XmippProgram Class Reference

#include <xmipp_program.h>

Inherited by Alignment::AProgAlignSignificant< T >, AProgMovieAlignmentCorrelation< T >, ML2DBaseProgram, MultireferenceAligneability, Phantom_transform_parameters, PhantomMovieProgram, ProgAdjustVolume, ProgAlign2d, ProgAlignDualTiltSeries, ProgAlignTiltPairs, ProgAlignVolumes, ProgAnalyzeCluster, ProgAngResAlign, ProgAngularAccuracyPCA, ProgAngularBreakSymmetry, ProgAngularDistance, ProgAngularDistributionShow, ProgAngularEstimateTiltAxis, ProgAngularNeighbourhood, ProgAngularProjectionMatching, ProgAngularProjectLibrary, ProgAngularRotate, ProgApplyCoeffZernike3D, ProgApplyVolDeformSph, ProgARTPseudo, ProgassignmentTiltPair, ProgClassifyCL2D, ProgClassifyCL2DCore, ProgClassifyCL3D, ProgClassifyFirstSplit, ProgClassifyFirstSplit3, ProgClassifyFTTRI, ProgClassifyKmeans2D, ProgClassifySignificant, ProgCommonLine, ProgCompareClass, ProgCompareDensity, ProgCompareViews, ProgCoordinatesNoisyZonesFilter, ProgCTFBasicParams, ProgCtfCorrectAmplitude3D, ProgCtfCreateCtfdat, ProgCTFEstimateFromMicrograph, ProgCtfGroup, ProgCTFPhaseFlipping, ProgCTFShow, ProgDetectMissingWedge, ProgDimRed, ProgEliminateEmptyParticles, ProgEvaluateClass, ProgEvaluateCoordinates, ProgExtractFeatures, ProgExtractSubset, ProgFindCenter2D, ProgForwardZernikeVol, ProgFSO, ProgGpuCorrelation, ProgHistogram, ProgIDRXrayTomo [virtual], ProgImagePeakHighContrast, ProgImageRotationalPCA, ProgImageVectorize, ProgKenderSOM, ProgLocalVolumeAdjust, ProgLocSharpening, ProgMakeSpectra, ProgMetadataHistogram, ProgMetadataImport, ProgMetadataSplit, ProgMetadataSplit3D, ProgMetadataUtilities, ProgMicrographAutomaticPicking2, ProgMicrographScissor, ProgMLRefine3D, ProgMLTomo, ProgMonogenicSignalRes, ProgMonoTomo, ProgMonoTomo, ProgMovieEstimateGain, ProgMovieFilterDose, ProgMPIRun, ProgMrcCreateMetaData, ProgOddEven, ProgOpticalAligment, ProgPdbAnalysis, ProgPdbConverter, ProgPDBDictionary, ProgPdbNmaDeform, ProgPdbReduce, ProgPdbSphDeform, ProgPdbValueToVol, ProgPerformanceTest, ProgPhantomCreate, ProgProject, ProgProjectTomography, ProgPSFXrCreate, ProgReconsADMM, ProgReconsBase [virtual], ProgReconstructSignificant, ProgResBFactor, ProgResDir, ProgResliceVol, ProgResLocalFilter, ProgResolutionFsc, ProgResolutionIBW, ProgScoreMicrograph, ProgSeparateObjects, ProgSortByStatistics, ProgSortImages, ProgSSNR, ProgTest, ProgTestWork, ProgTomoAlignRefinement, ProgTomoExtractParticleStacks, ProgTomoExtractSubtomograms, ProgTomoFilterCoordinates, ProgTomographAlignment, ProgTomoMapBack, ProgTomoRemoveFluctuations, ProgTomoSimulateTiltseries, ProgTomoTSFilterDose, ProgValidationNonTilt, ProgValidationTiltPairs, ProgVolDeformSph, ProgVolumeDeformSphGpu, ProgVolumeEnhanceContrast, ProgVolumeFindSymmetry, ProgVolumeHalvesRestoration, ProgVolumeHalvesRestorationGpu< T >, ProgVolumeHomogenizer, ProgVolumeInitialSimulatedAnnealing, ProgVolumePCA, ProgVolumeSegment, ProgVolumeStructureFactor, ProgVolumeSubtraction, ProgVolumeToPseudoatoms, ProgVolumeToWeb, ProgVolumeValidationPCA, ProgXrayImport, ProgXrayProject [virtual], PSDEstimatorProgram, PythonProgram, XmippMetadataProgram [virtual], and XmippMpiProgram [virtual].

Collaboration diagram for XmippProgram:

Public Member Functions
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	run ()
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 ()
Functions to be implemented by subclasses.
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
virtual void	defineParams ()
virtual void	readParams ()
Program definitions
Following functions will be used in defineParams() for define the arguments of a program. Very useful for checking the command line parameters and for standard usage message.
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)
Public common functions
The functions in this section are available for all programs and should not be reimplemented in derived class, since they are thought to have the same behaivor and it depends on the definition of each program.
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)
Constructors
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Public Attributes
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Protected Member Functions
void	defineCommons ()

Protected Attributes
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

This class represent an Xmipp Program. It have some of the basic functionalities of the programs like argument parsing, checking, usage printing.

Definition at line 52 of file xmipp_program.h.

Constructor & Destructor Documentation

XmippProgram() [1/2]

XmippProgram::XmippProgram

(

)

Constructor

Definition at line 146 of file xmipp_program.cpp.

{
    //by defaul all programs have verbose = 1
    // this can be changed on mpi slaves node for no output at all
    verbose = 1;
    progDef = NULL;
    runWithoutArgs = doRun = false;
    errorCode = 0;
}

XmippProgram() [2/2]

XmippProgram::XmippProgram	(	int	argc,
		const char **	argv
	)

Constructor for read params

Definition at line 156 of file xmipp_program.cpp.

{
    runWithoutArgs = doRun = false;
    errorCode = 0;
    init();
    read(argc, argv);
}

~XmippProgram()

XmippProgram::~XmippProgram ( )

virtual

Destructor

Definition at line 164 of file xmipp_program.cpp.

{
    delete progDef;
}

Member Function Documentation

addExampleLine()

void XmippProgram::addExampleLine	(	const char *	example,
		bool	verbatim = true
	)

Add examples

Definition at line 286 of file xmipp_program.cpp.

{
    progDef->examples.addComment(example, verbatim);
}

addKeywords()

void XmippProgram::addKeywords

(

const char *

keywords

)

Add keywords to the program definition

Definition at line 315 of file xmipp_program.cpp.

{
    progDef->keywords += " ";
    progDef->keywords += keywords;
}

addParamsLine() [1/2]

void XmippProgram::addParamsLine

(

const String &

line

)

Add a params definition line

Definition at line 305 of file xmipp_program.cpp.

{
    progDef->pLexer->addLine(line);
}

addParamsLine() [2/2]

void XmippProgram::addParamsLine

(

const char *

line

)

Definition at line 310 of file xmipp_program.cpp.

{
    progDef->pLexer->addLine((String)line);
}

addSeeAlsoLine()

void XmippProgram::addSeeAlsoLine

(

const char *

seeAlso

)

Add other programs. Separated by commas and without xmipp_

Definition at line 290 of file xmipp_program.cpp.

{
    if (progDef->seeAlso=="")
        progDef->seeAlso = seeAlso;
    else
    {
        progDef->seeAlso +=", ";
        progDef->seeAlso +=seeAlso;
    }
}

addUsageLine()

void XmippProgram::addUsageLine	(	const char *	line,
		bool	verbatim = false
	)

Add usage line

Definition at line 282 of file xmipp_program.cpp.

{
    progDef->usageComments.addComment(line,verbatim);
}

checkParam()

bool XmippProgram::checkParam

(

const char *

param

)

Check if the param was supplied to command line

Definition at line 379 of file xmipp_program.cpp.

{
    ParamDef * paramDef = progDef->findParam(param);
    if (paramDef == NULL)
        REPORT_ERROR(ERR_ARG_INCORRECT, ((String)"Doesn't exists param: " + param));
    return paramDef->counter == 1;
}

clearUsage()

void XmippProgram::clearUsage

(

)

Clear usage

Definition at line 301 of file xmipp_program.cpp.

{
    progDef->usageComments.clear();
}

defineCommons()

void XmippProgram::defineCommons ( )

protected

Define Commons

Add some common definitions to all Xmipp programs

This are a set of internal command for MetaProgram usage they should be hidden

Definition at line 54 of file xmipp_program.cpp.

{
    addParamsLine("== Common options ==");
    processDefaultComment("-v","[-v+ <verbose_level=1>]");
    addParamsLine("alias --verbose;");
    addParamsLine("[-h+* <param=\"\">]      : If not param is supplied show this help message.");
    addParamsLine("                         : Otherwise, specific param help is showed,");
    addParamsLine("                         : param should be provided without the '-'");
    addParamsLine("alias --help;");
    addParamsLine("[--more*]                : Show additional options.");

    addParamsLine("==+++++ Internal section ==");
    addParamsLine("[--xmipp_write_definition* <dbname>] : Print metadata info about the program to sqlite database");
    addParamsLine("[--xmipp_write_wiki* ] : Print metadata info about the program in wiki format");
    addParamsLine("[--xmipp_write_autocomplete* <scriptfile>] : Add program autocomplete bash options to script file");
    addParamsLine("[--xmipp_protocol_script <script>] : This is only meanful when execute throught protocols");
    addParamsLine("[--xmipp_validate_params] : Validate input params");
}

defineParams()

void XmippProgram::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented in ProgMask, ProgFindCenter2D, ProgMicrographAutomaticPicking2, ProgClassifyCL3D, ProgClassifyCL2D, ProgNormalize, ProgMLTomo, BasicMpiMetadataProgram< BASE_CLASS >, BasicMpiMetadataProgram< ProgAngularContinuousAssign >, BasicMpiMetadataProgram< ProgPSDSort >, BasicMpiMetadataProgram< ProgEliminateByEnergy >, BasicMpiMetadataProgram< ProgThreshold >, BasicMpiMetadataProgram< ProgCorrectWiener2D >, BasicMpiMetadataProgram< ProgAngularDiscreteAssign >, BasicMpiMetadataProgram< ProgMask >, BasicMpiMetadataProgram< ProgTomoExtractSubvolume >, BasicMpiMetadataProgram< ProgFilter >, BasicMpiMetadataProgram< ProgTransformGeometry >, BasicMpiMetadataProgram< ProgImageSSNR >, BasicMpiMetadataProgram< ProgNormalize >, BasicMpiMetadataProgram< ProgImageResize >, BasicMpiMetadataProgram< ProgCorrectPhaseFlip2D >, BasicMpiMetadataProgram< ProgOperate >, BasicMpiMetadataProgram< ProgSymmetrize >, BasicMpiMetadataProgram< ProgCtfCorrectIdr >, MpiMetadataProgram, ProgRecFourier, ProgRecFourierAccel, ProgRecFourierGPU, ProgForwardZernikeSubtomos, ProgForwardZernikeImages, ProgForwardZernikeImagesPriors, ProgTomographAlignment, ProgAngularProjectLibrary, ProgMLF2D, ProgFlexibleAlignment, ProgParallelForwardArtZernike3D, ProgAngularSphAlignment, ProgAngularSphAlignmentGpu, ProgAngularContinuousAssign2, ProgForwardArtZernike3D, ProgFSO, ProgForwardArtZernike3DSubtomos, MpiProgAngularClassAverage, ProgNmaAlignmentVol, ProgAngularProjectionMatching, ProgVolumeToPseudoatoms, ProgConstructPDBDictionary, ProgCTFBasicParams, ProgNmaAlignment, ProgSubtractProjection, ProgReconstructSignificant, ProgArtZernike3D, ProgCtfGroup, ProgAlignVolumes, ProgRecFourierStarPU, ProgClassifyFTTRI, ProgImagePeakHighContrast, ProgAngResAlign, ProgImageRotationalPCA, XmippMetadataProgram, ProgSubtomoSubtraction, ProgForwardZernikeVol, ProgTomoTSFilterDose, ProgMovieFilterDose, ProgVolumeInitialSimulatedAnnealing, ProgMLRefine3D, ProgAngularDiscreteAssign, ProgML2D, ProgVolumeDeformSphGpu, ProgXrayImport, ProgMatrixDimRed, ProgXrayProject, ProgSortImages, ProgVolDeformSph, ProgReconsADMM, ProgClassifySignificant, ProgTomoExtractSubvolume, ProgCommonLine, ProgOpticalAligment, ProgProject, ProgIDRXrayTomo, ProgTomoAlignRefinement, ProgPSDSort, ProgRecWbp, ProgDimRed, ProgMPIRecFourier, MpiProgAngularProjectionMatching, ProgClassifyCL2DCore, ProgMpiAngularProjectLibrary, ProgTomoSimulateTiltseries, ProgCTFEstimateFromMicrograph, ProgSSNR, ProgSimulateMicroscope, ProgAnalyzeCluster, ProgTransformImageGreyLevels, ProgPdbConverter, ProgVolumeSetAlign, ProgReconsXrayART, ProgExtractFeatures, ProgScoreMicrograph, ProgPDBDictionary, ProgAngularDistance, ProgVolumeHalvesRestoration, ProgVolumeSegment, ProgAngularContinuousAssign, ProgDetectMissingWedge, ProgVolumeCorrectBfactor, ProgTomoExtractSubtomograms, ProgPdbValueToVol, ProgSymmetrize, ProgCtfCorrectIdr, ProgVolumePCA, ProgResDir, ProgOperate, MultireferenceAligneability, ProgConvImg, ProgCtfCorrectAmplitude3D, ProgMonogenicSignalRes, ProgEvaluateClass, ProgClassifyFirstSplit3, ProgARTPseudo, ProgVolumeValidationPCA, ProgCTFEnhancePSD, ProgResLocalFilter, ProgRecFourierMpiStarPU, ProgMonoTomo, ProgMonoTomo, ProgAngularDistributionShow, ProgAngularNeighbourhood, ProgMetadataSplit3D, ProgVolumeHomogenizer, ProgVolumeEnhanceContrast, ProgVolumeHalvesRestorationGpu< T >, ProgEvaluateCoordinates, ProgEliminateEmptyParticles, ProgVolumeToWeb, ProgTransformDimRed, ProgAlign2d, ProgCorrectWiener2D, ProgassignmentTiltPair, AProgMovieAlignmentCorrelation< T >, ProgPdbSphDeform, ProgClassifyFirstSplit, ProgClassifyKmeans2D, ProgThreshold, ProgTomoExtractParticleStacks, ProgGpuCorrelation, ProgMPIRun, ProgAdjustVolume, ProgTomoRemoveFluctuations, ProgImageResize, ProgAngularAccuracyPCA, ProgCTFEstimateFromPSD, ProgLocSharpening, ProgResolutionIBW, ProgAlignDualTiltSeries, ProgTransformDownsample, ProgPerformanceTest, ProgCompareDensity, ProgCompareViews, ProgAngularBreakSymmetry, ProgStatistics, ProgTomoMapBack, ProgAlignTiltPairs, ProgVolumeFindSymmetry, ProgCtfCreateCtfdat, ProgApplyVolDeformSph, ProgMakeSpectra, ProgCTFEstimateFromPSDFast, ProgValidationNonTilt, ProgValidationTiltPairs, ProgCTFPhaseFlipping, ProgSortByStatistics, ProgMovieEstimateGain, ProgPdbAnalysis, ProgCoordinatesNoisyZonesFilter, PythonProgram, ProgPdbNmaDeform, ProgMorphology, ProgTransformGeometry, ProgAngularAssignmentMag, ProgCompareClass, Alignment::AProgAlignSignificant< T >, ProgKenderSOM, ProgPdbReduce, ProgReconsART, Alignment::ProgAlignSignificantGPU< T >, ProgTransRangeAdjust, ProgWindow, ProgAngularEstimateTiltAxis, ProgEliminateByEnergy, ProgFilter, ProgCTFShow, ProgSeparateObjects, ProgMetadataSplit, Phantom_transform_parameters, ProgProjectTomography, ProgMPIXrayProject, ProgCorrectPhaseFlip2D, ProgMetadataUtilities, ProgResolutionFsc, ProgHistogram, MpiProgAngularAssignmentMag, ProgMetadataHistogram, ProgHeader, ProgImageSSNR, ProgAddNoise, ProgRestoreWithPDBDictionary, ProgMPIRecWbp, ProgAngularRotate, ProgMovieAlignmentCorrelation< T >, ProgTestWork, ProgPSFXrCreate, MpiProgAngularSphAlignment, MpiProgForwardZernikeImages, MpiProgForwardZernikeImagesPriors, MpiProgForwardZernikeSubtomos, ProgMovieAlignmentCorrelationGPU< T >, ProgSpiderTranslate, ProgCenterImage, ProgPhantomCreate, ProgMetadataImport, FlipParameters, ProgImageVectorize, ProgMicrographScissor, ProgImageResiduals, ProgVolumeStructureFactor, ProgRandomizePhases, ProgVolumeCenter, ProgExtractSubset, ProgMrcCreateMetaData, MpiProgTransformImageGreyLevels, MpiProgAngularContinuousAssign2, MpiProgSubtomoSubtraction, and MpiProgSubtractProjection.

Definition at line 169 of file xmipp_program.cpp.

{
    REPORT_ERROR(ERR_NOT_IMPLEMENTED, "function 'defineParams'");
}

endProgress()

void XmippProgram::endProgress

(

)

Notify end of work

Definition at line 271 of file xmipp_program.cpp.

{
    if (verbose)
        progress_bar(progressTotal);
}

existsParam()

bool XmippProgram::existsParam

(

const char *

param

)

Return true if the program is defined

Definition at line 387 of file xmipp_program.cpp.

{
    ParamDef * paramDef = progDef->findParam(param);
    return paramDef != NULL;
}

getCountParam()

int XmippProgram::getCountParam

(

const char *

param

)

Get the number of arguments supplied to the param

Definition at line 371 of file xmipp_program.cpp.

{
    ParamDef * paramDef = progDef->findParam(param);
    if (paramDef == NULL)
        REPORT_ERROR(ERR_ARG_INCORRECT, ((String)"Doesn't exists param: " + param));
    return paramDef->cmdArguments.size();
}

getDoubleParam() [1/2]

double XmippProgram::getDoubleParam	(	const char *	param,
		int	arg = 0
	)

Definition at line 341 of file xmipp_program.cpp.

{
    return textToFloat(progDef->getParam(param, arg));
}

getDoubleParam() [2/2]

double XmippProgram::getDoubleParam	(	const char *	param,
		const char *	subparam,
		int	arg = 0
	)

Definition at line 346 of file xmipp_program.cpp.

{
    return textToFloat(progDef->getParam(param, subparam, arg));
}

getFloatParam() [1/2]

float XmippProgram::getFloatParam	(	const char *	param,
		int	arg = 0
	)

Definition at line 351 of file xmipp_program.cpp.

{
    return textToFloat(progDef->getParam(param, arg));
}

getFloatParam() [2/2]

float XmippProgram::getFloatParam	(	const char *	param,
		const char *	subparam,
		int	arg = 0
	)

Definition at line 356 of file xmipp_program.cpp.

{
    return textToFloat(progDef->getParam(param, subparam, arg));
}

getIntParam() [1/2]

int XmippProgram::getIntParam	(	const char *	param,
		int	arg = 0
	)

Definition at line 331 of file xmipp_program.cpp.

{
    return textToInteger(progDef->getParam(param, arg));
}

getIntParam() [2/2]

int XmippProgram::getIntParam	(	const char *	param,
		const char *	subparam,
		int	arg = 0
	)

Definition at line 336 of file xmipp_program.cpp.

{
    return textToInteger(progDef->getParam(param, subparam, arg));
}

getListParam()

void XmippProgram::getListParam	(	const char *	param,
		StringVector &	list
	)

Get arguments supplied to param as a list

Definition at line 361 of file xmipp_program.cpp.

{
    ParamDef * paramDef = progDef->findParam(param);
    if (paramDef == NULL)
        REPORT_ERROR(ERR_ARG_INCORRECT, ((String)"Doesn't exists param: " + param));
    list.clear();
    for (size_t i = 0; i < paramDef->cmdArguments.size(); ++i)
        list.push_back(paramDef->cmdArguments[i]);
}

getParam() [1/2]

const char * XmippProgram::getParam	(	const char *	param,
		int	arg = 0
	)

Get the argument of this param, first start at 0 position

Definition at line 321 of file xmipp_program.cpp.

{
    return progDef->getParam(param, arg);
}

getParam() [2/2]

const char * XmippProgram::getParam	(	const char *	param,
		const char *	subparam,
		int	arg = 0
	)

Definition at line 326 of file xmipp_program.cpp.

{
    return progDef->getParam(param, subparam, arg);
}

getParamDef()

ParamDef * XmippProgram::getParamDef

(

const char *

param

)

const

Get Parameter definition

Definition at line 394 of file xmipp_program.cpp.

{
    return progDef->findParam(param);
}

initComments()

void XmippProgram::initComments ( )

virtual

Initialize comments for -v, ...

Reimplemented in XmippMetadataProgram.

Definition at line 33 of file xmipp_program.cpp.

{
    CommentList comments;
    comments.addComment("Verbosity level, 0 means no output.");
    defaultComments["-v"] = comments;
}

initProgress()

void XmippProgram::initProgress	(	size_t	total,
		size_t	stepBin = 60
	)

Functions related to progress notification Set the total amount of work and initialize the progress to 0 The update step is calculated as step = XMIPP_MAX(1, total/stepBin) so, the updates only are done at step multiples

Init progress

Definition at line 251 of file xmipp_program.cpp.

{
    if (verbose)
    {
        progressTotal = total;
        progressStep = XMIPP_MAX(1, total / stepBin);
        progressLast = 0;
        init_progress_bar(total);
    }
}

name()

const char * XmippProgram::name

(

)

const

Returns the name of the program the name of the program is defined by each subclass of this base class.

Definition at line 399 of file xmipp_program.cpp.

{
    return progDef->name.c_str();
}

processDefaultComment()

void XmippProgram::processDefaultComment	(	const char *	param,
		const char *	left
	)

Add the comments for a given default parameter

Definition at line 40 of file xmipp_program.cpp.

{
    addParamsLine(((String)left+":"+defaultComments[param].comments[0]).c_str());
    int imax=defaultComments[param].comments.size();
    for (int i=1; i<imax; ++i)
        addParamsLine(((String)":"+defaultComments[param].comments[i]).c_str());
}

quit()

void XmippProgram::quit ( int  exit_code = 0 ) const

virtual

function to exit the program can be useful redefined for mpi programs

Definition at line 179 of file xmipp_program.cpp.

{
    exit(exit_code);
}

read() [1/3]

void XmippProgram::read ( int  argc, const char **  argv, bool  reportErrors = true  )

virtual

Read the command line arguments If an error occurs while reading arguments, the error message will be printed and the usage of the program showed. So you don't need to do that in readParams();

If not arguments are provided show the console program help

Reimplemented in PythonProgram.

Definition at line 191 of file xmipp_program.cpp.

{
    if (progDef == NULL)
        init();

    setProgramName(argv[0]);

    doRun = false;
    errorCode = 0; //suppose no errors
    //this behavior will be defined with environment variable XMIPP_BEHAVIOR
    if (argc == 1)
    {
        if (runWithoutArgs) {
            doRun = true;
        } else {
            usage();
        }
    }
    else
    {
       
        this->argc = argc;
        this->argv = argv;
        progDef->read(argc, argv, reportErrors);
        if (!checkBuiltIns())
        {
            if (verbose) //if 0, ignore the parameter, useful for mpi programs
                verbose = getIntParam("--verbose");
            this->readParams();
            doRun = !checkParam("--xmipp_validate_params"); //just validation, not run
        }
    }
}

read() [2/3]

void XmippProgram::read ( int  argc, char **  argv, bool  reportErrors = true  )

virtual

Read the command line arguments A convenience wrapper

Reimplemented in ProgRecFourierMpiStarPU, MpiProgVolumeSetAlign, PythonProgram, MpiProgAngularSphAlignment, MpiProgForwardZernikeImages, MpiProgForwardZernikeImagesPriors, MpiProgForwardZernikeSubtomos, MpiProgTransformImageGreyLevels, MpiProgAngularContinuousAssign2, MpiProgSubtomoSubtraction, and MpiProgSubtractProjection.

Definition at line 226 of file xmipp_program.cpp.

{
    read(argc,(const char **)argv,reportErrors);
}

read() [3/3]

void XmippProgram::read

(

const String &

argumentsLine

)

Read arguments from an string. This function should do the same as reading arguments but first convert the string to arguments.

Definition at line 231 of file xmipp_program.cpp.

{
    int argc;
    char ** argv=NULL;
    char * copy=NULL;

    generateCommandLine(argumentsLine, argc, argv, copy);
    read(argc, (const char **)argv);
    delete[] copy;
    delete[] argv[0]; // the only one allocated, the rest is pointing to 'copy'
    delete[] argv;
}

readParams()

void XmippProgram::readParams ( )

virtual

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

Reimplemented in ProgMask, ProgFindCenter2D, ProgMicrographAutomaticPicking2, ProgClassifyCL3D, ProgNormalize, ProgClassifyCL2D, ProgMLTomo, BasicMpiMetadataProgram< BASE_CLASS >, BasicMpiMetadataProgram< ProgAngularContinuousAssign >, BasicMpiMetadataProgram< ProgPSDSort >, BasicMpiMetadataProgram< ProgEliminateByEnergy >, BasicMpiMetadataProgram< ProgThreshold >, BasicMpiMetadataProgram< ProgCorrectWiener2D >, BasicMpiMetadataProgram< ProgAngularDiscreteAssign >, BasicMpiMetadataProgram< ProgMask >, BasicMpiMetadataProgram< ProgTomoExtractSubvolume >, BasicMpiMetadataProgram< ProgFilter >, BasicMpiMetadataProgram< ProgTransformGeometry >, BasicMpiMetadataProgram< ProgImageSSNR >, BasicMpiMetadataProgram< ProgNormalize >, BasicMpiMetadataProgram< ProgImageResize >, BasicMpiMetadataProgram< ProgCorrectPhaseFlip2D >, BasicMpiMetadataProgram< ProgOperate >, BasicMpiMetadataProgram< ProgSymmetrize >, BasicMpiMetadataProgram< ProgCtfCorrectIdr >, MpiMetadataProgram, ProgRecFourier, ProgMetadataUtilities, ProgRecFourierAccel, ProgRecFourierGPU, ProgAlignVolumes, ProgTomographAlignment, ProgForwardZernikeSubtomos, ProgMLF2D, ProgFlexibleAlignment, ProgAngularProjectLibrary, ProgForwardZernikeImages, ProgWindow, ProgForwardZernikeImagesPriors, ProgFSO, ProgParallelForwardArtZernike3D, ProgAngularSphAlignment, MpiProgAngularClassAverage, ProgNmaAlignmentVol, ProgAngularSphAlignmentGpu, ProgAngularContinuousAssign2, ProgForwardArtZernike3D, ProgForwardArtZernike3DSubtomos, ProgNmaAlignment, ProgConstructPDBDictionary, ProgAngularProjectionMatching, ProgVolumeToPseudoatoms, ProgReconstructSignificant, ProgSubtractProjection, ProgRecFourierStarPU, ProgAngResAlign, ProgCTFBasicParams, ProgCtfGroup, ProgArtZernike3D, XmippMetadataProgram, ProgClassifyFTTRI, ProgImagePeakHighContrast, ProgOpticalAligment, ProgForwardZernikeVol, ProgImageRotationalPCA, ProgMLRefine3D, ProgSubtomoSubtraction, ProgVolumeDeformSphGpu, ProgVolumeInitialSimulatedAnnealing, ProgML2D, ProgTomoTSFilterDose, ProgMovieFilterDose, ProgXrayProject, ProgAngularDiscreteAssign, ProgXrayImport, ProgMatrixDimRed, ProgVolDeformSph, ProgVolumeFindSymmetry, ProgReconsADMM, ProgTomoExtractSubvolume, ProgMetadataHistogram, ProgKenderSOM, ProgMicrographScissor, ProgMorphology, ProgIDRXrayTomo, ProgClassifySignificant, ProgCommonLine, MpiProgAngularProjectionMatching, ProgProject, ProgPdbConverter, ProgPSDSort, ProgVolumeSetAlign, ProgSSNR, ProgSortImages, ProgTomoAlignRefinement, ProgReconsXrayART, ProgRecWbp, ProgValidationTiltPairs, ProgDimRed, ProgMPIRecFourier, ProgCTFEstimateFromMicrograph, ProgPDBDictionary, ProgClassifyCL2DCore, ProgSimulateMicroscope, ProgScoreMicrograph, ProgAnalyzeCluster, ProgMpiAngularProjectLibrary, ProgPdbValueToVol, ProgTransformImageGreyLevels, ProgExtractFeatures, ProgHeader, ProgStatistics, ProgVolumeCorrectBfactor, ProgAngularDistance, ProgMetadataSplit, ProgTomoExtractSubtomograms, ProgOperate, ProgVolumeHalvesRestoration, ProgResDir, ProgVolumeSegment, ProgTomoSimulateTiltseries, ProgARTPseudo, ProgConvImg, ProgAngularContinuousAssign, ProgMonogenicSignalRes, ProgSymmetrize, ProgRecFourierMpiStarPU, ProgVolumeEnhanceContrast, ProgTomoExtractParticleStacks, ProgTransRangeAdjust, MultireferenceAligneability, ProgResLocalFilter, ProgMonoTomo, ProgMonoTomo, ProgDetectMissingWedge, ProgVolumePCA, ProgPdbSphDeform, ProgAddNoise, ProgEvaluateClass, ProgassignmentTiltPair, ProgVolumeValidationPCA, ProgCTFEnhancePSD, Phantom_transform_parameters, ProgVolumeHomogenizer, ProgCtfCorrectIdr, ProgCtfCorrectAmplitude3D, ProgClassifyFirstSplit3, ProgAdjustVolume, ProgCompareDensity, ProgCompareViews, ProgCorrectWiener2D, ProgHistogram, ProgPSFXrCreate, ProgImageResize, ProgAngularNeighbourhood, ProgMetadataSplit3D, ProgLocSharpening, ProgVolumeHalvesRestorationGpu< T >, ProgAlignTiltPairs, ProgEvaluateCoordinates, ProgAngularRotate, ProgEliminateEmptyParticles, ProgThreshold, ProgApplyVolDeformSph, ProgMakeSpectra, ProgTransformDimRed, ProgAlign2d, ProgAngularAccuracyPCA, AProgMovieAlignmentCorrelation< T >, ProgCenterImage, ProgMetadataImport, ProgSpiderTranslate, ProgTomoRemoveFluctuations, ProgClassifyFirstSplit, ProgPdbAnalysis, ProgClassifyKmeans2D, ProgResolutionIBW, ProgTransformDownsample, ProgCTFPhaseFlipping, ProgGpuCorrelation, ProgImageVectorize, ProgMovieEstimateGain, ProgPdbNmaDeform, ProgCoordinatesNoisyZonesFilter, ProgCTFEstimateFromPSD, ProgPdbReduce, PythonProgram, ProgAlignDualTiltSeries, ProgPerformanceTest, ProgMPIRun, ProgValidationNonTilt, ProgTransformGeometry, ProgAngularAssignmentMag, ProgAngularBreakSymmetry, ProgSortByStatistics, ProgTomoMapBack, ProgPhantomCreate, ProgAngularEstimateTiltAxis, ProgCTFEstimateFromPSDFast, ProgReconsART, ProgVolumeToWeb, Alignment::ProgAlignSignificantGPU< T >, ProgRandomizePhases, FlipParameters, ProgTestWork, ProgCTFShow, Alignment::AProgAlignSignificant< T >, ProgFilter, ProgCompareClass, ProgProjectTomography, ProgVolumeStructureFactor, ProgVolumeCenter, ProgResolutionFsc, MpiProgAngularSphAlignment, MpiProgForwardZernikeImages, MpiProgForwardZernikeImagesPriors, MpiProgForwardZernikeSubtomos, ProgEliminateByEnergy, ProgMrcCreateMetaData, MpiProgAngularAssignmentMag, ProgAngularDistributionShow, ProgCorrectPhaseFlip2D, ProgImageSSNR, ProgRestoreWithPDBDictionary, ProgMPIRecWbp, MpiProgTransformImageGreyLevels, ProgMovieAlignmentCorrelation< T >, ProgMovieAlignmentCorrelationGPU< T >, ProgCtfCreateCtfdat, MpiProgAngularContinuousAssign2, ProgImageResiduals, ProgSeparateObjects, MpiProgSubtomoSubtraction, MpiProgSubtractProjection, and ProgExtractSubset.

Definition at line 184 of file xmipp_program.cpp.

{
    REPORT_ERROR(ERR_NOT_IMPLEMENTED, "function 'readParams'");
}

run()

void XmippProgram::run ( )

virtual

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

Reimplemented in ProgFindCenter2D, ProgMetadataUtilities, ProgMpiAngularProjectLibrary, ProgOpticalAligment, ProgMicrographAutomaticPicking2, ProgClassifyCL3D, ProgClassifyCL2D, ML2DBaseProgram, ProgSortImages, ProgAlignVolumes, ProgMLTomo, ProgTomographAlignment, ProgImagePeakHighContrast, ProgVolumeFindSymmetry, ProgRecFourier, ProgClassifyFTTRI, XmippMetadataProgram, ProgAngularProjectLibrary, ProgFSO, ProgCtfGroup, Phantom_transform_parameters, ProgImageRotationalPCA, MpiProgAngularClassAverage, ProgAngularProjectionMatching, ProgVolumeToPseudoatoms, ProgKenderSOM, ProgConstructPDBDictionary, ProgReconstructSignificant, ProgRecFourierStarPU, ProgAngResAlign, ProgMicrographScissor, ProgMLRefine3D, ProgForwardZernikeVol, ProgVolumeDeformSphGpu, ProgVolumeInitialSimulatedAnnealing, ProgResDir, ProgExtractFeatures, ProgTomoTSFilterDose, ProgCommonLine, ProgMovieFilterDose, ProgXrayImport, ProgMatrixDimRed, ProgXrayProject, ProgVolDeformSph, ProgMetadataHistogram, ProgMetadataSplit, ProgClassifySignificant, ProgClassifyCL2DCore, ProgRecFourierAccel, ProgMonoTomo, ProgTomoAlignRefinement, ProgAngularRotate, ProgReconsADMM, ProgPdbConverter, ProgIDRXrayTomo, ProgMonoTomo, ProgCTFEstimateFromMicrograph, ProgMPIRecFourier, ProgHistogram, ProgProject, ProgAnalyzeCluster, ProgRecWbp, ProgLocSharpening, ProgVolumeSegment, ProgTomoSimulateTiltseries, ProgSSNR, ProgAngularDistance, ProgMonogenicSignalRes, ProgPdbValueToVol, ProgResLocalFilter, ProgCtfCorrectAmplitude3D, ProgReconsXrayART, ProgValidationTiltPairs, ProgPDBDictionary, ProgScoreMicrograph, ProgAlignDualTiltSeries, ProgAngularDistributionShow, ProgPSFXrCreate, ProgVolumeHalvesRestoration, ProgTomoExtractSubtomograms, ProgVolumeHomogenizer, ProgCtfCreateCtfdat, ProgARTPseudo, ProgDetectMissingWedge, ProgVolumePCA, ProgMPIRun, ProgAlign2d, ProgAngularNeighbourhood, ProgRecFourierMpiStarPU, ProgVolumeToWeb, ProgassignmentTiltPair, ProgEvaluateClass, ProgImageVectorize, ProgVolumeValidationPCA, ProgCTFEstimateFromPSD, ProgAdjustVolume, MultireferenceAligneability, ProgPdbSphDeform, ProgVolumeEnhanceContrast, ProgClassifyFirstSplit3, ProgTomoExtractParticleStacks, ProgVolumeHalvesRestorationGpu< T >, ProgTransformDimRed, ProgMetadataSplit3D, ProgTomoRemoveFluctuations, ProgAlignTiltPairs, ProgEvaluateCoordinates, ProgCompareDensity, ProgCompareViews, ProgEliminateEmptyParticles, AProgMovieAlignmentCorrelation< T >, ProgGpuCorrelation, ProgAngularBreakSymmetry, ProgClassifyFirstSplit, ProgRecFourierGPU, ProgMetadataImport, ProgClassifyKmeans2D, ProgMakeSpectra, ProgResolutionIBW, ProgPerformanceTest, ProgApplyVolDeformSph, ProgVolumeStructureFactor, ProgSeparateObjects, ProgTomoMapBack, ProgSortByStatistics, ProgPdbAnalysis, ProgProjectTomography, ProgAngularAccuracyPCA, ProgCTFEstimateFromPSDFast, ProgPdbNmaDeform, ProgPdbReduce, ProgMrcCreateMetaData, ProgResolutionFsc, ProgPhantomCreate, ProgCTFPhaseFlipping, ProgMovieEstimateGain, ProgValidationNonTilt, ProgCompareClass, ProgCoordinatesNoisyZonesFilter, PythonProgram, ProgAngularEstimateTiltAxis, ProgTestWork, ProgReconsART, Alignment::AProgAlignSignificant< T >, ProgCTFShow, ProgMPIReconsArt, ProgRestoreWithPDBDictionary, ProgMPIXrayProject, and ProgExtractSubset.

Definition at line 174 of file xmipp_program.cpp.

{
    REPORT_ERROR(ERR_NOT_IMPLEMENTED, "function 'run'");
}

setDefaultComment()

void XmippProgram::setDefaultComment	(	const char *	param,
		const char *	comment
	)

Set default comment

Definition at line 48 of file xmipp_program.cpp.

{
    defaultComments[param].clear();
    defaultComments[param].addComment(comment);
}

setProgramName()

void XmippProgram::setProgramName

(

const char *

name

)

Set the program name

Definition at line 277 of file xmipp_program.cpp.

{
    progDef->name = name;
}

setProgress()

void XmippProgram::setProgress

(

size_t

value = 0

)

Notify progress on work

Definition at line 263 of file xmipp_program.cpp.

{
    progressLast = value ? value : progressLast + 1;
    if (verbose && progressLast % progressStep == 0)
        progress_bar(progressLast);
}

show()

void XmippProgram::show ( ) const

virtual

Show parameters

Reimplemented in ProgClassifyCL3D, ProgClassifyCL2D, ProgAngularSphAlignmentGpu, ProgVolumeToPseudoatoms, ProgSubtractProjection, ProgRecFourierStarPU, XmippMetadataProgram, ProgSubtomoSubtraction, ProgVolumeDeformSphGpu, ProgXrayImport, ProgVolumeSegment, ProgARTPseudo, ProgDetectMissingWedge, ProgVolumePCA, ProgPdbSphDeform, ProgTomoRemoveFluctuations, ProgResolutionIBW, ProgApplyVolDeformSph, ProgTomoMapBack, PythonProgram, ProgAngularAssignmentMag, Alignment::ProgAlignSignificantGPU< T >, Alignment::AProgAlignSignificant< T >, and ProgExtractSubset.

Definition at line 429 of file xmipp_program.cpp.

{}

tryRun()

int XmippProgram::tryRun ( )

virtual

Call the run function inside a try/catch block The function will return the error code when 0 means success and a value greater than 0 represents the error type

Reimplemented in XmippMpiProgram, and ProgRecFourierMpiStarPU.

Definition at line 244 of file xmipp_program.cpp.

{
    if (doRun)
        this->run();
    return errorCode;
}

usage() [1/2]

void XmippProgram::usage ( int  verb = 0 ) const

virtual

Print the usage of the program, reduced version

Reimplemented in MpiProgML2D.

Definition at line 404 of file xmipp_program.cpp.

{
    if (verbose)
    {
        ConsolePrinter cp;
        char * var = getenv("XMIPP_COLOR_OFF");
        if (var != NULL)
            cp.color = false;
        cp.printProgram(*progDef, verb);
    }
}

usage() [2/2]

void XmippProgram::usage ( const String &  param, int  verb = 2  )

virtual

Print help about specific parameter

Definition at line 416 of file xmipp_program.cpp.

{
    if (verbose)
    {
        ConsolePrinter cp;
        ParamDef * paramDef = progDef->findParam(param);
        if (paramDef == NULL)
            REPORT_ERROR(ERR_ARG_INCORRECT, ((String)"Doesn't exists param: " + param));
        cp.printParam(*paramDef, verb);
    }
    quit(0);
}

version()

int XmippProgram::version

(

)

const

Return the version of the program

Definition at line 432 of file xmipp_program.cpp.

{
    REPORT_ERROR(ERR_NOT_IMPLEMENTED,"");
}

Member Data Documentation

argc

int XmippProgram::argc

protected

Original command line arguments.

Definition at line 86 of file xmipp_program.h.

argv

const char** XmippProgram::argv

protected

Definition at line 87 of file xmipp_program.h.

debug

int XmippProgram::debug

debug flag

Definition at line 163 of file xmipp_program.h.

defaultComments

std::map<String, CommentList> XmippProgram::defaultComments

protected

Default comments

Definition at line 83 of file xmipp_program.h.

doRun

bool XmippProgram::doRun

Flag to check whether to run or not

Definition at line 91 of file xmipp_program.h.

errorCode

int XmippProgram::errorCode

protected

Value to store possible error codes

Definition at line 78 of file xmipp_program.h.

progDef

ProgramDef* XmippProgram::progDef

protected

Program definition and arguments parser.

Definition at line 80 of file xmipp_program.h.

runWithoutArgs

bool XmippProgram::runWithoutArgs

Flag to mark if the program should run without arguments or just print the usage(default behavior)

Definition at line 95 of file xmipp_program.h.

verbose

int XmippProgram::verbose

Verbosity level.

Definition at line 161 of file xmipp_program.h.

---

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

• xmippCore/core/xmipp_program.h
• xmippCore/core/xmipp_program.cpp