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
|
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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
*
* http://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
//
// This example shows how to use the \doxygen{ImageLinearIteratorWithIndex} for
// computing the mean across time of a 4D image where the first three
// dimensions correspond to spatial coordinates and the fourth dimension
// corresponds to time. The result of the mean across time is to be stored in a
// 3D image.
//
// \index{Iterators!and 4D images}
// \index{ImageLinearIteratorWithIndex!4D images}
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginCodeSnippet
#include "itkImageLinearConstIteratorWithIndex.h"
// Software Guide : EndCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
int main( int argc, char *argv[] )
{
// Verify the number of parameters on the command line.
if ( argc < 3 )
{
std::cerr << "Missing parameters. " << std::endl;
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0]
<< " input4DImageFile output3DImageFile"
<< std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// First we declare the types of the images
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef unsigned char PixelType;
typedef itk::Image< PixelType, 3 > Image3DType;
typedef itk::Image< PixelType, 4 > Image4DType;
typedef itk::ImageFileReader< Image4DType > Reader4DType;
typedef itk::ImageFileWriter< Image3DType > Writer3DType;
Reader4DType::Pointer reader4D = Reader4DType::New();
reader4D->SetFileName( argv[1] );
try
{
reader4D->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Error reading the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
Image4DType::ConstPointer image4D = reader4D->GetOutput();
Image3DType::Pointer image3D = Image3DType::New();
typedef Image3DType::IndexType Index3DType;
typedef Image3DType::SizeType Size3DType;
typedef Image3DType::RegionType Region3DType;
typedef Image3DType::SpacingType Spacing3DType;
typedef Image3DType::PointType Origin3DType;
typedef Image4DType::IndexType Index4DType;
typedef Image4DType::SizeType Size4DType;
typedef Image4DType::SpacingType Spacing4DType;
typedef Image4DType::PointType Origin4DType;
Index3DType index3D;
Size3DType size3D;
Spacing3DType spacing3D;
Origin3DType origin3D;
Image4DType::RegionType region4D = image4D->GetBufferedRegion();
Index4DType index4D = region4D.GetIndex();
Size4DType size4D = region4D.GetSize();
Spacing4DType spacing4D = image4D->GetSpacing();
Origin4DType origin4D = image4D->GetOrigin();
for( unsigned int i=0; i < 3; i++)
{
size3D[i] = size4D[i];
index3D[i] = index4D[i];
spacing3D[i] = spacing4D[i];
origin3D[i] = origin4D[i];
}
image3D->SetSpacing( spacing3D );
image3D->SetOrigin( origin3D );
Region3DType region3D;
region3D.SetIndex( index3D );
region3D.SetSize( size3D );
image3D->SetRegions( region3D );
image3D->Allocate();
typedef itk::NumericTraits< PixelType >::AccumulateType SumType;
typedef itk::NumericTraits< SumType >::RealType MeanType;
const unsigned int timeLength = region4D.GetSize()[3];
typedef itk::ImageLinearConstIteratorWithIndex<
Image4DType > IteratorType;
IteratorType it( image4D, region4D );
it.SetDirection( 3 ); // Walk along time dimension
it.GoToBegin();
while( !it.IsAtEnd() )
{
SumType sum = itk::NumericTraits< SumType >::Zero;
it.GoToBeginOfLine();
index4D = it.GetIndex();
while( !it.IsAtEndOfLine() )
{
sum += it.Get();
++it;
}
MeanType mean = static_cast< MeanType >( sum ) /
static_cast< MeanType >( timeLength );
index3D[0] = index4D[0];
index3D[1] = index4D[1];
index3D[2] = index4D[2];
image3D->SetPixel( index3D, static_cast< PixelType >( mean ) );
it.NextLine();
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// As you can see, we avoid to use a 3D iterator to walk
// over the mean image. The reason is that there is no
// guarantee that the 3D iterator will walk in the same
// order as the 4D. Iterators just adhere to their contract
// of visiting all the pixel, but do not enforce any particular
// order for the visits. The linear iterator guarantees to
// visit the pixels along a line of the image in the order
// in which they are placed in the line, but do not states
// in what order one line will be visited with respect to
// other lines. Here we simply take advantage of knowing
// the first three components of the 4D iterator index,
// and use them to place the resulting mean value in the
// output 3D image.
//
// Software Guide : EndLatex
Writer3DType::Pointer writer3D = Writer3DType::New();
writer3D->SetFileName( argv[2] );
writer3D->SetInput( image3D );
try
{
writer3D->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Error writing the image" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
|
