#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 6895 of file processor.h.
string EMAN::ModelEMCylinderProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 6910 of file processor.h.
06911 { 06912 return "Adds a cylinder with a radial density profile similar to that of an alpha helix."; 06913 }
string EMAN::ModelEMCylinderProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 6900 of file processor.h.
References NAME.
06901 { 06902 return NAME; 06903 }
virtual TypeDict EMAN::ModelEMCylinderProcessor::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.
Reimplemented from EMAN::Processor.
Definition at line 6915 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
06916 { 06917 TypeDict d; 06918 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"); 06919 d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)"); 06920 d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06921 d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06922 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06923 //TODO: Check with Matt Baker about description strings 06924 return d; 06925 }
static Processor* EMAN::ModelEMCylinderProcessor::NEW | ( | ) | [inline, static] |
Definition at line 6905 of file processor.h.
06906 { 06907 return new ModelEMCylinderProcessor(); 06908 }
void ModelEMCylinderProcessor::process_inplace | ( | EMData * | in | ) | [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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 9957 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(), in, EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Dict::set_default(), and x.
09958 : modified from EMAN1 Cylinder.C by Wen Jiang 09959 { 09960 // synthesize model alpha helix, len is Angstrom, default to 2 turns 09961 //The helical axis is parallel to the z axis. 09962 EMData * cyl = in; 09963 int nx = cyl->get_xsize(); 09964 int ny = cyl->get_ysize(); 09965 int nz = cyl->get_zsize(); 09966 09967 int type = params.set_default("type", 2); 09968 float len = params.set_default("length", 16.2f); //in angstroms 09969 int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down 09970 int y0 = params.set_default("y0", -1); //in voxels 09971 int z0 = params.set_default("z0", -1); //in voxels 09972 //TODO: check with Matt about default values 09973 09974 if (x0 < 0 || x0 >= nx) 09975 x0 = nx / 2; 09976 if (y0 < 0 || y0 >= ny) 09977 y0 = ny / 2; 09978 if (z0 < 0 || z0 >= nz) 09979 z0 = nz / 2; 09980 09981 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 09982 float apix_y = cyl->get_attr("apix_y"); 09983 float apix_z = cyl->get_attr("apix_z"); 09984 09985 float * dat = cyl->get_data(); 09986 int cyl_voxel_len = (int) (len / apix_z); 09987 int cyl_k_min = z0 - cyl_voxel_len / 2; 09988 int cyl_k_max = z0 + cyl_voxel_len / 2; 09989 09990 int x, y; 09991 for (int k = 0; k < nz; k++) { 09992 for (int j = 0; j < ny; j++) { 09993 for (int i = 0; i < nx; i++, dat++) { 09994 x = i - x0;//coordinate sys centered on cylinder 09995 y = j - y0;//coordinate sys centered on cylinder 09996 float radius = (float)hypot(x * apix_x, y * apix_y); 09997 if ((k > cyl_k_min) && (k < cyl_k_max)) 09998 *dat += radprofile(radius, type); //pointer arithmetic for array done in loop 09999 //else 10000 //continue; 10001 10002 } 10003 } 10004 } 10005 }
const string ModelEMCylinderProcessor::NAME = "math.model_em_cylinder" [static] |