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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 ShapeDetection image filter for segmenting the
volume. It requires seed points and the original image as inputs. */
#include "vvITKShapeDetectionModule.txx"
template <class InputPixelType>
class ShapeDetectionModuleRunner
{
public:
typedef VolView::PlugIn::ShapeDetectionModule<
InputPixelType > ModuleType;
public:
ShapeDetectionModuleRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const float distanceFromSeeds = atof( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ));
const float gaussianSigma = 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 ));
const float curvatureScaling = atof( info->GetGUIProperty(info, 4, VVP_GUI_VALUE ));
const float propagationScaling = 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;
itk::Index<3> seedPosition;
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing Shape Detection Module...");
module.SetDistanceFromSeeds( distanceFromSeeds );
module.SetSigma( gaussianSigma );
module.SetLowestBasinValue( lowestBasinValue );
module.SetLowestBorderValue( lowestBorderValue );
module.SetCurvatureScaling( curvatureScaling );
module.SetPropagationScaling( propagationScaling );
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 );
char tmp[1024];
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:
{
ShapeDetectionModuleRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
ShapeDetectionModuleRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
ShapeDetectionModuleRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
ShapeDetectionModuleRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
ShapeDetectionModuleRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
ShapeDetectionModuleRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
ShapeDetectionModuleRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
ShapeDetectionModuleRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
ShapeDetectionModuleRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
ShapeDetectionModuleRunner<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, "Shape Detection 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, "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, "Sigma used by the smoothing previous to computing the gradient magnitude. Large values of sigma will reduce noise in the image but will also degrade contours. Sigma is measured in millimeters, not pixels");
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->SetGUIProperty(info, 4, VVP_GUI_LABEL, "Curvature 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 curvature contribution. Larger values will result in smoother contours");
info->SetGUIProperty(info, 4, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 5, VVP_GUI_LABEL, "Propagation 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 inflation factor. Larger factors will result in rapid expansion with irregular borders");
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 , "1.0 500.0 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 vvITKShapeDetectionModuleInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Shape Detection Module (ITK)");
info->SetProperty(info, VVP_GROUP, "Segmentation - Level Sets");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Shape Detection Module");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This module applies a Shape Detection 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 ShapeDetection 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 ShapeDetection 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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