Inheritance diagram for ProgHeader:

Collaboration diagram for ProgHeader:

Protected Member Functions
void	defineParams ()

void	readParams ()

void	show ()

void	roundShifts (MDRow &row)

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

void	finishProcessing ()

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	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes
HeaderOperation	operation

bool	round_shifts

MDRowVec	row

ApplyGeoParams	params

double	sampling

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 33 of file image_header.cpp.

Member Function Documentation

◆ defineParams()

void ProgHeader::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 42 of file image_header.cpp.

     {
         produces_an_output = true;
         get_image_info = false;
 
         XmippMetadataProgram::defineParams();
         addUsageLine("Operate with image files headers. By default in Xmipp, geometrical transformations");
         addUsageLine("coming in images files headers are ignored. Instead this information is read from");
         addUsageLine("the images metadata if exist. With this program geometrical transformations can be");
         addUsageLine("extracted to a metadata or assigned to header, also allows print or reset image file headers.");
         addParamsLine("[   --print <decompose=0>]    : Print the geometrical transformations in image file headers.");
         addParamsLine("                              : if input is stack and decompose=1 print header of each individual image.");
         addParamsLine("       alias -p;");
         addParamsLine("or --extract     : The output is a selfile with geometrical transformations read from image file headers.");
         addParamsLine("       alias -e;");
         addParamsLine("      requires -o;");
         addParamsLine("or --assign     : Write the geometrical transformations from selfile to the image file headers.");
         addParamsLine("       alias -a;");
         addParamsLine("or --reset      : Reset the geometrical transformations in image file headers.");
         addParamsLine("       alias -r;");
         addParamsLine("or --tree      : Print the tree scheme from file containers as hdf5 files.");
         addParamsLine("       alias -t;");
         addParamsLine("or --sampling_rate <Ts=-1>  : Change the sampling rate (in Angstrom units) in the image file header.");
         addParamsLine("          : If no value is passed then current value in header is print.");
         addParamsLine("       alias -s;");
         addParamsLine("   [--round_shifts]    :Round shifts to integers");
         addExampleLine("Print the header of the images in metadata: ", false);
         addExampleLine("xmipp_image_header -i images.sel");
         addExampleLine("Extract geometrical transformations from image file headers: ", false);
         addExampleLine("xmipp_image_header -i smallStack.stk --extract -o header.doc");
         addExampleLine("Assign the geometrical transformations from the metadata to header: ", false);
         addExampleLine("xmipp_image_header -i header.doc --assign");
         addSeeAlsoLine("transform_geometry");
         addKeywords("header, geometric, transformation, print");
     }

◆ finishProcessing()

void ProgHeader::finishProcessing ( )

inlineprotectedvirtual

Reimplemented from XmippMetadataProgram.

Definition at line 232 of file image_header.cpp.

     {
         if (operation ==HEADER_EXTRACT)
             single_image = false;
         XmippMetadataProgram::finishProcessing();
     }

◆ processImage()

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

inlineprotectedvirtual

Implements XmippMetadataProgram.

Definition at line 165 of file image_header.cpp.

     {
 
         ImageGeneric img;
 
         switch (operation)
         {
         case HEADER_PRINT:
             img.read(fnImg, _HEADER_ALL);
             img.print();
             break;
         case HEADER_EXTRACT:
             img.read(fnImg, _HEADER_ALL);
             rowOut = img.getGeometry();
             if (round_shifts)
                 roundShifts(rowOut);
             rowOut.setValue(MDL_IMAGE, fnImgOut);
             break;
         case HEADER_ASSIGN:
             rowOut = rowIn;
             if (round_shifts)
                 roundShifts(rowOut);
             img.readApplyGeo(fnImg, rowOut, params);
             img.setDataMode(_HEADER_ALL);
             img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
             break;
         case HEADER_RESET:
             img.read(fnImg, _HEADER_ALL);
             img.initGeometry();
             img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
             break;
         case HEADER_SAMPLINGRATE:
             {
                 img.read(fnImg, _HEADER_ALL);
                 if (sampling < 0)
                 {
                     double samplingRead;
                     img.image->MDMainHeader.getValue(MDL_SAMPLINGRATE_X, samplingRead);
                     std::cout << samplingRead << std::endl;
                 }
                 else
                 {
                     img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_X, sampling);
                     img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_Y, sampling);
                     img.image->MDMainHeader.setValue(MDL_SAMPLINGRATE_Z, sampling);
                     img.write(fnImg, ALL_IMAGES, fnImg.isInStack(), WRITE_REPLACE);
                     std::cout << "New sampling rate (Angstrom) = " << sampling << std::endl;
                 }
             }
             break;
         case HEADER_TREE:
             {
                 XmippH5File H5File;
                 FileName filename = fnImg.removeAllPrefixes().removeFileFormat();
 
                 if (H5File.isHdf5(filename.c_str()))
                 {
                     H5File.openFile(fnImg.removeAllPrefixes().removeFileFormat(), H5F_ACC_RDONLY);
                     H5File.showTree();
                 }
                 else
                     REPORT_ERROR(ERR_IMG_UNKNOWN, "Unknown file format to display its data structure.");
             }
             break;
         }
     }

◆ readParams()

void ProgHeader::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_header.cpp.

     {
         if (checkParam("--extract"))
         {
             operation = HEADER_EXTRACT;
             produces_a_metadata = true;
         }
         else if (checkParam("--assign"))
             operation = HEADER_ASSIGN;
         else if (checkParam("--reset"))
             operation = HEADER_RESET;
         else if (checkParam("--sampling_rate"))
         {
             operation = HEADER_SAMPLINGRATE;
             sampling = getDoubleParam("--sampling_rate");
             allow_time_bar = false;
         }
         else if (checkParam("--tree"))
         {
             operation = HEADER_TREE;
             decompose_stacks = false;
         }
         else
         {
             operation = HEADER_PRINT;
             allow_time_bar = false;
             decompose_stacks = getIntParam("--print") == 1;
         }
         XmippMetadataProgram::readParams();
         round_shifts = checkParam("--round_shifts");
         if (operation != HEADER_EXTRACT && checkParam("-o"))
             REPORT_ERROR(ERR_PARAM_INCORRECT, "Argument -o is not valid for this operation");
         params.datamode = HEADER;
     }

◆ roundShifts()

void ProgHeader::roundShifts ( MDRow & row )

inlineprotected

Definition at line 150 of file image_header.cpp.

     {
         double aux = 0.;
         if (row.getValue(MDL_SHIFT_X, aux))
         {
             aux = (double)ROUND(aux);
             row.setValue(MDL_SHIFT_X, aux);
         }
         if (row.getValue(MDL_SHIFT_Y, aux))
         {
             aux = (double)ROUND(aux);
             row.setValue(MDL_SHIFT_Y, aux);
         }
     }

◆ show()

void ProgHeader::show ( )

inlineprotected

Definition at line 113 of file image_header.cpp.

     {
         if (verbose == 0)
             return;
 
         String msg;
         switch (operation)
         {
         case HEADER_PRINT:
             msg = "Printing headers...";
             break;
         case HEADER_EXTRACT:
             msg = "Extracting image(s) geometrical transformations from header to metadata...";
             break;
         case HEADER_ASSIGN:
             msg = "Assigning image(s) geometrical transformations from metadata to header...";
             break;
         case HEADER_RESET:
             msg = "Reseting geometrical transformations from headers...";
             break;
         case HEADER_SAMPLINGRATE:
             if (sampling > 0)
                 msg = "Setting sampling rate into headers...";
             else
                 msg = "Showing sampling rate from headers...";
             break;
         case HEADER_TREE:
             msg = "Printing tree structure...";
             break;
         }
         std::cout << msg << std::endl << "Input: " << fn_in << std::endl;
 
         if (checkParam("-o"))
             std::cout << "Output: " << fn_out << std::endl;
 
     }

Member Data Documentation

◆ operation

HeaderOperation ProgHeader::operation

protected

Definition at line 36 of file image_header.cpp.

◆ params

ApplyGeoParams ProgHeader::params

protected

Definition at line 39 of file image_header.cpp.

◆ round_shifts

bool ProgHeader::round_shifts

protected

Definition at line 37 of file image_header.cpp.

◆ row

MDRowVec ProgHeader::row

protected

Definition at line 38 of file image_header.cpp.

◆ sampling

double ProgHeader::sampling

protected

Definition at line 40 of file image_header.cpp.

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

xmipp/libraries/reconstruction/image_header.cpp

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ finishProcessing()

◆ processImage()

◆ readParams()

◆ roundShifts()

◆ show()

Member Data Documentation

◆ operation

◆ params

◆ round_shifts

◆ row

◆ sampling