#include <score_micrograph.h>

Inheritance diagram for ProgScoreMicrograph:

Collaboration diagram for ProgScoreMicrograph:

Public Member Functions
void	readParams ()

void	defineParams ()

void	run ()

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
int	particleSize

ProgCTFEstimateFromMicrograph	prmEstimateCTFFromMicrograph

ProgCTFEstimateFromPSD	prmEstimateCTFFromPSD
	Parameters for adjust_CTF program. More...

FileName	fn_micrograph
	Micrograph filename. More...

int	pieceDim
	Dimension of micrograph pieces. More...

double	overlap

int	skipBorders

int	Nsubpiece

int	bootstrapN

bool	estimate_ctf
	Estimate a CTF for each PSD. More...

double	defocus_range
	Defocus range. More...

ProgCTFEstimateFromMicrograph::TPSD_mode	PSDEstimator_mode

ProgCTFEstimateFromMicrograph::TPSD_mode	psd_mode

ProgPSDSort	prmPSDSort

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

Parameter class for the project program

Definition at line 41 of file score_micrograph.h.

Member Function Documentation

◆ defineParams()

void ProgScoreMicrograph::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 53 of file score_micrograph.cpp.

 {
     addUsageLine("Estimate the score of a given Micrograph attending on different parameters.");
     addParamsLine("   --micrograph <file>         : File with the micrograph");
     addParamsLine("  [--particleSize <p=100>]       : Size of the particle");
     ProgCTFEstimateFromPSD::defineBasicParams(this);
 }

◆ readParams()

void ProgScoreMicrograph::readParams ( )

virtual

Read from a command line.

Reimplemented from XmippProgram.

Definition at line 35 of file score_micrograph.cpp.

 {
 
     pieceDim = 256;
     overlap = 0.5;
     skipBorders = 2;
     Nsubpiece = 1;
     bootstrapN = -1;
     estimate_ctf = true;
     defocus_range = 1000;
     fn_micrograph = getParam("--micrograph");
     particleSize = getIntParam("--particleSize");
 
      prmEstimateCTFFromPSD.readBasicParams(this);
 
 }

◆ run()

void ProgScoreMicrograph::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 62 of file score_micrograph.cpp.

 {
 
     std::cout << particleSize << std::endl;
     char bufferDW[200];
     FileName fn_micrographBadPxl;
     fn_micrographBadPxl = fn_micrograph.withoutExtension()+"bp__tmp."+fn_micrograph.getExtension();
     sprintf(bufferDW, "xmipp_transform_filter -i %s -o %s --bad_pixels outliers 2", fn_micrograph.c_str(), fn_micrographBadPxl.c_str());
     if (!system(bufferDW))
         REPORT_ERROR(ERR_UNCLASSIFIED,"Cannot filter");
 
     FileName fn_micrographDwn;
     fn_micrographDwn = fn_micrograph.withoutExtension()+"_tmp."+fn_micrograph.getExtension();
     sprintf(bufferDW, "xmipp_transform_downsample -i %s -o %s --step 2.0 --method fourier" ,    fn_micrographBadPxl.c_str(), fn_micrographDwn.c_str());
     if (!system(bufferDW))
         REPORT_ERROR(ERR_UNCLASSIFIED,"Cannot downsample");
 
     prmEstimateCTFFromPSD.defocus_range = defocus_range;
     prmEstimateCTFFromPSD.downsampleFactor = 2.0;
     prmEstimateCTFFromPSD.Tm = prmEstimateCTFFromPSD.Tm*prmEstimateCTFFromPSD.downsampleFactor;
     prmEstimateCTFFromMicrograph.prmEstimateCTFFromPSD = prmEstimateCTFFromPSD;
     prmEstimateCTFFromMicrograph.pieceDim = pieceDim;
     prmEstimateCTFFromMicrograph.overlap = overlap;
     prmEstimateCTFFromMicrograph.skipBorders = skipBorders;
     prmEstimateCTFFromMicrograph.Nsubpiece = 1;
     prmEstimateCTFFromMicrograph.bootstrapN = bootstrapN;
     prmEstimateCTFFromMicrograph.estimate_ctf = estimate_ctf;
     prmEstimateCTFFromMicrograph.fn_micrograph = fn_micrographDwn;
     prmEstimateCTFFromMicrograph.fn_root = "/home/jvargas/Linux/Proyectos/LUMC/set_001_challenge/kk";
     prmEstimateCTFFromMicrograph.run();
 
     MetaDataVec MD;
     size_t id=MD.addObject();
     MD.setValue(MDL_MICROGRAPH,fn_micrographDwn,id);
     MD.setValue(MDL_PSD,prmEstimateCTFFromMicrograph.fn_root+".psd",id);
     MD.setValue(MDL_PSD_ENHANCED,prmEstimateCTFFromMicrograph.fn_root+"_enhanced_psd.xmp",id);
     MD.setValue(MDL_PSD_ENHANCED,prmEstimateCTFFromMicrograph.fn_root+"_enhanced_psd.xmp",id);
     MD.setValue(MDL_CTF_MODEL,prmEstimateCTFFromMicrograph.fn_root+".ctfparam",id);
     MD.setValue(MDL_IMAGE1,prmEstimateCTFFromMicrograph.fn_root+"_ctfmodel_quadrant.xmp",id);
     MD.setValue(MDL_IMAGE2,prmEstimateCTFFromMicrograph.fn_root+"_ctfmodel_halfplane.xmp",id);
     MD.setValue(MDL_CTF_DOWNSAMPLE_PERFORMED,2.000000,id);
     MD.write("auxiliaryFile.xmd");
 
     //prmPSDSort.downsampling =
     prmPSDSort.fn_in = "auxiliaryFile.xmd";
     prmPSDSort.fn_out = "kkauxiliaryFile.xmd";
     // COSS prmPSDSort.downsampling = 2.000000; // this parameter must be written in the metadata
 
     char buffer[200];
     sprintf(buffer, "xmipp_ctf_sort_psds -i %s -o %s --downsampling %f",    prmPSDSort.fn_in.c_str(), prmPSDSort.fn_out.c_str(),2.000000);
     if (!system(bufferDW))
         REPORT_ERROR(ERR_UNCLASSIFIED,"Cannot sort psds");
 
     //Spiral Phase Transform
     MultidimArray<double> im, In, Mod, Part, Ice;
     MultidimArray<bool> ROI1, ROI2;
     Image<double> img;
     img.read(fn_micrographDwn);
     im = img();
     im.statisticsAdjust(0.,1.);
     In.resizeNoCopy(im);
     Part.resizeNoCopy(im);
     Ice.resizeNoCopy(im);
     Mod.resizeNoCopy(im);
     ROI1.resizeNoCopy(im);
     ROI1.setXmippOrigin();
     ROI2.resizeNoCopy(im);
     ROI2.setXmippOrigin();
     Ice.setXmippOrigin();
     Part.setXmippOrigin();
     FOR_ALL_ELEMENTS_IN_ARRAY2D(ROI1)
         A2D_ELEM(ROI1,i,j)= true;
 
     //aprox  Xdim/particleSize is the particle frequency
     size_t Xdim, Ydim, Zdim,Ndim;
     im.getDimensions(Xdim, Ydim,Zdim,Ndim);
 
     double avg, stdv;
     im.computeAvgStdev(avg,stdv);
     double R = Xdim/particleSize;
     double S = Xdim/particleSize;
     FourierTransformer ftrans(FFTW_BACKWARD);
     normalize(ftrans,im,In,Mod,R,S,ROI1);
 
     double partDensity = (Mod.sum()/(Xdim*Ydim))*100;
 
     double th=EntropyOtsuSegmentation(Mod,0.005,false);
     //th *= 2;
     FOR_ALL_ELEMENTS_IN_ARRAY2D(ROI1)
     {
         if (A2D_ELEM(Mod,i,j) < th)
         {
             A2D_ELEM(ROI1,i,j) = false;
             A2D_ELEM(ROI2,i,j) = true;
         }
     }
 
     double min_val, max_val, avg1, avg2, stdv1, stdv2;
     computeStats_within_binary_mask(ROI1, im, min_val, max_val,avg1,stdv1);
     computeStats_within_binary_mask(ROI2, im, min_val, max_val,avg2,stdv2);
     double snr = (stdv1/stdv2)*(stdv1/stdv2);
 
 
     double maxFreq;
     double fitting;
     double psdCorr90;
     double psdRadialInt;
 
     std::cout << prmPSDSort.fn_in.c_str() << std::endl;
     std::cout << prmPSDSort.fn_out.c_str() << std::endl;
 
     MD.read(prmPSDSort.fn_out);
     for (size_t objId : MD.ids())
     {
         MD.getValue(MDL_CTF_CRIT_MAXFREQ,maxFreq,objId);
         MD.getValue(MDL_CTF_CRIT_FITTINGSCORE,fitting,objId);
         MD.getValue(MDL_CTF_CRIT_PSDCORRELATION90,psdCorr90,objId);
         MD.getValue(MDL_CTF_CRIT_PSDRADIALINTEGRAL,psdRadialInt,objId);
         std::cout << "partDensity : " << partDensity << std::endl;
         std::cout << "snr :" << snr << std::endl;
         std::cout << "maxFreq :" << maxFreq << std::endl;
         std::cout << "fitting :" << fitting << std::endl;
         std::cout << "psdCorr90 :" << psdCorr90 << std::endl;
         std::cout << "psdRadialInt :" << psdRadialInt << std::endl;
     }
 
     img()=Part;
     img.write("kk1.mrc");
     img()=Ice;
     img.write("kk2.mrc");
 
 }

Member Data Documentation

◆ bootstrapN

int ProgScoreMicrograph::bootstrapN

Bootstrap N

Definition at line 65 of file score_micrograph.h.

◆ defocus_range

double ProgScoreMicrograph::defocus_range

Defocus range.

Definition at line 69 of file score_micrograph.h.

◆ estimate_ctf

bool ProgScoreMicrograph::estimate_ctf

Estimate a CTF for each PSD.

Definition at line 67 of file score_micrograph.h.

◆ fn_micrograph

FileName ProgScoreMicrograph::fn_micrograph

Micrograph filename.

Definition at line 54 of file score_micrograph.h.

◆ Nsubpiece

int ProgScoreMicrograph::Nsubpiece

Number of pieces (Nsubpiece x Nsubpiece) for the piece averaging

Definition at line 63 of file score_micrograph.h.

◆ overlap

double ProgScoreMicrograph::overlap

Overlap among pieces (0=No overlap, 1=Full overlap

Definition at line 58 of file score_micrograph.h.

◆ particleSize

int ProgScoreMicrograph::particleSize

Definition at line 46 of file score_micrograph.h.

◆ pieceDim

int ProgScoreMicrograph::pieceDim

Dimension of micrograph pieces.

Definition at line 56 of file score_micrograph.h.

◆ prmEstimateCTFFromMicrograph

ProgCTFEstimateFromMicrograph ProgScoreMicrograph::prmEstimateCTFFromMicrograph

Definition at line 48 of file score_micrograph.h.

◆ prmEstimateCTFFromPSD

ProgCTFEstimateFromPSD ProgScoreMicrograph::prmEstimateCTFFromPSD

Parameters for adjust_CTF program.

Definition at line 51 of file score_micrograph.h.

◆ prmPSDSort

ProgPSDSort ProgScoreMicrograph::prmPSDSort

Definition at line 75 of file score_micrograph.h.

◆ psd_mode

ProgCTFEstimateFromMicrograph::TPSD_mode ProgScoreMicrograph::psd_mode

Definition at line 73 of file score_micrograph.h.

◆ PSDEstimator_mode

ProgCTFEstimateFromMicrograph::TPSD_mode ProgScoreMicrograph::PSDEstimator_mode

Definition at line 71 of file score_micrograph.h.

◆ skipBorders

int ProgScoreMicrograph::skipBorders

Skip borders. The number of pieces around the border that must be skipped.

Definition at line 61 of file score_micrograph.h.

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ readParams()

◆ run()

Member Data Documentation

◆ bootstrapN

◆ defocus_range

◆ estimate_ctf

◆ fn_micrograph

◆ Nsubpiece

◆ overlap

◆ particleSize

◆ pieceDim

◆ prmEstimateCTFFromMicrograph

◆ prmEstimateCTFFromPSD

◆ prmPSDSort

◆ psd_mode

◆ PSDEstimator_mode

◆ skipBorders