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 Processor *	NEW ()
Static Public Attributes
static const string	NAME = "threshold.binary.fourier"

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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 1805 of file processor.h.

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Member Function Documentation

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 1808 of file processor.h.

References NAME.

                        {
                                return NAME;
                        }

static Processor* EMAN::BinarizeFourierProcessor::NEW

(

)

[inline, static]

Definition at line 1812 of file processor.h.

                        {
                                return new BinarizeFourierProcessor();
                        }

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 3708 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.

                                                            {
        ENTERFUNC;
        if (!image->is_complex()) throw ImageFormatException("Fourier binary thresholding processor only works for complex images");

        float threshold = params.set_default("value",-1.0f);
        if (threshold < 0) throw InvalidParameterException("For fourier amplitude-based thresholding, the threshold must be greater than or equal to 0.");

        image->ri2ap(); //  works for cuda

#ifdef EMAN2_USING_CUDA
        if (image->gpu_operation_preferred()) {
                EMDataForCuda tmp = image->get_data_struct_for_cuda();
                binarize_fourier_amp_processor(&tmp,threshold);
                image->set_ri(true); // So it can be used for fourier multiplaction, for example
                image->gpu_update();
                EXITFUNC;
                return;
        }
#endif

        float* d = image->get_data();
        for( size_t i = 0; i < image->get_size()/2; ++i, d+=2) {
                float v = *d;
                if ( v >= threshold ) {
                        *d = 1;
                        *(d+1) = 0;
                } else {
                        *d = 0;
                        *(d+1) = 0;
                }
        }

        // No need to run ap2ri, because 1+0i is the same in either notation
        image->set_ri(true); // So it can be used for fourier multiplaction, for example
        image->update();
        EXITFUNC;
}

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 1825 of file processor.h.

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

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

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 1832 of file processor.h.

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

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Member Data Documentation

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

Definition at line 1837 of file processor.h.

Referenced by get_name().

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

• processor.h
• processor.cpp