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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 5980 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 5990 of file processor.h.

05991                 {
05992                         return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
05993                 }

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 5985 of file processor.h.

05986                 {
05987                         return NAME;
05988                 }

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 6000 of file processor.h.

References EMAN::TypeDict::put().

06001                 {
06002                         TypeDict d;
06003                         d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
06004                         return d;
06005                 }

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

Definition at line 5995 of file processor.h.

05996                 {
05997                         return new TestImageFourierNoiseProfile();
05998                 }

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 7137 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.

07137                                                                  {
07138 
07139         if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
07140 
07141         if (!image->is_complex()) {
07142                 int nx = image->get_xsize();
07143                 int offset = 2 - nx%2;
07144 
07145                 image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
07146                 image->set_complex(true);
07147                 if (1 == offset) image->set_fftodd(true);
07148                 else image->set_fftodd(false);
07149                 image->set_fftpad(true);
07150         }
07151         image->to_zero();
07152         image->ri2ap();
07153 
07154         vector<float> profile = params["profile"];
07155         transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
07156 
07157         int i = static_cast<int>(profile.size());
07158 
07159         float * d = image->get_data();
07160         int nx = image->get_xsize();
07161         int ny = image->get_ysize();
07162         int nxy = image->get_ysize()*nx;
07163         int nzon2 = image->get_zsize()/2;
07164         int nyon2 = image->get_ysize()/2;
07165         float rx, ry, rz, amp, phase;
07166         int length;
07167         int twox;
07168         for (int z = 0; z< image->get_zsize(); ++z) {
07169                 for (int y = 0; y < image->get_ysize(); ++y) {
07170                         for (int x = 0; x < image->get_xsize()/2; ++x) {
07171                                 rx = (float)x;
07172                                 ry = (float)nyon2 - (float)y;
07173                                 rz = (float)nzon2 - (float)z;
07174                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
07175 
07176                                 twox = 2*x;
07177                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
07178                                 size_t idx2 = idx1 + 1;
07179 
07180 
07181                                 if (length >= i) {
07182                                         d[idx1] = 0;
07183                                         d[idx2] = 0;
07184                                         continue;
07185                                 }
07186                                 amp = profile[length];
07187                                 phase = Util::get_frand(0,1)*2*M_PI;
07188 
07189 
07190                                 d[idx1] = amp;
07191                                 d[idx2] = phase;
07192 
07193                         }
07194                 }
07195         }
07196 
07197         image->ap2ri();
07198         if (image->get_ndim() == 2) {
07199                 bool yodd = image->get_ysize() % 2 == 1;
07200 
07201                 int yit = image->get_ysize()/2-1;
07202                 int offset = 1;
07203                 if (yodd) {
07204                         offset = 0;
07205                 }
07206                 for (int y = 0; y < yit; ++y) {
07207                         int bot_idx = (y+offset)*nx;
07208                         int top_idx = (ny-1-y)*nx;
07209                         float r1 = d[bot_idx];
07210                         float i1 = d[bot_idx+1];
07211                         float r2 = d[top_idx];
07212                         float i2 = d[top_idx+1];
07213                         float r = (r1 + r2)/2.0f;
07214                         float i = (i1 + i2)/2.0f;
07215                         d[bot_idx] = r;
07216                         d[top_idx] = r;
07217                         d[bot_idx+1] = i;
07218                         d[top_idx+1] = -i;
07219 
07220                         bot_idx = (y+offset)*nx+nx-2;
07221                         top_idx = (ny-1-y)*nx+nx-2;
07222                         r1 = d[bot_idx];
07223                         i1 = d[bot_idx+1];
07224                         r2 = d[top_idx];
07225                         i2 = d[top_idx+1];
07226                         r = (r1 + r2)/2.0f;
07227                         i = (i1 + i2)/2.0f;
07228                         d[bot_idx] = r;
07229                         d[top_idx] = r;
07230                         d[bot_idx+1] = i;
07231                         d[top_idx+1] = -i;
07232                 }
07233 
07234                 d[1] = 0; // 0 phase for this componenet
07235                 d[nx-1] = 0; // 0 phase for this component
07236                 d[ny/2*nx+nx-1] = 0;// 0 phase for this component
07237                 d[ny/2*nx+1] = 0;// 0 phase for this component
07238         }
07239 
07240         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
07241         image->do_ift_inplace();
07242         image->depad();
07243 }


Member Data Documentation

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

Definition at line 193 of file processor.cpp.


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