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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 DeformableModel image filter for segmenting the
volume. It requires seed points and the original image as inputs. */
#include "vvITKSplineBoundedConnectedThreshold.txx"
template <class InputPixelType>
class SplineBoundedConnectedThresholdRunner
{
public:
typedef VolView::PlugIn::SplineBoundedConnectedThreshold<
InputPixelType > ModuleType;
public:
SplineBoundedConnectedThresholdRunner() {}
void Execute( vtkVVPluginInfo *info, vtkVVProcessDataStruct *pds )
{
const bool engraveSurface = atoi( info->GetGUIProperty(info, 0, VVP_GUI_VALUE ));
const bool doSegmentation = atoi( info->GetGUIProperty(info, 1, VVP_GUI_VALUE ));
const bool compositeOutput = atoi( info->GetGUIProperty(info, 2, VVP_GUI_VALUE ));
const double stiffness = atof( info->GetGUIProperty(info, 3, VVP_GUI_VALUE ));
const float upper = atof( info->GetGUIProperty(info, 4, VVP_GUI_VALUE ) );
const float lower = atof( info->GetGUIProperty(info, 5, VVP_GUI_VALUE ) );
const int replaceValue = atoi( info->GetGUIProperty(info, 6, VVP_GUI_VALUE ) );
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing...");
module.SetNumberOfPointsAlongRows( 100 );
module.SetNumberOfPointsAlongColumns( 100 );
module.SetStiffness( stiffness );
module.SetDoSegmentation( doSegmentation );
module.SetProduceDoubleOutput( compositeOutput );
module.SetEngraveSurface( engraveSurface );
// Set the parameters on it
module.GetFilter()->SetUpper( static_cast<InputPixelType>( upper ) );
module.GetFilter()->SetLower( static_cast<InputPixelType>( lower ) );
module.GetFilter()->SetReplaceValue( replaceValue );
// Execute the filter
module.ProcessData( pds );
}
};
static int ProcessData(void *inf, vtkVVProcessDataStruct *pds)
{
vtkVVPluginInfo *info = (vtkVVPluginInfo *)inf;
try
{
switch( info->InputVolumeScalarType )
{
case VTK_CHAR:
{
SplineBoundedConnectedThresholdRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
SplineBoundedConnectedThresholdRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
SplineBoundedConnectedThresholdRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
SplineBoundedConnectedThresholdRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
SplineBoundedConnectedThresholdRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
SplineBoundedConnectedThresholdRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
SplineBoundedConnectedThresholdRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
SplineBoundedConnectedThresholdRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
SplineBoundedConnectedThresholdRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
SplineBoundedConnectedThresholdRunner<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, "Engrave Surface");
info->SetGUIProperty(info, 0, VVP_GUI_TYPE, VVP_GUI_CHECKBOX);
info->SetGUIProperty(info, 0, VVP_GUI_DEFAULT, "0");
info->SetGUIProperty(info, 0, VVP_GUI_HELP, "Selects whether the surfaces should be engraved in the image values or not.");
info->SetGUIProperty(info, 1, VVP_GUI_LABEL, "Segment Inside Region");
info->SetGUIProperty(info, 1, VVP_GUI_TYPE, VVP_GUI_CHECKBOX);
info->SetGUIProperty(info, 1, VVP_GUI_DEFAULT, "0");
info->SetGUIProperty(info, 1, VVP_GUI_HELP, "Enabling this option will make the filter run a region growing segmenation bounded by the mask defined by the 3D markers.");
info->SetGUIProperty(info, 2, VVP_GUI_LABEL, "Produce composite output");
info->SetGUIProperty(info, 2, VVP_GUI_TYPE, VVP_GUI_CHECKBOX);
info->SetGUIProperty(info, 2, VVP_GUI_DEFAULT, "0");
info->SetGUIProperty(info, 2, 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.");
info->SetGUIProperty(info, 3, VVP_GUI_LABEL, "Stiffness");
info->SetGUIProperty(info, 3, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 3, VVP_GUI_DEFAULT, "0.0");
info->SetGUIProperty(info, 3, VVP_GUI_HELP, "Stiffness allows to modify the spline for doing interpolation or approximation. A value of zero will result in the standard interpolating spline. A non-zero stiffness allows the spline to approximate rather thatn interpolate the landmarks.");
info->SetGUIProperty(info, 3, VVP_GUI_HINTS , "0.0 0.1 0.001");
info->SetGUIProperty(info, 4, VVP_GUI_LABEL,"Upper Threshold");
info->SetGUIProperty(info, 4, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 4, VVP_GUI_DEFAULT, VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarMaximum( info ) );
info->SetGUIProperty(info, 4, VVP_GUI_HELP, "Upper threshold. Only pixels with intensities lower than this threshold will be considered to be added to the region.");
info->SetGUIProperty(info, 4, VVP_GUI_HINTS , VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarRange( info ) );
info->SetGUIProperty(info, 5, VVP_GUI_LABEL,"Lower Threshold");
info->SetGUIProperty(info, 5, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 5, VVP_GUI_DEFAULT, VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarMinimum( info ) );
info->SetGUIProperty(info, 5, 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, 5, VVP_GUI_HINTS , VolView::PlugIn::FilterModuleBase::GetInputVolumeScalarRange( info ) );
info->SetGUIProperty(info, 6, VVP_GUI_LABEL, "Replace Value");
info->SetGUIProperty(info, 6, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 6, VVP_GUI_DEFAULT, "255");
info->SetGUIProperty(info, 6, 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, 6, VVP_GUI_HINTS , "1 255.0 1.0");
// Depending on this option the plugin will return the same input volume with
// all pixels outside the curvilinear box set to zero.
const char * gui0 = info->GetGUIProperty(info, 0, VVP_GUI_VALUE );
const char * gui1 = info->GetGUIProperty(info, 1, VVP_GUI_VALUE );
const char * gui2 = info->GetGUIProperty(info, 2, VVP_GUI_VALUE );
const bool engraveSurface = ( gui0 && bool ( atoi( gui0 ) ) );
const bool doSegmentation = ( gui1 && bool ( atoi( gui1 ) ) );
const bool doCompositeOutput = ( gui2 && bool ( atoi( gui2 ) ) );
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1");
info->SetProperty(info, VVP_PRODUCES_MESH_ONLY, "1");
if( engraveSurface && !doSegmentation )
{
info->OutputVolumeScalarType = info->InputVolumeScalarType;
info->OutputVolumeNumberOfComponents = 1;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1"); // FIXME: It should depend on the input pixel type...
info->SetProperty(info, VVP_PRODUCES_MESH_ONLY, "0");
// During the startup of the application this string is not yet defined.
// We should then check for it before trying to use it.
if( doCompositeOutput )
{
info->OutputVolumeScalarType = info->InputVolumeScalarType;
info->OutputVolumeNumberOfComponents = 2;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "2");
}
}
else
{
if( doSegmentation )
{
info->OutputVolumeScalarType = VTK_UNSIGNED_CHAR;
info->OutputVolumeNumberOfComponents = 1;
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "1"); // FIXME: It should depend on the input pixel type...
info->SetProperty(info, VVP_PRODUCES_MESH_ONLY, "0");
// During the startup of the application this string is not yet defined.
// We should then check for it before trying to use it.
if( doCompositeOutput )
{
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 vvITKSplineBoundedConnectedThresholdInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Spline Bounded Connected Threshold (ITK)");
info->SetProperty(info, VVP_GROUP, "Segmentation - Region Growing");
info->SetProperty(info, VVP_TERSE_DOCUMENTATION,
"Computes region growing in a bounded region");
info->SetProperty(info, VVP_FULL_DOCUMENTATION,
"This plugins computes a region growing segmentation limited to a curvilinear region defined by spline surfaces. The splines are defined with sets of 3D markers. Three groups of 3D markers are expected.");
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, "7");
info->SetProperty(info, VVP_REQUIRED_Z_OVERLAP, "0");
info->SetProperty(info, VVP_PER_VOXEL_MEMORY_REQUIRED, "0");
info->SetProperty(info, VVP_PRODUCES_MESH_ONLY, "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");
}
}
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