ProgCTFPhaseFlipping Class Reference

#include <ctf_phase_flip.h>

Inheritance diagram for ProgCTFPhaseFlipping:

Collaboration diagram for ProgCTFPhaseFlipping:

Public Member Functions
void	defineParams ()
void	readParams ()
void	run ()
void	show ()
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Public Attributes
Micrograph	M_in
FileName	fn_in
FileName	fn_out
FileName	fnt_ctf
double	downsampling
double	Tm
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
Protected Attributes inherited from XmippProgram
int	errorCode
ProgramDef *	progDef
	Program definition and arguments parser. More...
std::map< String, CommentList >	defaultComments
int	argc
	Original command line arguments. More...
const char **	argv

Detailed Description

Definition at line 38 of file ctf_phase_flip.h.

Member Function Documentation

defineParams()

void ProgCTFPhaseFlipping::defineParams ( )

virtual

Define parameters

Reimplemented from XmippProgram.

Definition at line 29 of file ctf_phase_flip.cpp.

{
    addUsageLine("Correct the phase of micrographs");
    addUsageLine("+This program flips the phase of those frequencies that were already ");
    addUsageLine("+flipped by the CTF. Flipping the phase at the level of the micrograph is recommended.");
    addParamsLine(" -i <file>               : Input micrograph");
    addParamsLine(" -o <file>               : Output micrograph");
    addParamsLine(" --ctf <ctfparam_file>   : CTF description");
    addParamsLine(" [--sampling <T=-1>]     : Sampling rate of the input micrograph.");
    addParamsLine("                         : If not given, then it is assumed to be the sampling rate in the ctfparam times the downsampling.");
    addParamsLine(" [--downsampling <D=1>]  : Downsampling factor of the input micrograph with respect to the original");
    addParamsLine("                         : micrograph.");
}

readParams()

void ProgCTFPhaseFlipping::readParams ( )

virtual

Read parameters

Reimplemented from XmippProgram.

Definition at line 43 of file ctf_phase_flip.cpp.

{
    fn_in        = getParam("-i");
    fn_out       = getParam("-o");
    fnt_ctf      = getParam("--ctf");
    downsampling = getDoubleParam("--downsampling");
    Tm           = getDoubleParam("--sampling");
}

run()

void ProgCTFPhaseFlipping::run ( )

virtual

Do_all.

Reimplemented from XmippProgram.

Definition at line 65 of file ctf_phase_flip.cpp.

{
    show();

    // Read the micrograph in an array of doubles
    Image<double> M_in;
    M_in.read(fn_in);

    // Read CTF
    CTFDescription ctf;
    ctf.clear();
    ctf.read(fnt_ctf);
    if (Tm<0)
        ctf.changeSamplingRate(ctf.Tm*downsampling);
    else
        ctf.changeSamplingRate(Tm);
    ctf.produceSideInfo();

    actualPhaseFlip(M_in(),ctf);

    M_in.write(fn_out);
}

show()

void ProgCTFPhaseFlipping::show

(

)

Show parameters.

Definition at line 52 of file ctf_phase_flip.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "input_micrograph:      " << fn_in        << std::endl
    << "output_micrograph:     " << fn_out       << std::endl
    << "ctf_param_file:        " << fnt_ctf      << std::endl
    << "sampling:              " << Tm           << std::endl
    << "downsampling:          " << downsampling << std::endl
    ;
}

Member Data Documentation

downsampling

double ProgCTFPhaseFlipping::downsampling

Downsampling factor

Definition at line 50 of file ctf_phase_flip.h.

fn_in

FileName ProgCTFPhaseFlipping::fn_in

Input micrograph file name

Definition at line 44 of file ctf_phase_flip.h.

fn_out

FileName ProgCTFPhaseFlipping::fn_out

Out flipped micrograph

Definition at line 46 of file ctf_phase_flip.h.

fnt_ctf

FileName ProgCTFPhaseFlipping::fnt_ctf

CTF param file name

Definition at line 48 of file ctf_phase_flip.h.

M_in

Micrograph ProgCTFPhaseFlipping::M_in

Input micrograph

Definition at line 42 of file ctf_phase_flip.h.

Tm

double ProgCTFPhaseFlipping::Tm

Sampling rate of the input micrograph

Definition at line 52 of file ctf_phase_flip.h.

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

• xmipp/libraries/reconstruction/ctf_phase_flip.h
• xmipp/libraries/reconstruction/ctf_phase_flip.cpp