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EMAN::BinarySkeletonizerProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::BinarySkeletonizerProcessor:

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Collaboration diagram for EMAN::BinarySkeletonizerProcessor:

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List of all members.

Public Member Functions

virtual EMDataprocess (EMData *image)
virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
string get_desc () const
 Get the descrition of this specific processor.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

ProcessorNEW ()

Static Public Attributes

const string NAME = "gorgon.binary_skel"

Member Function Documentation

string EMAN::BinarySkeletonizerProcessor::get_desc  )  const [inline, virtual]
 

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 7058 of file processor.h.

07059                 {
07060                         return "Creates a skeleton of the 3D image by considering whether density is above or below a threshold value.";
07061                 }

virtual string EMAN::BinarySkeletonizerProcessor::get_name  )  const [inline, virtual]
 

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 7049 of file processor.h.

07050                 {
07051                         return NAME;
07052 //                      return "gorgon.binary_skel";
07053                 }

virtual TypeDict EMAN::BinarySkeletonizerProcessor::get_param_types  )  const [inline, virtual]
 

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 7062 of file processor.h.

References EMAN::TypeDict::put().

07063                 {
07064                         TypeDict d;
07065                         d.put("threshold", EMObject::FLOAT, "Threshold value.");
07066                         d.put("min_curve_width", EMObject::INT, "Minimum curve width.");
07067                         d.put("min_surface_width", EMObject::INT, "Minimum surface width.");
07068                         d.put("mark_surfaces", EMObject::BOOL, "Mark surfaces with a value of 2.0f, whereas curves are 1.0f.");
07069                         return d;
07070                 }

Processor* EMAN::BinarySkeletonizerProcessor::NEW  )  [inline, static]
 

Definition at line 7054 of file processor.h.

07055                 {
07056                         return new BinarySkeletonizerProcessor();
07057                 }

EMData * BinarySkeletonizerProcessor::process EMData image  )  [virtual]
 

Definition at line 9966 of file processor.cpp.

References wustl_mm::SkeletonMaker::Volume::get_emdata(), wustl_mm::SkeletonMaker::Volume::getVolumeData(), wustl_mm::SkeletonMaker::VolumeData::owns_emdata, EMAN::Dict::set_default(), and EMAN::EMData::update().

Referenced by process_inplace().

09967 {
09968         using namespace wustl_mm::GraySkeletonCPP;
09969         using namespace wustl_mm::SkeletonMaker;
09970 
09971         Volume * vimage = new Volume(image);
09972         float threshold = params["threshold"];
09973         int min_curvew = params.set_default("min_curve_width", 4);
09974         int min_srfcw = params.set_default("min_surface_width", 4);
09975         bool mark_surfaces = params.set_default("mark_surfaces", true);
09976         Volume* vskel = VolumeSkeletonizer::PerformPureJuSkeletonization(vimage, "unused", static_cast<double>(threshold), min_curvew, min_srfcw);
09977         //VolumeSkeletonizer::CleanUpSkeleton(vskel, 4, 0.01f);
09978         if (mark_surfaces) {
09979                 VolumeSkeletonizer::MarkSurfaces(vskel);
09980         }
09981 
09982         vskel->getVolumeData()->owns_emdata = false; //ensure the EMData object will remain when the Volume and its VolumeData object are freed
09983         EMData* skel = vskel->get_emdata();
09984         skel->update();
09985         return skel;
09986 }

void BinarySkeletonizerProcessor::process_inplace EMData image  )  [virtual]
 

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 9988 of file processor.cpp.

References process(), and EMAN::EMData::update().

09989 {
09990         EMData* em_skel = this->process(image);
09991         //TODO: use memcpy and copy metadata explicitly
09992         *image = *em_skel; //Deep copy performed by EMData::operator=
09993         image->update();
09994         delete em_skel;
09995         em_skel = NULL;
09996         return;
09997 }


Member Data Documentation

const string BinarySkeletonizerProcessor::NAME = "gorgon.binary_skel" [static]
 

Definition at line 220 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:42:51 2013 for EMAN2 by  doxygen 1.3.9.1