forked from InsightSoftwareConsortium/ITK
-
Notifications
You must be signed in to change notification settings - Fork 0
/
DeformationFieldInitialization.cxx
189 lines (130 loc) · 4.93 KB
/
DeformationFieldInitialization.cxx
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: DeformationFieldInitialization.cxx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
// Software Guide : BeginLatex
//
// In order to initialize deformable registration algorithme it is often
// convenient to generate a deformation fields from a set of feature
// correspondances provided by the user. The following example illustrates how
// to use the \doxygen{itkDeformableFieldSource} class in order to generate a
// deformation field from the specification of two sets of landmarks.
// Landmarks from one set are associated one-to-one to the landmarks in the
// other set. Each landmark pair defines one deformation vector. This class
// interpolates the values of all other deformation vectors using
// \doxygen{KernelBasedTransform}
//
//
// \index{Registration!Finite Element-Based}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkVector.h"
#include "itkDeformationFieldSource.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImageFileWriter.h"
#include <fstream>
int main( int argc, char * argv[] )
{
if( argc < 3 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " landmarksFile fixedImage outputDeformationField" << std::endl;
return 1;
}
const unsigned int Dimension = 2;
typedef float VectorComponentType;
typedef itk::Vector< VectorComponentType, Dimension > VectorType;
typedef itk::Image< VectorType, Dimension > DeformationFieldType;
typedef unsigned char PixelType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::ImageFileReader< FixedImageType > FixedReaderType;
FixedReaderType::Pointer fixedReader = FixedReaderType::New();
fixedReader->SetFileName( argv[2] );
try
{
fixedReader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
FixedImageType::ConstPointer fixedImage = fixedReader->GetOutput();
typedef itk::DeformationFieldSource<
DeformationFieldType
> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetOutputSpacing( fixedImage->GetSpacing() );
filter->SetOutputOrigin( fixedImage->GetOrigin() );
filter->SetOutputRegion( fixedImage->GetLargestPossibleRegion() );
// Create source and target landmarks.
//
typedef FilterType::LandmarkContainerPointer LandmarkContainerPointer;
typedef FilterType::LandmarkContainer LandmarkContainerType;
typedef FilterType::LandmarkPointType LandmarkPointType;
LandmarkContainerType::Pointer sourceLandmarks = LandmarkContainerType::New();
LandmarkContainerType::Pointer targetLandmarks = LandmarkContainerType::New();
LandmarkPointType sourcePoint;
LandmarkPointType targetPoint;
std::ifstream pointsFile;
pointsFile.open( argv[1] );
unsigned int pointId = 0;
pointsFile >> sourcePoint;
pointsFile >> targetPoint;
while( !pointsFile.fail() )
{
sourceLandmarks->InsertElement( pointId, sourcePoint );
targetLandmarks->InsertElement( pointId, targetPoint );
pointId++;
pointsFile >> sourcePoint;
pointsFile >> targetPoint;
}
pointsFile.close();
filter->SetSourceLandmarks( sourceLandmarks.GetPointer() );
filter->SetTargetLandmarks( targetLandmarks.GetPointer() );
try
{
filter->UpdateLargestPossibleRegion();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Write an image for regression testing
typedef itk::ImageFileWriter< DeformationFieldType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput ( filter->GetOutput() );
writer->SetFileName( argv[3] );
filter->Print( std::cout );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown by writer" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
// Software Guide : EndLatex
}