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   //reading first line of input file to chck thw dimension of data
  79   double x = 0;
  80   //clitk::skipComment(is);
  81   is >> x;
  82
  83     typedef   unsigned char  PixelType;
  84
  85
  86
  87
  88
  89     unsigned int Dimension_temp = (unsigned int)x;
  90
  91
  92
  93         if (Dimension_temp==2)
  94         {
  95             const     unsigned int   Dimension = 2;
  96             typedef   itk::Image< PixelType, Dimension > ImageType;
  97             typedef   float          VectorComponentType;
  98             typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
  99             //Typ LandmarkBasedTransormInitializer
 100             typedef itk::Rigid2DTransform< double > Rigid2DTransformType;
 101             typedef itk::LandmarkBasedTransformInitializer< Rigid2DTransformType,ImageType, ImageType>
 102                 LandmarkBasedTransformInitializerType;
 103
 104             LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
 105
 106             //  Create source and target landmarks.
 107             typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer     LandmarkContainerType;
 108             typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;
 109
 110             LandmarkContainerType imageLandmarks;
 111             LandmarkContainerType trackerLandmarks;
 112
 113             LandmarkPointType imagePoint;
 114             LandmarkPointType trackerPoint;
 115
 116             is >> x;
 117
 118
 119             while (is && !is.eof()) {
 120                 trackerPoint[0] = x;
 121                 is >> trackerPoint[1];
 122
 123
 124                 is >> imagePoint[0];
 125                 is >> imagePoint[1];
 126
 127                 imageLandmarks.push_back(imagePoint );
 128                 trackerLandmarks.push_back(trackerPoint );
 129
 130
 131               is >> x;
 132             }
 133
 134             is.close();
 135
 136             landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
 137             landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
 138
 139             Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
 140
 141             transform->SetIdentity();
 142
 143             landmarkBasedTransformInitializer->SetTransform(transform);
 144             landmarkBasedTransformInitializer->InitializeTransform();
 145
 146             Rigid2DTransformType::MatrixType matrix = transform->GetMatrix();
 147             Rigid2DTransformType::OffsetType offset = transform->GetOffset();
 148
 149             // Write result
 150               std::ofstream out;
 151               clitk::openFileForWriting(out, args_info.output_arg);
 152
 153               out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << offset[0] << std::endl;
 154               out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << offset[1] << std::endl;
 155               out << 0.0  << ' ' << 0.0 << ' ' << 1.0;
 156               out.close();
 157
 158
 159         }
 160         else if (Dimension_temp==3)
 161         {
 162
 163             const     unsigned int   Dimension = 3;
 164             typedef   itk::Image< PixelType, Dimension > ImageType;
 165             typedef   float          VectorComponentType;
 166             typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
 167             //Typ LandmarkBasedTransormInitializer
 168             typedef itk::VersorRigid3DTransform< double > Rigid3DTransformType;
 169             typedef itk::LandmarkBasedTransformInitializer< Rigid3DTransformType,ImageType, ImageType>
 170                 LandmarkBasedTransformInitializerType;
 171
 172             LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
 173
 174             //  Create source and target landmarks.
 175             typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer     LandmarkContainerType;
 176             typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;
 177
 178             LandmarkContainerType imageLandmarks;
 179             LandmarkContainerType trackerLandmarks;
 180
 181             LandmarkPointType imagePoint;
 182             LandmarkPointType trackerPoint;
 183
 184             is >> x;
 185
 186             while (is && !is.eof()) {
 187                 trackerPoint[0] = x;
 188                 is >> trackerPoint[1];
 189                 is >> trackerPoint[2];
 190
 191                 is >> imagePoint[0];
 192                 is >> imagePoint[1];
 193                 is >> imagePoint[2];
 194
 195                 imageLandmarks.push_back(imagePoint );
 196                 trackerLandmarks.push_back(trackerPoint );
 197
 198                 is >> x;
 199             }
 200
 201             is.close();
 202
 203             landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
 204             landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
 205
 206             Rigid3DTransformType::Pointer transform = Rigid3DTransformType::New();
 207
 208             transform->SetIdentity();
 209
 210             landmarkBasedTransformInitializer->SetTransform(transform);
 211             landmarkBasedTransformInitializer->InitializeTransform();
 212
 213             Rigid3DTransformType::MatrixType matrix = transform->GetMatrix();
 214             Rigid3DTransformType::OffsetType offset = transform->GetOffset();
 215
 216             // Write result
 217               std::ofstream out;
 218               clitk::openFileForWriting(out, args_info.output_arg);
 219
 220               out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << matrix[0][2] << ' '<< offset[0] << std::endl;
 221               out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << matrix[1][2] << ' '<< offset[1] << std::endl;
 222               out << matrix[2][0] << ' ' << matrix[2][1] << ' ' << matrix[2][2] << ' '<< offset[2] << std::endl;
 223               out << 0.0  << ' ' << 0.0 << ' ' << 0.0 << ' ' << 1.0;
 224               out.close();
 225
 226
 227
 228         }
 229         else
 230         {
 231               is.close();
 232               return EXIT_FAILURE;
 233
 234         }
 235
 236
 237
 238
 239
 240   return EXIT_SUCCESS;
 241 }// end main
 242 //--------------------------------------------------------------------