#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 6890 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 6905 of file processor.h.
06906 { 06907 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 06908 }
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 6895 of file processor.h.
References NAME.
06896 { 06897 return NAME; 06898 }
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 6909 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
06910 { 06911 TypeDict d; 06912 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 06913 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06914 return d; 06915 }
static Processor* EMAN::ApplyPolynomialProfileToHelix::NEW | ( | ) | [inline, static] |
Definition at line 6900 of file processor.h.
06901 { 06902 return new ApplyPolynomialProfileToHelix(); 06903 }
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 9900 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().
09901 { 09902 EMData * cyl = in; 09903 int nx = cyl->get_xsize(); 09904 int ny = cyl->get_ysize(); 09905 int nz = cyl->get_zsize(); 09906 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 09907 float apix_y = cyl->get_attr("apix_y"); 09908 float apix_z = cyl->get_attr("apix_z"); 09909 float lengthAngstroms = params["length"]; 09910 int z0 = params.set_default("z0", -1); //in voxels 09911 09912 if (z0 < 0 || z0 >= nz) 09913 z0 = nz / 2; 09914 09915 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09916 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09917 09918 float * dat = cyl->get_data(); 09919 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09920 09921 for (int k = 0; k < nz; k++) //taking slices along z axis 09922 { 09923 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09924 09925 if (k >= z_start && k <= z_stop) 09926 //Apply the radial profile only between z_start and z_stop on the z axis 09927 { 09928 //Calculating CM for the slice... 09929 for (int j = 0; j < ny; j++) 09930 { 09931 for (int i = 0; i < nx; i++, dat++) 09932 { 09933 rho_x_sum += (*dat)*i; 09934 rho_y_sum += (*dat)*j; 09935 rho_sum += *dat; 09936 } 09937 } 09938 if (rho_sum != 0) 09939 { 09940 dat -= nx*ny;//going back to the beginning of the dat array 09941 x_cm = rho_x_sum/rho_sum; 09942 y_cm = rho_y_sum/rho_sum; 09943 09944 //Applying radial profile... 09945 for (int j=0; j<ny;j++) 09946 { 09947 for (int i=0;i<nx;i++,dat++) 09948 { 09949 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09950 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09951 } 09952 } 09953 } 09954 } 09955 else 09956 //Clear the map, setting the density to zero everywhere else. 09957 { 09958 for (int j=0; j<ny; j++) 09959 for(int i=0; i<nx; i++) 09960 { 09961 *dat = 0; 09962 dat++; 09963 } 09964 } 09965 09966 } 09967 }
const string ApplyPolynomialProfileToHelix::NAME = "math.poly_radial_profile" [static] |