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
|
/*=========================================================================
*
* 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.
*
*=========================================================================*/
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkSimpleFilterWatcher.h"
#include "itkLabelImageToStatisticsLabelMapFilter.h"
#include "itkStatisticsUniqueLabelMapFilter.h"
#include "itkTestingMacros.h"
#include "itkFlatStructuringElement.h"
#include "itkGrayscaleDilateImageFilter.h"
#include "itkObjectByObjectLabelMapFilter.h"
template <typename TLabelMap>
int
CheckLabelMapOverlap(TLabelMap * labelMap)
{
int exitCode = EXIT_SUCCESS;
for (auto & labelObject : labelMap->GetLabelObjects())
{
// Manually check each label object against all other label objects, to ensure that no two label objects share an
// index.
for (itk::SizeValueType lineNumber = 0; lineNumber < labelObject->GetNumberOfLines(); ++lineNumber)
{
auto line = labelObject->GetLine(lineNumber);
auto idx = line.GetIndex();
ITK_TEST_EXPECT_TRUE(line.GetLength() <= labelObject->GetNumberOfPixels());
for (itk::SizeValueType lengthIndex = 0; lengthIndex < line.GetLength(); ++lengthIndex)
{
for (auto & checkObject : labelMap->GetLabelObjects())
{
if (checkObject != labelObject && checkObject->HasIndex(idx))
{
std::cerr << "Label: " << int(labelObject->GetLabel()) << " and " << int(checkObject->GetLabel())
<< " has index " << idx << std::endl;
exitCode = EXIT_FAILURE;
}
}
++idx[0];
}
}
}
return exitCode;
}
int
itkStatisticsUniqueLabelMapFilterTest1(int argc, char * argv[])
{
if (argc != 6)
{
std::cerr << "Missing parameters." << std::endl;
std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv);
std::cerr << " input feature output";
std::cerr << " reverseOrdering attribute";
std::cerr << std::endl;
return EXIT_FAILURE;
}
const char * inputImage = argv[1];
const char * featureImage = argv[2];
const char * outputImage = argv[3];
const bool reverseOrdering = std::stoi(argv[4]);
const unsigned int attribute = std::stoi(argv[5]);
constexpr unsigned int Dimension = 2;
using PixelType = unsigned char;
using ImageType = itk::Image<PixelType, Dimension>;
using StatisticsLabelObjectType = itk::StatisticsLabelObject<PixelType, Dimension>;
using LabelMapType = itk::LabelMap<StatisticsLabelObjectType>;
using ReaderType = itk::ImageFileReader<ImageType>;
auto reader = ReaderType::New();
reader->SetFileName(inputImage);
auto reader2 = ReaderType::New();
reader2->SetFileName(featureImage);
// Dilate each label object to form overlapping label objects.
constexpr unsigned int radiusValue = 5;
using LabelImageToLabelMapFilterType = itk::LabelImageToLabelMapFilter<ImageType, LabelMapType>;
auto labelMapConverter = LabelImageToLabelMapFilterType::New();
labelMapConverter->SetInput(reader->GetOutput());
labelMapConverter->SetBackgroundValue(PixelType{});
using StructuringElementType = itk::FlatStructuringElement<Dimension>;
StructuringElementType::RadiusType radius;
radius.Fill(radiusValue);
StructuringElementType structuringElement = StructuringElementType::Box(radius);
using MorphologicalFilterType = itk::GrayscaleDilateImageFilter<ImageType, ImageType, StructuringElementType>;
auto grayscaleDilateFilter = MorphologicalFilterType::New();
grayscaleDilateFilter->SetInput(reader->GetOutput());
grayscaleDilateFilter->SetKernel(structuringElement);
using ObjectByObjectLabelMapFilterType = itk::ObjectByObjectLabelMapFilter<LabelMapType>;
auto objectByObjectLabelMapFilter = ObjectByObjectLabelMapFilterType::New();
objectByObjectLabelMapFilter->SetInput(labelMapConverter->GetOutput());
objectByObjectLabelMapFilter->SetBinaryInternalOutput(false);
objectByObjectLabelMapFilter->SetFilter(grayscaleDilateFilter);
using StatisticsFilterType = itk::StatisticsLabelMapFilter<LabelMapType, ImageType>;
auto statisticsFilter = StatisticsFilterType::New();
statisticsFilter->SetInput1(objectByObjectLabelMapFilter->GetOutput());
statisticsFilter->SetFeatureImage(reader2->GetOutput());
using LabelUniqueType = itk::StatisticsUniqueLabelMapFilter<LabelMapType>;
auto unique = LabelUniqueType::New();
// testing boolean macro for ReverseOrdering
unique->ReverseOrderingOn();
ITK_TEST_SET_GET_VALUE(true, unique->GetReverseOrdering());
unique->ReverseOrderingOff();
ITK_TEST_SET_GET_VALUE(false, unique->GetReverseOrdering());
// testing get and set macros for ReverseOrdering
// ToDo: decrease reverseOrdering argv index once the JIRA issue 3370 has been solved
// Then, argv[4]
unique->SetReverseOrdering(reverseOrdering);
ITK_TEST_SET_GET_VALUE(reverseOrdering, unique->GetReverseOrdering());
// testing get and set macros for Attribute
// ToDo: decrease attribute argv index once the JIRA issue 3370 has been solved
// Then, argv[5]
unique->SetAttribute(attribute);
ITK_TEST_SET_GET_VALUE(attribute, unique->GetAttribute());
unique->SetInput(statisticsFilter->GetOutput());
itk::SimpleFilterWatcher watcher(unique, "filter");
ITK_TRY_EXPECT_NO_EXCEPTION(unique->Update());
int exitCode = CheckLabelMapOverlap(unique->GetOutput());
if (exitCode == EXIT_FAILURE)
{
std::cerr << "Overlap detected in the label map." << std::endl;
}
using LabelMapToImageFilterType = itk::LabelMapToLabelImageFilter<LabelMapType, ImageType>;
auto labelMapToImageFilter = LabelMapToImageFilterType::New();
labelMapToImageFilter->SetInput(unique->GetOutput());
using WriterType = itk::ImageFileWriter<ImageType>;
auto writer = WriterType::New();
writer->SetInput(labelMapToImageFilter->GetOutput());
writer->SetFileName(outputImage);
writer->UseCompressionOn();
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
return exitCode;
}
|
