#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" |
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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 6904 of file processor.h. 06905 { 06906 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 06907 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6894 of file processor.h. 06895 {
06896 return NAME;
06897 }
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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 6908 of file processor.h. References EMAN::TypeDict::put(). 06909 { 06910 TypeDict d; 06911 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 06912 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06913 return d; 06914 }
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Definition at line 6899 of file processor.h. 06900 { 06901 return new ApplyPolynomialProfileToHelix(); 06902 }
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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 9869 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(). 09870 { 09871 EMData * cyl = in; 09872 int nx = cyl->get_xsize(); 09873 int ny = cyl->get_ysize(); 09874 int nz = cyl->get_zsize(); 09875 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 09876 float apix_y = cyl->get_attr("apix_y"); 09877 float apix_z = cyl->get_attr("apix_z"); 09878 float lengthAngstroms = params["length"]; 09879 int z0 = params.set_default("z0", -1); //in voxels 09880 09881 if (z0 < 0 || z0 >= nz) 09882 z0 = nz / 2; 09883 09884 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09885 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09886 09887 float * dat = cyl->get_data(); 09888 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09889 09890 for (int k = 0; k < nz; k++) //taking slices along z axis 09891 { 09892 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09893 09894 if (k >= z_start && k <= z_stop) 09895 //Apply the radial profile only between z_start and z_stop on the z axis 09896 { 09897 //Calculating CM for the slice... 09898 for (int j = 0; j < ny; j++) 09899 { 09900 for (int i = 0; i < nx; i++, dat++) 09901 { 09902 rho_x_sum += (*dat)*i; 09903 rho_y_sum += (*dat)*j; 09904 rho_sum += *dat; 09905 } 09906 } 09907 if (rho_sum != 0) 09908 { 09909 dat -= nx*ny;//going back to the beginning of the dat array 09910 x_cm = rho_x_sum/rho_sum; 09911 y_cm = rho_y_sum/rho_sum; 09912 09913 //Applying radial profile... 09914 for (int j=0; j<ny;j++) 09915 { 09916 for (int i=0;i<nx;i++,dat++) 09917 { 09918 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09919 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09920 } 09921 } 09922 } 09923 } 09924 else 09925 //Clear the map, setting the density to zero everywhere else. 09926 { 09927 for (int j=0; j<ny; j++) 09928 for(int i=0; i<nx; i++) 09929 { 09930 *dat = 0; 09931 dat++; 09932 } 09933 } 09934 09935 } 09936 }
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Definition at line 218 of file processor.cpp. |