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
189
190
191
192
193
194
195
196
197
198
199
200
|
/*=========================================================================
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt for
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.
=========================================================================*/
#include "antsUtilities.h"
#include "antsAllocImage.h"
#include <algorithm>
#include "ReadWriteData.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkAvantsMutualInformationRegistrationFunction.h"
#include "itkProbabilisticRegistrationFunction.h"
#include "itkCrossCorrelationRegistrationFunction.h"
namespace ants
{
template <unsigned int ImageDimension>
int
MemoryTest(unsigned int argc, char * argv[])
{
using PixelType = float;
using VectorType = itk::Vector<float, ImageDimension>;
using FieldType = itk::Image<VectorType, ImageDimension>;
using ImageType = itk::Image<PixelType, ImageDimension>;
using Iterator = itk::ImageRegionIteratorWithIndex<ImageType>;
// get command line params
unsigned int argct = 2;
unsigned int whichmetric = std::stoi(argv[argct]);
argct++;
std::string fn1 = std::string(argv[argct]);
argct++;
std::string fn2 = std::string(argv[argct]);
argct++;
unsigned int numberoffields = 11;
if (argc > argct)
{
numberoffields = std::stoi(argv[argct]);
}
argct++;
typename ImageType::Pointer image1 = nullptr;
ReadImage<ImageType>(image1, fn1.c_str());
typename ImageType::Pointer image2 = nullptr;
ReadImage<ImageType>(image2, fn2.c_str());
std::vector<typename FieldType::Pointer> fieldvec;
for (unsigned int i = 0; i < numberoffields; i++)
{
std::cout << " NFields " << i << " of " << numberoffields << std::endl;
VectorType zero;
zero.Fill(0);
// ORIENTATION ALERT: Original code set spacing/origin without
// also setting directions.
typename FieldType::Pointer field = AllocImage<FieldType>(image1, zero);
fieldvec.push_back(field);
}
typename ImageType::Pointer metricimg = AllocImage<ImageType>(image1, 0);
Iterator iter(metricimg, metricimg->GetLargestPossibleRegion());
using FixedImageType = ImageType;
using MovingImageType = ImageType;
using DisplacementFieldType = FieldType;
// Choose the similarity metric
using MIMetricType =
itk::AvantsMutualInformationRegistrationFunction<FixedImageType, MovingImageType, DisplacementFieldType>;
using CCMetricType =
itk::CrossCorrelationRegistrationFunction<FixedImageType, MovingImageType, DisplacementFieldType>;
// typedef itk::LandmarkCrossCorrelationRegistrationFunction<FixedImageType,MovingImageType,DisplacementFieldType>
// MetricType;
// typename
typename MIMetricType::Pointer mimet = MIMetricType::New();
typename CCMetricType::Pointer ccmet = CCMetricType::New();
// int nbins=32;
typename CCMetricType::RadiusType ccradius;
ccradius.Fill(4);
typename MIMetricType::RadiusType miradius;
miradius.Fill(0);
// mimet->SetDisplacementField(field);
mimet->SetFixedImage(image1);
mimet->SetMovingImage(image2);
mimet->SetRadius(miradius);
mimet->SetGradientStep(1.e2);
mimet->SetNormalizeGradient(false);
// ccmet->SetDisplacementField(field);
ccmet->SetFixedImage(image1);
ccmet->SetMovingImage(image2);
ccmet->SetRadius(ccradius);
ccmet->SetGradientStep(1.e2);
ccmet->SetNormalizeGradient(false);
if (whichmetric == 1) // imagedifference
{
ccmet->InitializeIteration();
}
else if (whichmetric != 0)
{
mimet->InitializeIteration();
}
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
MemoryTest(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "MemoryTest");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = nullptr;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
// antscout->set_stream( out_stream );
if (argc < 3)
{
std::cout << "Basic useage ex: " << std::endl;
std::cout << argv[0] << " ImageDimension whichmetric image1.ext image2.ext NumberOfFieldsToAllocate " << std::endl;
std::cout << " outimage and logfile are optional " << std::endl;
std::cout << " Metric 0 - MeanSquareDifference, 1 - Cross-Correlation, 2-Mutual Information " << std::endl;
if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
{
return EXIT_SUCCESS;
}
return EXIT_FAILURE;
}
// Get the image dimension
switch (std::stoi(argv[1]))
{
case 2:
{
return MemoryTest<2>(argc, argv);
}
break;
case 3:
{
return MemoryTest<3>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
|
