EMAN::BinarizeFourierProcessor Class Reference
[a function or class that is CUDA enabled]

A thresholding processor for Fourier images based on the amplitude component. More...

#include <processor.h>

Inheritance diagram for EMAN::BinarizeFourierProcessor:

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Collaboration diagram for EMAN::BinarizeFourierProcessor:

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List of all members.

Public Member Functions

virtual string get_name () const
 Get the processor's name.
virtual void process_inplace (EMData *image)
 
Exceptions:
ImageFormatException if the input image is not complex
InvalidParameterException if the threshold is less than 0 Note result is always in real-imaginary format Note input can be real-imaginary or amplitude-phase

virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
virtual string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "threshold.binary.fourier"

Detailed Description

A thresholding processor for Fourier images based on the amplitude component.

Useful in tomography when you want to count large complex pixels. Not the fastest approach, if you were going for efficiency it would probably be better just to iterate through the pixels and count. But if you do it this way you can just get the mean of the resulting image (and multiplying by 2). So it's basically easier, but lazy. Originally added for use by e2tomohunter.py

Author:
David Woolford
Date:
April 29th 2009
Parameters:
value The Fourier amplitude threshold cutoff

Definition at line 1905 of file processor.h.


Member Function Documentation

virtual string EMAN::BinarizeFourierProcessor::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 1932 of file processor.h.

01933                         {
01934                                 return "f(k) = 0 + 0i if ||f(k)|| < value; f(k) = 1 + 0i if ||f(k)|| >= value.";
01935                         }

virtual string EMAN::BinarizeFourierProcessor::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 1908 of file processor.h.

References NAME.

01909                         {
01910                                 return NAME;
01911                         }

virtual TypeDict EMAN::BinarizeFourierProcessor::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 1925 of file processor.h.

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

01926                         {
01927                                 TypeDict d;
01928                                 d.put("value", EMObject::FLOAT, "The Fourier amplitude threshold cutoff" );
01929                                 return d;
01930                         }

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

Definition at line 1912 of file processor.h.

01913                         {
01914                                 return new BinarizeFourierProcessor();
01915                         }

void BinarizeFourierProcessor::process_inplace ( EMData image  )  [virtual]

Exceptions:
ImageFormatException if the input image is not complex
InvalidParameterException if the threshold is less than 0 Note result is always in real-imaginary format Note input can be real-imaginary or amplitude-phase

Implements EMAN::Processor.

Definition at line 3909 of file processor.cpp.

References binarize_fourier_amp_processor(), ENTERFUNC, EXITFUNC, EMAN::EMData::get_data(), EMAN::EMData::get_size(), ImageFormatException, InvalidParameterException, EMAN::EMData::is_complex(), EMAN::Processor::params, EMAN::EMData::ri2ap(), EMAN::Dict::set_default(), EMAN::EMData::set_ri(), EMAN::EMData::update(), and v.

03909                                                             {
03910         ENTERFUNC;
03911         if (!image->is_complex()) throw ImageFormatException("Fourier binary thresholding processor only works for complex images");
03912 
03913         float threshold = params.set_default("value",-1.0f);
03914         if (threshold < 0) throw InvalidParameterException("For fourier amplitude-based thresholding, the threshold must be greater than or equal to 0.");
03915 
03916         image->ri2ap(); //  works for cuda
03917 
03918 #ifdef EMAN2_USING_CUDA
03919         if (image->gpu_operation_preferred()) {
03920                 EMDataForCuda tmp = image->get_data_struct_for_cuda();
03921                 binarize_fourier_amp_processor(&tmp,threshold);
03922                 image->set_ri(true); // So it can be used for fourier multiplaction, for example
03923                 image->gpu_update();
03924                 EXITFUNC;
03925                 return;
03926         }
03927 #endif
03928 
03929         float* d = image->get_data();
03930         for( size_t i = 0; i < image->get_size()/2; ++i, d+=2) {
03931                 float v = *d;
03932                 if ( v >= threshold ) {
03933                         *d = 1;
03934                         *(d+1) = 0;
03935                 } else {
03936                         *d = 0;
03937                         *(d+1) = 0;
03938                 }
03939         }
03940 
03941         // No need to run ap2ri, because 1+0i is the same in either notation
03942         image->set_ri(true); // So it can be used for fourier multiplaction, for example
03943         image->update();
03944         EXITFUNC;
03945 }


Member Data Documentation

const string BinarizeFourierProcessor::NAME = "threshold.binary.fourier" [static]

Definition at line 1937 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:43:14 2010 for EMAN2 by  doxygen 1.4.7