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EMAN::TestImageFourierNoiseProfile Class Reference

#include <processor.h>

Inheritance diagram for EMAN::TestImageFourierNoiseProfile:

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Collaboration diagram for EMAN::TestImageFourierNoiseProfile:
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List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual 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

ProcessorNEW ()

Static Public Attributes

const string NAME = "testimage.noise.fourier.profile"

Detailed Description

Author:
David Woolford
Date:
June 15th 2009

Definition at line 5856 of file processor.h.


Member Function Documentation

virtual string EMAN::TestImageFourierNoiseProfile::get_desc  )  const [inline, virtual]
 

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 5866 of file processor.h.

05867                 {
05868                         return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
05869                 }

virtual string EMAN::TestImageFourierNoiseProfile::get_name  )  const [inline, virtual]
 

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 5861 of file processor.h.

05862                 {
05863                         return NAME;
05864                 }

virtual TypeDict EMAN::TestImageFourierNoiseProfile::get_param_types  )  const [inline, virtual]
 

Get processor parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 5876 of file processor.h.

References EMAN::TypeDict::put().

05877                 {
05878                         TypeDict d;
05879                         d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05880                         return d;
05881                 }

Processor* EMAN::TestImageFourierNoiseProfile::NEW  )  [inline, static]
 

Definition at line 5871 of file processor.h.

05872                 {
05873                         return new TestImageFourierNoiseProfile();
05874                 }

void TestImageFourierNoiseProfile::process_inplace EMData image  )  [virtual]
 

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.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 6769 of file processor.cpp.

References EMAN::EMData::ap2ri(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_data(), EMAN::Util::get_frand(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::EMData::is_complex(), EMAN::length(), nx, ny, phase(), EMAN::EMData::process_inplace(), EMAN::EMData::ri2ap(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftodd(), EMAN::EMData::set_fftpad(), EMAN::EMData::set_size(), sqrt(), EMAN::EMData::to_zero(), x, and y.

06769                                                                  {
06770 
06771         if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
06772 
06773         if (!image->is_complex()) {
06774                 int nx = image->get_xsize();
06775                 int offset = 2 - nx%2;
06776 
06777                 image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
06778                 image->set_complex(true);
06779                 if (1 == offset) image->set_fftodd(true);
06780                 else image->set_fftodd(false);
06781                 image->set_fftpad(true);
06782         }
06783         image->to_zero();
06784         image->ri2ap();
06785 
06786         vector<float> profile = params["profile"];
06787         transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
06788 
06789         int i = static_cast<int>(profile.size());
06790 
06791         float * d = image->get_data();
06792         int nx = image->get_xsize();
06793         int ny = image->get_ysize();
06794         int nxy = image->get_ysize()*nx;
06795         int nzon2 = image->get_zsize()/2;
06796         int nyon2 = image->get_ysize()/2;
06797         float rx, ry, rz, amp, phase;
06798         int length;
06799         int twox;
06800         for (int z = 0; z< image->get_zsize(); ++z) {
06801                 for (int y = 0; y < image->get_ysize(); ++y) {
06802                         for (int x = 0; x < image->get_xsize()/2; ++x) {
06803                                 rx = (float)x;
06804                                 ry = (float)nyon2 - (float)y;
06805                                 rz = (float)nzon2 - (float)z;
06806                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06807 
06808                                 twox = 2*x;
06809                                 size_t idx1 = twox + y*nx+z*nxy;
06810                                 size_t idx2 = idx1 + 1;
06811 
06812 
06813                                 if (length >= i) {
06814                                         d[idx1] = 0;
06815                                         d[idx2] = 0;
06816                                         continue;
06817                                 }
06818                                 amp = profile[length];
06819                                 phase = Util::get_frand(0,1)*2*M_PI;
06820 
06821 
06822                                 d[idx1] = amp;
06823                                 d[idx2] = phase;
06824 
06825                         }
06826                 }
06827         }
06828 
06829         image->ap2ri();
06830         if (image->get_ndim() == 2) {
06831                 bool yodd = image->get_ysize() % 2 == 1;
06832 
06833                 int yit = image->get_ysize()/2-1;
06834                 int offset = 1;
06835                 if (yodd) {
06836                         offset = 0;
06837                 }
06838                 for (int y = 0; y < yit; ++y) {
06839                         int bot_idx = (y+offset)*nx;
06840                         int top_idx = (ny-1-y)*nx;
06841                         float r1 = d[bot_idx];
06842                         float i1 = d[bot_idx+1];
06843                         float r2 = d[top_idx];
06844                         float i2 = d[top_idx+1];
06845                         float r = (r1 + r2)/2.0f;
06846                         float i = (i1 + i2)/2.0f;
06847                         d[bot_idx] = r;
06848                         d[top_idx] = r;
06849                         d[bot_idx+1] = i;
06850                         d[top_idx+1] = -i;
06851 
06852                         bot_idx = (y+offset)*nx+nx-2;
06853                         top_idx = (ny-1-y)*nx+nx-2;
06854                         r1 = d[bot_idx];
06855                         i1 = d[bot_idx+1];
06856                         r2 = d[top_idx];
06857                         i2 = d[top_idx+1];
06858                         r = (r1 + r2)/2.0f;
06859                         i = (i1 + i2)/2.0f;
06860                         d[bot_idx] = r;
06861                         d[top_idx] = r;
06862                         d[bot_idx+1] = i;
06863                         d[top_idx+1] = -i;
06864                 }
06865 
06866                 d[1] = 0; // 0 phase for this componenet
06867                 d[nx-1] = 0; // 0 phase for this component
06868                 d[ny/2*nx+nx-1] = 0;// 0 phase for this component
06869                 d[ny/2*nx+1] = 0;// 0 phase for this component
06870         }
06871 
06872         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06873         image->do_ift_inplace();
06874         image->depad();
06875 }


Member Data Documentation

const string TestImageFourierNoiseProfile::NAME = "testimage.noise.fourier.profile" [static]
 

Definition at line 192 of file processor.cpp.


The documentation for this class was generated from the following files:
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