1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
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
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.
13 It is distributed under dual licence
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
22 * @file clitkVFMerge.cxx
23 * @author Jef Vandemeulebroucke <jefvdmb@gmail.com>
24 * @date June 15 10:14:53 2007
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 .
32 #include "clitkVFMerge_ggo.h"
34 #include "clitkImageCommon.h"
37 //#include "itkReadTransform.h"
38 #include "itkImageFileWriter.h"
40 #include "itkImageFileReader.h"
41 //#include "itkRawImageIO.h"
44 int main( int argc, char *argv[] )
48 GGO(clitkVFMerge, args_info);
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;
61 DynamicDeformationFieldType::Pointer dynamicDeformationField=DynamicDeformationFieldType::New();
64 //declare their iterators
65 typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
66 DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
68 for (unsigned int i=0 ; i< args_info.inputs_num ; i ++)
70 //read in the deformation field i
71 DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
72 deformationFieldReader->SetFileName( args_info.inputs[i]);
73 if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
74 deformationFieldReader->Update();
75 DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
77 //create an iterator for the current deformation field
78 typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
79 FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
81 //Allocate memory for the dynamic components
84 DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
85 DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
86 DeformationFieldType::RegionType::SizeType deformationFieldSize;
87 deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
88 dynamicDeformationFieldSize[0]=deformationFieldSize[0];
89 dynamicDeformationFieldSize[1]=deformationFieldSize[1];
90 dynamicDeformationFieldSize[2]=deformationFieldSize[2];
91 dynamicDeformationFieldSize[3]=args_info.inputs_num;
92 dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
93 DynamicDeformationFieldType::IndexType start;
95 dynamicDeformationFieldRegion.SetIndex(start);
96 dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
97 dynamicDeformationField->Allocate();
101 DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
102 DynamicDeformationFieldType::SpacingType dynamicSpacing;
103 dynamicSpacing[0]=spacing[0];
104 dynamicSpacing[1]=spacing[1];
105 dynamicSpacing[2]=spacing[2];
106 dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
107 dynamicDeformationField->SetSpacing(dynamicSpacing);
108 DynamicDeformationFieldType::PointType origin;
109 origin[0]=args_info.xorigin_arg;
110 origin[1]=args_info.yorigin_arg;
111 origin[2]=args_info.zorigin_arg;
112 origin[3]=0; //temporal origin is always 0
113 dynamicDeformationField->SetOrigin(origin);
115 // Creating iterators for the currentDeformationField and the DynamicDeformationField
116 DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
117 dynamicIteratorPointer=dynamicIterator;
118 dynamicIteratorPointer->GoToBegin();
120 if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
121 //Copy the current component of the input into dynamicDeformationFieldComponent
122 fieldIterator.GoToBegin();
123 while(!fieldIterator.IsAtEnd())
125 dynamicIteratorPointer->Set(fieldIterator.Get());
127 ++(*dynamicIteratorPointer);
132 //Write the vector field
133 DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
134 writer->SetInput( dynamicDeformationField );
135 writer->SetFileName( args_info.output_arg );
136 if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
143 catch( itk::ExceptionObject & excp ) {
144 std::cerr << "Problem writing the output file" << std::endl;
145 std::cerr << excp << std::endl;