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
|
/*=========================================================================
Copyright (c) Kitware, Inc.
All rights reserved.
See Copyright.txt or http://www.kitware.com/VolViewCopyright.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.
=========================================================================*/
/* perform segmentation using the Isolated Connected image filter */
#include "vvITKFilterModuleDoubleOutput.h"
#include "itkIsolatedConnectedImageFilter.h"
template <class InputPixelType>
class IsolatedConnectedRunner
{
public:
itkStaticConstMacro( Dimension, unsigned int, 3);
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef typename InputImageType::IndexType IndexType;
typedef itk::IsolatedConnectedImageFilter< InputImageType,
OutputImageType > FilterType;
public:
IsolatedConnectedRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const float lower = atof( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ) );
const float upperLimit = atof( info->GetGUIProperty(info, 1, VVP_GUI_VALUE ) );
const float upperTolerance = atof( info->GetGUIProperty(info, 2, VVP_GUI_VALUE ) );
const int replaceValue = atoi( info->GetGUIProperty(info, 3, VVP_GUI_VALUE ) );
const bool compositeOutput = atoi( info->GetGUIProperty(info, 4, VVP_GUI_VALUE ) );
if( static_cast<InputPixelType>(upperTolerance) == itk::NumericTraits<InputPixelType>::Zero )
{
itk::ExceptionObject excp;
excp.SetDescription(" The current tolerance is truncated to zero. Please select a larger tolerance value." );
excp.SetLocation("");
throw excp;
}
itk::Index<Dimension> seed1;
itk::Index<Dimension> seed2;
VolView::PlugIn::FilterModuleBase::Convert3DMarkerToIndex( info, 0, seed1 );
VolView::PlugIn::FilterModuleBase::Convert3DMarkerToIndex( info, 1, seed2 );
VolView::PlugIn::FilterModuleDoubleOutput< FilterType > module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Isolated Connected Region Growing...");
// Set the parameters on it
module.GetFilter()->SetIsolatedValueTolerance( static_cast<InputPixelType>( upperTolerance ) );
module.GetFilter()->SetUpperValueLimit( static_cast<InputPixelType>( upperLimit ) );
module.GetFilter()->SetLower( static_cast<InputPixelType>( lower ) );
module.GetFilter()->SetReplaceValue( replaceValue );
module.GetFilter()->SetSeed1( seed1 );
module.GetFilter()->SetSeed2( seed2 );
module.SetProduceDoubleOutput( compositeOutput );
// Execute the filter
module.ProcessData( pds );
const float isolatedValue = static_cast<float>( module.GetFilter()->GetIsolatedValue() );
char tmp[1024];
sprintf( tmp, "Upper threshold found = %g\n This is the intensity value that disconnects the two seeds",
isolatedValue );
info->SetProperty( info, VVP_REPORT_TEXT, tmp );
}
};
static int ProcessData(void *inf, vtkVVProcessDataStruct *pds)
{
vtkVVPluginInfo *info = (vtkVVPluginInfo *)inf;
if( info->InputVolumeNumberOfComponents != 1 )
{
info->SetProperty( info, VVP_ERROR, "This filter requires a single-component data set as input" );
return -1;
}
if( info->NumberOfMarkers < 2 )
{
info->SetProperty( info, VVP_ERROR, "Please select two seed point using the 3D Markers in the Annotation menu. The first seed point in the region to segment, the second seed point in the region to reject." );
return -1;
}
try
{
switch( info->InputVolumeScalarType )
{
case VTK_CHAR:
{
IsolatedConnectedRunner<char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
IsolatedConnectedRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
IsolatedConnectedRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
IsolatedConnectedRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
IsolatedConnectedRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
IsolatedConnectedRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
IsolatedConnectedRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
IsolatedConnectedRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
IsolatedConnectedRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
IsolatedConnectedRunner<double> runner;
runner.Execute( info, pds );
break;
}
}
}
catch( itk::ExceptionObject & except )
{
info->SetProperty( info, VVP_ERROR, except.what() );
return -1;
}
return 0;
}
static int UpdateGUI(void *inf)
{
vtkVVPluginInfo *info = (vtkVVPluginInfo *)inf;
info->SetGUIProperty(info, 0, VVP_GUI_LABEL,"Lower Threshold");
info->SetGUIProperty(info, 0, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 0, VVP_GUI_DEFAULT, VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarMinimum( info ) );
info->SetGUIProperty(info, 0, VVP_GUI_HELP, "Lower threshold. Only pixels with intensities higher than this threshold will be considered to be added to the region.");
info->SetGUIProperty(info, 0, VVP_GUI_HINTS , VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarRange( info ) );
info->SetGUIProperty(info, 1, VVP_GUI_LABEL,"Upper Limit");
info->SetGUIProperty(info, 1, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 1, VVP_GUI_DEFAULT, VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarMaximum( info ) );
info->SetGUIProperty(info, 1, VVP_GUI_HELP, "This is the maximum value that will be attempted for the upper threshold that will separate the two seeds.");
info->SetGUIProperty(info, 1, VVP_GUI_HINTS , VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarRange( info ) );
info->SetGUIProperty(info, 2, VVP_GUI_LABEL,"Upper Tolerance");
info->SetGUIProperty(info, 2, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 2, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 2, VVP_GUI_HELP, "Precision required for the upper threshold that will separate the two seeds. The upper threshold is found using a bipartition algorithm, this tolerance defines the stopping criterion for the bipartition.");
info->SetGUIProperty(info, 2, VVP_GUI_HINTS , VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarRangeFraction( info, 0.001, 100 ) );
info->SetGUIProperty(info, 3, VVP_GUI_LABEL, "Replace Value");
info->SetGUIProperty(info, 3, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 3, VVP_GUI_DEFAULT, "255");
info->SetGUIProperty(info, 3, VVP_GUI_HELP, "Value to assign to the binary mask of the segmented region. The rest of the image will be set to zero.");
info->SetGUIProperty(info, 3, VVP_GUI_HINTS , "1 255.0 1.0");
info->SetGUIProperty(info, 4, VVP_GUI_LABEL, "Produce composite output");
info->SetGUIProperty(info, 4, VVP_GUI_TYPE, VVP_GUI_CHECKBOX);
info->SetGUIProperty(info, 4, VVP_GUI_DEFAULT, "0");
info->SetGUIProperty(info, 4, VVP_GUI_HELP, "This filter produce by default a binary image as output. Enabling this option will instead generate a composite output combining the input image and the binary mask as an image of two components. This is convenient for evaluating the quality of a segmentation.");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
// Depending on this option, the filter will produce a
// single component or a double component output.
// When single component is used, the output type is 'unsigned char'
info->OutputVolumeScalarType = VTK_UNSIGNED_CHAR;
info->OutputVolumeNumberOfComponents = 1;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1");
const char * compositeOutputProperty = info->GetGUIProperty(info, 4, VVP_GUI_VALUE );
// During the startup of the application this string is not yet defined.
// We should then check for it before trying to use it.
if( compositeOutputProperty )
{
const bool compositeOutput = atoi( compositeOutputProperty );
if( compositeOutput )
{
info->OutputVolumeScalarType = info->InputVolumeScalarType;
info->OutputVolumeNumberOfComponents = 2;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "2");
}
}
memcpy(info->OutputVolumeDimensions,info->InputVolumeDimensions,
3*sizeof(int));
memcpy(info->OutputVolumeSpacing,info->InputVolumeSpacing,
3*sizeof(float));
memcpy(info->OutputVolumeOrigin,info->InputVolumeOrigin,
3*sizeof(float));
return 1;
}
extern "C" {
void VV_PLUGIN_EXPORT vvITKIsolatedConnectedInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Isolated Connected (ITK) ");
info->SetProperty(info, VVP_GROUP, "Segmentation - Region Growing");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Isolated Connedted Segmentation");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This filter applies a region growing algorithm for segmentation. You must provide two seed points, the filter will extract a region connected to the first seed point and not connected to the second one. This is quite useful for separating adjacent structures. The method will grow a region around the first seed point in such a way that the pixels in the region have intensities higher than the lower threshold. The upper threshold is computed by the filter as the value that prevents the seed2 point to be included in the region of seed1.");
info->SetProperty(info, VVP_SUPPORTS_IN_PLACE_PROCESSING, "0");
info->SetProperty(info, VVP_SUPPORTS_PROCESSING_PIECES, "0");
info->SetProperty(info, VVP_NUMBER_OF_GUI_ITEMS, "5");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1");// It is actually dependent of the complexity of the shape to segment
info->OutputVolumeScalarType = VTK_UNSIGNED_CHAR;
info->OutputVolumeNumberOfComponents = 1;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1");
info->SetProperty(info, VVP_REQUIRES_SERIES_INPUT, "0");
info->SetProperty(info, VVP_SUPPORTS_PROCESSING_SERIES_BY_VOLUMES, "0");
info->SetProperty(info, VVP_PRODUCES_OUTPUT_SERIES, "0");
info->SetProperty(info, VVP_PRODUCES_PLOTTING_OUTPUT, "0");
}
}
|
