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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

static ProcessorNEW ()

Static Public Attributes

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

Detailed Description

Author:
David Woolford
Date:
June 15th 2009

Definition at line 5857 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 5867 of file processor.h.

05868                 {
05869                         return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
05870                 }

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 5862 of file processor.h.

References NAME.

05863                 {
05864                         return NAME;
05865                 }

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 5877 of file processor.h.

References EMAN::EMObject::FLOATARRAY, and EMAN::TypeDict::put().

05878                 {
05879                         TypeDict d;
05880                         d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05881                         return d;
05882                 }

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

Definition at line 5872 of file processor.h.

05873                 {
05874                         return new TestImageFourierNoiseProfile();
05875                 }

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 6800 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(), get_xsize(), EMAN::EMData::get_xsize(), get_ysize(), EMAN::EMData::get_ysize(), get_zsize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::EMData::is_complex(), EMAN::length(), EMAN::Processor::params, 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(), and x.

06800                                                                  {
06801 
06802         if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
06803 
06804         if (!image->is_complex()) {
06805                 int nx = image->get_xsize();
06806                 int offset = 2 - nx%2;
06807 
06808                 image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
06809                 image->set_complex(true);
06810                 if (1 == offset) image->set_fftodd(true);
06811                 else image->set_fftodd(false);
06812                 image->set_fftpad(true);
06813         }
06814         image->to_zero();
06815         image->ri2ap();
06816 
06817         vector<float> profile = params["profile"];
06818         transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
06819 
06820         int i = static_cast<int>(profile.size());
06821 
06822         float * d = image->get_data();
06823         int nx = image->get_xsize();
06824         int ny = image->get_ysize();
06825         int nxy = image->get_ysize()*nx;
06826         int nzon2 = image->get_zsize()/2;
06827         int nyon2 = image->get_ysize()/2;
06828         float rx, ry, rz, amp, phase;
06829         int length;
06830         int twox;
06831         for (int z = 0; z< image->get_zsize(); ++z) {
06832                 for (int y = 0; y < image->get_ysize(); ++y) {
06833                         for (int x = 0; x < image->get_xsize()/2; ++x) {
06834                                 rx = (float)x;
06835                                 ry = (float)nyon2 - (float)y;
06836                                 rz = (float)nzon2 - (float)z;
06837                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06838 
06839                                 twox = 2*x;
06840                                 size_t idx1 = twox + y*nx+z*nxy;
06841                                 size_t idx2 = idx1 + 1;
06842 
06843 
06844                                 if (length >= i) {
06845                                         d[idx1] = 0;
06846                                         d[idx2] = 0;
06847                                         continue;
06848                                 }
06849                                 amp = profile[length];
06850                                 phase = Util::get_frand(0,1)*2*M_PI;
06851 
06852 
06853                                 d[idx1] = amp;
06854                                 d[idx2] = phase;
06855 
06856                         }
06857                 }
06858         }
06859 
06860         image->ap2ri();
06861         if (image->get_ndim() == 2) {
06862                 bool yodd = image->get_ysize() % 2 == 1;
06863 
06864                 int yit = image->get_ysize()/2-1;
06865                 int offset = 1;
06866                 if (yodd) {
06867                         offset = 0;
06868                 }
06869                 for (int y = 0; y < yit; ++y) {
06870                         int bot_idx = (y+offset)*nx;
06871                         int top_idx = (ny-1-y)*nx;
06872                         float r1 = d[bot_idx];
06873                         float i1 = d[bot_idx+1];
06874                         float r2 = d[top_idx];
06875                         float i2 = d[top_idx+1];
06876                         float r = (r1 + r2)/2.0f;
06877                         float i = (i1 + i2)/2.0f;
06878                         d[bot_idx] = r;
06879                         d[top_idx] = r;
06880                         d[bot_idx+1] = i;
06881                         d[top_idx+1] = -i;
06882 
06883                         bot_idx = (y+offset)*nx+nx-2;
06884                         top_idx = (ny-1-y)*nx+nx-2;
06885                         r1 = d[bot_idx];
06886                         i1 = d[bot_idx+1];
06887                         r2 = d[top_idx];
06888                         i2 = d[top_idx+1];
06889                         r = (r1 + r2)/2.0f;
06890                         i = (i1 + i2)/2.0f;
06891                         d[bot_idx] = r;
06892                         d[top_idx] = r;
06893                         d[bot_idx+1] = i;
06894                         d[top_idx+1] = -i;
06895                 }
06896 
06897                 d[1] = 0; // 0 phase for this componenet
06898                 d[nx-1] = 0; // 0 phase for this component
06899                 d[ny/2*nx+nx-1] = 0;// 0 phase for this component
06900                 d[ny/2*nx+1] = 0;// 0 phase for this component
06901         }
06902 
06903         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06904         image->do_ift_inplace();
06905         image->depad();
06906 }


Member Data Documentation

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

Definition at line 5884 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:37:45 2010 for EMAN2 by  doxygen 1.4.4