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 5894 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 5904 of file processor.h.

05905                 {
05906                         return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
05907                 }

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 5899 of file processor.h.

References NAME.

05900                 {
05901                         return NAME;
05902                 }

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 5914 of file processor.h.

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

05915                 {
05916                         TypeDict d;
05917                         d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05918                         return d;
05919                 }

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

Definition at line 5909 of file processor.h.

05910                 {
05911                         return new TestImageFourierNoiseProfile();
05912                 }

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 6985 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.

06985                                                                  {
06986 
06987         if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
06988 
06989         if (!image->is_complex()) {
06990                 int nx = image->get_xsize();
06991                 int offset = 2 - nx%2;
06992 
06993                 image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
06994                 image->set_complex(true);
06995                 if (1 == offset) image->set_fftodd(true);
06996                 else image->set_fftodd(false);
06997                 image->set_fftpad(true);
06998         }
06999         image->to_zero();
07000         image->ri2ap();
07001 
07002         vector<float> profile = params["profile"];
07003         transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
07004 
07005         int i = static_cast<int>(profile.size());
07006 
07007         float * d = image->get_data();
07008         int nx = image->get_xsize();
07009         int ny = image->get_ysize();
07010         int nxy = image->get_ysize()*nx;
07011         int nzon2 = image->get_zsize()/2;
07012         int nyon2 = image->get_ysize()/2;
07013         float rx, ry, rz, amp, phase;
07014         int length;
07015         int twox;
07016         for (int z = 0; z< image->get_zsize(); ++z) {
07017                 for (int y = 0; y < image->get_ysize(); ++y) {
07018                         for (int x = 0; x < image->get_xsize()/2; ++x) {
07019                                 rx = (float)x;
07020                                 ry = (float)nyon2 - (float)y;
07021                                 rz = (float)nzon2 - (float)z;
07022                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
07023 
07024                                 twox = 2*x;
07025                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
07026                                 size_t idx2 = idx1 + 1;
07027 
07028 
07029                                 if (length >= i) {
07030                                         d[idx1] = 0;
07031                                         d[idx2] = 0;
07032                                         continue;
07033                                 }
07034                                 amp = profile[length];
07035                                 phase = Util::get_frand(0,1)*2*M_PI;
07036 
07037 
07038                                 d[idx1] = amp;
07039                                 d[idx2] = phase;
07040 
07041                         }
07042                 }
07043         }
07044 
07045         image->ap2ri();
07046         if (image->get_ndim() == 2) {
07047                 bool yodd = image->get_ysize() % 2 == 1;
07048 
07049                 int yit = image->get_ysize()/2-1;
07050                 int offset = 1;
07051                 if (yodd) {
07052                         offset = 0;
07053                 }
07054                 for (int y = 0; y < yit; ++y) {
07055                         int bot_idx = (y+offset)*nx;
07056                         int top_idx = (ny-1-y)*nx;
07057                         float r1 = d[bot_idx];
07058                         float i1 = d[bot_idx+1];
07059                         float r2 = d[top_idx];
07060                         float i2 = d[top_idx+1];
07061                         float r = (r1 + r2)/2.0f;
07062                         float i = (i1 + i2)/2.0f;
07063                         d[bot_idx] = r;
07064                         d[top_idx] = r;
07065                         d[bot_idx+1] = i;
07066                         d[top_idx+1] = -i;
07067 
07068                         bot_idx = (y+offset)*nx+nx-2;
07069                         top_idx = (ny-1-y)*nx+nx-2;
07070                         r1 = d[bot_idx];
07071                         i1 = d[bot_idx+1];
07072                         r2 = d[top_idx];
07073                         i2 = d[top_idx+1];
07074                         r = (r1 + r2)/2.0f;
07075                         i = (i1 + i2)/2.0f;
07076                         d[bot_idx] = r;
07077                         d[top_idx] = r;
07078                         d[bot_idx+1] = i;
07079                         d[top_idx+1] = -i;
07080                 }
07081 
07082                 d[1] = 0; // 0 phase for this componenet
07083                 d[nx-1] = 0; // 0 phase for this component
07084                 d[ny/2*nx+nx-1] = 0;// 0 phase for this component
07085                 d[ny/2*nx+1] = 0;// 0 phase for this component
07086         }
07087 
07088         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
07089         image->do_ift_inplace();
07090         image->depad();
07091 }


Member Data Documentation

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

Definition at line 5921 of file processor.h.

Referenced by get_name().


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