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
|
/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// In order to initialize deformable registration algorithm it is often
// convenient to generate a displacement field from a set of feature
// correspondences provided by the user. The following example illustrates
// how to use the \doxygen{itkLandmarkDisplacementFieldSource} class in order
// to generate a displacement 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 displacement
// vector. This class interpolates the values of all other displacement
// 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 "itkLandmarkDisplacementFieldSource.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 outputDisplacementField"
<< std::endl;
return EXIT_FAILURE;
}
constexpr unsigned int Dimension = 2;
using VectorComponentType = float;
using VectorType = itk::Vector<VectorComponentType, Dimension>;
using DisplacementFieldType = itk::Image<VectorType, Dimension>;
using PixelType = unsigned char;
using FixedImageType = itk::Image<PixelType, Dimension>;
using FixedReaderType = itk::ImageFileReader<FixedImageType>;
auto fixedReader = FixedReaderType::New();
fixedReader->SetFileName(argv[2]);
try
{
fixedReader->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
FixedImageType::ConstPointer fixedImage = fixedReader->GetOutput();
using FilterType =
itk::LandmarkDisplacementFieldSource<DisplacementFieldType>;
auto filter = FilterType::New();
filter->SetOutputSpacing(fixedImage->GetSpacing());
filter->SetOutputOrigin(fixedImage->GetOrigin());
filter->SetOutputRegion(fixedImage->GetLargestPossibleRegion());
filter->SetOutputDirection(fixedImage->GetDirection());
// Create source and target landmarks.
//
using LandmarkContainerType = FilterType::LandmarkContainer;
using LandmarkPointType = FilterType::LandmarkPointType;
auto sourceLandmarks = LandmarkContainerType::New();
auto targetLandmarks = LandmarkContainerType::New();
std::ifstream pointsFile;
pointsFile.open(argv[1]);
LandmarkPointType sourcePoint;
pointsFile >> sourcePoint;
LandmarkPointType targetPoint;
pointsFile >> targetPoint;
unsigned int pointId = 0;
while (!pointsFile.fail())
{
sourceLandmarks->InsertElement(pointId, sourcePoint);
targetLandmarks->InsertElement(pointId, targetPoint);
pointId++;
pointsFile >> sourcePoint;
pointsFile >> targetPoint;
}
pointsFile.close();
filter->SetSourceLandmarks(sourceLandmarks);
filter->SetTargetLandmarks(targetLandmarks);
try
{
filter->UpdateLargestPossibleRegion();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Write an image for regression testing
using WriterType = itk::ImageFileWriter<DisplacementFieldType>;
auto writer = WriterType::New();
writer->SetInput(filter->GetOutput());
writer->SetFileName(argv[3]);
filter->Print(std::cout);
try
{
writer->Update();
}
catch (const 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
}
|
