Threshold Parameters. More...

#include <threshold.h>

Inheritance diagram for ProgThreshold:

Collaboration diagram for ProgThreshold:

Public Member Functions
void	readParams ()

void	defineParams ()

void	show ()

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
	Process image or volume. More...

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	selectionMethod

double	threshold

String	substitutionMethod

double	newValue

double	noiseAvg

double	noiseStddev

int	iSelectionMethod

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

Threshold Parameters.

Definition at line 38 of file threshold.h.

Member Function Documentation

◆ defineParams()

void ProgThreshold::defineParams ( )

virtual

Define Parameters

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgThreshold >.

Definition at line 51 of file threshold.cpp.

 {
     addUsageLine("Threshold volumes and images ");
     each_image_produces_an_output=true;
     XmippMetadataProgram::defineParams();
     addSeeAlsoLine("transform_mask, transform_morphology");
     addParamsLine("   --select <mode>                        : Select pixels meeting");
     addParamsLine("     where <mode>");
     addParamsLine("           abs_below <th>                 : Absolute value below a threshold");
     addParamsLine("           below <th>                     : Below a threshold");
     addParamsLine("           above <th>                     : Above a threshold");
     addParamsLine("   --substitute <substitutionMode=value>  : Substitute selected pixels by");
     addParamsLine("     where <substitutionMode>");
     addParamsLine("           binarize                       : Selected are set to 0, non-selected to 1");
     addParamsLine("           value <new=0>                  : New value");
     addParamsLine("           noise <avg=0> <stddev=1>       : Gaussian noise");
     addParamsLine("           avg                            : Average of non-selected");
     addExampleLine("Threshold a volume below a threshold",false);
     addExampleLine("xmipp_transform_threshold -i volume.vol -o volumeThresholded.vol --select below 0.01 --substitute value 0");
     addExampleLine("Generate a binary mask based on a threshold and apply it",false);
     addExampleLine("xmipp_transform_threshold -i volume.vol -o mask.vol --select below 0.5 --substitute binarize");
     addExampleLine("xmipp_transform_morphology -i mask.vol --dil");
     addExampleLine("xmipp_transform_mask -i volume.vol -o volumeMasked.vol --mask mask.vol");
 }

◆ processImage()

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

virtual

Process image or volume.

Implements XmippMetadataProgram.

Definition at line 96 of file threshold.cpp.

 {
     Image<double> I;
     I.read(fnImg);
     MultidimArray<double> &mI=I();
 
     // Compute substitute value
     double substituteValue=0.0;
     if (substitutionMethod=="value")
         substituteValue=newValue;
     else if (substitutionMethod=="noise")
         substituteValue=rnd_gaus(noiseAvg,noiseStddev);
     else if (substitutionMethod=="avg")
     {
         double N=0;
         switch (iSelectionMethod)
         {
         case 0:
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
             {
                 double pixval=DIRECT_MULTIDIM_ELEM(mI,n);
                 if (fabs(pixval)>threshold)
                 {
                     substituteValue+=pixval;
                     ++N;
                 }
             }
             break;
         case 1:
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
             {
                 double pixval=DIRECT_MULTIDIM_ELEM(mI,n);
                 if (pixval>threshold)
                 {
                     substituteValue+=pixval;
                     ++N;
                 }
             }
             break;
         case 2:
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
             {
                 double pixval=DIRECT_MULTIDIM_ELEM(mI,n);
                 if (pixval<threshold)
                 {
                     substituteValue+=pixval;
                     ++N;
                 }
             }
             break;
         }
         substituteValue/=N;
     }
 
     // Apply threshold
     bool binarize=substitutionMethod=="binarize";
     switch (iSelectionMethod)
     {
     case 0:
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
         {
             if (fabs(DIRECT_MULTIDIM_ELEM(mI,n))<threshold)
                 DIRECT_MULTIDIM_ELEM(mI,n)=substituteValue;
             else if (binarize)
                 DIRECT_MULTIDIM_ELEM(mI,n)=1;
         }
         break;
     case 1:
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
         {
             if (DIRECT_MULTIDIM_ELEM(mI,n)<threshold)
                 DIRECT_MULTIDIM_ELEM(mI,n)=substituteValue;
             else if (binarize)
                 DIRECT_MULTIDIM_ELEM(mI,n)=1;
         }
         break;
     case 2:
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
         {
             if (DIRECT_MULTIDIM_ELEM(mI,n)>threshold)
                 DIRECT_MULTIDIM_ELEM(mI,n)=substituteValue;
             else if (binarize)
                 DIRECT_MULTIDIM_ELEM(mI,n)=1;
         }
         break;
     }
 
     // Write result
     I.write(fnImgOut);
 }

◆ readParams()

void ProgThreshold::readParams ( )

virtual

Read parameters from command line.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgThreshold >.

Definition at line 29 of file threshold.cpp.

 {
     XmippMetadataProgram::readParams();
     selectionMethod=getParam("--select");
     if (selectionMethod=="abs_below")
         iSelectionMethod=0;
     else if (selectionMethod=="below")
         iSelectionMethod=1;
     else if (selectionMethod=="above")
         iSelectionMethod=2;
     threshold=getDoubleParam("--select",1);
     substitutionMethod=getParam("--substitute");
     if (substitutionMethod=="value")
         newValue=getDoubleParam("--substitute",1);
     else if (substitutionMethod=="noise")
     {
         noiseAvg=getDoubleParam("--substitute",1);
         noiseStddev=getDoubleParam("--substitute",2);
     }
 }

◆ show()

void ProgThreshold::show ( )

Show parameters

Definition at line 77 of file threshold.cpp.

 {
     if (verbose==0)
         return;
     XmippMetadataProgram::show();
     std::cout
     << "Selection method:    " << selectionMethod    << std::endl
     << "Threshold:           " << threshold          << std::endl
     << "Substitution method: " << substitutionMethod << std::endl;
     if (substitutionMethod=="value")
         std::cout << "New value:           " << newValue << std::endl;
     else if (substitutionMethod=="noise")
     {
         std::cout << "Noise average:       " << noiseAvg << std::endl;
         std::cout << "Noise std.dev.:      " << noiseStddev << std::endl;
     }
 }

Member Data Documentation

◆ iSelectionMethod

int ProgThreshold::iSelectionMethod

Definition at line 72 of file threshold.h.

◆ newValue

double ProgThreshold::newValue

Definition at line 51 of file threshold.h.

◆ noiseAvg

double ProgThreshold::noiseAvg

Definition at line 54 of file threshold.h.

◆ noiseStddev

double ProgThreshold::noiseStddev

Definition at line 57 of file threshold.h.

◆ selectionMethod

String ProgThreshold::selectionMethod

Definition at line 42 of file threshold.h.

◆ substitutionMethod

String ProgThreshold::substitutionMethod

Definition at line 48 of file threshold.h.

◆ threshold

double ProgThreshold::threshold

Definition at line 45 of file threshold.h.

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

xmipp/libraries/reconstruction/threshold.h
xmipp/libraries/reconstruction/threshold.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ processImage()

◆ readParams()

◆ show()

Member Data Documentation

◆ iSelectionMethod

◆ newValue

◆ noiseAvg

◆ noiseStddev

◆ selectionMethod

◆ substitutionMethod

◆ threshold