Inheritance diagram for ProgMetadataHistogram:

Collaboration diagram for ProgMetadataHistogram:

Public Member Functions
void	defineParams ()

void	readColumn (MDLabel &column, bool &automatic, double &m, double &M, int &steps, bool second=false)

void	getColumnValues (const MDLabel column, MultidimArray< double > &values, const bool automatic, double &m, double &M)

void	readParams ()

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
MetaDataVec	mdIn

FileName	fn_in

FileName	fn_out

FileName	fn_img

MDLabel	col

MDLabel	col2

double	m

double	M

double	m2

double	M2

bool	do_hist2d

bool	write_img

bool	automatic_range

bool	automatic_range2

int	StepsNo

int	StepsNo2

Histogram1D	hist

Histogram2D	hist2

double	percentil

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 30 of file metadata_histogram.cpp.

Member Function Documentation

◆ defineParams()

void ProgMetadataHistogram::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 43 of file metadata_histogram.cpp.

     {
         addUsageLine("Calculate histogram from a metadata column(1D) or from a couple of columns(2D)");
         addParamsLine("   -i <input_metadata>          : input metadata");
         addParamsLine("  [-o <text_file=\"/dev/stdout\">] : output text file with histogram, by default standard output");
         addParamsLine("  --col <label>                 : column to create the histogram");
         addParamsLine("  [--range <m> <M>]             : range for the histogram, automatic calculated if not provided");
         addParamsLine("  [--steps <N=100>]             : number of subdivisions");
         addParamsLine("  [--col2 <label=\"\"> ]        : if specified, a 2D histogram is calculated");
         addParamsLine("  [--range2 <m> <M>]            : range for second column in 2D histogram");
         addParamsLine("       requires --col2;");
         addParamsLine("  [--steps2 <N=100>]            : number of subdivisions in second column");
         addParamsLine("       requires --col2;");
         addParamsLine("  [--percentil <p=50.>]         : Only for 1D histograms");
         addParamsLine("  [--write_as_image <image_file>]   : Only for 2D histograms");
         addParamsLine("       requires --col2;");
 
         addExampleLine("Calculate the histogram of the column 'angleRot' from a metadata:", false);
         addExampleLine("xmipp_metadata_histogram -i images.xmd --col angleRot -o hist.txt");
 
         addSeeAlsoLine("image_histogram");
 
     }

◆ getColumnValues()

void ProgMetadataHistogram::getColumnValues	(	const MDLabel	column,
		MultidimArray< double > &	values,
		const bool	automatic,
		double &	m,
		double &	M
	)

inline

Definition at line 90 of file metadata_histogram.cpp.

     {
         std::vector<double> columnValues;
         mdIn.getColumnValues(column, columnValues);
         values = columnValues;
         if (automatic)
            values.computeDoubleMinMax(m, M);
     }

◆ readColumn()

void ProgMetadataHistogram::readColumn	(	MDLabel &	column,
		bool &	automatic,
		double &	m,
		double &	M,
		int &	steps,
		bool	second = `false`
	)

inline

Definition at line 67 of file metadata_histogram.cpp.

     {
         const char* colStr = second ? "--col2" : "--col";
         const char* rangeStr = second ? "--range2" : "--range";
         const char* stepStr = second ? "--steps2" : "--steps";
 
         column = MDL::str2Label(getParam(colStr));
         steps = getIntParam(stepStr);
         automatic = true;
         if (checkParam(rangeStr))
         {
             m = getDoubleParam(rangeStr, 0);
             M = getDoubleParam(rangeStr, 1);
             automatic = false;
         }
 
         // Check if valid columns where provided
         if (column == MDL_UNDEFINED)
             REPORT_ERROR(ERR_MD_UNDEFINED, "Metadata Histogram: Column for histogram not valid");
         else if (!MDL::isDouble(column))
             REPORT_ERROR(ERR_MD_BADTYPE, "Metadata Histogram: Column type for histogram should be double");
     }

◆ readParams()

void ProgMetadataHistogram::readParams ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 99 of file metadata_histogram.cpp.

     {
         fn_in = getParam("-i");
         mdIn.read(fn_in);
         fn_out = getParam("-o");
         percentil = getDoubleParam("--percentil");
         readColumn(col, automatic_range, m, M, StepsNo);
 
         if ((do_hist2d = checkParam("--col2")))
             readColumn(col2, automatic_range2, m2, M2, StepsNo2, true);
 
         if ((write_img = checkParam("--write_as_image")))
             fn_img = getParam("--write_as_image");
     }

◆ run()

void ProgMetadataHistogram::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 114 of file metadata_histogram.cpp.

     {
         double avg=0., stddev=0., dummy;
         MultidimArray<double> C;
         getColumnValues(col, C, automatic_range, m, M);
 
         if (!do_hist2d)
         {
             compute_hist(C, hist, m, M, StepsNo);
             std::cout << formatString("min: %f max: %f steps: %d", m, M, StepsNo) << std::endl;
             C.computeStats(avg, stddev, dummy, dummy);
             std::cout << formatString("mean: %f stddev: %f", avg, stddev) << std::endl;
             std::cout << formatString("percentil (%f)", hist.percentil(percentil)) << std::endl;
             hist.write(fn_out);
         }
         else
         {
             MultidimArray<double> C2;
             getColumnValues(col2, C2, automatic_range2, m2, M2);
             compute_hist(C, C2, hist2, m, M, m2, M2, StepsNo, StepsNo2);
             //stats for column 1
             std::cout << formatString("min1: %f max1: %f steps1: %d", m, M, StepsNo) << std::endl;
             C.computeStats(avg, stddev, dummy, dummy);
             std::cout << formatString("mean: %f stddev: %f", avg, stddev) << std::endl;
             //stats for column 2
             std::cout << formatString("min2: %f max2: %f steps2: %d", m2, M2, StepsNo2) << std::endl;
             C2.computeStats(avg, stddev, dummy, dummy);
             std::cout << formatString("mean: %f stddev: %f", avg, stddev) << std::endl;
             hist2.write(fn_out);
 
             if (write_img)
             {
               Image<double> img;
               img() = hist2;
               img.write(fn_img);
             }
         }
     }

Member Data Documentation

◆ automatic_range

bool ProgMetadataHistogram::automatic_range

Definition at line 37 of file metadata_histogram.cpp.

◆ automatic_range2

bool ProgMetadataHistogram::automatic_range2

Definition at line 37 of file metadata_histogram.cpp.

◆ col

MDLabel ProgMetadataHistogram::col

Definition at line 35 of file metadata_histogram.cpp.

◆ col2

MDLabel ProgMetadataHistogram::col2

Definition at line 35 of file metadata_histogram.cpp.

◆ do_hist2d

bool ProgMetadataHistogram::do_hist2d

Definition at line 37 of file metadata_histogram.cpp.

◆ fn_img

FileName ProgMetadataHistogram::fn_img

Definition at line 34 of file metadata_histogram.cpp.

◆ fn_in

FileName ProgMetadataHistogram::fn_in

Definition at line 34 of file metadata_histogram.cpp.

◆ fn_out

FileName ProgMetadataHistogram::fn_out

Definition at line 34 of file metadata_histogram.cpp.

◆ hist

Histogram1D ProgMetadataHistogram::hist

Definition at line 39 of file metadata_histogram.cpp.

◆ hist2

Histogram2D ProgMetadataHistogram::hist2

Definition at line 40 of file metadata_histogram.cpp.

◆ M

double ProgMetadataHistogram::M

Definition at line 36 of file metadata_histogram.cpp.

◆ m

double ProgMetadataHistogram::m

Definition at line 36 of file metadata_histogram.cpp.

◆ M2

double ProgMetadataHistogram::M2

Definition at line 36 of file metadata_histogram.cpp.

◆ m2

double ProgMetadataHistogram::m2

Definition at line 36 of file metadata_histogram.cpp.

◆ mdIn

MetaDataVec ProgMetadataHistogram::mdIn

Definition at line 33 of file metadata_histogram.cpp.

◆ percentil

double ProgMetadataHistogram::percentil

Definition at line 41 of file metadata_histogram.cpp.

◆ StepsNo

int ProgMetadataHistogram::StepsNo

Definition at line 38 of file metadata_histogram.cpp.

◆ StepsNo2

int ProgMetadataHistogram::StepsNo2

Definition at line 38 of file metadata_histogram.cpp.

◆ write_img

bool ProgMetadataHistogram::write_img

Definition at line 37 of file metadata_histogram.cpp.

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

xmipp/libraries/reconstruction/metadata_histogram.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ getColumnValues()

◆ readColumn()

◆ readParams()

◆ run()

Member Data Documentation

◆ automatic_range

◆ automatic_range2

◆ col

◆ col2

◆ do_hist2d

◆ fn_img

◆ fn_in

◆ fn_out

◆ hist

◆ hist2

◆ M

◆ m

◆ M2

◆ m2

◆ mdIn

◆ percentil

◆ StepsNo

◆ StepsNo2

◆ write_img