#include <processor.h>
Inheritance diagram for EMAN::ApplyPolynomialProfileToHelix:
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.poly_radial_profile" |
Definition at line 6974 of file processor.h.
string EMAN::ApplyPolynomialProfileToHelix::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 6989 of file processor.h.
06990 { 06991 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 06992 }
string EMAN::ApplyPolynomialProfileToHelix::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 6979 of file processor.h.
References NAME.
06980 { 06981 return NAME; 06982 }
virtual TypeDict EMAN::ApplyPolynomialProfileToHelix::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 6993 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
06994 { 06995 TypeDict d; 06996 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 06997 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06998 return d; 06999 }
static Processor* EMAN::ApplyPolynomialProfileToHelix::NEW | ( | ) | [inline, static] |
Definition at line 6984 of file processor.h.
06985 { 06986 return new ApplyPolynomialProfileToHelix(); 06987 }
void ApplyPolynomialProfileToHelix::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 9833 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::Util::round(), and EMAN::Dict::set_default().
09834 { 09835 EMData * cyl = in; 09836 int nx = cyl->get_xsize(); 09837 int ny = cyl->get_ysize(); 09838 int nz = cyl->get_zsize(); 09839 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 09840 float apix_y = cyl->get_attr("apix_y"); 09841 float apix_z = cyl->get_attr("apix_z"); 09842 float lengthAngstroms = params["length"]; 09843 int z0 = params.set_default("z0", -1); //in voxels 09844 09845 if (z0 < 0 || z0 >= nz) 09846 z0 = nz / 2; 09847 09848 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09849 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09850 09851 float * dat = cyl->get_data(); 09852 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09853 09854 for (int k = 0; k < nz; ++k) //taking slices along z axis 09855 { 09856 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09857 09858 if (k >= z_start && k <= z_stop) 09859 //Apply the radial profile only between z_start and z_stop on the z axis 09860 { 09861 //Calculating CM for the slice... 09862 for (int j = 0; j < ny; ++j) 09863 { 09864 for (int i = 0; i < nx; ++i, ++dat) 09865 { 09866 rho_x_sum += (*dat)*i; 09867 rho_y_sum += (*dat)*j; 09868 rho_sum += *dat; 09869 } 09870 } 09871 if (rho_sum != 0) 09872 { 09873 dat -= nx*ny;//going back to the beginning of the dat array 09874 x_cm = rho_x_sum/rho_sum; 09875 y_cm = rho_y_sum/rho_sum; 09876 09877 //Applying radial profile... 09878 for (int j=0; j<ny;++j) 09879 { 09880 for (int i=0;i<nx;++i,++dat) 09881 { 09882 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09883 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09884 } 09885 } 09886 } 09887 } 09888 else 09889 //Clear the map, setting the density to zero everywhere else. 09890 { 09891 for (int j=0; j<ny; j++) 09892 for(int i=0; i<nx; i++) 09893 { 09894 *dat = 0; 09895 dat++; 09896 } 09897 } 09898 09899 } 09900 }
const string ApplyPolynomialProfileToHelix::NAME = "math.poly_radial_profile" [static] |