tools/clitkVFMerge.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 #ifndef CLITKVFMERGE_CXX
  19 #define CLITKVFMERGE_CXX
  20
  21 /**
  22  * @file   clitkVFMerge.cxx
  23  * @author Jef Vandemeulebroucke <jefvdmb@gmail.com>
  24  * @date   June 15  10:14:53 2007
  25  *
  26  * @brief  Read in one VF (ex mhd, vf)  and write to another.  Transforming from mm to voxels needed for the vf format is implemented in clitkVfImageIO.cxx .
  27  *
  28  *
  29  */
  30
  31 // clitk include
  32 #include "clitkVFMerge_ggo.h"
  33 #include "clitkIO.h"
  34 #include "clitkImageCommon.h"
  35 #include "clitkCommon.h"
  36
  37 // itk include
  38 #include "itkImageFileWriter.h"
  39 #include <iostream>
  40 #include "itkImageFileReader.h"
  41
  42 int main( int argc, char *argv[] )
  43 {
  44
  45   // Init command line
  46   GGO(clitkVFMerge, args_info);
  47   CLITK_INIT;
  48
  49   const unsigned int SpaceDimension = 3;
  50   const unsigned int ModelDimension = 4;
  51   typedef itk::Vector< float, SpaceDimension > Displacement;
  52   typedef itk::Image< Displacement, SpaceDimension > DeformationFieldType;
  53   typedef itk::Image< Displacement, ModelDimension > DynamicDeformationFieldType;
  54   typedef itk::ImageFileReader< DeformationFieldType > DeformationFieldReaderType;
  55   typedef itk::ImageFileWriter< DynamicDeformationFieldType > DynamicDeformationFieldWriterType;
  56
  57
  58 //declare the dynamic
  59   DynamicDeformationFieldType::Pointer  dynamicDeformationField=DynamicDeformationFieldType::New();
  60
  61
  62 //declare their iterators
  63   typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
  64   DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
  65
  66   for (unsigned int i=0 ; i< args_info.inputs_num ; i ++) {
  67     //read in the deformation field i
  68     DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
  69     deformationFieldReader->SetFileName( args_info.inputs[i]);
  70     if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
  71     deformationFieldReader->Update();
  72     DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
  73
  74     //create an iterator for the current deformation field
  75     typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
  76     FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
  77
  78     //Allocate memory for the dynamic components
  79     if (i==0) {
  80       DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
  81       DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
  82       DeformationFieldType::RegionType::SizeType deformationFieldSize;
  83       deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
  84       dynamicDeformationFieldSize[0]=deformationFieldSize[0];
  85       dynamicDeformationFieldSize[1]=deformationFieldSize[1];
  86       dynamicDeformationFieldSize[2]=deformationFieldSize[2];
  87       dynamicDeformationFieldSize[3]=args_info.inputs_num;
  88       dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
  89       DynamicDeformationFieldType::IndexType start;
  90       start.Fill(0);
  91       dynamicDeformationFieldRegion.SetIndex(start);
  92       dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
  93       dynamicDeformationField->Allocate();
  94
  95
  96       //Set the spacing
  97       DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
  98       DynamicDeformationFieldType::SpacingType dynamicSpacing;
  99       dynamicSpacing[0]=spacing[0];
 100       dynamicSpacing[1]=spacing[1];
 101       dynamicSpacing[2]=spacing[2];
 102       dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
 103       dynamicDeformationField->SetSpacing(dynamicSpacing);
 104       DynamicDeformationFieldType::PointType origin;
 105       origin[0]=args_info.xorigin_arg;
 106       origin[1]=args_info.yorigin_arg;
 107       origin[2]=args_info.zorigin_arg;
 108       origin[3]=0; //temporal origin is always 0
 109       dynamicDeformationField->SetOrigin(origin);
 110
 111       // Creating iterators for the currentDeformationField and the DynamicDeformationField
 112       DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
 113       dynamicIteratorPointer=dynamicIterator;
 114       dynamicIteratorPointer->GoToBegin();
 115     }
 116     if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
 117     //Copy the current component of the input into dynamicDeformationFieldComponent
 118     fieldIterator.GoToBegin();
 119     while(!fieldIterator.IsAtEnd()) {
 120       dynamicIteratorPointer->Set(fieldIterator.Get());
 121       ++fieldIterator;
 122       ++(*dynamicIteratorPointer);
 123     }
 124   }
 125
 126
 127 //Write the vector field
 128   DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
 129   writer->SetInput( dynamicDeformationField );
 130   writer->SetFileName( args_info.output_arg );
 131   if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
 132
 133
 134   try {
 135
 136     writer->Update( );
 137   } catch( itk::ExceptionObject & excp ) {
 138     std::cerr << "Problem writing the output file" << std::endl;
 139     std::cerr << excp << std::endl;
 140     return EXIT_FAILURE;
 141   }
 142   return EXIT_SUCCESS;
 143 }
 144 #endif
 145
 146