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
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
|
/*=========================================================================
*
* 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.
*
*=========================================================================*/
#ifndef itkHistogramThresholdImageFilter_h
#define itkHistogramThresholdImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkHistogram.h"
#include "itkHistogramThresholdCalculator.h"
namespace itk
{
/** \class HistogramThresholdImageFilter
* \brief Threshold an image using a HistogramThresholdCalculator
*
* This filter creates a binary thresholded image that separates an
* image into foreground and background components. The filter
* computes the threshold using a user provided HistogramThresholdCalculator and
* applies that threshold to the input image using the
* BinaryThresholdImageFilter.
*
* The filter also has the option of providing a mask, in which case
* the histogram and therefore the threshold is computed from the
* parts of the mask with values indicated by MaskValue. The output
* image is, by default, masked by the same image. This output
* masking can be disabled using SetMaskOutput(false). Note that there
* is an inconsistency here. The MaskImageFilter (used internally)
* masks by non zero values, where as the MaskedImageToHistogramFilter
* uses explicit values. If this does not match your usage then the
* output masking will need to be managed by the user.
*
* \author Richard Beare. Department of Medicine, Monash University,
* Melbourne, Australia.
* \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.
*
* This implementation was taken from the Insight Journal paper:
* https://hdl.handle.net/10380/3279 or
* http://www.insight-journal.org/browse/publication/811
*
* \ingroup Multithreaded
* \ingroup ITKThresholding
*/
template<typename TInputImage, typename TOutputImage, typename TMaskImage=TOutputImage>
class ITK_TEMPLATE_EXPORT HistogramThresholdImageFilter :
public ImageToImageFilter<TInputImage, TOutputImage>
{
public:
/** Standard Self typedef */
typedef HistogramThresholdImageFilter Self;
typedef ImageToImageFilter<TInputImage,TOutputImage> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Runtime information support. */
itkTypeMacro(HistogramThresholdImageFilter, ImageToImageFilter);
typedef TInputImage InputImageType;
typedef TOutputImage OutputImageType;
typedef TMaskImage MaskImageType;
/** Image pixel value typedef. */
typedef typename InputImageType::PixelType InputPixelType;
typedef typename OutputImageType::PixelType OutputPixelType;
typedef typename MaskImageType::PixelType MaskPixelType;
/** Image related typedefs. */
typedef typename InputImageType::Pointer InputImagePointer;
typedef typename OutputImageType::Pointer OutputImagePointer;
typedef typename MaskImageType::Pointer MaskImagePointer;
typedef typename InputImageType::SizeType InputSizeType;
typedef typename InputImageType::IndexType InputIndexType;
typedef typename InputImageType::RegionType InputImageRegionType;
typedef typename OutputImageType::SizeType OutputSizeType;
typedef typename OutputImageType::IndexType OutputIndexType;
typedef typename OutputImageType::RegionType OutputImageRegionType;
typedef typename MaskImageType::SizeType MaskSizeType;
typedef typename MaskImageType::IndexType MaskIndexType;
typedef typename MaskImageType::RegionType MaskImageRegionType;
typedef typename NumericTraits< InputPixelType >::ValueType ValueType;
typedef typename NumericTraits< ValueType >::RealType ValueRealType;
typedef Statistics::Histogram< ValueRealType > HistogramType;
typedef typename HistogramType::Pointer HistogramPointer;
typedef typename HistogramType::ConstPointer HistogramConstPointer;
typedef typename HistogramType::SizeType HistogramSizeType;
typedef typename HistogramType::MeasurementType HistogramMeasurementType;
typedef typename HistogramType::MeasurementVectorType HistogramMeasurementVectorType;
typedef HistogramThresholdCalculator<HistogramType, InputPixelType>
CalculatorType;
typedef typename CalculatorType::Pointer CalculatorPointer;
/** Image related typedefs. */
itkStaticConstMacro(InputImageDimension, unsigned int,
InputImageType::ImageDimension );
itkStaticConstMacro(OutputImageDimension, unsigned int,
OutputImageType::ImageDimension );
itkStaticConstMacro(MaskImageDimension, unsigned int,
MaskImageType::ImageDimension );
/** Set and Get the mask image */
itkSetInputMacro(MaskImage, TMaskImage);
itkGetInputMacro(MaskImage, TMaskImage);
/** Set the input image */
void SetInput1(const TInputImage *input)
{
this->SetInput(input);
}
/** Set the marker image */
void SetInput2(const TMaskImage *input)
{
this->SetMaskImage(input);
}
/** Set the "outside" pixel value. The default value
* NumericTraits<OutputPixelType>::ZeroValue(). */
itkSetMacro(OutsideValue, OutputPixelType);
/** Get the "outside" pixel value. */
itkGetConstMacro(OutsideValue, OutputPixelType);
/** Set the "inside" pixel value. The default value
* NumericTraits<OutputPixelType>::max() */
itkSetMacro(InsideValue, OutputPixelType);
/** Get the "inside" pixel value. */
itkGetConstMacro(InsideValue, OutputPixelType);
/** Set the number of histogram bins */
itkSetMacro(NumberOfHistogramBins, unsigned int);
itkGetConstMacro(NumberOfHistogramBins, unsigned int);
/** Does histogram generator compute min and max from data?
* Default is true for all but char types */
itkSetMacro(AutoMinimumMaximum, bool);
itkGetConstMacro(AutoMinimumMaximum, bool);
itkBooleanMacro(AutoMinimumMaximum);
/** Do you want the output to be masked by the mask used in
* histogram construction. Only relevant if masking is in
* use. Default is true. */
itkSetMacro(MaskOutput, bool);
itkGetConstMacro(MaskOutput, bool);
itkBooleanMacro(MaskOutput);
/** The value in the mask image, if used, indicating voxels that
should be included. Default is the max of pixel type, as in the
MaskedImageToHistogramFilter */
itkSetMacro(MaskValue, MaskPixelType);
itkGetConstMacro(MaskValue, MaskPixelType);
/** Get the computed threshold. */
itkGetConstMacro(Threshold, InputPixelType);
/** Set/Get the calculator to use to compute the threshold */
itkSetObjectMacro(Calculator, CalculatorType);
itkGetModifiableObjectMacro(Calculator, CalculatorType);
#ifdef ITK_USE_CONCEPT_CHECKING
// Begin concept checking
itkConceptMacro(OutputEqualityComparableCheck,
(Concept::EqualityComparable<OutputPixelType>));
itkConceptMacro(InputOStreamWritableCheck,
(Concept::OStreamWritable<InputPixelType>));
itkConceptMacro(OutputOStreamWritableCheck,
(Concept::OStreamWritable<OutputPixelType>));
// End concept checking
#endif
protected:
HistogramThresholdImageFilter();
~HistogramThresholdImageFilter() ITK_OVERRIDE {};
void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
void GenerateInputRequestedRegion() ITK_OVERRIDE;
void GenerateData () ITK_OVERRIDE;
private:
ITK_DISALLOW_COPY_AND_ASSIGN(HistogramThresholdImageFilter);
OutputPixelType m_InsideValue;
OutputPixelType m_OutsideValue;
InputPixelType m_Threshold;
MaskPixelType m_MaskValue;
CalculatorPointer m_Calculator;
unsigned m_NumberOfHistogramBins;
bool m_AutoMinimumMaximum;
bool m_MaskOutput;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkHistogramThresholdImageFilter.hxx"
#endif
#endif
|
