#include <volume_correct_bfactor.h>

Inheritance diagram for ProgVolumeCorrectBfactor:

Collaboration diagram for ProgVolumeCorrectBfactor:

Public Member Functions
	ProgVolumeCorrectBfactor ()

	~ProgVolumeCorrectBfactor ()

void	make_guinier_plot (MultidimArray< std::complex< double > > &m1, std::vector< fit_point2D > &guinier)

void	apply_bfactor (MultidimArray< std::complex< double > > &FT1, double bfactor)

void	apply_allpoints (MultidimArray< std::complex< double > > &FT1, std::vector< fit_point2D > &guinier_diff)

void	get_snr_weights (std::vector< double > &snr)

void	apply_snr_weights (MultidimArray< std::complex< double > > &FT1, std::vector< double > &snr)

void	write_guinierfile (const FileName &fn_guinier, std::vector< fit_point2D > &guinierin, std::vector< fit_point2D > &guinierweighted, std::vector< fit_point2D > &guiniernew, double intercept, std::vector< fit_point2D > &guinierref)

void	bfactor_correction (MultidimArray< double > &m1, const FileName &fn_guinier)

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 ()

Protected Types
enum	MODES { MODES::BFACTOR_AUTO = 1, MODES::BFACTOR_REF = 2, MODES::BFACTOR_ADHOC = 3, MODES::ALLPOINTS_REF = 4 }

Protected Member Functions
void	show ()

void	defineParams ()

void	readParams ()

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

Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

virtual void	preProcess ()

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
double	fit_minres

double	fit_maxres

double	apply_maxres

double	sampling_rate

MODES	bMode

int	xsize

FileName	fn_ref

double	adhocB

FileName	fn_fsc

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

Additional Inherited Members
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

Detailed Description

correct_bfactor parameters.

Definition at line 37 of file volume_correct_bfactor.h.

Member Enumeration Documentation

◆ MODES

enum ProgVolumeCorrectBfactor::MODES

strongprotected

Mode for B-factor correction Three modes are provided:

automated fit according to Rosenthal and Henderson (2003)
fit according to a reference map
ad-hoc correction with a user-defined B-factor

Enumerator
BFACTOR_AUTO
BFACTOR_REF
BFACTOR_ADHOC
ALLPOINTS_REF

Definition at line 53 of file volume_correct_bfactor.h.

                      {
         BFACTOR_AUTO = 1,
         BFACTOR_REF = 2,
         BFACTOR_ADHOC = 3,
         ALLPOINTS_REF = 4
     };

Constructor & Destructor Documentation

◆ ProgVolumeCorrectBfactor()

ProgVolumeCorrectBfactor::ProgVolumeCorrectBfactor ( )

Constructor

Definition at line 133 of file volume_correct_bfactor.cpp.

 {
     fit_minres    = -1.;
     fit_maxres    = -1.;
     apply_maxres  = -1.;
     sampling_rate = 1.;
     bMode          = MODES::BFACTOR_AUTO;
     xsize         = -1;
     fn_ref        = "";
     fn_fsc        = "";
     adhocB        = 0.;
 }

◆ ~ProgVolumeCorrectBfactor()

ProgVolumeCorrectBfactor::~ProgVolumeCorrectBfactor ( )

inline

Destructor

Definition at line 87 of file volume_correct_bfactor.h.

88 { }

Member Function Documentation

◆ bfactor_correction()

void ProgVolumeCorrectBfactor::bfactor_correction	(	MultidimArray< double > &	m1,
		const FileName &	fn_guinier
	)

B-factor correction (sharpening)

Definition at line 347 of file volume_correct_bfactor.cpp.

 {
     MultidimArray< std::complex< double > > FT1, FT2;
     FourierTransformer transformer;
     double slope;
     double intercept = 0.;
     std::vector<fit_point2D>  guinierin, guinierweighted, guinierref, guinierdiff;
     std::vector<double> snr;
 
     // Transform
     xsize=XSIZE(m1);
     transformer.FourierTransform(m1, FT1, true);
     make_guinier_plot(FT1,guinierin);
 
     // Get SNR weights and apply to guinier1
     if (fn_fsc != "")
     {
         get_snr_weights(snr);
         apply_snr_weights(FT1,snr);
         make_guinier_plot(FT1,guinierweighted);
     }
     else
         guinierweighted=guinierin;
 
     if (bMode == MODES::BFACTOR_AUTO)
     {
         least_squares_line_fit(guinierweighted, slope, intercept);
         std::cerr<<" Fitted slope= "<<slope<<" intercept= "<<intercept<<std::endl;
         adhocB = 4. * slope;
     }
     else if (bMode == MODES::BFACTOR_REF || bMode == MODES::ALLPOINTS_REF)
     {
         Image<double> ref;
         ref.read(fn_ref);
         ref().setXmippOrigin();
         transformer.FourierTransform(ref(), FT2, true);
         make_guinier_plot(FT2,guinierref);
         guinierdiff = guinierweighted;
         for (size_t i = 0; i < guinierdiff.size(); i++)
         {
             (guinierdiff[i]).y -= (guinierref[i]).y;
         }
         if (bMode == MODES::BFACTOR_REF)
         {
             least_squares_line_fit(guinierdiff, slope, intercept);
             std::cerr<<" Fitted slope= "<<slope<<" intercept= "<<intercept<<std::endl;
             adhocB = 4. * slope;
         }
     }
 
     if (bMode == MODES::ALLPOINTS_REF)
     {
         // Now apply the allpoints correction
         std::cerr<<"Adjust power spectrum to that of reference "<<std::endl;
         apply_allpoints(FT1,guinierdiff);
     }
     else
     {
         // Now apply the B-factor
         std::cerr<<"Applying B-factor of "<< adhocB << " squared Angstroms"<<std::endl;
         apply_bfactor(FT1,adhocB);
     }
     // Now backtransform
     transformer.inverseFourierTransform(FT1,m1);
 
     // Write Guinier-plot
     std::vector<fit_point2D>  guiniernew;
     make_guinier_plot(FT1,guiniernew);
     write_guinierfile(fn_guinier, guinierin, guinierweighted, guiniernew, intercept, guinierref);
 }

◆ defineParams()

void ProgVolumeCorrectBfactor::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 31 of file volume_correct_bfactor.cpp.

 {
     addUsageLine("Sharpen a volume by applying a negative B-factor");
     addUsageLine("+The high-resolution features are enhanced, thereby correcting ");
     addUsageLine("+the envelope functions of the microscope, detector etc. Three ");
     addUsageLine("+modes are available:");
     addUsageLine("+");
     addUsageLine("+1. An automated mode based on methodology developed by [[http://www.ncbi.nlm.nih.gov/pubmed/14568533][Rosenthal and Henderson]]");
     addUsageLine("+");
     addUsageLine("+2. Based on the fall-off in a reference map (possibly obtained using xmipp_volume_from_pdb)");
     addUsageLine("+");
     addUsageLine("+3. An user-provided (ad hoc) B-factor");
     addSeeAlsoLine("volume_from_pdb, resolution_fsc");
     XmippMetadataProgram::defineParams();
     addParamsLine(" --auto                              : Use automated B-factor fit in flat Wilson region");
     addParamsLine("                                     : Note: do not use the automated mode for maps with resolutions");
     addParamsLine("                                     : lower than 12-15 Angstroms!");
     addParamsLine(" or --ref <fn_ref> <mode=bfactorref> : Fit B-factor according to the reference ");
     addParamsLine("         where <mode>");
     addParamsLine("                  bfactorref         : Fit B-factor");
     addParamsLine("                  allpoints          : Adjust power spectrum to reference");
     addParamsLine(" or --adhoc <B>              : Use a user-provided (negative) B-factor");
     addParamsLine("== Specific parameters == ");
     addParamsLine("  --sampling <float>         : Pixel size of the input volume (in Angstroms/pixel) ");
     addParamsLine("  --maxres <float>           : High-resolution limit for B-factor correction (in Ang.) ");
     addParamsLine("  -o <filename>              : Output file Name with corrected volume ");
     addParamsLine(" [--fit_minres+ <f=15>]      : Low-resolution  limit (in Ang.) for fit in --auto or --ref ");
     addParamsLine(" [--fit_maxres+ <f=-1>]      : High-resolution limit (in Ang.) for fit in --auto or --ref,");
     addParamsLine("                             : -1 means maximum resolution ");
     addParamsLine(" [--fsc+ <fscFile=\"\">]     : FSC file produced by xmipp_resolution_fsc");
     addExampleLine("xmipp_correct_bfactor -i volume.vol -o correctedVolume.vol --auto --sampling 1.4 --maxres 10");
     addExampleLine("To plot the Guinier file you may use:",false);
     addExampleLine("gnuplot");
     addExampleLine("set xlabel \"d^(-2)\"");
     addExampleLine("plot \"correctedVolume.vol.guinier\" using 1:2 title \"log F\" with line, \"correctedVolume.vol.guinier\" using 1:4 title \"Corrected log F\"with line");
 }

◆ processImage()

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

protectedvirtual

Implements XmippMetadataProgram.

Definition at line 123 of file volume_correct_bfactor.cpp.

 {
     Image<double> vol;
     vol.read(fnImg);
     vol().checkDimensionWithDebug(3,__FILE__,__LINE__);
     FileName fn_guinier = fn_out + ".guinier";
     bfactor_correction(vol(), fn_guinier);
     vol.write(fn_out);
 }

◆ readParams()

void ProgVolumeCorrectBfactor::readParams ( )

protectedvirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippMetadataProgram.

Definition at line 68 of file volume_correct_bfactor.cpp.

 {
     produces_an_output = true;
 
     XmippMetadataProgram::readParams();
     if (checkParam("--ref"))
     {
         fn_ref= getParam("--ref");
         String strMode=getParam("--ref",1);
         bMode = strMode=="allpoints" ? MODES::ALLPOINTS_REF : MODES::BFACTOR_REF;
     }
     else if (checkParam("--adhoc"))
     {
         bMode = MODES::BFACTOR_ADHOC;
         adhocB = getDoubleParam("--adhoc");
     }
     else if (checkParam("--auto"))
         bMode = MODES::BFACTOR_AUTO;
     else
         REPORT_ERROR(ERR_DEBUG_IMPOSIBLE, "This should not happens, review program definition");
     sampling_rate = getDoubleParam("--sampling");
     apply_maxres = getDoubleParam("--maxres");
     fit_minres = getDoubleParam("--fit_minres");
     fit_maxres = getDoubleParam("--fit_maxres");
     fn_fsc = getParam("--fsc");
 
     if (fit_maxres < 0.)
         fit_maxres = apply_maxres;
 }

◆ show()

void ProgVolumeCorrectBfactor::show ( )

protected

Functions from XmippMetadataProgram

Definition at line 98 of file volume_correct_bfactor.cpp.

 {
     XmippMetadataProgram::show();
     std::cout << "Pixel size : " << sampling_rate << " Angstrom" << std::endl;
     std::cout << "Maximum resolution: " << apply_maxres << " Angstrom" << std::endl;
     if (bMode == MODES::BFACTOR_REF || bMode == MODES::BFACTOR_AUTO)
     {
         std::cerr<<"Fit within resolutions: " << fit_minres << " - " << fit_maxres << " Angstrom" << std::endl;
     }
     if (bMode == MODES::BFACTOR_REF)
     {
         std::cout << "Adjust B-factor according to reference "<<fn_ref<<std::endl;
     }
     else if (bMode == MODES::BFACTOR_ADHOC)
     {
         std::cout << "Apply ad-hoc B-factor of "<< adhocB <<" squared Angstroms" << std::endl;
     }
     else
     {
         std::cout << "Use automated B-factor fit (Rosenthal and Henderson, 2003) " << std::endl;
     }
     if (fn_fsc != "")
         std::cout << "Use signal-to-noise weight based on "<< fn_fsc <<std::endl;
 }

Member Data Documentation

◆ adhocB

double ProgVolumeCorrectBfactor::adhocB

protected

Ad hoc B-factor (for mode BFACTOR_ADHOC)

Definition at line 69 of file volume_correct_bfactor.h.

◆ apply_maxres

double ProgVolumeCorrectBfactor::apply_maxres

protected

Definition at line 42 of file volume_correct_bfactor.h.

◆ bMode

MODES ProgVolumeCorrectBfactor::bMode

protected

Definition at line 60 of file volume_correct_bfactor.h.

◆ fit_maxres

double ProgVolumeCorrectBfactor::fit_maxres

protected

Definition at line 42 of file volume_correct_bfactor.h.

◆ fit_minres

double ProgVolumeCorrectBfactor::fit_minres

protected

Low and high resolution limits for automated fit

Definition at line 42 of file volume_correct_bfactor.h.

◆ fn_fsc

FileName ProgVolumeCorrectBfactor::fn_fsc

protected

Filename for FSC curve

Definition at line 72 of file volume_correct_bfactor.h.

◆ fn_ref

FileName ProgVolumeCorrectBfactor::fn_ref

protected

Reference map file name (for mode BFACTOR_REF)

Definition at line 66 of file volume_correct_bfactor.h.

◆ sampling_rate

double ProgVolumeCorrectBfactor::sampling_rate

protected

Pixels size in Angstrom

Definition at line 44 of file volume_correct_bfactor.h.

◆ xsize

int ProgVolumeCorrectBfactor::xsize

protected

X-size of the original volume or image

Definition at line 63 of file volume_correct_bfactor.h.

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

xmipp/libraries/reconstruction/volume_correct_bfactor.h
xmipp/libraries/reconstruction/volume_correct_bfactor.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ MODES

Constructor & Destructor Documentation

◆ ProgVolumeCorrectBfactor()

◆ ~ProgVolumeCorrectBfactor()

Member Function Documentation

◆ bfactor_correction()

◆ defineParams()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ adhocB

◆ apply_maxres

◆ bMode

◆ fit_maxres

◆ fit_minres

◆ fn_fsc

◆ fn_ref

◆ sampling_rate

◆ xsize