#include <processor.h>
Inheritance diagram for EMAN::BinarySkeletonizerProcessor:
Public Member Functions | |
virtual EMData * | process (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 | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "gorgon.binary_skel" |
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
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 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 7008 of file processor.h. 07009 { 07010 return NAME; 07011 // return "gorgon.binary_skel"; 07012 }
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Get processor parameter information in a dictionary. Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Reimplemented from EMAN::Processor. Definition at line 7021 of file processor.h. References 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 }
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Definition at line 7013 of file processor.h. 07014 { 07015 return new BinarySkeletonizerProcessor(); 07016 }
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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::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 }
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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.
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 }
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Definition at line 219 of file processor.cpp. |