#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 | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "math.poly_radial_profile" |
|
Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 7028 of file processor.h. 07029 { 07030 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 07031 }
|
|
Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 7018 of file processor.h. 07019 {
07020 return NAME;
07021 }
|
|
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 7032 of file processor.h. References EMAN::TypeDict::put(). 07033 { 07034 TypeDict d; 07035 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 07036 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 07037 return d; 07038 }
|
|
Definition at line 7023 of file processor.h. 07024 { 07025 return new ApplyPolynomialProfileToHelix(); 07026 }
|
|
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 9896 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(), nx, ny, EMAN::ModelHelixProcessor::radprofile(), EMAN::Util::round(), and EMAN::Dict::set_default(). 09897 { 09898 EMData * cyl = in; 09899 int nx = cyl->get_xsize(); 09900 int ny = cyl->get_ysize(); 09901 int nz = cyl->get_zsize(); 09902 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 09903 float apix_y = cyl->get_attr("apix_y"); 09904 float apix_z = cyl->get_attr("apix_z"); 09905 float lengthAngstroms = params["length"]; 09906 int z0 = params.set_default("z0", -1); //in voxels 09907 09908 if (z0 < 0 || z0 >= nz) 09909 z0 = nz / 2; 09910 09911 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09912 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09913 09914 float * dat = cyl->get_data(); 09915 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09916 09917 for (int k = 0; k < nz; ++k) //taking slices along z axis 09918 { 09919 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09920 09921 if (k >= z_start && k <= z_stop) 09922 //Apply the radial profile only between z_start and z_stop on the z axis 09923 { 09924 //Calculating CM for the slice... 09925 for (int j = 0; j < ny; ++j) 09926 { 09927 for (int i = 0; i < nx; ++i, ++dat) 09928 { 09929 rho_x_sum += (*dat)*i; 09930 rho_y_sum += (*dat)*j; 09931 rho_sum += *dat; 09932 } 09933 } 09934 if (rho_sum != 0) 09935 { 09936 dat -= nx*ny;//going back to the beginning of the dat array 09937 x_cm = rho_x_sum/rho_sum; 09938 y_cm = rho_y_sum/rho_sum; 09939 09940 //Applying radial profile... 09941 for (int j=0; j<ny;++j) 09942 { 09943 for (int i=0;i<nx;++i,++dat) 09944 { 09945 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09946 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09947 } 09948 } 09949 } 09950 } 09951 else 09952 //Clear the map, setting the density to zero everywhere else. 09953 { 09954 for (int j=0; j<ny; j++) 09955 for(int i=0; i<nx; i++) 09956 { 09957 *dat = 0; 09958 dat++; 09959 } 09960 } 09961 09962 } 09963 }
|
|
Definition at line 219 of file processor.cpp. |