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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 "vvITKSurfaceBoundedConfidenceConnected.txx"
template <class InputPixelType>
class SurfaceBoundedConfidenceConnectedRunner
{
public:
typedef VolView::PlugIn::SurfaceBoundedConfidenceConnected<
InputPixelType > ModuleType;
public:
SurfaceBoundedConfidenceConnectedRunner() {}
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 unsigned int numberOfIterations = atoi( info->GetGUIProperty(info, 3, VVP_GUI_VALUE ) );
const float multiplier = atof( info->GetGUIProperty(info, 4, VVP_GUI_VALUE ) );
const unsigned int initialRadius = atoi( info->GetGUIProperty(info, 5, VVP_GUI_VALUE ) );
ModuleType module;
module.SetPluginInfo( info );
module.SetUpdateMessage("Computing...");
module.SetDoSegmentation( doSegmentation );
module.SetProduceDoubleOutput( compositeOutput );
module.SetEngraveSurface( engraveSurface );
// Set the parameters on it
module.GetFilter()->SetNumberOfIterations( numberOfIterations );
module.GetFilter()->SetMultiplier( multiplier );
module.GetFilter()->SetReplaceValue( 255 );
module.GetFilter()->SetInitialNeighborhoodRadius( initialRadius );
// Execute the filter
module.ProcessData( pds );
}
};
static int ProcessData(void *inf, vtkVVProcessDataStruct *pds)
{
vtkVVPluginInfo *info = (vtkVVPluginInfo *)inf;
try
{
switch( info->InputVolumeScalarType )
{
case VTK_CHAR:
{
SurfaceBoundedConfidenceConnectedRunner<signed char> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_CHAR:
{
SurfaceBoundedConfidenceConnectedRunner<unsigned char> runner;
runner.Execute( info, pds );
break;
}
case VTK_SHORT:
{
SurfaceBoundedConfidenceConnectedRunner<signed short> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_SHORT:
{
SurfaceBoundedConfidenceConnectedRunner<unsigned short> runner;
runner.Execute( info, pds );
break;
}
case VTK_INT:
{
SurfaceBoundedConfidenceConnectedRunner<signed int> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_INT:
{
SurfaceBoundedConfidenceConnectedRunner<unsigned int> runner;
runner.Execute( info, pds );
break;
}
case VTK_LONG:
{
SurfaceBoundedConfidenceConnectedRunner<signed long> runner;
runner.Execute( info, pds );
break;
}
case VTK_UNSIGNED_LONG:
{
SurfaceBoundedConfidenceConnectedRunner<unsigned long> runner;
runner.Execute( info, pds );
break;
}
case VTK_FLOAT:
{
SurfaceBoundedConfidenceConnectedRunner<float> runner;
runner.Execute( info, pds );
break;
}
case VTK_DOUBLE:
{
SurfaceBoundedConfidenceConnectedRunner<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, "Number of Iterations");
info->SetGUIProperty(info, 3, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 3, VVP_GUI_DEFAULT, "5");
info->SetGUIProperty(info, 3, VVP_GUI_HELP, "Number of times that region growing process should be repeated. If initial statistical estimations are good, further iterations may improve the segmentation. After a certain number of iterations the result will not change. ");
info->SetGUIProperty(info, 3, VVP_GUI_HINTS , "1 20 1");
info->SetGUIProperty(info, 4, VVP_GUI_LABEL, "Variance Multiplier");
info->SetGUIProperty(info, 4, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 4, VVP_GUI_DEFAULT, "2.5");
info->SetGUIProperty(info, 4, VVP_GUI_HELP, "Factor that will multiplies the variance of the pixels region in order to define the intensity range for which new pixels will be accepted in the region.");
info->SetGUIProperty(info, 4, VVP_GUI_HINTS , "0.1 10.0 0.1");
info->SetGUIProperty(info, 5, VVP_GUI_LABEL, "Initial Neighborhood Radius");
info->SetGUIProperty(info, 5, VVP_GUI_TYPE, VVP_GUI_SCALE);
info->SetGUIProperty(info, 5, VVP_GUI_DEFAULT, "2");
info->SetGUIProperty(info, 5, VVP_GUI_HELP, "Size of the initial neighborhood used to compute the statistics of the region. If the region in which the seed points are placed happens to be a homogeneous intensity distribution, increasing this radius will safely improve the statistical estimation of mean and variance. Make sure that the radius is not large enough to make contours participate in the computation of the estimation. That is, from any seed point to the nearest important edge, there should be a distance larger than this radius.");
info->SetGUIProperty(info, 5, VVP_GUI_HINTS , "1 20.0 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 vvITKSurfaceBoundedConfidenceConnectedInit(vtkVVPluginInfo *info)
{
vvPluginVersionCheck();
// setup information that never changes
info->ProcessData = ProcessData;
info->UpdateGUI = UpdateGUI;
info->SetProperty(info, VVP_NAME, "Surface Bounded Confidence Connected (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, "6");
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_SPLINE_SURFACES, "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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