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
|
/*=========================================================================
*
* 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.
*
*=========================================================================*/
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkSimpleFilterWatcher.h"
#include "vnl/vnl_sample.h"
int itkConnectedComponentImageFilterTest(int argc, char* argv[] )
{
if( argc < 5 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImage outputImage threshold_low threshold_hi [fully_connected] [minimum_object_size]" << std::endl;
return EXIT_FAILURE;
}
typedef unsigned short InternalPixelType;
const unsigned int Dimension = 2;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::Image<unsigned short,Dimension> OutputImageType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, Dimension> RGBImageType;
typedef itk::ImageFileReader< InternalImageType > ReaderType;
typedef itk::ImageFileWriter< RGBImageType > WriterType;
typedef itk::BinaryThresholdImageFilter< InternalImageType, InternalImageType > ThresholdFilterType;
typedef itk::ConnectedComponentImageFilter< InternalImageType, OutputImageType > FilterType;
typedef itk::RelabelComponentImageFilter< OutputImageType, OutputImageType > RelabelType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
ThresholdFilterType::Pointer threshold = ThresholdFilterType::New();
FilterType::Pointer filter = FilterType::New();
RelabelType::Pointer relabel = RelabelType::New();
itk::SimpleFilterWatcher watcher(filter);
watcher.QuietOn();
reader->SetFileName( argv[1] );
InternalPixelType threshold_low, threshold_hi;
threshold_low = atoi( argv[3]);
threshold_hi = atoi( argv[4]);
threshold->SetInput (reader->GetOutput());
threshold->SetInsideValue(itk::NumericTraits<InternalPixelType>::OneValue());
threshold->SetOutsideValue(itk::NumericTraits<InternalPixelType>::ZeroValue());
threshold->SetLowerThreshold(threshold_low);
threshold->SetUpperThreshold(threshold_hi);
threshold->Update();
filter->SetInput (threshold->GetOutput());
if (argc > 5)
{
int fullyConnected = atoi( argv[5] );
filter->SetFullyConnected( fullyConnected );
}
relabel->SetInput( filter->GetOutput() );
if (argc > 6)
{
int minSize = atoi( argv[6] );
relabel->SetMinimumObjectSize( minSize );
std::cerr << "minSize: " << minSize << std::endl;
}
try
{
relabel->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Relabel: exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
// Remap the labels to viewable colors
RGBImageType::Pointer colored = RGBImageType::New();
colored->SetRegions( filter->GetOutput()->GetBufferedRegion() );
colored->Allocate();
unsigned short numObjects = relabel->GetNumberOfObjects();
std::vector<RGBPixelType> colormap;
RGBPixelType px;
colormap.resize( numObjects+1 );
vnl_sample_reseed( 1031571 );
for (unsigned short i=0; i < colormap.size(); ++i)
{
px.SetRed(
static_cast<unsigned char>(255*vnl_sample_uniform( 0.3333, 1.0 ) ));
px.SetGreen(
static_cast<unsigned char>(255*vnl_sample_uniform( 0.3333, 1.0 ) ));
px.SetBlue(
static_cast<unsigned char>(255*vnl_sample_uniform( 0.3333, 1.0 ) ));
colormap[i] = px;
}
itk::ImageRegionIterator<OutputImageType>
it(relabel->GetOutput(), relabel->GetOutput()->GetBufferedRegion());
itk::ImageRegionIterator<RGBImageType> cit(colored,
colored->GetBufferedRegion());
while( !it.IsAtEnd() )
{
if (it.Get() == 0)
{
cit.Set(RGBPixelType(itk::NumericTraits< unsigned char >::ZeroValue() ));
}
else
{
cit.Set( colormap[it.Get()] );
}
++it;
++cit;
}
try
{
writer->SetInput (colored);
writer->SetFileName( argv[2] );
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
return EXIT_SUCCESS;
}
|
