#include <xmipp_metadata_program.h>

Inherits XmippProgram.

Inherited by FlipParameters, ProgAddNoise, ProgAngularAssignmentMag, ProgAngularContinuousAssign, ProgAngularContinuousAssign2, ProgAngularDiscreteAssign, ProgAngularSphAlignment, ProgAngularSphAlignmentGpu, ProgArtZernike3D, ProgCenterImage, ProgConvImg, ProgCorrectPhaseFlip2D, ProgCorrectWiener2D, ProgCtfCorrectIdr, ProgCTFEnhancePSD, ProgEliminateByEnergy, ProgFilter, ProgFlexibleAlignment, ProgForwardArtZernike3D, ProgForwardArtZernike3DSubtomos, ProgForwardZernikeImages, ProgForwardZernikeImagesPriors, ProgForwardZernikeSubtomos, ProgHeader, ProgImageResiduals, ProgImageResize, ProgImageSSNR, ProgMask, ProgMorphology, ProgNmaAlignment, ProgNmaAlignmentVol, ProgNormalize, ProgOperate, ProgParallelForwardArtZernike3D, ProgPSDSort, ProgRandomizePhases, ProgSimulateMicroscope, ProgSpiderTranslate, ProgStatistics, ProgSubtomoSubtraction, ProgSubtractProjection, ProgSymmetrize, ProgThreshold, ProgTomoExtractSubvolume, ProgTransformDownsample, ProgTransformGeometry, ProgTransformImageGreyLevels, ProgTransRangeAdjust, ProgVolumeCenter, ProgVolumeCorrectBfactor, ProgVolumeSetAlign, and ProgWindow.

Collaboration diagram for XmippMetadataProgram:

[legend]

Public Member Functions
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
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

Protected Member Functions
virtual void	initComments ()

virtual void	defineParams ()

virtual void	readParams ()

virtual void	preProcess ()

virtual void	postProcess ()

virtual void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)=0

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
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

Special class of XmippProgram that performs some operation related with processing images. It can receive a file with images(MetaData) or a single image. The function processImage is virtual here and needs to be implemented by derived classes. Optionally can be implemented preProcess and postProcess to perform some customs actions.

Definition at line 44 of file xmipp_metadata_program.h.

Constructor & Destructor Documentation

◆ XmippMetadataProgram()

XmippMetadataProgram::XmippMetadataProgram ( )

Empty constructor.

Definition at line 32 of file xmipp_metadata_program.cpp.

 {
     oroot = oext = fn_out = fn_in = "";
     mode = MD_OVERWRITE;
     apply_geo = false;
     allow_apply_geo = false;
     produces_an_output = false;
     produces_a_metadata = false;
     each_image_produces_an_output = false;
     allow_time_bar = true;
     decompose_stacks = true;
     delete_output_stack = true;
     get_image_info = true;
     remove_disabled = true;
     single_image = input_is_metadata = input_is_stack = output_is_stack = false;
     mdInSize = 0;
     ndimOut = zdimOut = ydimOut = xdimOut = 0;
     image_label = MDL_IMAGE;
     delete_mdIn = false;
     //Flags to store metadata when -o is stack
     save_metadata_stack = false;
     keep_input_columns = false;
     track_origin = false;
     create_empty_stackfile = false;
     datatypeOut = DT_Double;
     mdIn = nullptr;
 }

◆ ~XmippMetadataProgram()

XmippMetadataProgram::~XmippMetadataProgram ( )

virtual

Destructor

Definition at line 60 of file xmipp_metadata_program.cpp.

 {
     if (delete_mdIn)
         delete mdIn;
 }

Member Function Documentation

◆ checkPoint()

void XmippMetadataProgram::checkPoint ( )

virtual

For very long programs, it may be needed to write checkpoints.

Reimplemented in ProgForwardZernikeSubtomos, ProgForwardZernikeImages, ProgForwardZernikeImagesPriors, MpiProgForwardZernikeImagesPriors, MpiProgForwardZernikeImages, and MpiProgForwardZernikeSubtomos.

Definition at line 317 of file xmipp_metadata_program.cpp.

318 {

319 }

◆ defineLabelParam()

void XmippMetadataProgram::defineLabelParam ( )

protectedvirtual

Define the label param

Reimplemented in ProgPSDSort.

Definition at line 133 of file xmipp_metadata_program.cpp.

 {
     addParamsLine(" [--label+ <image_label=image>]   : Label to be used to read/write images.");
 }

◆ defineParams()

void XmippMetadataProgram::defineParams ( )

protectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 94 of file xmipp_metadata_program.cpp.

 {
     processDefaultComment("-i","-i <input_file>");
     addParamsLine("alias --input;");
     addParamsLine(" [--mode+ <mode=overwrite>]   : Metadata writing mode.");
     addParamsLine("    where <mode>");
     addParamsLine("     overwrite   : Replace the content of the file with the Metadata");
     addParamsLine("     append      : Write the Metadata as a new block, removing the old one");
     defineLabelParam();
 
     if (produces_a_metadata)
         produces_an_output = true;
 
     if (each_image_produces_an_output)
     {
         processDefaultComment("-o","[-o <output_file=\"\">]");
         addParamsLine("   alias --output;");
         processDefaultComment("--oroot","[--oroot <root=\"\">]");
     }
     else if (produces_an_output)
     {
         processDefaultComment("-o","[-o <output_file=\"\">]");
         addParamsLine("   alias --output;");
     }
 
     addParamsLine("  [--save_metadata_stack+ <output_md=\"\">]  : Create a metadata when the output (-o) is an stack");
     addParamsLine("                             : if --oroot is used, the metadata can be saved in -o param.");
     addParamsLine("                             : if output_md is empty, the name of the stack will be used, changing the extension to xmd.");
     addParamsLine(" [--track_origin+]   : Store the original image filename in the output ");
     addParamsLine("                     : metadata in column imageOriginal.");
     addParamsLine(" [--keep_input_columns+]   : Preserve the columns from the input metadata.");
     addParamsLine("                     : Some of the column values can be changed by the program.");
 
     if (allow_apply_geo)
     {
         addParamsLine("  [--dont_apply_geo]   : for 2D-images: do not apply transformation stored in metadata");
     }
 }//function defineParams

◆ finishProcessing()

void XmippMetadataProgram::finishProcessing ( )

protectedvirtual

Definition at line 269 of file xmipp_metadata_program.cpp.

 {
     if (allow_time_bar && verbose && !single_image)
         progress_bar(time_bar_size);
     writeOutput();
 }

◆ getImageToProcess()

bool XmippMetadataProgram::getImageToProcess	(	size_t &	objId,
		size_t &	objIndex
	)

protectedvirtual

Definition at line 321 of file xmipp_metadata_program.cpp.

 {
     if (nullptr == iter) {
         iter = std::unique_ptr<MetaData::id_iterator>(new MetaData::id_iterator(mdIn->ids().begin()));
         iterIndex = 0;
         time_bar_done = 0;
     } else {
         if (*iter == mdIn->ids().end()) {
             throw std::logic_error("Iterating behind the end of the metadata");
         }
         ++iterIndex;
         ++(*iter);
     }
     bool isValid = *iter != mdIn->ids().end();
     if (isValid) {
         ++time_bar_done;
         objId = **iter;
         objIndex = iterIndex;
     }
     return isValid;
 }

◆ getInputMd()

MetaData* XmippMetadataProgram::getInputMd ( )

inline

The input metadata should not be used if there is a very very special case you can use this function

Definition at line 58 of file xmipp_metadata_program.h.

58 { return mdIn; }

◆ getOutputMd()

MetaDataVec& XmippMetadataProgram::getOutputMd ( )

inline

Definition at line 59 of file xmipp_metadata_program.h.

59 { return mdOut; }

◆ init()

void XmippMetadataProgram::init ( void )

virtual

Initialization of variables should be done here

Reimplemented in ProgConvImg.

Definition at line 72 of file xmipp_metadata_program.cpp.

73 {}

◆ initComments()

void XmippMetadataProgram::initComments ( )

protectedvirtual

Initialize comments for -v, ...

Reimplemented from XmippProgram.

Definition at line 75 of file xmipp_metadata_program.cpp.

 {
     XmippProgram::initComments();
 
     CommentList comments;
     comments.addComment("Input file: metadata, stack, volume or image.");
     defaultComments["-i"]=comments;
 
     comments.clear();
     comments.addComment("Output file: metadata, stack, volume or image.");
     defaultComments["-o"]=comments;
 
     comments.clear();
     comments.addComment("Rootname of output individual images.");
     comments.addComment("Output image format can be set adding extension after rootname as \":ext\".");
     defaultComments["--oroot"]=comments;
 }

◆ postProcess()

void XmippMetadataProgram::postProcess ( )

protectedvirtual

Reimplemented in ProgMask, ProgWindow, ProgStatistics, ProgAngularContinuousAssign2, ProgSpiderTranslate, ProgSubtractProjection, ProgSubtomoSubtraction, ProgAngularDiscreteAssign, ProgTomoExtractSubvolume, ProgCorrectWiener2D, ProgImageResize, ProgAngularAssignmentMag, ProgImageSSNR, and ProgImageResiduals.

Definition at line 248 of file xmipp_metadata_program.cpp.

249 {}

◆ preProcess()

void XmippMetadataProgram::preProcess ( )

protectedvirtual

Definition at line 245 of file xmipp_metadata_program.cpp.

246 {}

◆ processImage()

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

protectedpure virtual

Implemented in ProgMask, ProgNormalize, ProgWindow, ProgFlexibleAlignment, ProgAngularDiscreteAssign, ProgForwardZernikeSubtomos, ProgMorphology, ProgForwardZernikeImages, ProgForwardZernikeImagesPriors, ProgNmaAlignment, ProgForwardArtZernike3DSubtomos, ProgNmaAlignmentVol, ProgAngularContinuousAssign2, ProgParallelForwardArtZernike3D, ProgAngularSphAlignment, ProgAngularSphAlignmentGpu, ProgForwardArtZernike3D, ProgHeader, ProgArtZernike3D, ProgSubtractProjection, ProgAddNoise, ProgStatistics, ProgSubtomoSubtraction, ProgSpiderTranslate, ProgTomoExtractSubvolume, ProgSimulateMicroscope, ProgPSDSort, ProgTransRangeAdjust, ProgVolumeSetAlign, ProgTransformImageGreyLevels, ProgAngularContinuousAssign, ProgSymmetrize, ProgVolumeCorrectBfactor, ProgOperate, ProgCtfCorrectIdr, ProgCenterImage, ProgCTFEnhancePSD, ProgConvImg, ProgRandomizePhases, ProgCorrectWiener2D, ProgThreshold, ProgTransformDownsample, ProgImageResize, ProgVolumeCenter, ProgTransformGeometry, FlipParameters, ProgAngularAssignmentMag, ProgEliminateByEnergy, ProgFilter, ProgCorrectPhaseFlip2D, ProgImageSSNR, and ProgImageResiduals.

◆ readParams()

void XmippMetadataProgram::readParams ( )

protectedvirtual

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 138 of file xmipp_metadata_program.cpp.

 {
     fn_in = getParam("-i");
     mode = metadataModeConvert(getParam("--mode"));
 
     if (produces_an_output)
         fn_out = checkParam("-o") ? getParam("-o") : "";
 
     if (each_image_produces_an_output)
     {
         fn_out = checkParam("-o") ? getParam("-o") : "";
         oroot = getParam("--oroot");
     }
 
     if (allow_apply_geo)
         apply_geo = !checkParam("--dont_apply_geo");
 
     // The following flags are an "advanced" options to allow save metadata
     // when the -o is an stack, each program can define its default value
     // that's why the || construct before checkParam call
     save_metadata_stack = save_metadata_stack || checkParam("--save_metadata_stack");
     track_origin = track_origin || checkParam("--track_origin");
     keep_input_columns = keep_input_columns || checkParam("--keep_input_columns");
 
     MetaData * md = new MetaDataVec();
     md->read(fn_in, NULL, decompose_stacks);
     delete_mdIn = true; // Only delete mdIn when called directly from command line
 
     setup(md, fn_out, oroot, apply_geo, MDL::str2Label(getParam("--label")));
 }//function readParams

◆ run()

void XmippMetadataProgram::run ( )

virtual

Run over all images.

When nor -o neither –oroot is passed and want to overwrite input metadata

Reimplemented from XmippProgram.

Definition at line 343 of file xmipp_metadata_program.cpp.

 {
     FileName fnImg, fnImgOut, fullBaseName;
     mdOut.clear(); //this allows multiple runs of the same Program object
 
     //Perform particular preprocessing
     preProcess();
 
     startProcessing();
 
     if (!oroot.empty())
     {
         if (oext.empty())
             oext           = oroot.getFileFormat();
         oextBaseName   = oext;
         fullBaseName   = oroot.removeFileFormat();
         baseName       = fullBaseName.getBaseName();
         pathBaseName   = fullBaseName.getDir();
     }
 
     size_t objId;
     size_t objIndex;
     while (getImageToProcess(objId, objIndex))
     {
         ++objIndex; //increment for composing starting at 1
         auto rowIn = mdIn->getRow(objId);
         rowIn->getValue(image_label, fnImg);
 
         if (fnImg.empty())
             break;
 
         fnImgOut = fnImg;
 
         MDRowVec rowOut;
 
         if (each_image_produces_an_output)
         {
             if (!oroot.empty()) // Compose out name to save as independent images
             {
                 if (oext.empty()) // If oext is still empty, then use ext of indep input images
                 {
                     if (input_is_stack)
                         oextBaseName = "spi";
                     else
                         oextBaseName = fnImg.getFileFormat();
                 }
 
                 if (!baseName.empty() )
                     fnImgOut.compose(fullBaseName, objIndex, oextBaseName);
                 else if (fnImg.isInStack())
                     fnImgOut.compose(pathBaseName + (fnImg.withoutExtension()).getDecomposedFileName(), objIndex, oextBaseName);
                 else
                     fnImgOut = pathBaseName + fnImg.withoutExtension()+ "." + oextBaseName;
             }
             else if (!fn_out.empty() )
             {
                 if (single_image)
                     fnImgOut = fn_out;
                 else
                     fnImgOut.compose(objIndex, fn_out); // Compose out name to save as stacks
             }
             else
                 fnImgOut = fnImg;
             setupRowOut(fnImg, *rowIn.get(), fnImgOut, rowOut);
         }
         else if (produces_a_metadata)
             setupRowOut(fnImg, *rowIn.get(), fnImgOut, rowOut);
 
         processImage(fnImg, fnImgOut, *rowIn.get(), rowOut);
 
         if (each_image_produces_an_output || produces_a_metadata)
             mdOut.addRow(rowOut);
 
         checkPoint();
         showProgress();
     }
     wait();
 
     /* Generate name to save mdOut when output are independent images. It uses as prefix
      * the dirBaseName in order not overwriting files when repeating same command on
      * different directories. If baseName is set it is used, otherwise, input name is used.
      * Then, the suffix _oext is added.*/
     if (fn_out.empty() )
     {
         if (!oroot.empty())
         {
             if (!baseName.empty() )
                 fn_out = findAndReplace(pathBaseName,"/","_") + baseName + "_" + oextBaseName + ".xmd";
             else
                 fn_out = findAndReplace(pathBaseName,"/","_") + fn_in.getBaseName() + "_" + oextBaseName + ".xmd";
         }
         else if (input_is_metadata) 
             fn_out = fn_in;
     }
 
     finishProcessing();
 
     postProcess();
 
     /* Reset the default values of the program in case
      * to be reused.*/
     init();
 }

◆ setMode()

void XmippMetadataProgram::setMode ( WriteModeMetaData _mode )

inline

Definition at line 173 of file xmipp_metadata_program.h.

     {
         mode = _mode;
     }

◆ setup()

void XmippMetadataProgram::setup	(	MetaData *	md,
		const FileName &	o = `""`,
		const FileName &	oroot = `""`,
		bool	applyGeo = `false`,
		MDLabel	label = `MDL_IMAGE`
	)

virtual

Setup of common XmippMetadataProgram arguments to be called from another program.

Definition at line 169 of file xmipp_metadata_program.cpp.

 {
     this->mdIn = md;
     this->fn_out = out;
     this->oroot = oroot;
     this->image_label = image_label;
     this->doRun = true;
     this->iter = nullptr;
 
     if (remove_disabled)
         mdIn->removeDisabled();
 
     if (mdIn->isEmpty())
         REPORT_ERROR(ERR_MD_NOOBJ, "Empty input Metadata.");
 
     mdInSize = mdIn->size();
 
     if (mdIn->isMetadataFile)
         input_is_metadata = true;
     else
     {
         if (mdInSize == 1)
             single_image = true;
         else
             input_is_stack = true;
     }
 
     String labelStr = MDL::label2Str(image_label);
 
     if (image_label == MDL_UNDEFINED)
         REPORT_ERROR(ERR_MD_BADLABEL, formatString("Unknown image label '%s'.", labelStr.c_str()));
 
     if (!mdIn->containsLabel(image_label))
         REPORT_ERROR(ERR_MD_MISSINGLABEL,
                      formatString("Image label '%s' is missing. See option --label.", labelStr.c_str()));
 
     /* Output is stack if, given a filename in fn_out, mdIn has multiple images.
      * In case no output name is given, then input is overwritten and we have to
      * check if it is stack. */
     output_is_stack = mdInSize > 1 && oroot.empty() && (!fn_out.empty() || input_is_stack);
 
     /* Save metadata related to output stack only if required,
      * and output is a stack.*/
     //save_metadata_stack = save_metadata_stack && output_is_stack;
 
     // Only delete output stack in case we are not overwriting input
     delete_output_stack = (output_is_stack && delete_output_stack) ?
                           !(fn_out.empty() && oroot.empty()) : false;
 
     // If the output is a stack, create empty stack file in advance to avoid concurrent access to the header
     create_empty_stackfile = (each_image_produces_an_output && output_is_stack && !fn_out.empty());
 
     // if create, then we need to read the dimensions of the input stack
     if (get_image_info || create_empty_stackfile)
         getImageInfo(*mdIn, xdimOut, ydimOut, zdimOut, ndimOut, datatypeOut, image_label);
 
     apply_geo = applyGeo;
     // if input is volume do not apply geo
     if (zdimOut > 1)
         apply_geo = false;
 }//function setup

◆ setupRowOut()

void XmippMetadataProgram::setupRowOut	(	const FileName &	fnImgIn,
		const MDRow &	rowIn,
		const FileName &	fnImgOut,
		MDRow &	rowOut
	)		const

Prepare rowout.

Definition at line 298 of file xmipp_metadata_program.cpp.

 {
     rowOut.clear();
     if (keep_input_columns) {
         for (const MDObject* col : rowIn)
             rowOut.setValue(*col);
     }
     rowOut.setValue(image_label, fnImgOut);
     rowOut.setValue(MDL_ENABLED, 1);
 
     if (track_origin)
         rowOut.setValue(MDL_IMAGE_ORIGINAL, fnImgIn);
 }

◆ show()

void XmippMetadataProgram::show ( ) const

overrideprotectedvirtual

Show parameters

Reimplemented from XmippProgram.

Definition at line 232 of file xmipp_metadata_program.cpp.

 {
     if (verbose==0)
         return;
     std::cout << "Input File: " << fn_in << std::endl;
     if (apply_geo)
         std::cout << "Reading geometrical transformations stored in metadata" << std::endl;
     if (!fn_out.empty())
         std::cout << "Output File: " << fn_out << std::endl;
     if (!oroot.empty())
         std::cout << "Output Root: " << oroot << std::endl;
 }

◆ showProgress()

void XmippMetadataProgram::showProgress ( )

protectedvirtual

Definition at line 292 of file xmipp_metadata_program.cpp.

 {
     if (time_bar_step>0 && time_bar_done % time_bar_step == 0 && allow_time_bar && verbose && !single_image)
         progress_bar(time_bar_done);
 }

◆ startProcessing()

void XmippMetadataProgram::startProcessing ( )

protectedvirtual

Do some stuff before starting processing in a parallel environment usually this only be executed by master.

Definition at line 251 of file xmipp_metadata_program.cpp.

 {
     if (delete_output_stack)
         fn_out.deleteFile();
 
     if (create_empty_stackfile)
         createEmptyFile(fn_out, xdimOut, ydimOut, zdimOut, mdInSize, true, WRITE_OVERWRITE);
 
     //Show some info
     show();
     // Initialize progress bar
     time_bar_size = mdInSize;
     if (allow_time_bar && verbose && !single_image)
         init_progress_bar(time_bar_size);
     time_bar_step = CEIL((double)time_bar_size / 60.0);
     time_bar_done = 0;
 }

◆ tryRead()

int XmippMetadataProgram::tryRead	(	int	argc,
		const char **	argv,
		bool	reportErrors = `true`
	)

virtual

Call the read 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

Definition at line 66 of file xmipp_metadata_program.cpp.

 {
     this->read( argc, argv,  reportErrors );
     return errorCode;
 }

◆ wait()

void XmippMetadataProgram::wait ( )

virtual

Wait for the distributor to finish.

Definition at line 312 of file xmipp_metadata_program.cpp.

 {
     // In the serial implementation, we don't have to wait. This will be useful for MPI programs
 }

◆ writeOutput()

void XmippMetadataProgram::writeOutput ( )

protectedvirtual

Definition at line 276 of file xmipp_metadata_program.cpp.

 {
     if (!single_image && !mdOut.isEmpty() && !fn_out.empty())
     {
         if (produces_an_output || produces_a_metadata || !oroot.empty()) // Out as independent images
             mdOut.write(fn_out.replaceExtension("xmd"));
         else if (save_metadata_stack) // Output is stack and also save its associated metadata
         {
             FileName outFileName = getParam("--save_metadata_stack");
             if (outFileName.empty())
                 outFileName = fn_out.replaceExtension("xmd");
             mdOut.write(outFileName);
         }
     }
 }

Member Data Documentation

◆ allow_apply_geo

bool XmippMetadataProgram::allow_apply_geo

protected

Provide the program with the param –dont_apply_geo to allow the user deciding whether or not applying the transformation info as stored in the input metadata

Definition at line 93 of file xmipp_metadata_program.h.

◆ allow_time_bar

bool XmippMetadataProgram::allow_time_bar

protected

Show process time bar.

Definition at line 109 of file xmipp_metadata_program.h.

◆ apply_geo

bool XmippMetadataProgram::apply_geo

Apply geo.

Definition at line 66 of file xmipp_metadata_program.h.

◆ baseName

FileName XmippMetadataProgram::baseName

Definition at line 64 of file xmipp_metadata_program.h.

◆ create_empty_stackfile

bool XmippMetadataProgram::create_empty_stackfile

protected

Definition at line 121 of file xmipp_metadata_program.h.

◆ datatypeOut

DataType XmippMetadataProgram::datatypeOut

Definition at line 69 of file xmipp_metadata_program.h.

◆ decompose_stacks

bool XmippMetadataProgram::decompose_stacks

protected

Input Metadata will treat a stack file as a set of images instead of a unique file.

Definition at line 95 of file xmipp_metadata_program.h.

◆ delete_mdIn

bool XmippMetadataProgram::delete_mdIn

protected

Definition at line 123 of file xmipp_metadata_program.h.

◆ delete_output_stack

bool XmippMetadataProgram::delete_output_stack

protected

Delete previous output stack file prior to process images.

Definition at line 97 of file xmipp_metadata_program.h.

◆ each_image_produces_an_output

bool XmippMetadataProgram::each_image_produces_an_output

protected

Indicate that an output is produced for each image in the input.

Definition at line 90 of file xmipp_metadata_program.h.

◆ fn_in

FileName XmippMetadataProgram::fn_in

Filenames of input and output Metadata.

Definition at line 64 of file xmipp_metadata_program.h.

◆ fn_out

FileName XmippMetadataProgram::fn_out

Definition at line 64 of file xmipp_metadata_program.h.

◆ get_image_info

bool XmippMetadataProgram::get_image_info

protected

Get the input image file dimensions to further operations.

Definition at line 99 of file xmipp_metadata_program.h.

◆ image_label

MDLabel XmippMetadataProgram::image_label

protected

MDLabel to be used to read/write images, usually will be MDL_IMAGE.

Definition at line 80 of file xmipp_metadata_program.h.

◆ input_is_metadata

bool XmippMetadataProgram::input_is_metadata

protected

Input is a metadata.

Definition at line 113 of file xmipp_metadata_program.h.

◆ input_is_stack

bool XmippMetadataProgram::input_is_stack

protected

Input is a stack.

Definition at line 117 of file xmipp_metadata_program.h.

◆ keep_input_columns

bool XmippMetadataProgram::keep_input_columns

protected

Keep input metadata columns.

Definition at line 105 of file xmipp_metadata_program.h.

◆ mdInSize

size_t XmippMetadataProgram::mdInSize

Number of input elements.

Definition at line 71 of file xmipp_metadata_program.h.

◆ mode

WriteModeMetaData XmippMetadataProgram::mode

protected

Metadata writing mode: OVERWRITE, APPEND.

Definition at line 75 of file xmipp_metadata_program.h.

◆ ndimOut

size_t XmippMetadataProgram::ndimOut

Output dimensions.

Definition at line 68 of file xmipp_metadata_program.h.

◆ oext

FileName XmippMetadataProgram::oext

protected

Output extension and root.

Definition at line 78 of file xmipp_metadata_program.h.

◆ oextBaseName

FileName XmippMetadataProgram::oextBaseName

Definition at line 64 of file xmipp_metadata_program.h.

◆ oroot

FileName XmippMetadataProgram::oroot

protected

Definition at line 78 of file xmipp_metadata_program.h.

◆ output_is_stack

bool XmippMetadataProgram::output_is_stack

protected

Output is a stack.

Definition at line 119 of file xmipp_metadata_program.h.

◆ pathBaseName

FileName XmippMetadataProgram::pathBaseName

Definition at line 64 of file xmipp_metadata_program.h.

◆ produces_a_metadata

bool XmippMetadataProgram::produces_a_metadata

protected

Indicate that the unique final output file is a Metadata.

Definition at line 88 of file xmipp_metadata_program.h.

◆ produces_an_output

bool XmippMetadataProgram::produces_an_output

protected

Indicate that a unique final output is produced.

Definition at line 86 of file xmipp_metadata_program.h.

◆ remove_disabled

bool XmippMetadataProgram::remove_disabled

protected

Remove disabled images from the input selfile.

Definition at line 107 of file xmipp_metadata_program.h.

◆ save_metadata_stack

bool XmippMetadataProgram::save_metadata_stack

protected

Save the associated output metadata when output file is a stack.

Definition at line 101 of file xmipp_metadata_program.h.

◆ single_image

bool XmippMetadataProgram::single_image

protected

Input is a single image.

Definition at line 115 of file xmipp_metadata_program.h.

◆ time_bar_done

size_t XmippMetadataProgram::time_bar_done

protected

Definition at line 126 of file xmipp_metadata_program.h.

◆ time_bar_size

size_t XmippMetadataProgram::time_bar_size

protected

Definition at line 126 of file xmipp_metadata_program.h.

◆ time_bar_step

size_t XmippMetadataProgram::time_bar_step

protected

Some time bar related counters.

Definition at line 126 of file xmipp_metadata_program.h.

◆ track_origin

bool XmippMetadataProgram::track_origin

protected

Include the original input image filename in the output stack.

Definition at line 103 of file xmipp_metadata_program.h.

◆ xdimOut

size_t XmippMetadataProgram::xdimOut

Definition at line 68 of file xmipp_metadata_program.h.

◆ ydimOut

size_t XmippMetadataProgram::ydimOut

Definition at line 68 of file xmipp_metadata_program.h.

◆ zdimOut

size_t XmippMetadataProgram::zdimOut

Definition at line 68 of file xmipp_metadata_program.h.

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

xmippCore/core/xmipp_metadata_program.h
xmippCore/core/xmipp_metadata_program.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XmippMetadataProgram()

◆ ~XmippMetadataProgram()

Member Function Documentation

◆ checkPoint()

◆ defineLabelParam()

◆ defineParams()

◆ finishProcessing()

◆ getImageToProcess()

◆ getInputMd()

◆ getOutputMd()

◆ init()

◆ initComments()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ run()

◆ setMode()

◆ setup()

◆ setupRowOut()

◆ show()

◆ showProgress()

◆ startProcessing()

◆ tryRead()

◆ wait()

◆ writeOutput()

Member Data Documentation

◆ allow_apply_geo

◆ allow_time_bar

◆ apply_geo

◆ baseName

◆ create_empty_stackfile

◆ datatypeOut

◆ decompose_stacks

◆ delete_mdIn

◆ delete_output_stack

◆ each_image_produces_an_output

◆ fn_in

◆ fn_out

◆ get_image_info

◆ image_label

◆ input_is_metadata

◆ input_is_stack

◆ keep_input_columns

◆ mdInSize

◆ mode

◆ ndimOut

◆ oext

◆ oextBaseName

◆ oroot

◆ output_is_stack

◆ pathBaseName

◆ produces_a_metadata

◆ produces_an_output

◆ remove_disabled

◆ save_metadata_stack

◆ single_image

◆ time_bar_done

◆ time_bar_size

◆ time_bar_step

◆ track_origin

◆ xdimOut

◆ ydimOut

◆ zdimOut