#include <ctf_enhance_psd.h>

Inheritance diagram for ProgCTFEnhancePSD:

Collaboration diagram for ProgCTFEnhancePSD:

Public Member Functions
void	readParams ()

void	defineParams ()

void	show ()

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

void	applyFilter (MultidimArray< double > &PSD)

void	applySPHT (MultidimArray< double > &PSD)

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
String	method
	Method. More...

double	filter_w1
	Bandpass filter low frequency (in Fourier space, max 0.5) More...

double	filter_w2
	Bandpass filter high frequency (in Fourier space, max 0.5) More...

double	decay_width
	Decay width (raised cosine) More...

int	N0
	Minimum number of fringes. More...

int	NF
	Maximum number of fringes. More...

double	mask_w1
	Lower frequency for the mask (in Fourier space, max 0.5) More...

double	mask_w2
	Higher frequency for the mask (in Fourier space, max 0.5) More...

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	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 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

Parameter class for the project program

Definition at line 38 of file ctf_enhance_psd.h.

Member Function Documentation

◆ applyFilter()

void ProgCTFEnhancePSD::applyFilter ( MultidimArray< double > & PSD )

Apply filter method to a single PSD. The steps are basically: outlier removal, band pass filtration, masking and normalization.

Definition at line 110 of file ctf_enhance_psd.cpp.

 {
     // Take the logarithm
     FOR_ALL_ELEMENTS_IN_ARRAY2D(PSD)
     A2D_ELEM(PSD, i, j) = log10(1 + A2D_ELEM(PSD, i, j));
 
     // Remove single outliers
     CenterFFT(PSD, true);
     MultidimArray<double> aux;
     medianFilter3x3(PSD, aux);
     PSD = aux;
 
     // Reject other outliers
     reject_outliers(PSD, 2);
 
     // Band pass filter
     FourierFilter Filter;
     Filter.FilterShape = RAISED_COSINE;
     Filter.FilterBand = BANDPASS;
     Filter.w1 = filter_w1;
     Filter.w2 = filter_w2;
     Filter.raised_w = decay_width;
     PSD.setXmippOrigin();
     Filter.generateMask(PSD);
     Filter.applyMaskSpace(PSD);
     STARTINGX(PSD) = STARTINGY(PSD) = 0;
     CenterFFT(PSD, false);
 
     // Mask the input PSD
     MultidimArray<int> mask;
     mask.resize(PSD);
     Matrix1D<double> freq(2); // Frequencies for Fourier plane
     double limit0_2 = mask_w1;
     limit0_2 = limit0_2 * limit0_2;
     double limitF_2 = mask_w2;
     limitF_2 = limitF_2 * limitF_2;
     for (int i = STARTINGY(PSD); i <= FINISHINGY(PSD); ++i)
     {
         FFT_IDX2DIGFREQ(i, YSIZE(PSD), YY(freq));
         double freqy2 = YY(freq) * YY(freq);
         for (int j = STARTINGX(PSD); j <= FINISHINGX(PSD); ++j)
         {
             FFT_IDX2DIGFREQ(j, XSIZE(PSD), XX(freq));
             double freq2 = XX(freq) * XX(freq) + freqy2;
             if (freq2 < limit0_2 || freq2 > limitF_2)
                 A2D_ELEM(PSD, i, j) = 0;
             else
                 A2D_ELEM(mask, i, j) = 1;
         }
     }
 
     //Compute the mean and the standard deviation under a tighter mask
     //close to the border and normalize the PSD image
     MultidimArray<int> tighterMask;
     tighterMask.resizeNoCopy(PSD);
     limit0_2 = mask_w2 * 0.9;
     limit0_2 = limit0_2 * limit0_2;
     limitF_2 = mask_w2;
     limitF_2 = limitF_2 * limitF_2;
     for (int i = STARTINGY(PSD); i <= FINISHINGY(PSD); ++i)
     {
         FFT_IDX2DIGFREQ(i, YSIZE(PSD), YY(freq));
         double freqy2 = YY(freq) * YY(freq);
         for (int j = STARTINGX(PSD); j <= FINISHINGX(PSD); ++j)
         {
             FFT_IDX2DIGFREQ(j, XSIZE(PSD), XX(freq));
             double freq2 = XX(freq) * XX(freq) + freqy2;
             A2D_ELEM(tighterMask, i, j) = freq2 > limit0_2 && freq2 < limitF_2;
         }
     }
 
     double avg, stddev;
     PSD.computeAvgStdev_within_binary_mask(tighterMask, avg, stddev);
     double istddev = 1.0 / stddev;
     FOR_ALL_ELEMENTS_IN_ARRAY2D(PSD)
     if (A2D_ELEM(mask, i, j))
         A2D_ELEM(PSD, i, j) = (A2D_ELEM(PSD, i, j) - avg) * istddev;
 
     // Mask again
     limit0_2 = mask_w1;
     limit0_2 = limit0_2 * limit0_2;
     limitF_2 = mask_w2 * 0.9;
     limitF_2 = limitF_2 * limitF_2;
     for (int i = STARTINGY(PSD); i <= FINISHINGY(PSD); ++i)
     {
         FFT_IDX2DIGFREQ(i, YSIZE(PSD), YY(freq));
         double freqy2 = YY(freq) * YY(freq);
         for (int j = STARTINGX(PSD); j <= FINISHINGX(PSD); ++j)
         {
             FFT_IDX2DIGFREQ(j, XSIZE(PSD), XX(freq));
             double freq2 = XX(freq) * XX(freq) + freqy2;
             if (freq2 < limit0_2 || freq2 > limitF_2)
                 A2D_ELEM(PSD, i, j) = 0;
         }
     }
 
     CenterFFT(PSD, true);
 }

◆ applySPHT()

void ProgCTFEnhancePSD::applySPHT ( MultidimArray< double > & PSD )

Apply SPHT to a single PSD.

Definition at line 209 of file ctf_enhance_psd.cpp.

 {
     FourierTransformer transformer;
     MultidimArray< std::complex<double> > PSDfourier;
     transformer.FourierTransform(PSD, PSDfourier, false);
 
     transformer.inverseFourierTransform();
 }

◆ defineParams()

void ProgCTFEnhancePSD::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 60 of file ctf_enhance_psd.cpp.

 {
     each_image_produces_an_output = true;
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with PSDs or a single PSD");
     XmippMetadataProgram::defineParams();
     addUsageLine(
         "Enhances the visibility of the Thon rings in a Power Spectrum Density (PSD).");
     addSeeAlsoLine("ctf_estimate_from_micrograph");
     addParamsLine("[--method <mth=filter>]        : Choose enhancing method");
     addParamsLine("       where <mth>");
     addParamsLine("             filter <freq_low=0.05> <freq_high=0.2> <freq_decay=0.02>: Ad hoc filters. The algorithm is fully described at [[http://www.ncbi.nlm.nih.gov/pubmed/16987671][this article]]");
     addParamsLine("                                                                     : The frequency limits define a raised-cosine bandpass filter, frequencies are normalized to 0.5");
     addParamsLine("             spht   <N0=1> <NF=10> : Spiral phase transform normalization.");
     addParamsLine("                                   : N0 and NF define the minimum and maximum number of fringes in the CTF");
     addParamsLine("==+ Output parameters");
     addParamsLine("  [--dont_center]            : By default, the output is centered");
     addParamsLine("  [--dont_log]               : Don't take log10 before working");
     addParamsLine("==+ Output mask parameters");
     addParamsLine("  [--m1 <freq_low=0.025>]    : Low freq. for frequency mask, max 0.5");
     addParamsLine("  [--m2 <freq_high=0.3>]     : High freq. for frequency mask, max 0.5");
     addExampleLine("xmipp_ctf_enhance_psd -i myPSD.psd -o myPSD_enhanced.psd");
 }

◆ processImage()

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

virtual

Process one image

Implements XmippMetadataProgram.

Definition at line 95 of file ctf_enhance_psd.cpp.

 {
     Image<double> PSD;
     PSD.read(fnImg);
     if (ZSIZE(PSD()) != 1)
         REPORT_ERROR(ERR_MATRIX_DIM,"This program is not intended for volumes");
     if (method=="filter")
         applyFilter(PSD());
     else
         applySPHT(PSD());
     PSD.write(fnImgOut);
 }

◆ readParams()

void ProgCTFEnhancePSD::readParams ( )

virtual

Read from a command line.

Reimplemented from XmippMetadataProgram.

Definition at line 40 of file ctf_enhance_psd.cpp.

 {
     XmippMetadataProgram::readParams();
     method = getParam("--method");
     if (method == "filter")
     {
         filter_w1 = getDoubleParam("--method", 1);
         filter_w2 = getDoubleParam("--method", 2);
         decay_width = getDoubleParam("--method", 3);
     }
     else
     {
         N0 = getIntParam("--method", 1);
         NF = getIntParam("--method", 2);
     }
     mask_w1 = getDoubleParam("--m1");
     mask_w2 = getDoubleParam("--m2");
 }

◆ show()

void ProgCTFEnhancePSD::show ( )

Show parameters.

Definition at line 85 of file ctf_enhance_psd.cpp.

 {
     XmippMetadataProgram::show();
     std::cout << "Filter w1:    " << filter_w1 << std::endl << "Filter w2:    "
     << filter_w2 << std::endl << "Filter decay: " << decay_width
     << std::endl << "Mask w1:      " << mask_w1 << std::endl
     << "Mask w2:      " << mask_w2 << std::endl;
 }

Member Data Documentation

◆ decay_width

double ProgCTFEnhancePSD::decay_width

Decay width (raised cosine)

Definition at line 51 of file ctf_enhance_psd.h.

◆ filter_w1

double ProgCTFEnhancePSD::filter_w1

Bandpass filter low frequency (in Fourier space, max 0.5)

Definition at line 45 of file ctf_enhance_psd.h.

◆ filter_w2

double ProgCTFEnhancePSD::filter_w2

Bandpass filter high frequency (in Fourier space, max 0.5)

Definition at line 48 of file ctf_enhance_psd.h.

◆ mask_w1

double ProgCTFEnhancePSD::mask_w1

Lower frequency for the mask (in Fourier space, max 0.5)

Definition at line 60 of file ctf_enhance_psd.h.

◆ mask_w2

double ProgCTFEnhancePSD::mask_w2

Higher frequency for the mask (in Fourier space, max 0.5)

Definition at line 63 of file ctf_enhance_psd.h.

◆ method

String ProgCTFEnhancePSD::method

Method.

Definition at line 42 of file ctf_enhance_psd.h.

◆ N0

int ProgCTFEnhancePSD::N0

Minimum number of fringes.

Definition at line 54 of file ctf_enhance_psd.h.

◆ NF

int ProgCTFEnhancePSD::NF

Maximum number of fringes.

Definition at line 57 of file ctf_enhance_psd.h.

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

xmipp/libraries/reconstruction/ctf_enhance_psd.h
xmipp/libraries/reconstruction/ctf_enhance_psd.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ applyFilter()

◆ applySPHT()

◆ defineParams()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ decay_width

◆ filter_w1

◆ filter_w2

◆ mask_w1

◆ mask_w2

◆ method

◆ N0

◆ NF