#include <processor.h>
Inheritance diagram for EMAN::ModelEMCylinderProcessor:


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.model_em_cylinder" |
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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 6838 of file processor.h. 06839 {
06840 return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
06841 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6828 of file processor.h. 06829 {
06830 return NAME;
06831 }
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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 6843 of file processor.h. References EMAN::TypeDict::put(). 06844 {
06845 TypeDict d;
06846 d.put("type", EMObject::INT, "Radial profile of density method, defaults to 2: 0 = pure Gaussian falloff; 1 = Gaussian falloff + dip, so mean is zero; 2 = polynomial fitting of real helix density");
06847 d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)");
06848 d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06849 d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06850 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06851 //TODO: Check with Matt Baker about description strings
06852 return d;
06853 }
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Definition at line 6833 of file processor.h. 06834 {
06835 return new ModelEMCylinderProcessor();
06836 }
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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 9578 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::Dict::set_default(), x, and y. 09579 : modified from EMAN1 Cylinder.C by Wen Jiang
09580 {
09581 // synthesize model alpha helix, len is Angstrom, default to 2 turns
09582 //The helical axis is parallel to the z axis.
09583 EMData * cyl = in;
09584 int nx = cyl->get_xsize();
09585 int ny = cyl->get_ysize();
09586 int nz = cyl->get_zsize();
09587
09588 int type = params.set_default("type", 2);
09589 float len = params.set_default("length", 16.2f); //in angstroms
09590 int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down
09591 int y0 = params.set_default("y0", -1); //in voxels
09592 int z0 = params.set_default("z0", -1); //in voxels
09593 //TODO: check with Matt about default values
09594
09595 if (x0 < 0 || x0 >= nx)
09596 x0 = nx / 2;
09597 if (y0 < 0 || y0 >= ny)
09598 y0 = ny / 2;
09599 if (z0 < 0 || z0 >= nz)
09600 z0 = nz / 2;
09601
09602 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
09603 float apix_y = cyl->get_attr("apix_y");
09604 float apix_z = cyl->get_attr("apix_z");
09605
09606 float * dat = cyl->get_data();
09607 int cyl_voxel_len = (int) (len / apix_z);
09608 int cyl_k_min = z0 - cyl_voxel_len / 2;
09609 int cyl_k_max = z0 + cyl_voxel_len / 2;
09610
09611 int x, y;
09612 for (int k = 0; k < nz; ++k) {
09613 for (int j = 0; j < ny; ++j) {
09614 for (int i = 0; i < nx; ++i, ++dat) {
09615 x = i - x0;//coordinate sys centered on cylinder
09616 y = j - y0;//coordinate sys centered on cylinder
09617 float radius = (float)hypot(x * apix_x, y * apix_y);
09618 if ((k > cyl_k_min) && (k < cyl_k_max))
09619 *dat += radprofile(radius, type); //pointer arithmetic for array done in loop
09620 //else
09621 //continue;
09622
09623 }
09624 }
09625 }
09626 }
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Definition at line 217 of file processor.cpp. |
1.3.9.1