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 5825 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 5835 of file processor.h.

05836                 {
05837                         return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
05838                 }

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 5830 of file processor.h.

References NAME.

05831                 {
05832                         return NAME;
05833                 }

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 5845 of file processor.h.

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

05846                 {
05847                         TypeDict d;
05848                         d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05849                         return d;
05850                 }

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

Definition at line 5840 of file processor.h.

05841                 {
05842                         return new TestImageFourierNoiseProfile();
05843                 }

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 6871 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(), 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.

06871                                                                  {
06872 
06873         if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
06874 
06875         if (!image->is_complex()) {
06876                 int nx = image->get_xsize();
06877                 int offset = 2 - nx%2;
06878 
06879                 image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
06880                 image->set_complex(true);
06881                 if (1 == offset) image->set_fftodd(true);
06882                 else image->set_fftodd(false);
06883                 image->set_fftpad(true);
06884         }
06885         image->to_zero();
06886         image->ri2ap();
06887 
06888         vector<float> profile = params["profile"];
06889         transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
06890 
06891         int i = static_cast<int>(profile.size());
06892 
06893         float * d = image->get_data();
06894         int nx = image->get_xsize();
06895         int ny = image->get_ysize();
06896         int nxy = image->get_ysize()*nx;
06897         int nzon2 = image->get_zsize()/2;
06898         int nyon2 = image->get_ysize()/2;
06899         float rx, ry, rz, amp, phase;
06900         int length;
06901         int twox;
06902         for (int z = 0; z< image->get_zsize(); ++z) {
06903                 for (int y = 0; y < image->get_ysize(); ++y) {
06904                         for (int x = 0; x < image->get_xsize()/2; ++x) {
06905                                 rx = (float)x;
06906                                 ry = (float)nyon2 - (float)y;
06907                                 rz = (float)nzon2 - (float)z;
06908                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06909 
06910                                 twox = 2*x;
06911                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
06912                                 size_t idx2 = idx1 + 1;
06913 
06914 
06915                                 if (length >= i) {
06916                                         d[idx1] = 0;
06917                                         d[idx2] = 0;
06918                                         continue;
06919                                 }
06920                                 amp = profile[length];
06921                                 phase = Util::get_frand(0,1)*2*M_PI;
06922 
06923 
06924                                 d[idx1] = amp;
06925                                 d[idx2] = phase;
06926 
06927                         }
06928                 }
06929         }
06930 
06931         image->ap2ri();
06932         if (image->get_ndim() == 2) {
06933                 bool yodd = image->get_ysize() % 2 == 1;
06934 
06935                 int yit = image->get_ysize()/2-1;
06936                 int offset = 1;
06937                 if (yodd) {
06938                         offset = 0;
06939                 }
06940                 for (int y = 0; y < yit; ++y) {
06941                         int bot_idx = (y+offset)*nx;
06942                         int top_idx = (ny-1-y)*nx;
06943                         float r1 = d[bot_idx];
06944                         float i1 = d[bot_idx+1];
06945                         float r2 = d[top_idx];
06946                         float i2 = d[top_idx+1];
06947                         float r = (r1 + r2)/2.0f;
06948                         float i = (i1 + i2)/2.0f;
06949                         d[bot_idx] = r;
06950                         d[top_idx] = r;
06951                         d[bot_idx+1] = i;
06952                         d[top_idx+1] = -i;
06953 
06954                         bot_idx = (y+offset)*nx+nx-2;
06955                         top_idx = (ny-1-y)*nx+nx-2;
06956                         r1 = d[bot_idx];
06957                         i1 = d[bot_idx+1];
06958                         r2 = d[top_idx];
06959                         i2 = d[top_idx+1];
06960                         r = (r1 + r2)/2.0f;
06961                         i = (i1 + i2)/2.0f;
06962                         d[bot_idx] = r;
06963                         d[top_idx] = r;
06964                         d[bot_idx+1] = i;
06965                         d[top_idx+1] = -i;
06966                 }
06967 
06968                 d[1] = 0; // 0 phase for this componenet
06969                 d[nx-1] = 0; // 0 phase for this component
06970                 d[ny/2*nx+nx-1] = 0;// 0 phase for this component
06971                 d[ny/2*nx+1] = 0;// 0 phase for this component
06972         }
06973 
06974         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06975         image->do_ift_inplace();
06976         image->depad();
06977 }


Member Data Documentation

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

Definition at line 5852 of file processor.h.

Referenced by get_name().


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