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
|
/*=========================================================================
*
* 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.
*
*=========================================================================*/
#ifndef itkShapeKeepNObjectsLabelMapFilter_h
#define itkShapeKeepNObjectsLabelMapFilter_h
#include "itkInPlaceLabelMapFilter.h"
#include "itkShapeLabelObjectAccessors.h"
#include "itkProgressReporter.h"
namespace itk
{
/**
* \class ShapeKeepNObjectsLabelMapFilter
* \brief Keep N objects according to their shape attributes.
*
* The ShapeKeepNObjectsLabelMapFilter keeps N objects in a label collection image with the
* highest (or lowest) attribute value. The attributes values are those of the ShapeLabelObject.
*
* This implementation was taken from the Insight Journal paper:
* https://www.insight-journal.org/browse/publication/176
*
* \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.
*
* \sa ShapeLabelObject, BinaryShapeKeepNObjectsImageFilter, LabelStatisticsKeepNObjectsImageFilter
* \ingroup ImageEnhancement MathematicalMorphologyImageFilters
* \ingroup ITKLabelMap
*/
template <typename TImage>
class ITK_TEMPLATE_EXPORT ShapeKeepNObjectsLabelMapFilter : public InPlaceLabelMapFilter<TImage>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(ShapeKeepNObjectsLabelMapFilter);
/** Standard class type aliases. */
using Self = ShapeKeepNObjectsLabelMapFilter;
using Superclass = InPlaceLabelMapFilter<TImage>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** Some convenient type alias. */
using ImageType = TImage;
using ImagePointer = typename ImageType::Pointer;
using ImageConstPointer = typename ImageType::ConstPointer;
using PixelType = typename ImageType::PixelType;
using IndexType = typename ImageType::IndexType;
using LabelObjectType = typename ImageType::LabelObjectType;
using AttributeType = typename LabelObjectType::AttributeType;
/** ImageDimension constants */
static constexpr unsigned int ImageDimension = TImage::ImageDimension;
/** Standard New method. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(ShapeKeepNObjectsLabelMapFilter);
#ifdef ITK_USE_CONCEPT_CHECKING
// Begin concept checking
/* itkConceptMacro(InputEqualityComparableCheck,
(Concept::EqualityComparable<InputImagePixelType>));
itkConceptMacro(IntConvertibleToInputCheck,
(Concept::Convertible<int, InputImagePixelType>));
itkConceptMacro(InputOStreamWritableCheck,
(Concept::OStreamWritable<InputImagePixelType>));*/
// End concept checking
#endif
/**
* Set/Get the ordering of the objects. By default, the ones with the
* highest value are kept. Turning ReverseOrdering to true make this filter
* keep the objects with the smallest values
*/
itkSetMacro(ReverseOrdering, bool);
itkGetConstReferenceMacro(ReverseOrdering, bool);
itkBooleanMacro(ReverseOrdering);
/**
* Set/Get the number of objects to keep
*/
itkSetMacro(NumberOfObjects, SizeValueType);
itkGetConstReferenceMacro(NumberOfObjects, SizeValueType);
/**
* Set/Get the attribute to use to select the object to keep.
* Default is "Size".
*/
itkGetConstMacro(Attribute, AttributeType);
itkSetMacro(Attribute, AttributeType);
void
SetAttribute(const std::string & s)
{
this->SetAttribute(LabelObjectType::GetAttributeFromName(s));
}
protected:
ShapeKeepNObjectsLabelMapFilter();
~ShapeKeepNObjectsLabelMapFilter() override = default;
void
GenerateData() override;
template <typename TAttributeAccessor>
void
TemplatedGenerateData(const TAttributeAccessor &)
{
// Allocate the output
this->AllocateOutputs();
ImageType * output = this->GetOutput();
ImageType * output2 = this->GetOutput(1);
// set the background value for the second output - this is not done in the
// superclasses
output2->SetBackgroundValue(output->GetBackgroundValue());
using LabelObjectPointer = typename LabelObjectType::Pointer;
using VectorType = std::vector<LabelObjectPointer>;
ProgressReporter progress(this, 0, 2 * output->GetNumberOfLabelObjects());
// get the label objects in a vector, so they can be sorted
VectorType labelObjects;
labelObjects.reserve(output->GetNumberOfLabelObjects());
typename ImageType::Iterator it(output);
while (!it.IsAtEnd())
{
labelObjects.push_back(it.GetLabelObject());
progress.CompletedPixel();
++it;
}
// instantiate the comparator and sort the vector
if (m_NumberOfObjects < output->GetNumberOfLabelObjects())
{
auto end = labelObjects.begin() + m_NumberOfObjects;
if (m_ReverseOrdering)
{
Functor::LabelObjectReverseComparator<LabelObjectType, TAttributeAccessor> comparator;
std::nth_element(labelObjects.begin(), end, labelObjects.end(), comparator);
}
else
{
Functor::LabelObjectComparator<LabelObjectType, TAttributeAccessor> comparator;
std::nth_element(labelObjects.begin(), end, labelObjects.end(), comparator);
}
progress.CompletedPixel();
// and remove the last objects of the map
for (typename VectorType::const_iterator it2 = end; it2 != labelObjects.end(); ++it2)
{
output2->AddLabelObject(*it2);
output->RemoveLabelObject(*it2);
progress.CompletedPixel();
}
}
}
void
PrintSelf(std::ostream & os, Indent indent) const override;
bool m_ReverseOrdering{};
SizeValueType m_NumberOfObjects{};
AttributeType m_Attribute{};
}; // end of class
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkShapeKeepNObjectsLabelMapFilter.hxx"
#endif
#endif
|
