forked from InsightSoftwareConsortium/ITK
-
Notifications
You must be signed in to change notification settings - Fork 0
/
itkFastMarchingUpwindGradientImageFilter.txx
325 lines (272 loc) · 9.28 KB
/
itkFastMarchingUpwindGradientImageFilter.txx
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
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkFastMarchingUpwindGradientImageFilter.txx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkFastMarchingUpwindGradientImageFilter_txx
#define __itkFastMarchingUpwindGradientImageFilter_txx
#include "itkFastMarchingUpwindGradientImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkNumericTraits.h"
#include "vnl/vnl_math.h"
#include <algorithm>
namespace itk
{
/**
*
*/
template <class TLevelSet, class TSpeedImage>
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::FastMarchingUpwindGradientImageFilter()
{
m_TargetPoints = NULL;
m_ReachedTargetPoints = NULL;
m_GradientImage = GradientImageType::New();
m_GenerateGradientImage = false;
m_TargetOffset = 1.0;
m_TargetReachedMode = NoTargets;
m_TargetValue = 0.0;
m_NumberOfTargets = 0;
}
/**
*
*/
template <class TLevelSet, class TSpeedImage>
void
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::PrintSelf(std::ostream& os, Indent indent) const
{
Superclass::PrintSelf(os,indent);
os << indent << "Target points: " << m_TargetPoints.GetPointer() << std::endl;
os << indent << "Reached points: " << m_ReachedTargetPoints.GetPointer() << std::endl;
os << indent << "Gradient image: " << m_GradientImage.GetPointer() << std::endl;
os << indent << "Generate gradient image: " << m_GenerateGradientImage << std::endl;
os << indent << "Number of targets: " << m_NumberOfTargets << std::endl;
os << indent << "Target offset: " << m_TargetOffset << std::endl;
os << indent << "Target reach mode: " << m_TargetReachedMode << std::endl;
os << indent << "Target value: " << m_TargetValue << std::endl;
}
/**
*
*/
template <class TLevelSet, class TSpeedImage>
void
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::Initialize( LevelSetImageType * output )
{
Superclass::Initialize(output);
// allocate memory for the GradientImage if requested
if (m_GenerateGradientImage)
{
m_GradientImage->CopyInformation( this->GetInput() );
m_GradientImage->SetBufferedRegion( output->GetBufferedRegion() );
m_GradientImage->Allocate();
}
// set all gradient vectors to zero
if (m_GenerateGradientImage)
{
typedef ImageRegionIterator< GradientImageType > GradientIterator;
GradientIterator gradientIt( m_GradientImage,
m_GradientImage->GetBufferedRegion() );
GradientPixelType zeroGradient;
typedef typename GradientPixelType::ValueType GradientPixelValueType;
zeroGradient.Fill(NumericTraits< GradientPixelValueType >::Zero);
for ( gradientIt.GoToBegin(); !gradientIt.IsAtEnd(); ++gradientIt )
{
gradientIt.Set( zeroGradient );
}
}
// Need to reset the target value.
m_TargetValue = 0.0;
if ( m_TargetReachedMode == SomeTargets || m_TargetReachedMode == AllTargets)
{
m_ReachedTargetPoints = NodeContainer::New();
}
}
template <class TLevelSet, class TSpeedImage>
void
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::GenerateData()
{
// cache the original stopping value that was set by the user
// because this subclass may change it once a target point is
// reached in order to control the execution of the superclass.
double stoppingValue = this->GetStoppingValue();
// run the GenerateData() method of the superclass
try
{
Superclass::GenerateData();
}
catch (ProcessAborted &exc)
{
// process was aborted, clean up the state of the filter
// (most of the cleanup will have already been done by the
// superclass)
// restore the original stopping value
this->SetStoppingValue( stoppingValue );
throw exc;
}
// restore the original stopping value
this->SetStoppingValue( stoppingValue );
}
template <class TLevelSet, class TSpeedImage>
void
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::UpdateNeighbors(
const IndexType& index,
const SpeedImageType * speedImage,
LevelSetImageType * output )
{
Superclass::UpdateNeighbors(index,speedImage,output);
if (m_GenerateGradientImage)
{
this->ComputeGradient(index, output, this->GetLabelImage(), m_GradientImage);
}
AxisNodeType node;
// Only check for reached targets if the mode is not NoTargets and
// there is at least one TargetPoint.
if( m_TargetReachedMode != NoTargets && m_TargetPoints )
{
bool targetReached = false;
if (m_TargetReachedMode == OneTarget)
{
typename NodeContainer::ConstIterator pointsIter = m_TargetPoints->Begin();
typename NodeContainer::ConstIterator pointsEnd = m_TargetPoints->End();
for (; pointsIter != pointsEnd; ++pointsIter )
{
node = pointsIter.Value();
if (node.GetIndex() == index)
{
targetReached = true;
break;
}
}
}
else if (m_TargetReachedMode == SomeTargets)
{
typename NodeContainer::ConstIterator pointsIter = m_TargetPoints->Begin();
typename NodeContainer::ConstIterator pointsEnd = m_TargetPoints->End();
for (; pointsIter != pointsEnd; ++pointsIter )
{
node = pointsIter.Value();
if (node.GetIndex() == index)
{
m_ReachedTargetPoints->InsertElement(m_ReachedTargetPoints->Size(),node);
break;
}
}
if (static_cast<long>(m_ReachedTargetPoints->Size()) == m_NumberOfTargets)
{
targetReached = true;
}
}
else if (m_TargetReachedMode == AllTargets)
{
typename NodeContainer::ConstIterator pointsIter = m_TargetPoints->Begin();
typename NodeContainer::ConstIterator pointsEnd = m_TargetPoints->End();
for (; pointsIter != pointsEnd; ++pointsIter )
{
node = pointsIter.Value();
if (node.GetIndex() == index)
{
m_ReachedTargetPoints->InsertElement(m_ReachedTargetPoints->Size(),node);
break;
}
}
if (m_ReachedTargetPoints->Size() == m_TargetPoints->Size())
{
targetReached = true;
}
}
if (targetReached)
{
m_TargetValue = static_cast<double>(output->GetPixel(index));
double newStoppingValue = m_TargetValue + m_TargetOffset;
if (newStoppingValue < this->GetStoppingValue())
{
// This changes the stopping value that may have been set by
// the user. Therefore, the value set by the user needs to be
// cached in GenerateUpdate() so that it will be correct for
// future Update() commands.
this->SetStoppingValue(newStoppingValue);
}
}
}
}
/**
*
*/
template <class TLevelSet, class TSpeedImage>
void
FastMarchingUpwindGradientImageFilter<TLevelSet,TSpeedImage>
::ComputeGradient( const IndexType& index,
const LevelSetImageType * output,
const LabelImageType * itkNotUsed(labelImage),
GradientImageType * gradientImage)
{
IndexType neighIndex = index;
typedef typename TLevelSet::PixelType LevelSetPixelType;
LevelSetPixelType centerPixel;
LevelSetPixelType dx_forward;
LevelSetPixelType dx_backward;
GradientPixelType gradientPixel;
const LevelSetIndexType & lastIndex = this->GetLastIndex();
const LevelSetIndexType & startIndex = this->GetStartIndex();
const LevelSetPixelType ZERO =
NumericTraits< LevelSetPixelType >::Zero;
OutputSpacingType spacing = this->GetOutput()->GetSpacing();
unsigned int xStride[itkGetStaticConstMacro(SetDimension)];
for ( unsigned int j = 0; j < SetDimension; j++ )
{
centerPixel = output->GetPixel(index);
neighIndex = index;
// Set stride of one in each direction
xStride[j] = 1;
// Compute one-sided finite differences with alive neighbors
// (the front can only come from there)
dx_backward = 0.0;
neighIndex[j] = index[j] - xStride[j];
if(! (neighIndex[j] > lastIndex[j] ||
neighIndex[j] < startIndex[j]) )
{
if ( this->GetLabelImage()->GetPixel( neighIndex ) == Superclass::AlivePoint )
{
dx_backward = centerPixel - output->GetPixel( neighIndex );
}
}
dx_forward = 0.0;
neighIndex[j] = index[j] + xStride[j];
if(! (neighIndex[j] > lastIndex[j] ||
neighIndex[j] < startIndex[j]) )
{
if ( this->GetLabelImage()->GetPixel( neighIndex ) == Superclass::AlivePoint )
{
dx_forward = output->GetPixel( neighIndex ) - centerPixel;
}
}
// Compute upwind finite differences
if (vnl_math_max(dx_backward,-dx_forward) < ZERO)
{
gradientPixel[j] = ZERO;
}
else if (dx_backward > -dx_forward)
{
gradientPixel[j] = dx_backward;
}
else
{
gradientPixel[j] = dx_forward;
}
gradientPixel[j] /= spacing[j];
}
gradientImage->SetPixel( index, gradientPixel );
}
} // namespace itk
#endif