#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 6732 of file processor.h. 06733 { 06734 return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it."; 06735 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6722 of file processor.h. 06723 {
06724 return NAME;
06725 }
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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 6736 of file processor.h. References EMAN::TypeDict::put(). 06737 { 06738 TypeDict d; 06739 d.put("length", EMObject::FLOAT, "Helix length in angstroms."); 06740 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map"); 06741 return d; 06742 }
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Definition at line 6727 of file processor.h. 06728 { 06729 return new ApplyPolynomialProfileToHelix(); 06730 }
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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 9915 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(). 09916 { 09917 EMData * cyl = in; 09918 int nx = cyl->get_xsize(); 09919 int ny = cyl->get_ysize(); 09920 int nz = cyl->get_zsize(); 09921 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 09922 float apix_y = cyl->get_attr("apix_y"); 09923 float apix_z = cyl->get_attr("apix_z"); 09924 float lengthAngstroms = params["length"]; 09925 int z0 = params.set_default("z0", -1); //in voxels 09926 09927 if (z0 < 0 || z0 >= nz) 09928 z0 = nz / 2; 09929 09930 int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z ); 09931 int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z ); 09932 09933 float * dat = cyl->get_data(); 09934 double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius; 09935 09936 for (int k = 0; k < nz; k++) //taking slices along z axis 09937 { 09938 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice 09939 09940 if (k >= z_start && k <= z_stop) 09941 //Apply the radial profile only between z_start and z_stop on the z axis 09942 { 09943 //Calculating CM for the slice... 09944 for (int j = 0; j < ny; j++) 09945 { 09946 for (int i = 0; i < nx; i++, dat++) 09947 { 09948 rho_x_sum += (*dat)*i; 09949 rho_y_sum += (*dat)*j; 09950 rho_sum += *dat; 09951 } 09952 } 09953 if (rho_sum != 0) 09954 { 09955 dat -= nx*ny;//going back to the beginning of the dat array 09956 x_cm = rho_x_sum/rho_sum; 09957 y_cm = rho_y_sum/rho_sum; 09958 09959 //Applying radial profile... 09960 for (int j=0; j<ny;j++) 09961 { 09962 for (int i=0;i<nx;i++,dat++) 09963 { 09964 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y ); 09965 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile. 09966 } 09967 } 09968 } 09969 } 09970 else 09971 //Clear the map, setting the density to zero everywhere else. 09972 { 09973 for (int j=0; j<ny; j++) 09974 for(int i=0; i<nx; i++) 09975 { 09976 *dat = 0; 09977 dat++; 09978 } 09979 } 09980 09981 } 09982 }
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Definition at line 213 of file processor.cpp. |