#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 6911 of file processor.h. 06912 { 06913 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 06914 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6901 of file processor.h. 06902 {
06903 return NAME;
06904 }
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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 6915 of file processor.h. References EMAN::TypeDict::put(). 06916 { 06917 TypeDict d; 06918 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 06919 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06920 return d; 06921 }
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Definition at line 6906 of file processor.h. 06907 { 06908 return new ApplyPolynomialProfileToHelix(); 06909 }
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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 9660 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(). 09661 { 09662 EMData * cyl = in; 09663 int nx = cyl->get_xsize(); 09664 int ny = cyl->get_ysize(); 09665 int nz = cyl->get_zsize(); 09666 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 09667 float apix_y = cyl->get_attr("apix_y"); 09668 float apix_z = cyl->get_attr("apix_z"); 09669 float lengthAngstroms = params["length"]; 09670 int z0 = params.set_default("z0", -1); //in voxels 09671 09672 if (z0 < 0 || z0 >= nz) 09673 z0 = nz / 2; 09674 09675 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09676 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09677 09678 float * dat = cyl->get_data(); 09679 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09680 09681 for (int k = 0; k < nz; ++k) //taking slices along z axis 09682 { 09683 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09684 09685 if (k >= z_start && k <= z_stop) 09686 //Apply the radial profile only between z_start and z_stop on the z axis 09687 { 09688 //Calculating CM for the slice... 09689 for (int j = 0; j < ny; ++j) 09690 { 09691 for (int i = 0; i < nx; ++i, ++dat) 09692 { 09693 rho_x_sum += (*dat)*i; 09694 rho_y_sum += (*dat)*j; 09695 rho_sum += *dat; 09696 } 09697 } 09698 if (rho_sum != 0) 09699 { 09700 dat -= nx*ny;//going back to the beginning of the dat array 09701 x_cm = rho_x_sum/rho_sum; 09702 y_cm = rho_y_sum/rho_sum; 09703 09704 //Applying radial profile... 09705 for (int j=0; j<ny;++j) 09706 { 09707 for (int i=0;i<nx;++i,++dat) 09708 { 09709 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09710 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09711 } 09712 } 09713 } 09714 } 09715 else 09716 //Clear the map, setting the density to zero everywhere else. 09717 { 09718 for (int j=0; j<ny; j++) 09719 for(int i=0; i<nx; i++) 09720 { 09721 *dat = 0; 09722 dat++; 09723 } 09724 } 09725 09726 } 09727 }
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Definition at line 223 of file processor.cpp. |