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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 "vvITKFastMarchingModule.txx"
template <class InputPixelType>
class FastMarchingModuleRunner
{
public:
typedef VolView::PlugIn::FastMarchingModule<
InputPixelType > ModuleType;
public:
FastMarchingModuleRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const float stoppingValue = atof( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ));
const float sigma = atof( info->GetGUIProperty(info, 1, VVP_GUI_VALUE ));
const float lowestBasinValue = atof( info->GetGUIProperty(info, 2, VVP_GUI_VALUE ));
const float lowestBorderValue = atof( info->GetGUIProperty(info, 3, VVP_GUI_VALUE ));
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing Fast Marching Module...");
module.SetStoppingValue( stoppingValue );
module.SetSigma( sigma );
module.SetLowestBasinValue( lowestBasinValue );
module.SetLowestBorderValue( lowestBorderValue );
itk::Index<3> seedPosition;
const unsigned int numberOfSeeds = info->NumberOfMarkers;
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 seed points using the 3D Markers in the Annotation menu" );
return -1;
}
try
{
switch( info->InputVolumeScalarType )
{
case VTK_CHAR:
{
FastMarchingModuleRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
FastMarchingModuleRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
FastMarchingModuleRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
FastMarchingModuleRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
FastMarchingModuleRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
FastMarchingModuleRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
FastMarchingModuleRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
FastMarchingModuleRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
FastMarchingModuleRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
FastMarchingModuleRunner<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, "Stopping Value");
info->SetGUIProperty(info, 0, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 0, VVP_GUI_DEFAULT, "50.0");
info->SetGUIProperty(info, 0, VVP_GUI_HELP, "Defines a stopping value for the time up to which the front propagation will be computed.");
info->SetGUIProperty(info, 0, VVP_GUI_HINTS , "1 200 1");
info->SetGUIProperty(info, 1, VVP_GUI_LABEL, "Sigma for gradient magnitude.");
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, "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 level set front from getting close to the edges of objects in the image.");
info->SetGUIProperty(info, 1, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 2, VVP_GUI_LABEL, "Bottom of basin.");
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, "The lowest value of the gradient magnitude in the inside of the region to be segmented. This value will be mapped by the Sigmoid into the fastest propagation in the speed image.");
info->SetGUIProperty(info, 2, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 3, VVP_GUI_LABEL, "Lowest of basin border.");
info->SetGUIProperty(info, 3, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 3, VVP_GUI_DEFAULT, "6.0");
info->SetGUIProperty(info, 3, VVP_GUI_HELP, "The lowest value of the gradient magnitude in the border of the region to be segmented. This value will be mapped by the Sigmoid into the slowest propagation in the speed image.");
info->SetGUIProperty(info, 3, VVP_GUI_HINTS , "0.1 50.0 0.1");
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 vvITKFastMarchingModuleInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Fast Marching Module (ITK)");
info->SetProperty(info, VVP_GROUP, "Segmentation - Level Sets");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Fast Marching Module");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This module applies a Fast Marching level set method for segmenting a volume. 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 FastMarching 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, "4");
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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