmarks;
 188             LandmarkContainerType trackerLandmarks;
 189
 190             //bufory na pojedyncze punkty
 191             LandmarkPointType imagePoint; // dane z CT
 192             LandmarkPointType trackerPoint; //dane z tracking system
 193
 194             is >> x;
 195
 196             while (is && !is.eof()) {
 197                 trackerPoint[0] = x;
 198                 is >> trackerPoint[1];
 199                 is >> trackerPoint[2];
 200
 201                 is >> imagePoint[0];
 202                 is >> imagePoint[1];
 203                 is >> imagePoint[2];
 204
 205                 imageLandmarks.push_back(imagePoint );
 206                 trackerLandmarks.push_back(trackerPoint );
 207
 208                 is >> x;
 209             }
 210
 211             is.close();
 212
 213             landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
 214             landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
 215
 216             Rigid3DTransformType::Pointer transform = Rigid3DTransformType::New();
 217
 218             transform->SetIdentity();
 219
 220             // Versor rotacji i macierz translacji
 221             landmarkBasedTransformInitializer->SetTransform(transform);
 222             landmarkBasedTransformInitializer->InitializeTransform();
 223
 224             Rigid3DTransformType::MatrixType matrix = transform->GetMatrix();
 225             Rigid3DTransformType::OffsetType offset = transform->GetOffset();
 226
 227             // Write result
 228               std::ofstream out;
 229               clitk::openFileForWriting(out, args_info.output_arg);
 230
 231               out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << matrix[0][2] << ' '<< offset[0] << std::endl;
 232               out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << matrix[1][2] << ' '<< offset[1] << std::endl;
 233               out << matrix[2][0] << ' ' << matrix[2][1] << ' ' << matrix[2][2] << ' '<< offset[2] << std::endl;
 234               out << 0.0  << ' ' << 0.0 << ' ' << 0.0 << ' ' << 1.0;
 235               out.close();
 236
 237
 238
 239         }
 240         else
 241         {
 242               is.close();
 243               return EXIT_FAILURE;
 244
 245         }
 246
 247
 248
 249
 250
 251   return EXIT_SUCCESS;
 252 }// end main
 253 //--------------------------------------------------------------------