#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 6972 of file processor.h. 06973 { 06974 return "Creates a skeleton of the 3D image by considering whether density is above or below a threshold value."; 06975 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6963 of file processor.h. 06964 { 06965 return NAME; 06966 // return "gorgon.binary_skel"; 06967 }
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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 6976 of file processor.h. References EMAN::TypeDict::put(). 06977 { 06978 TypeDict d; 06979 d.put("threshold", EMObject::FLOAT, "Threshold value."); 06980 d.put("min_curve_width", EMObject::INT, "Minimum curve width."); 06981 d.put("min_surface_width", EMObject::INT, "Minimum surface width."); 06982 d.put("mark_surfaces", EMObject::BOOL, "Mark surfaces with a value of 2.0f, whereas curves are 1.0f."); 06983 return d; 06984 }
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Definition at line 6968 of file processor.h. 06969 { 06970 return new BinarySkeletonizerProcessor(); 06971 }
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Definition at line 9816 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(). 09817 { 09818 using namespace wustl_mm::GraySkeletonCPP; 09819 using namespace wustl_mm::SkeletonMaker; 09820 09821 Volume * vimage = new Volume(image); 09822 float threshold = params["threshold"]; 09823 int min_curvew = params.set_default("min_curve_width", 4); 09824 int min_srfcw = params.set_default("min_surface_width", 4); 09825 bool mark_surfaces = params.set_default("mark_surfaces", true); 09826 Volume* vskel = VolumeSkeletonizer::PerformPureJuSkeletonization(vimage, "unused", static_cast<double>(threshold), min_curvew, min_srfcw); 09827 //VolumeSkeletonizer::CleanUpSkeleton(vskel, 4, 0.01f); 09828 if (mark_surfaces) { 09829 VolumeSkeletonizer::MarkSurfaces(vskel); 09830 } 09831 09832 vskel->getVolumeData()->owns_emdata = false; //ensure the EMData object will remain when the Volume and its VolumeData object are freed 09833 EMData* skel = vskel->get_emdata(); 09834 skel->update(); 09835 return skel; 09836 }
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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 9838 of file processor.cpp. References process(), and EMAN::EMData::update(). 09839 { 09840 EMData* em_skel = this->process(image); 09841 //TODO: use memcpy and copy metadata explicitly 09842 *image = *em_skel; //Deep copy performed by EMData::operator= 09843 image->update(); 09844 delete em_skel; 09845 em_skel = NULL; 09846 return; 09847 }
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Definition at line 219 of file processor.cpp. |