EMAN::BinarySkeletonizerProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::BinarySkeletonizerProcessor:

Inheritance graph
[legend]
Collaboration diagram for EMAN::BinarySkeletonizerProcessor:

Collaboration graph
[legend]
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

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "gorgon.binary_skel"

Detailed Description

Definition at line 7002 of file processor.h.


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 7017 of file processor.h.

07018                 {
07019                         return "Creates a skeleton of the 3D image by considering whether density is above or below a threshold value.";
07020                 }

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 7008 of file processor.h.

References NAME.

07009                 {
07010                         return NAME;
07011 //                      return "gorgon.binary_skel";
07012                 }

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 7021 of file processor.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

07022                 {
07023                         TypeDict d;
07024                         d.put("threshold", EMObject::FLOAT, "Threshold value.");
07025                         d.put("min_curve_width", EMObject::INT, "Minimum curve width.");
07026                         d.put("min_surface_width", EMObject::INT, "Minimum surface width.");
07027                         d.put("mark_surfaces", EMObject::BOOL, "Mark surfaces with a value of 2.0f, whereas curves are 1.0f.");
07028                         return d;
07029                 }

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

Definition at line 7013 of file processor.h.

07014                 {
07015                         return new BinarySkeletonizerProcessor();
07016                 }

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

Definition at line 9888 of file processor.cpp.

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

Referenced by process_inplace().

09889 {
09890         using namespace wustl_mm::GraySkeletonCPP;
09891         using namespace wustl_mm::SkeletonMaker;
09892 
09893         Volume * vimage = new Volume(image);
09894         float threshold = params["threshold"];
09895         int min_curvew = params.set_default("min_curve_width", 4);
09896         int min_srfcw = params.set_default("min_surface_width", 4);
09897         bool mark_surfaces = params.set_default("mark_surfaces", true);
09898         Volume* vskel = VolumeSkeletonizer::PerformPureJuSkeletonization(vimage, "unused", static_cast<double>(threshold), min_curvew, min_srfcw);
09899         //VolumeSkeletonizer::CleanUpSkeleton(vskel, 4, 0.01f);
09900         if (mark_surfaces) {
09901                 VolumeSkeletonizer::MarkSurfaces(vskel);
09902         }
09903 
09904         vskel->getVolumeData()->owns_emdata = false; //ensure the EMData object will remain when the Volume and its VolumeData object are freed
09905         EMData* skel = vskel->get_emdata();
09906         skel->update();
09907         return skel;
09908 }

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 9910 of file processor.cpp.

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

09911 {
09912         EMData* em_skel = this->process(image);
09913         //TODO: use memcpy and copy metadata explicitly
09914         *image = *em_skel; //Deep copy performed by EMData::operator=
09915         image->update();
09916         delete em_skel;
09917         em_skel = NULL;
09918         return;
09919 }


Member Data Documentation

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

Definition at line 7030 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:11:03 2012 for EMAN2 by  doxygen 1.4.7