forked from Kitware/VTK
-
Notifications
You must be signed in to change notification settings - Fork 0
/
vtkImageMedian3D.cxx
321 lines (281 loc) · 9.78 KB
/
vtkImageMedian3D.cxx
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
/*=========================================================================
Program: Visualization Toolkit
Module: vtkImageMedian3D.cxx
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.kitware.com/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 notice for more information.
=========================================================================*/
#include "vtkImageMedian3D.h"
#include "vtkCellData.h"
#include "vtkDataArray.h"
#include "vtkImageData.h"
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include <algorithm> // for std::nth_element
vtkStandardNewMacro(vtkImageMedian3D);
//-----------------------------------------------------------------------------
// Construct an instance of vtkImageMedian3D fitler.
vtkImageMedian3D::vtkImageMedian3D()
{
this->NumberOfElements = 0;
this->SetKernelSize(1,1,1);
this->HandleBoundaries = 1;
}
//-----------------------------------------------------------------------------
vtkImageMedian3D::~vtkImageMedian3D()
{
}
//-----------------------------------------------------------------------------
void vtkImageMedian3D::PrintSelf(ostream& os, vtkIndent indent)
{
this->Superclass::PrintSelf(os, indent);
os << indent << "NumberOfElements: " << this->NumberOfElements << endl;
}
//-----------------------------------------------------------------------------
// This method sets the size of the neighborhood. It also sets the
// default middle of the neighborhood
void vtkImageMedian3D::SetKernelSize(int size0, int size1, int size2)
{
int volume;
int modified = 1;
if (this->KernelSize[0] == size0 && this->KernelSize[1] == size1 &&
this->KernelSize[2] == size2)
{
modified = 0;
}
// Set the kernel size and middle
volume = 1;
this->KernelSize[0] = size0;
this->KernelMiddle[0] = size0 / 2;
volume *= size0;
this->KernelSize[1] = size1;
this->KernelMiddle[1] = size1 / 2;
volume *= size1;
this->KernelSize[2] = size2;
this->KernelMiddle[2] = size2 / 2;
volume *= size2;
this->NumberOfElements = volume;
if ( modified )
{
this->Modified();
}
}
namespace {
//-----------------------------------------------------------------------------
// Compute the median with std::nth_element
template<class T>
T vtkComputeMedianOfArray(T *aBegin, T *aEnd)
{
T *aMid = aBegin + (aEnd - aBegin)/2;
std::nth_element(aBegin, aMid, aEnd);
T m = *aMid;
// if even size, get max of lower part of array and compute the average
if (aMid - aBegin == aEnd - aMid)
{
T *lowMid = std::max_element(aBegin, aMid);
m = *lowMid + (m - *lowMid)/2;
}
return m;
}
} // end anonymous namespace
//-----------------------------------------------------------------------------
// This method contains the second switch statement that calls the correct
// templated function for the mask types.
template <class T>
void vtkImageMedian3DExecute(vtkImageMedian3D *self,
vtkImageData *inData, T *inPtr,
vtkImageData *outData, T *outPtr,
int outExt[6], int id,
vtkDataArray *inArray)
{
int *kernelMiddle, *kernelSize;
// For looping though output (and input) pixels.
int outIdx0, outIdx1, outIdx2;
vtkIdType inInc0, inInc1, inInc2;
int outIdxC;
vtkIdType outIncX, outIncY, outIncZ;
T *inPtr0, *inPtr1, *inPtr2;
// For looping through hood pixels
int hoodMin0, hoodMax0, hoodMin1, hoodMax1, hoodMin2, hoodMax2;
int hoodStartMin0, hoodStartMax0, hoodStartMin1, hoodStartMax1;
int hoodIdx0, hoodIdx1, hoodIdx2;
T *tmpPtr0, *tmpPtr1, *tmpPtr2;
// The portion of the out image that needs no boundary processing.
int middleMin0, middleMax0, middleMin1, middleMax1, middleMin2, middleMax2;
int numComp;
int *inExt;
unsigned long count = 0;
unsigned long target;
if (!inArray)
{
return;
}
// Array used to compute the median
T *workArray = new T[self->GetNumberOfElements()];
// Get information to march through data
inData->GetIncrements(inInc0, inInc1, inInc2);
outData->GetContinuousIncrements(outExt, outIncX, outIncY, outIncZ);
kernelMiddle = self->GetKernelMiddle();
kernelSize = self->GetKernelSize();
numComp = inArray->GetNumberOfComponents();
hoodMin0 = outExt[0] - kernelMiddle[0];
hoodMin1 = outExt[2] - kernelMiddle[1];
hoodMin2 = outExt[4] - kernelMiddle[2];
hoodMax0 = kernelSize[0] + hoodMin0 - 1;
hoodMax1 = kernelSize[1] + hoodMin1 - 1;
hoodMax2 = kernelSize[2] + hoodMin2 - 1;
// Clip by the input image extent
inExt = inData->GetExtent();
hoodMin0 = (hoodMin0 > inExt[0]) ? hoodMin0 : inExt[0];
hoodMin1 = (hoodMin1 > inExt[2]) ? hoodMin1 : inExt[2];
hoodMin2 = (hoodMin2 > inExt[4]) ? hoodMin2 : inExt[4];
hoodMax0 = (hoodMax0 < inExt[1]) ? hoodMax0 : inExt[1];
hoodMax1 = (hoodMax1 < inExt[3]) ? hoodMax1 : inExt[3];
hoodMax2 = (hoodMax2 < inExt[5]) ? hoodMax2 : inExt[5];
// Save the starting neighborhood dimensions (2 loops only once)
hoodStartMin0 = hoodMin0; hoodStartMax0 = hoodMax0;
hoodStartMin1 = hoodMin1; hoodStartMax1 = hoodMax1;
// The portion of the output that needs no boundary computation.
middleMin0 = inExt[0] + kernelMiddle[0];
middleMax0 = inExt[1] - (kernelSize[0] - 1) + kernelMiddle[0];
middleMin1 = inExt[2] + kernelMiddle[1];
middleMax1 = inExt[3] - (kernelSize[1] - 1) + kernelMiddle[1];
middleMin2 = inExt[4] + kernelMiddle[2];
middleMax2 = inExt[5] - (kernelSize[2] - 1) + kernelMiddle[2];
target = static_cast<unsigned long>((outExt[5] - outExt[4] + 1)*
(outExt[3] - outExt[2] + 1)/50.0);
target++;
// loop through pixel of output
inPtr = static_cast<T *>(
inArray->GetVoidPointer((hoodMin0 - inExt[0])* inInc0 +
(hoodMin1 - inExt[2])* inInc1 +
(hoodMin2 - inExt[4])* inInc2));
inPtr2 = inPtr;
for (outIdx2 = outExt[4]; outIdx2 <= outExt[5]; ++outIdx2)
{
inPtr1 = inPtr2;
hoodMin1 = hoodStartMin1;
hoodMax1 = hoodStartMax1;
for (outIdx1 = outExt[2];
!self->AbortExecute && outIdx1 <= outExt[3]; ++outIdx1)
{
if (!id)
{
if (!(count%target))
{
self->UpdateProgress(count/(50.0*target));
}
count++;
}
inPtr0 = inPtr1;
hoodMin0 = hoodStartMin0;
hoodMax0 = hoodStartMax0;
for (outIdx0 = outExt[0]; outIdx0 <= outExt[1]; ++outIdx0)
{
for (outIdxC = 0; outIdxC < numComp; outIdxC++)
{
// Compute median of neighborhood
T *workEnd = workArray;
// loop through neighborhood pixels
tmpPtr2 = inPtr0 + outIdxC;
for (hoodIdx2 = hoodMin2; hoodIdx2 <= hoodMax2; ++hoodIdx2)
{
tmpPtr1 = tmpPtr2;
for (hoodIdx1 = hoodMin1; hoodIdx1 <= hoodMax1; ++hoodIdx1)
{
tmpPtr0 = tmpPtr1;
for (hoodIdx0 = hoodMin0; hoodIdx0 <= hoodMax0; ++hoodIdx0)
{
// Add this pixel to the median
*workEnd++ = *tmpPtr0;
tmpPtr0 += inInc0;
}
tmpPtr1 += inInc1;
}
tmpPtr2 += inInc2;
}
// Replace this pixel with the hood median
*outPtr++ = vtkComputeMedianOfArray(workArray, workEnd);
}
// shift neighborhood considering boundaries
if (outIdx0 >= middleMin0)
{
inPtr0 += inInc0;
++hoodMin0;
}
if (outIdx0 < middleMax0)
{
++hoodMax0;
}
}
// shift neighborhood considering boundaries
if (outIdx1 >= middleMin1)
{
inPtr1 += inInc1;
++hoodMin1;
}
if (outIdx1 < middleMax1)
{
++hoodMax1;
}
outPtr += outIncY;
}
// shift neighborhood considering boundaries
if (outIdx2 >= middleMin2)
{
inPtr2 += inInc2;
++hoodMin2;
}
if (outIdx2 < middleMax2)
{
++hoodMax2;
}
outPtr += outIncZ;
}
delete [] workArray;
}
//-----------------------------------------------------------------------------
// This method contains the first switch statement that calls the correct
// templated function for the input and output region types.
void vtkImageMedian3D::ThreadedRequestData(
vtkInformation *vtkNotUsed(request),
vtkInformationVector **inputVector,
vtkInformationVector *vtkNotUsed(outputVector),
vtkImageData ***inData,
vtkImageData **outData,
int outExt[6], int id)
{
void *inPtr;
void *outPtr = outData[0]->GetScalarPointerForExtent(outExt);
vtkDataArray *inArray = this->GetInputArrayToProcess(0,inputVector);
if (id == 0)
{
outData[0]->GetPointData()->GetScalars()->SetName(inArray->GetName());
}
inPtr = inArray->GetVoidPointer(0);
// this filter expects that input is the same type as output.
if (inArray->GetDataType() != outData[0]->GetScalarType())
{
vtkErrorMacro(<< "Execute: input data type, " << inArray->GetDataType()
<< ", must match out ScalarType "
<< outData[0]->GetScalarType());
return;
}
switch (inArray->GetDataType())
{
vtkTemplateMacro(
vtkImageMedian3DExecute(this,inData[0][0],
static_cast<VTK_TT *>(inPtr),
outData[0], static_cast<VTK_TT *>(outPtr),
outExt, id,inArray));
default:
vtkErrorMacro(<< "Execute: Unknown input ScalarType");
return;
}
}