Inheritance diagram for ProgStatistics:

Collaboration diagram for ProgStatistics:

Protected Member Functions
void	defineParams ()

void	readParams ()

void	show ()

void	preProcess ()

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

void	postProcess ()

Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

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
MetaDataVec	DF_stats

ImageGeneric	image

MultidimArray< double >	averageArray

MultidimArray< double >	stdArray

MultidimArray< double >	dummyArray

Mask	mask

int	short_format

int	save_mask

int	repair

bool	show_angles

bool	save_image_stats

bool	apply_mask

double	min_val

double	max_val

double	avg

double	stddev

double	mean_min_val

double	mean_max_val

double	mean_avg

double	mean_stddev

int	max_length

FileName	maskFileName

FileName	statsRoot

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 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 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

Definition at line 35 of file image_statistics.cpp.

Member Function Documentation

◆ defineParams()

void ProgStatistics::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 59 of file image_statistics.cpp.

     {
         each_image_produces_an_output = false;
         allow_apply_geo = true;
         allow_time_bar = false;
         addUsageLine("Display statistics of 2D/3Dimages. A mask can be applied. Average Images may be computed");
         addUsageLine("All images must have same size");
         XmippMetadataProgram::defineParams();
         addParamsLine("[-o <metadata>]   : Save the statistics in this metadata file.");
         addParamsLine("[--short_format]  : Do not show labels for statistics.");
         addParamsLine("[--show_angles]   : Also show angles in the image header.");
         addParamsLine("[--save_mask        <maskFileName>] : Save 2D and 3D masks.");
         addParamsLine("[--save_image_stats <stats_root=\"\">]: Save average and standard deviation images");
         addUsageLine ("           Mask is ignored  for this operation");
         mask.defineParams(this,INT_MASK,nullptr,"Statistics restricted to the mask area.");
         addUsageLine ("NOTE: Geometry will NOT be applied to volumes even if apply_geo flag is on");
         addKeywords("statistics average mean std");
     }

◆ postProcess()

void ProgStatistics::postProcess ( )

inlineprotectedvirtual

Reimplemented from XmippMetadataProgram.

Definition at line 204 of file image_statistics.cpp.

     {
 
         if (mdInSize > 1)
         {
             mean_min_val /= mdInSize;
             mean_max_val /= mdInSize;
             mean_avg     /= mdInSize;
             mean_stddev  /= mdInSize;
 
             if (verbose)
             {
               // Show total statistics ------------------------------------------------
               std::cout << "==================================================\n";
               std::cout << "Total number of images/volumes: " << mdInSize << std::endl;
               std::cout << stringToString(" ", max_length + 13);
               if (!short_format)
                   std::cout << formatString("min=%10f max=%10f avg=%10f stddev=%10f",
                                             mean_min_val, mean_max_val, mean_avg, mean_stddev);
               else
                   std::cout << formatString("%10f %10f %10f %10f", mean_min_val, mean_max_val, mean_avg, mean_stddev);
               std::cout << std::endl;
             }
 
             if (save_image_stats)
             {
                 averageArray /= mdInSize;
                 if (mdInSize > 1)
                 {
                     stdArray= stdArray / mdInSize - averageArray * averageArray;
                     stdArray *= mdInSize / (mdInSize - 1);
                     //Do this as an image since it is not define for arrays
                     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(stdArray)
                     DIRECT_MULTIDIM_ELEM(stdArray,n) = sqrt(fabs(DIRECT_MULTIDIM_ELEM(stdArray,n)));
                 }
                 else
                     stdArray.initZeros();
             }
         }
 
         // Save masks -----------------------------------------------------------
         if (save_mask)
             mask.write_mask(maskFileName);
         // Save statistics ------------------------------------------------------
         if (fn_out != "")
             DF_stats.write(fn_out,MD_APPEND);
 
         //save average and std images
         if(save_image_stats)
         {
             Image<double> dummyImage;
             dummyImage() = averageArray;
             dummyImage.write(statsRoot  + "average.xmp");
             dummyImage() = stdArray;
             dummyImage.write(statsRoot + "stddev.xmp");
         }
     }

◆ preProcess()

void ProgStatistics::preProcess ( )

inlineprotectedvirtual

Reimplemented from XmippMetadataProgram.

Definition at line 103 of file image_statistics.cpp.

     {
         DF_stats.setComment((std::string)"Statistics of " + fn_in);
         // Get maximum filename size ---------------------------------------------
         max_length = getInputMd()->getMaxStringLength(image_label);
 
         // Process each file -----------------------------------------------------
         mean_min_val = 0, mean_max_val = 0, mean_avg = 0, mean_stddev = 0;
 
         if (verbose > 0)
         {
           if (short_format)
           {
               std::cout << "Format: Name ZxYxX min max avg stddev ";
               if (show_angles)
                   std::cout << " <rot tilt psi>";
               std::cout << '>' << std::endl;
           }
         }
 
         // get xdim, ydim,zdim
         //getImageSize(mdIn, xDim, yDim, zDim, nDim, image_label);
         averageArray.resize(ndimOut, zdimOut, ydimOut, xdimOut);
         stdArray.resize(ndimOut,zdimOut,ydimOut,xdimOut);
         averageArray.setXmippOrigin();
         stdArray.setXmippOrigin();
 
         // Generate mask if necessary
         if (apply_mask)
             mask.generate_mask(zdimOut, ydimOut, xdimOut);
 
     }

◆ processImage()

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

inlineprotectedvirtual

Implements XmippMetadataProgram.

Definition at line 136 of file image_statistics.cpp.

     {
         if (apply_geo)
             image.readApplyGeo(fnImg, rowIn);
         else
             image.read(fnImg, DATA, ALL_IMAGES, true);
 
         image().setXmippOrigin();
 
         double rot = 0, tilt = 0, psi = 0;
         if (show_angles)
             image.getEulerAngles(rot,tilt,psi);
 
         if (apply_mask)
         {
             computeStats_within_binary_mask(mask.get_binary_mask(), image(), min_val, max_val,
                                             avg, stddev);
         }
         else
             image().computeStats(avg, stddev, min_val, max_val);
 
         if(save_image_stats)
         {
             //copy image from imageGeneric
             image().getImage( dummyArray );
             averageArray     += dummyArray;
             stdArray         += dummyArray * dummyArray;
         }
 
         // Show information
         if (verbose > 0)
         {
           std::cout << stringToString(fnImg, max_length + 1);
           if (zdimOut > 1)
               formatString("%4dx%4dx%4d ", zdimOut, ydimOut, xdimOut);
           else
               formatString("%4dx%4d", ydimOut, xdimOut);
 
           if (!short_format)
           {
               std::cout << formatString("min=%10f max=%10f avg=%10f stddev=%10f",
                                         min_val, max_val, avg, stddev);
 
               if (show_angles)
                   std::cout << formatString("rot=%10f tilt=%10f psi=%10f", rot, tilt, psi);
           }
           else
               std::cout << formatString("%10f %10f %10f %10f", min_val, max_val, avg, stddev);
         }
         size_t id;
         id = DF_stats.addObject();
         DF_stats.setRow(rowIn,id);
         DF_stats.setValue(MDL_MIN,min_val,id);
         DF_stats.setValue(MDL_MAX,max_val,id);
         DF_stats.setValue(MDL_AVG,avg,id);
         DF_stats.setValue(MDL_STDDEV,stddev,id);
 
         // Total statistics
         mean_min_val += min_val;
         mean_max_val += max_val;
         mean_avg     += avg;
         mean_stddev  += stddev;
 
         // Finish information .................................................
         if (verbose > 0)
           std::cout << std::endl;
     }

◆ readParams()

void ProgStatistics::readParams ( )

inlineprotectedvirtual

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 78 of file image_statistics.cpp.

     {
         XmippMetadataProgram::readParams();
         short_format = checkParam("--short_format");
 
         if ((save_mask = checkParam("--save_mask")))
             maskFileName = getParam("--save_mask");
 
         if ((save_image_stats = checkParam("--save_image_stats")))
             statsRoot = getParam("--save_image_stats");
 
         show_angles  = checkParam("--show_angles");
         fn_out = (checkParam("-o"))? getParam("-o"): "";
 
         mask.allowed_data_types = INT_MASK;
 
         if ((apply_mask = checkParam("--mask")))
             mask.readParams(this);
     }

◆ show()

void ProgStatistics::show ( )

inlineprotected

Definition at line 98 of file image_statistics.cpp.

     {
         std::cout << " Statistics of " << fn_in << std::endl;
     }

Member Data Documentation

◆ apply_mask

bool ProgStatistics::apply_mask

protected

Definition at line 50 of file image_statistics.cpp.

◆ averageArray

MultidimArray<double> ProgStatistics::averageArray

protected

Definition at line 40 of file image_statistics.cpp.

◆ avg

double ProgStatistics::avg

protected

Definition at line 52 of file image_statistics.cpp.

◆ DF_stats

MetaDataVec ProgStatistics::DF_stats

protected

Definition at line 38 of file image_statistics.cpp.

◆ dummyArray

MultidimArray<double> ProgStatistics::dummyArray

protected

Definition at line 42 of file image_statistics.cpp.

◆ image

ImageGeneric ProgStatistics::image

protected

Definition at line 39 of file image_statistics.cpp.

◆ mask

Mask ProgStatistics::mask

protected

Definition at line 44 of file image_statistics.cpp.

◆ maskFileName

FileName ProgStatistics::maskFileName

protected

Definition at line 57 of file image_statistics.cpp.

◆ max_length

int ProgStatistics::max_length

protected

Definition at line 54 of file image_statistics.cpp.

◆ max_val

double ProgStatistics::max_val

protected

Definition at line 52 of file image_statistics.cpp.

◆ mean_avg

double ProgStatistics::mean_avg

protected

Definition at line 53 of file image_statistics.cpp.

◆ mean_max_val

double ProgStatistics::mean_max_val

protected

Definition at line 53 of file image_statistics.cpp.

◆ mean_min_val

double ProgStatistics::mean_min_val

protected

Definition at line 53 of file image_statistics.cpp.

◆ mean_stddev

double ProgStatistics::mean_stddev

protected

Definition at line 53 of file image_statistics.cpp.

◆ min_val

double ProgStatistics::min_val

protected

Definition at line 52 of file image_statistics.cpp.

◆ repair

int ProgStatistics::repair

protected

Definition at line 47 of file image_statistics.cpp.

◆ save_image_stats

bool ProgStatistics::save_image_stats

protected

Definition at line 49 of file image_statistics.cpp.

◆ save_mask

int ProgStatistics::save_mask

protected

Definition at line 46 of file image_statistics.cpp.

◆ short_format

int ProgStatistics::short_format

protected

Definition at line 45 of file image_statistics.cpp.

◆ show_angles

bool ProgStatistics::show_angles

protected

Definition at line 48 of file image_statistics.cpp.

◆ statsRoot

FileName ProgStatistics::statsRoot

protected

Definition at line 57 of file image_statistics.cpp.

◆ stdArray

MultidimArray<double> ProgStatistics::stdArray

protected

Definition at line 41 of file image_statistics.cpp.

◆ stddev

double ProgStatistics::stddev

protected

Definition at line 52 of file image_statistics.cpp.

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

xmipp/libraries/reconstruction/image_statistics.cpp

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ apply_mask

◆ averageArray

◆ avg

◆ DF_stats

◆ dummyArray

◆ image

◆ mask

◆ maskFileName

◆ max_length

◆ max_val

◆ mean_avg

◆ mean_max_val

◆ mean_min_val

◆ mean_stddev

◆ min_val

◆ repair

◆ save_image_stats

◆ save_mask

◆ short_format

◆ show_angles

◆ statsRoot

◆ stdArray

◆ stddev