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/*=========================================================================
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 FastMarching image filter for segmenting the
volume. It requires seed points and the original image as inputs. */
#include "vvITKCannySegmentationLevelSetModule.txx"
template <class InputPixelType>
class CannySegmentationLevelSetModuleRunner
{
public:
typedef VolView::PlugIn::CannySegmentationLevelSetModule< InputPixelType > ModuleType;
public:
CannySegmentationLevelSetModuleRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const float distanceFromSeeds = atof( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ));
const float cannyVariance = atof( info->GetGUIProperty(info, 1, VVP_GUI_VALUE ));
const float cannyThreshold = atof( info->GetGUIProperty(info, 2, VVP_GUI_VALUE ));
const float curvatureScaling = atof( info->GetGUIProperty(info, 3, VVP_GUI_VALUE ));
const float propagationScaling = atof( info->GetGUIProperty(info, 4, VVP_GUI_VALUE ));
const float advectionScaling = atof( info->GetGUIProperty(info, 5, VVP_GUI_VALUE ));
const float maximumRMSError = atof( info->GetGUIProperty(info, 6, VVP_GUI_VALUE ));
const unsigned int maximumNumberOfIterations = atoi( info->GetGUIProperty(info, 7, VVP_GUI_VALUE ));
const unsigned int numberOfSeeds = info->NumberOfMarkers;
char tmp[1024];
itk::Index<3> seedPosition;
// Take the first marker as the seed point
const MarkersCoordinatesType * seedCoordinates = info->Markers;
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing Canny Segmentation LevelSet Module...");
module.SetDistanceFromSeeds( distanceFromSeeds );
module.SetVariance( cannyVariance );
module.SetThreshold( cannyThreshold );
module.SetCurvatureScaling( curvatureScaling );
module.SetPropagationScaling( propagationScaling );
module.SetAdvectionScaling( advectionScaling );
module.SetMaximumRMSError( maximumRMSError );
module.SetNumberOfIterations( maximumNumberOfIterations );
for(unsigned int i=0; i< numberOfSeeds; i++)
{
VolView::PlugIn::FilterModuleBase::Convert3DMarkerToIndex( info, i, seedPosition );
module.AddSeed( seedPosition );
}
// Execute the filter
module.ProcessData( pds );
sprintf(tmp,"Total number of iterations = %d \n Final RMS error = %g",
module.GetElapsedIterations(),
module.GetRMSChange());
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 < 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:
{
CannySegmentationLevelSetModuleRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
CannySegmentationLevelSetModuleRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
CannySegmentationLevelSetModuleRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
CannySegmentationLevelSetModuleRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
CannySegmentationLevelSetModuleRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
CannySegmentationLevelSetModuleRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
CannySegmentationLevelSetModuleRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
CannySegmentationLevelSetModuleRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
CannySegmentationLevelSetModuleRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
CannySegmentationLevelSetModuleRunner<double> runner;
runner.Execute( info, pds );
break;
}
}
}
catch( itk::ExceptionObject & except )
{
info->SetProperty( info, VVP_ERROR, except.what() );
return -1;
}
info->UpdateProgress( info, 1.0, "Canny Segmentation Done !");
return 0;
}
static int UpdateGUI(void *inf)
{
vtkVVPluginInfo *info = (vtkVVPluginInfo *)inf;
info->SetGUIProperty(info, 0, VVP_GUI_LABEL, "Distance from seeds.");
info->SetGUIProperty(info, 0, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 0, VVP_GUI_DEFAULT, "5.0");
info->SetGUIProperty(info, 0, VVP_GUI_HELP, "An initial level will be created using the seed points. The zero set will be placed at a certain distance from the seed points. The value set in this scale is the distance to be used");
info->SetGUIProperty(info, 0, VVP_GUI_HINTS , "1.0 100.0 1.0");
info->SetGUIProperty(info, 1, VVP_GUI_LABEL, "Variance for Canny filter.");
info->SetGUIProperty(info, 1, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 1, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 1, VVP_GUI_HELP, "Variance used by the smoothing stage of the edge detection filter. Larger variances will reduce noise sensitivity but will also increase the uncertainty of edges location");
info->SetGUIProperty(info, 1, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 2, VVP_GUI_LABEL, "Threshold for Canny filter.");
info->SetGUIProperty(info, 2, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 2, VVP_GUI_DEFAULT, "0.0");
info->SetGUIProperty(info, 2, VVP_GUI_HELP, "");
info->SetGUIProperty(info, 2, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 3, VVP_GUI_LABEL, "Curvature scaling.");
info->SetGUIProperty(info, 3, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 3, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 3, VVP_GUI_HELP, "Scaling factor for the curvature contribution. Larger values will result in smoother contours");
info->SetGUIProperty(info, 3, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 4, VVP_GUI_LABEL, "Propagation scaling.");
info->SetGUIProperty(info, 4, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 4, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 4, VVP_GUI_HELP, "Scaling factor for the inflation factor. Larger factors will result in rapid expansion with irregular borders");
info->SetGUIProperty(info, 4, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 5, VVP_GUI_LABEL, "Advection scaling.");
info->SetGUIProperty(info, 5, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 5, VVP_GUI_DEFAULT, "1.0");
info->SetGUIProperty(info, 5, VVP_GUI_HELP, "Scaling factor for the advection factor. This factor generates a force that is proportional to the slant of the level set at a point.");
info->SetGUIProperty(info, 5, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 6, VVP_GUI_LABEL, "Maximum RMS Error.");
info->SetGUIProperty(info, 6, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 6, VVP_GUI_DEFAULT, "0.06");
info->SetGUIProperty(info, 6, VVP_GUI_HELP, "Threshold of the RMS change between one iteration and the previous one. This is a convergence criteria, the process will stop when the RMS change is lower than the value set here");
info->SetGUIProperty(info, 6, VVP_GUI_HINTS , "0.01 0.5 0.01");
info->SetGUIProperty(info, 7, VVP_GUI_LABEL, "Maximum iterations.");
info->SetGUIProperty(info, 7, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 7, VVP_GUI_DEFAULT, "100.0");
info->SetGUIProperty(info, 7, VVP_GUI_HELP, "The maximum number of iteration to apply the time step in the partial differental equation.");
info->SetGUIProperty(info, 7, VVP_GUI_HINTS , "1.0 1000.0 1.0");
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 vvITKCannySegmentationLevelSetModuleInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Canny Segmentation LevelSet Module (ITK)");
info->SetProperty(info, VVP_GROUP, "Segmentation - Level Sets");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Canny Segmentation LevelSet Module");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This module applies the Canny Segmentation Level Set method for segmenting a volume. A Canny edge detection filter is used to produce a set of edges that will be used to atract the zero set to them. 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 CannySegmentationLevelSet to a new data set, you may want to rather go step by step using each one the individual filters. Please experience first with the FastMarching modules, since it is used here for preprocessing the data set before applying the CannySegmentationLevelSet filter.");
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, "8");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "16");
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");
}
}
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