#include <processor.h>
Inheritance diagram for EMAN::ModelEMCylinderProcessor:
Public Member Functions | |
void | process_inplace (EMData *in) |
To process an image in-place. | |
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "math.model_em_cylinder" |
Definition at line 6855 of file processor.h.
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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 6870 of file processor.h. 06871 { 06872 return "Adds a cylinder with a radial density profile similar to that of an alpha helix."; 06873 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6860 of file processor.h. References NAME. 06861 { 06862 return NAME; 06863 }
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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 6875 of file processor.h. References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put(). 06876 { 06877 TypeDict d; 06878 d.put("type", EMObject::INT, "Radial profile of density method, defaults to 2: 0 = pure Gaussian falloff; 1 = Gaussian falloff + dip, so mean is zero; 2 = polynomial fitting of real helix density"); 06879 d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)"); 06880 d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06881 d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06882 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06883 //TODO: Check with Matt Baker about description strings 06884 return d; 06885 }
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Definition at line 6865 of file processor.h. 06866 { 06867 return new ModelEMCylinderProcessor(); 06868 }
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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 9850 of file processor.cpp. References EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Dict::set_default(), and x. 09851 : modified from EMAN1 Cylinder.C by Wen Jiang 09852 { 09853 // synthesize model alpha helix, len is Angstrom, default to 2 turns 09854 //The helical axis is parallel to the z axis. 09855 EMData * cyl = in; 09856 int nx = cyl->get_xsize(); 09857 int ny = cyl->get_ysize(); 09858 int nz = cyl->get_zsize(); 09859 09860 int type = params.set_default("type", 2); 09861 float len = params.set_default("length", 16.2); //in angstroms 09862 int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down 09863 int y0 = params.set_default("y0", -1); //in voxels 09864 int z0 = params.set_default("z0", -1); //in voxels 09865 //TODO: check with Matt about default values 09866 09867 if (x0 < 0 || x0 >= nx) 09868 x0 = nx / 2; 09869 if (y0 < 0 || y0 >= ny) 09870 y0 = ny / 2; 09871 if (z0 < 0 || z0 >= nz) 09872 z0 = nz / 2; 09873 09874 float apix_x = cyl->get_attr("apix_x"); //TODO: Ask Matt if I correctly handled cases where apix_x != apix_y or apix_x != apix_z are not equal 09875 float apix_y = cyl->get_attr("apix_y"); 09876 float apix_z = cyl->get_attr("apix_z"); 09877 09878 float * dat = cyl->get_data(); 09879 int cyl_voxel_len = (int) (len / apix_z); 09880 int cyl_k_min = z0 - cyl_voxel_len / 2; 09881 int cyl_k_max = z0 + cyl_voxel_len / 2; 09882 09883 int x, y; 09884 for (int k = 0; k < nz; k++) { 09885 for (int j = 0; j < ny; j++) { 09886 for (int i = 0; i < nx; i++, dat++) { 09887 x = i - x0;//coordinate sys centered on cylinder 09888 y = j - y0;//coordinate sys centered on cylinder 09889 float radius = (float)hypot(x * apix_x, y * apix_y); 09890 if ((k > cyl_k_min) && (k < cyl_k_max)) 09891 *dat += radprofile(radius, type); //pointer arithmetic for array done in loop 09892 //else 09893 //continue; 09894 09895 } 09896 } 09897 } 09898 }
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Definition at line 6887 of file processor.h. Referenced by get_name(). |