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://oncora1.lyon.fnclcc.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
  36 // itk include
  37 //#include "itkReadTransform.h"
  38 #include "itkImageFileWriter.h"
  39 #include <iostream>
  40 #include "itkImageFileReader.h"
  41 //#include "itkRawImageIO.h"
  42 //#include "macro.h"
  43
  44 int main( int argc, char *argv[] )
  45 {
  46
  47   // Init command line
  48   GGO(clitkVFMerge, args_info);
  49   CLITK_INIT;
  50
  51   const unsigned int SpaceDimension = 3;
  52   const unsigned int ModelDimension = 4;
  53   typedef itk::Vector< float, SpaceDimension > Displacement;
  54   typedef itk::Image< Displacement, SpaceDimension > DeformationFieldType;
  55   typedef itk::Image< Displacement, ModelDimension > DynamicDeformationFieldType;
  56   typedef itk::ImageFileReader< DeformationFieldType > DeformationFieldReaderType;
  57   typedef itk::ImageFileWriter< DynamicDeformationFieldType > DynamicDeformationFieldWriterType;
  58
  59
  60 //declare the dynamic
  61   DynamicDeformationFieldType::Pointer  dynamicDeformationField=DynamicDeformationFieldType::New();
  62
  63
  64 //declare their iterators
  65   typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
  66   DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
  67
  68   for (unsigned int i=0 ; i< args_info.inputs_num ; i ++) {
  69     //read in the deformation field i
  70     DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
  71     deformationFieldReader->SetFileName( args_info.inputs[i]);
  72     if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
  73     deformationFieldReader->Update();
  74     DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
  75
  76     //create an iterator for the current deformation field
  77     typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
  78     FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
  79
  80     //Allocate memory for the dynamic components
  81     if (i==0) {
  82       DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
  83       DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
  84       DeformationFieldType::RegionType::SizeType deformationFieldSize;
  85       deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
  86       dynamicDeformationFieldSize[0]=deformationFieldSize[0];
  87       dynamicDeformationFieldSize[1]=deformationFieldSize[1];
  88       dynamicDeformationFieldSize[2]=deformationFieldSize[2];
  89       dynamicDeformationFieldSize[3]=args_info.inputs_num;
  90       dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
  91       DynamicDeformationFieldType::IndexType start;
  92       start.Fill(0);
  93       dynamicDeformationFieldRegion.SetIndex(start);
  94       dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
  95       dynamicDeformationField->Allocate();
  96
  97
  98       //Set the spacing
  99       DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
 100       DynamicDeformationFieldType::SpacingType dynamicSpacing;
 101       dynamicSpacing[0]=spacing[0];
 102       dynamicSpacing[1]=spacing[1];
 103       dynamicSpacing[2]=spacing[2];
 104       dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
 105       dynamicDeformationField->SetSpacing(dynamicSpacing);
 106       DynamicDeformationFieldType::PointType origin;
 107       origin[0]=args_info.xorigin_arg;
 108       origin[1]=args_info.yorigin_arg;
 109       origin[2]=args_info.zorigin_arg;
 110       origin[3]=0; //temporal origin is always 0
 111       dynamicDeformationField->SetOrigin(origin);
 112
 113       // Creating iterators for the currentDeformationField and the DynamicDeformationField
 114       DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
 115       dynamicIteratorPointer=dynamicIterator;
 116       dynamicIteratorPointer->GoToBegin();
 117     }
 118     if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
 119     //Copy the current component of the input into dynamicDeformationFieldComponent
 120     fieldIterator.GoToBegin();
 121     while(!fieldIterator.IsAtEnd()) {
 122       dynamicIteratorPointer->Set(fieldIterator.Get());
 123       ++fieldIterator;
 124       ++(*dynamicIteratorPointer);
 125     }
 126   }
 127
 128
 129 //Write the vector field
 130   DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
 131   writer->SetInput( dynamicDeformationField );
 132   writer->SetFileName( args_info.output_arg );
 133   if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
 134
 135
 136   try {
 137
 138     writer->Update( );
 139   } catch( itk::ExceptionObject & excp ) {
 140     std::cerr << "Problem writing the output file" << std::endl;
 141     std::cerr << excp << std::endl;
 142     return EXIT_FAILURE;
 143   }
 144   return EXIT_SUCCESS;
 145 }
 146 #endif
 147
 148