#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 6903 of file processor.h. 06904 { 06905 return "Creates a skeleton of the 3D image by considering whether density is above or below a threshold value."; 06906 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6894 of file processor.h. 06895 { 06896 return NAME; 06897 // return "gorgon.binary_skel"; 06898 }
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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 6907 of file processor.h. References EMAN::TypeDict::put(). 06908 { 06909 TypeDict d; 06910 d.put("threshold", EMObject::FLOAT, "Threshold value."); 06911 d.put("min_curve_width", EMObject::INT, "Minimum curve width."); 06912 d.put("min_surface_width", EMObject::INT, "Minimum surface width."); 06913 d.put("mark_surfaces", EMObject::BOOL, "Mark surfaces with a value of 2.0f, whereas curves are 1.0f."); 06914 return d; 06915 }
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Definition at line 6899 of file processor.h. 06900 { 06901 return new BinarySkeletonizerProcessor(); 06902 }
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Definition at line 9698 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(). 09699 { 09700 using namespace wustl_mm::GraySkeletonCPP; 09701 using namespace wustl_mm::SkeletonMaker; 09702 09703 Volume * vimage = new Volume(image); 09704 float threshold = params["threshold"]; 09705 int min_curvew = params.set_default("min_curve_width", 4); 09706 int min_srfcw = params.set_default("min_surface_width", 4); 09707 bool mark_surfaces = params.set_default("mark_surfaces", true); 09708 Volume* vskel = VolumeSkeletonizer::PerformPureJuSkeletonization(vimage, "unused", static_cast<double>(threshold), min_curvew, min_srfcw); 09709 //VolumeSkeletonizer::CleanUpSkeleton(vskel, 4, 0.01f); 09710 if (mark_surfaces) { 09711 VolumeSkeletonizer::MarkSurfaces(vskel); 09712 } 09713 09714 vskel->getVolumeData()->owns_emdata = false; //ensure the EMData object will remain when the Volume and its VolumeData object are freed 09715 EMData* skel = vskel->get_emdata(); 09716 skel->update(); 09717 return skel; 09718 }
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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 9720 of file processor.cpp. References process(), and EMAN::EMData::update(). 09721 { 09722 EMData* em_skel = this->process(image); 09723 //TODO: use memcpy and copy metadata explicitly 09724 *image = *em_skel; //Deep copy performed by EMData::operator= 09725 image->update(); 09726 delete em_skel; 09727 em_skel = NULL; 09728 return; 09729 }
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Definition at line 219 of file processor.cpp. |