#include <ctf_correct_idr.h>

Inheritance diagram for ProgCtfCorrectIdr:

Collaboration diagram for ProgCtfCorrectIdr:

Public Member Functions
void	readParams ()
	Read params. More...

void	preProcess ()
	Preprocess. More...

void	show ()
	Show parameters. More...

void	defineParams ()
	Define parameters. More...

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
	Process one image. More...

Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()

MetaDataVec &	getOutputMd ()

	XmippMetadataProgram ()
	Empty constructor. More...

virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)

virtual void	init ()

virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)

virtual	~XmippMetadataProgram ()

void	setMode (WriteModeMetaData _mode)

void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...

virtual void	wait ()
	Wait for the distributor to finish. More...

virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...

virtual void	run ()
	Run over all images. More...

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)

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	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
FileName	fn_vol
	Reference volume. More...

double	mu
	Relaxation factor. More...

FileName	fnRoot
	Output filename root. More...

Image< double >	V

Projection	Ireal

Projection	Itheo

MultidimArray< double >	Inorm

MultidimArray< double >	Itheo_CTF

FourierFilter	ctf

FileName	last_fn_ctf

Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...

FileName	fn_out

FileName	baseName

FileName	pathBaseName

FileName	oextBaseName

bool	apply_geo
	Apply geo. More...

size_t	ndimOut
	Output dimensions. More...

size_t	zdimOut

size_t	ydimOut

size_t	xdimOut

DataType	datatypeOut

size_t	mdInSize
	Number of input elements. More...

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

virtual void	postProcess ()

virtual bool	getImageToProcess (size_t &objId, size_t &objIndex)

void	show () const override

virtual void	startProcessing ()

virtual void	finishProcessing ()

virtual void	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes inherited from XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...

FileName	oext
	Output extension and root. More...

FileName	oroot

MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...

bool	produces_an_output
	Indicate that a unique final output is produced. More...

bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...

bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...

bool	allow_apply_geo

bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...

bool	delete_output_stack
	Delete previous output stack file prior to process images. More...

bool	get_image_info
	Get the input image file dimensions to further operations. More...

bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...

bool	track_origin
	Include the original input image filename in the output stack. More...

bool	keep_input_columns
	Keep input metadata columns. More...

bool	remove_disabled
	Remove disabled images from the input selfile. More...

bool	allow_time_bar
	Show process time bar. More...

bool	input_is_metadata
	Input is a metadata. More...

bool	single_image
	Input is a single image. More...

bool	input_is_stack
	Input is a stack. More...

bool	output_is_stack
	Output is a stack. More...

bool	create_empty_stackfile

bool	delete_mdIn

size_t	time_bar_step
	Some time bar related counters. More...

size_t	time_bar_size

size_t	time_bar_done

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

IDR Parameters.

Definition at line 38 of file ctf_correct_idr.h.

Member Function Documentation

◆ defineParams()

void ProgCtfCorrectIdr::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgCtfCorrectIdr >.

Definition at line 51 of file ctf_correct_idr.cpp.

 {
     each_image_produces_an_output = true;
     addUsageLine("Correct CTF by using IDR");
     addUsageLine("+This utility allows you to make reconstructions removing the effect ");
     addUsageLine("+of the CTF. The projection images are modified according to a current ");
     addUsageLine("+guess of the reconstruction and the CTF definition. The modified images ");
     addUsageLine("+should be used for reconstruction which now serves as a new current guess ");
     addUsageLine("+for a new IDR iteration.");
     addUsageLine("+The method is fully described at http://www.ncbi.nlm.nih.gov/pubmed/15005161");
     addUsageLine("+");
     addUsageLine("+The program will assume that the image phase have already been corrected");
     addUsageLine("+(otherwise the initial solution is too far from the true solution and the ");
     addUsageLine("+algorithm does not converge).");
     addSeeAlsoLine("ctf_phase_flip");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with images and corresponding CTFs (ctfdat)");
     XmippMetadataProgram::defineParams();
     addParamsLine("   --vol <volume>  : Volume with the current reconstruction");
     addParamsLine("  [--mu <s=1.8>]   : Relaxation factor");
     addExampleLine("xmipp_ctf_correct_idr -i images.sel --vol currentGuess.vol -o idrCorrectedImages.stk");
 }

◆ preProcess()

void ProgCtfCorrectIdr::preProcess ( )

virtual

Preprocess.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgCtfCorrectIdr >.

Definition at line 36 of file ctf_correct_idr.cpp.

 {
     V.read(fn_vol);
     V().setXmippOrigin();
 }

◆ processImage()

void ProgCtfCorrectIdr::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

virtual

Process one image.

Implements XmippMetadataProgram.

Definition at line 76 of file ctf_correct_idr.cpp.

 {
     FileName fn_ctf;
     rowIn.getValue(MDL_CTF_MODEL,fn_ctf);
 
     // Read current input image
     Ireal.readApplyGeo(fnImg, rowIn);
     int Ydim = YSIZE(Ireal());
     int Xdim = XSIZE(Ireal());
 
     // Project the volume in the same direction
     projectVolume(V(), Itheo, Ydim, Xdim, Ireal.rot(), Ireal.tilt(), Ireal.psi());
 
     // Copy to theo_CTF and resize
     Itheo_CTF = Itheo();
     Itheo_CTF.setXmippOrigin();
     Itheo_CTF.selfWindow(FIRST_XMIPP_INDEX(2*Ydim), FIRST_XMIPP_INDEX(2*Xdim),
                          LAST_XMIPP_INDEX(2*Ydim), LAST_XMIPP_INDEX(2*Xdim));
 
     // Read CTF file
     if (last_fn_ctf!=fn_ctf)
     {
         ctf.FilterBand = CTF;
         ctf.ctf.read(fn_ctf);
         ctf.ctf.enable_CTFnoise = false;
         ctf.ctf.produceSideInfo();
         ctf.generateMask(Itheo_CTF);
         ctf.correctPhase();
         last_fn_ctf=fn_ctf;
     }
 
     // Apply CTF
     ctf.applyMaskSpace(Itheo_CTF);
     Itheo_CTF.selfWindow(FIRST_XMIPP_INDEX(Ydim), FIRST_XMIPP_INDEX(Xdim),
                          LAST_XMIPP_INDEX(Ydim), LAST_XMIPP_INDEX(Xdim));
 
 #ifdef DEBUG
 
     Itheo.write("PPPtheo.xmp");
     Ireal.write("PPPreal.xmp");
 #endif
 
     // Apply IDR process
     MultidimArray<double> &mItheo=Itheo();
     const MultidimArray<double> &mIreal=Ireal();
     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mItheo)
     DIRECT_MULTIDIM_ELEM(mItheo, n) = mu * DIRECT_MULTIDIM_ELEM(mIreal, n) +
                                       (DIRECT_MULTIDIM_ELEM(mItheo, n) -
                                        mu * DIRECT_MULTIDIM_ELEM(Itheo_CTF, n));
 
     // Save output image
     Itheo.write(fnImgOut);
 
 #ifdef DEBUG
 
     Image<double> save;
     save()=Itheo_CTF;
     save.write("PPPtheo_CTF.xmp");
     save() = Itheo() - mu * Itheo_CTF;
     save.write("PPPdiff.xmp");
     Itheo.write("PPPidr.xmp");
     std::cout << "Press any key to continue\n";
     char c;
     std::cin >> c;
 #endif
 }

◆ readParams()

void ProgCtfCorrectIdr::readParams ( )

virtual

Read params.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgCtfCorrectIdr >.

Definition at line 29 of file ctf_correct_idr.cpp.

 {
     XmippMetadataProgram::readParams();
     fn_vol = getParam("--vol");
     mu = getDoubleParam("--mu");
 }

◆ show()

void ProgCtfCorrectIdr::show ( )

Show parameters.

Definition at line 42 of file ctf_correct_idr.cpp.

 {
     if (!verbose)
         return;
     XmippMetadataProgram::show();
     std::cout << "Input volume: " << fn_vol << std::endl
     << "Relaxation factor: " << mu << std::endl;
 }

Member Data Documentation

◆ ctf

FourierFilter ProgCtfCorrectIdr::ctf

Definition at line 58 of file ctf_correct_idr.h.

◆ fn_vol

FileName ProgCtfCorrectIdr::fn_vol

Reference volume.

Definition at line 42 of file ctf_correct_idr.h.

◆ fnRoot

FileName ProgCtfCorrectIdr::fnRoot

Output filename root.

Definition at line 48 of file ctf_correct_idr.h.

◆ Inorm

MultidimArray<double> ProgCtfCorrectIdr::Inorm

Definition at line 55 of file ctf_correct_idr.h.

◆ Ireal

Projection ProgCtfCorrectIdr::Ireal

Definition at line 54 of file ctf_correct_idr.h.

◆ Itheo

Projection ProgCtfCorrectIdr::Itheo

Definition at line 54 of file ctf_correct_idr.h.

◆ Itheo_CTF

MultidimArray<double> ProgCtfCorrectIdr::Itheo_CTF

Definition at line 55 of file ctf_correct_idr.h.

◆ last_fn_ctf

FileName ProgCtfCorrectIdr::last_fn_ctf

Definition at line 61 of file ctf_correct_idr.h.

◆ mu

double ProgCtfCorrectIdr::mu

Relaxation factor.

Definition at line 45 of file ctf_correct_idr.h.

◆ V

Image<double> ProgCtfCorrectIdr::V

Definition at line 51 of file ctf_correct_idr.h.

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

xmipp/legacy/libraries/reconstruction/ctf_correct_idr.h
xmipp/legacy/libraries/reconstruction/ctf_correct_idr.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ ctf

◆ fn_vol

◆ fnRoot

◆ Inorm

◆ Ireal

◆ Itheo

◆ Itheo_CTF

◆ last_fn_ctf

◆ mu

◆ V