#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 6876 of file processor.h. 06877 {
06878 return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
06879 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 6866 of file processor.h. 06867 {
06868 return NAME;
06869 }
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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 6881 of file processor.h. References EMAN::TypeDict::put(). 06882 {
06883 TypeDict d;
06884 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");
06885 d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)");
06886 d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06887 d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06888 d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06889 //TODO: Check with Matt Baker about description strings
06890 return d;
06891 }
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Definition at line 6871 of file processor.h. 06872 {
06873 return new ModelEMCylinderProcessor();
06874 }
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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 9610 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. 09611 : modified from EMAN1 Cylinder.C by Wen Jiang
09612 {
09613 // synthesize model alpha helix, len is Angstrom, default to 2 turns
09614 //The helical axis is parallel to the z axis.
09615 EMData * cyl = in;
09616 int nx = cyl->get_xsize();
09617 int ny = cyl->get_ysize();
09618 int nz = cyl->get_zsize();
09619
09620 int type = params.set_default("type", 2);
09621 float len = params.set_default("length", 16.2f); //in angstroms
09622 int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down
09623 int y0 = params.set_default("y0", -1); //in voxels
09624 int z0 = params.set_default("z0", -1); //in voxels
09625 //TODO: check with Matt about default values
09626
09627 if (x0 < 0 || x0 >= nx)
09628 x0 = nx / 2;
09629 if (y0 < 0 || y0 >= ny)
09630 y0 = ny / 2;
09631 if (z0 < 0 || z0 >= nz)
09632 z0 = nz / 2;
09633
09634 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
09635 float apix_y = cyl->get_attr("apix_y");
09636 float apix_z = cyl->get_attr("apix_z");
09637
09638 float * dat = cyl->get_data();
09639 int cyl_voxel_len = (int) (len / apix_z);
09640 int cyl_k_min = z0 - cyl_voxel_len / 2;
09641 int cyl_k_max = z0 + cyl_voxel_len / 2;
09642
09643 int x, y;
09644 for (int k = 0; k < nz; ++k) {
09645 for (int j = 0; j < ny; ++j) {
09646 for (int i = 0; i < nx; ++i, ++dat) {
09647 x = i - x0;//coordinate sys centered on cylinder
09648 y = j - y0;//coordinate sys centered on cylinder
09649 float radius = (float)hypot(x * apix_x, y * apix_y);
09650 if ((k > cyl_k_min) && (k < cyl_k_max))
09651 *dat += radprofile(radius, type); //pointer arithmetic for array done in loop
09652 //else
09653 //continue;
09654
09655 }
09656 }
09657 }
09658 }
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Definition at line 222 of file processor.cpp. |
1.3.9.1