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
|
/*=========================================================================
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.
=========================================================================*/
/* This module encapsulates the full preprocessing required for
applying the Watershed image filter for segmenting the
volume. It requires seed points and the original image as inputs. */
#include "vvITKWatershedModule.txx"
template <class InputPixelType>
class WatershedModuleRunner
{
public:
typedef VolView::PlugIn::WatershedModule< InputPixelType > ModuleType;
public:
WatershedModuleRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const float sigma = atof( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ));
const float threshold = atof( info->GetGUIProperty(info, 1, VVP_GUI_VALUE ));
const float waterLevel = atof( info->GetGUIProperty(info, 2, VVP_GUI_VALUE ));
const unsigned int numberOfSeeds = info->NumberOfMarkers;
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing Watershed Module...");
module.SetSigma( sigma );
module.SetThreshold( threshold );
module.SetWaterLevel( waterLevel );
itk::Index<3> seedPosition;
for(unsigned int i=0; i< numberOfSeeds; i++)
{
VolView::PlugIn::FilterModuleBase::Convert3DMarkerToIndex( info, i, seedPosition );
module.AddSeed( seedPosition );
}
// Execute the filter
module.ProcessData( pds );
}
};
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 < 1 )
{
info->SetProperty( info, VVP_ERROR, "Please select points using the 3D Markers in the Annotation menu" );
return -1;
}
try
{
switch( info->InputVolumeScalarType )
{
case VTK_CHAR:
{
WatershedModuleRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
WatershedModuleRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
WatershedModuleRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
WatershedModuleRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
WatershedModuleRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
WatershedModuleRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
WatershedModuleRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
WatershedModuleRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
WatershedModuleRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
WatershedModuleRunner<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, "Sigma for gradient magnitude.");
info->SetGUIProperty(info, 0, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 0, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 0, VVP_GUI_HELP, "The input image is smoothed with a Gaussian during the computation of the Gradient Magnitude. This sigma value should be large enough to attenuate image noise, but not as large as to prevent the basins from being separated.");
info->SetGUIProperty(info, 0, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 1, VVP_GUI_LABEL, "Threshold for minimum basin.");
info->SetGUIProperty(info, 1, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 1, VVP_GUI_DEFAULT, "0.01");
info->SetGUIProperty(info, 1, VVP_GUI_HELP, "The lowest value of water level for which basins will be computed. This prevents to spend time in computing micro basins at the lowest levels.");
info->SetGUIProperty(info, 1, VVP_GUI_HINTS , "0.001 0.1 0.001");
info->SetGUIProperty(info, 2, VVP_GUI_LABEL, "Water Level.");
info->SetGUIProperty(info, 2, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 2, VVP_GUI_DEFAULT, "0.1");
info->SetGUIProperty(info, 2, VVP_GUI_HELP, "The level of water at which the basins will be identified. It is expressed as a fraction of the maximum possible level.");
info->SetGUIProperty(info, 2, VVP_GUI_HINTS , "0.01 0.5 0.01");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
info->OutputVolumeScalarType = VTK_UNSIGNED_CHAR;
info->OutputVolumeNumberOfComponents = 1;
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 vvITKWatershedModuleInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Watershed Module (ITK)");
info->SetProperty(info, VVP_GROUP, "Segmentation - Level Sets");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Watershed Module");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This module applies a Watershed method for segmenting a volume. Before running this filter you must set one 3D marker on the region that you want to segment. This marker will be used to select the water basin to be binarized in order to produce the output binary mask at the end of the processing. All the necessary preprocessing is packaged in this module. This makes it a good choice when you are already familiar with the parameters settings requires for you particular data set. When you are applying Watershed to a new data set, you may want to rather go step by step using each one the individual filters.");
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, "3");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "10");
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");
}
}
|
