Typical usage of Processors are as follows: More...

#include <processor.h>

Collaboration diagram for EMAN::Processor:

[legend]

Public Types
enum	fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...

Public Member Functions
virtual	~Processor ()

virtual void	process_inplace (EMData *image)=0
	To process an image in-place. More...

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...

virtual string	get_name () const =0
	Get the processor's name. More...

virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...

virtual void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...

virtual string	get_desc () const =0
	Get the descrition of this specific processor. More...

Static Public Member Functions
static string	get_group_desc ()
	Get the description of this group of processors. More...

static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...

static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Protected Attributes
Dict	params

Static Private Member Functions
static EMData *	EMFourierFilterFunc (EMData *fimage, Dict params, bool doInPlace=true)
	Compute a Fourier-filter processed image. More...

Detailed Description

Typical usage of Processors are as follows:

How to get all the processor names
vector<string> all_processors = Factory<Processor>::get_list();

EMAN::Factory::get_list
static vector< string > get_list()
Definition: emobject.h:837
How to use a processor
EMData *img = ...;

img->process_inplace("PROCESSORNAME", Dict("sigma", 12));
How to define a new XYZProcessor
XYZProcessor should either extend the base class 'Processor' or a subclass of 'Processor'. At a minimum, it should define: (Please replace 'XYZ' with your own class name).
string get_name() const { return "processorname"; }

static Processor *NEW() { return XYZProcessor(); }

EMAN::Processor::get_name
virtual string get_name() const =0
Get the processor's name.

If XYZProcessor is a parent class, it should define:
static string get_group_desc();

EMAN::Processor::get_group_desc
static string get_group_desc()
Get the description of this group of processors.
Definition: processor.h:159

Otherwise, it should define:
string get_desc() const;

EMAN::Processor::get_desc
virtual string get_desc() const =0
Get the descrition of this specific processor.

If XYZProcessor need parameters not defined by its parent class, it should define:
Dict get_params() const;

void set_params(const Dict & new_params);

TypeDict get_param_types() const;

EMAN::Processor::set_params
virtual void set_params(const Dict &new_params)
Set the processor parameters using a key/value dictionary.
Definition: processor.h:137

EMAN::Processor::get_params
virtual Dict get_params() const
Get the processor parameters in a key/value dictionary.
Definition: processor.h:129

EMAN::Processor::get_param_types
virtual TypeDict get_param_types() const
Get processor parameter information in a dictionary.
Definition: processor.h:148

Definition at line 89 of file processor.h.

Member Enumeration Documentation

◆ fourier_filter_types

enum EMAN::Processor::fourier_filter_types

Fourier filter Processor type enum.

New Fourier filter processors are computed in a single function, EMFourierFilterFunc, that uses a large switch statement to apply the correct filter processor. This enum specifies the filter processor to be applied.

Enumerator
TOP_HAT_LOW_PASS
TOP_HAT_HIGH_PASS
TOP_HAT_BAND_PASS
TOP_HOMOMORPHIC
GAUSS_LOW_PASS
GAUSS_HIGH_PASS
GAUSS_BAND_PASS
GAUSS_INVERSE
GAUSS_HOMOMORPHIC
BUTTERWORTH_LOW_PASS
BUTTERWORTH_HIGH_PASS
BUTTERWORTH_HOMOMORPHIC
KAISER_I0
KAISER_SINH
KAISER_I0_INVERSE
KAISER_SINH_INVERSE
SHIFT
TANH_LOW_PASS
TANH_HIGH_PASS
TANH_HOMOMORPHIC
TANH_BAND_PASS
RADIAL_TABLE
CTF_

Definition at line 182 of file processor.h.

                                          {
                        TOP_HAT_LOW_PASS,
                        TOP_HAT_HIGH_PASS,
                        TOP_HAT_BAND_PASS,
                        TOP_HOMOMORPHIC,
                        GAUSS_LOW_PASS,
                        GAUSS_HIGH_PASS,
                        GAUSS_BAND_PASS,
                        GAUSS_INVERSE,
                        GAUSS_HOMOMORPHIC,
                        BUTTERWORTH_LOW_PASS,
                        BUTTERWORTH_HIGH_PASS,
                        BUTTERWORTH_HOMOMORPHIC,
                        KAISER_I0,
                        KAISER_SINH,
                        KAISER_I0_INVERSE,
                        KAISER_SINH_INVERSE,
                        SHIFT,
                        TANH_LOW_PASS,
                        TANH_HIGH_PASS,
                        TANH_HOMOMORPHIC,
                        TANH_BAND_PASS,
                        RADIAL_TABLE,
                        CTF_,
                };

Constructor & Destructor Documentation

◆ ~Processor()

virtual EMAN::Processor::~Processor ( )

inlinevirtual

Definition at line 92 of file processor.h.

93 {

94 }

Member Function Documentation

◆ EMFourierFilter()

static EMData * EMAN::Processor::EMFourierFilter	(	EMData *	fimage,
		Dict	params
	)

inlinestatic

Compute a Fourier-processor processed image without altering the original image.

Purpose: Apply selected Fourier space processor to 1-,2-, or 3-D image.

Method:

Parameters

	fimage	Input image object to be processeded, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional.
[in]	params	Processor parameters. Different processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0).

Returns: 1-, 2-, or 3-dimensional filter processed image. If the input image is a real-space image, then the returned output image will also be a real-space image. Similarly, if the input image is already a Fourier image, then the output image will be a Fourier image.

Definition at line 264 of file processor.h.

                                                             {
                        bool doInPlace = false;
                        return EMFourierFilterFunc(fimage, params, doInPlace);
                }

References EMFourierFilterFunc(), and params.

◆ EMFourierFilterFunc()

static EMData * EMAN::Processor::EMFourierFilterFunc	(	EMData *	fimage,
		Dict	params,
		bool	doInPlace = `true`
	)

staticprivate

Compute a Fourier-filter processed image.

This function is called by either of the convience functions EMFourierFilter or EMFourierFilterInPlace.

Purpose: Apply selected Fourier space processor to 1-,2-, or 3-D image.

Method:

Parameters

	fimage	Input image object to be processed, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional. Image fimage will not be changed unless inplace == true.
[in]	params	Processor parameters. Different processor processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0).
[in]	doInPlace	Inplace flag. If this flag is true then fimage will contain the processeded image when this function returns.

Returns: 1-, 2-, or 3-dimensional filter processed image. If the input image is a real-space image, then the returned output image will also be a real-space image. Similarly, if the input image is already a Fourier image, then the output image will be a Fourier image. In either case, if inplace == true then the output image (pointer) will be the same as the input image (pointer).

Referenced by EMFourierFilter(), and EMFourierFilterInPlace().

◆ EMFourierFilterInPlace()

static void EMAN::Processor::EMFourierFilterInPlace	(	EMData *	fimage,
		Dict	params
	)

inlinestatic

Compute a Fourier-filter processed image in place.

Purpose: Apply selected Fourier space processor to 1-,2-, or 3-D image.

Method:

Parameters

	fimage	Input image object to be processed, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional. The original input image is not touched by this routine.
[in]	params	Processor parameters. Different processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0).

Returns: No explicit return. The image fimage is modified in place.

Definition at line 233 of file processor.h.

                                                                    {
                        bool doInPlace = true;
                        EMFourierFilterFunc(fimage, params, doInPlace);
                }

References EMFourierFilterFunc(), and params.

◆ get_desc()

virtual string EMAN::Processor::get_desc ( ) const

pure virtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns: The description of this processor.

◆ get_group_desc()

static string EMAN::Processor::get_group_desc ( )

inlinestatic

Get the description of this group of processors.

This function is defined in a parent class. It gives a introduction to a group of processors.

Returns: The description of this group of processors.

Definition at line 159 of file processor.h.

                {
                        return "EMAN processors are in-place image processors. You may apply a processor to process a single image or process multiple images. Processor class is the base class for all processor. <br> \
The basic design of EMAN Processors: <br>\
    1) Each Processor class defines an image-processinging algorithm. <br>\
    2) All the Processor classes in EMAN are managed by a Factory pattern. So each Processor class must define: <br> a) a unique name to idenfity itself in the factory. <br>b) a static method to register itself in the factory.<br>\
    3) Each Processor class defines its own parameter set.<br>\
    4) Each Processor class defines functions to return its documentation including parameter information, and processor description. These functions enable EMAN to generate processor manuals dynamically.";
                }

◆ get_name()

virtual string EMAN::Processor::get_name ( ) const

pure virtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Referenced by EMAN::group_processors().

◆ get_param_types()

virtual TypeDict EMAN::Processor::get_param_types ( ) const

inlinevirtual

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.

Definition at line 148 of file processor.h.

                {
                        return TypeDict();
                }

◆ get_params()

virtual Dict EMAN::Processor::get_params ( ) const

inlinevirtual

Get the processor parameters in a key/value dictionary.

Returns: A key/value pair dictionary containing the parameters.

Definition at line 129 of file processor.h.

                {
                        return params;
                }

References params.

◆ process()

EMData * Processor::process ( const EMData *const image )

virtual

To proccess an image out-of-place.

For those processors which can only be processed out-of-place, override this function to give the right behavior.

Parameters

image The image will be copied, actual process happen on copy of image.

Returns: the image processing result, may or may not be the same size of the input image

Definition at line 637 of file processor.cpp.

{
        EMData * result = image->copy();
//      printf("Default copy called\n");
        process_inplace(result);
        return result;
}

References process_inplace().

◆ process_inplace()

virtual void EMAN::Processor::process_inplace ( EMData * image )

pure 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.

Referenced by process(), and process_list_inplace().

◆ process_list_inplace()

virtual void EMAN::Processor::process_list_inplace ( vector< EMData * > & images )

inlinevirtual

To process multiple images using the same algorithm.

Parameters

images Multiple images to be processed.

Definition at line 114 of file processor.h.

                {
                        for (size_t i = 0; i < images.size(); i++) {
                                process_inplace(images[i]);
                        }
                }

References images, and process_inplace().

◆ set_params()

virtual void EMAN::Processor::set_params ( const Dict & new_params )

inlinevirtual

Set the processor parameters using a key/value dictionary.

Parameters

new_params A dictionary containing the new parameters.

Reimplemented in EMAN::SNREvalProcessor, EMAN::Axis0FourierProcessor, EMAN::GaussZFourierProcessor, EMAN::AmpweightFourierProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::Wiener2DFourierProcessor, EMAN::LinearRampProcessor, EMAN::LoGFourierProcessor, EMAN::DoGFourierProcessor, EMAN::RealPixelProcessor, EMAN::FixSignProcessor, EMAN::RecipCarefullyProcessor, EMAN::ValuePowProcessor, EMAN::DiscritizeProcessor, EMAN::RangeZeroProcessor, EMAN::CollapseProcessor, EMAN::LinearXformProcessor, EMAN::ExpProcessor, EMAN::FiniteProcessor, EMAN::RangeThresholdProcessor, EMAN::SigmaProcessor, EMAN::CircularMaskProcessor, EMAN::MaskSharpProcessor, EMAN::MaskSoftProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskGaussProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::AreaProcessor, EMAN::PeakOnlyProcessor, EMAN::PaintProcessor, EMAN::RadialProcessor, EMAN::MorphologicalProcessor, and EMAN::PolyMaskProcessor.

Definition at line 137 of file processor.h.

                {
                        params = new_params;
                }

References params.

Member Data Documentation

◆ params

Dict EMAN::Processor::params

mutableprotected

Definition at line 309 of file processor.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Static Private Member Functions

Detailed Description

Member Enumeration Documentation

◆ fourier_filter_types

Constructor & Destructor Documentation

◆ ~Processor()

Member Function Documentation

◆ EMFourierFilter()

◆ EMFourierFilterFunc()

◆ EMFourierFilterInPlace()

◆ get_desc()

◆ get_group_desc()

◆ get_name()

◆ get_param_types()

◆ get_params()

◆ process()

◆ process_inplace()

◆ process_list_inplace()

◆ set_params()

Member Data Documentation

◆ params