Inheritance diagram for ProgMrcCreateMetaData:

Collaboration diagram for ProgMrcCreateMetaData:

Public Member Functions
void	defineParams ()

void	readParams ()

void	show ()

void	run ()

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)

virtual void	initComments ()

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	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)

	XmippProgram ()

	XmippProgram (int argc, const char **argv)

virtual	~XmippProgram ()

Public Attributes
FileName	fnStack

FileName	fnAngles

FileName	fnOut

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

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

Definition at line 31 of file mrc_create_metadata_main.cpp.

Member Function Documentation

◆ defineParams()

void ProgMrcCreateMetaData::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 36 of file mrc_create_metadata_main.cpp.

     {
         addUsageLine("Produces a selfile valid for tomography with an MRC stack and a list of angles");
         addParamsLine(" --stack <stack>       : Stack file (not necessarily MRC)");
         addParamsLine(" --tiltAngles <rawtlt> : Tilt angle file");
         addParamsLine(" -o <metadata>         : Output metadata");
     }

◆ readParams()

void ProgMrcCreateMetaData::readParams ( )

inlinevirtual

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 44 of file mrc_create_metadata_main.cpp.

     {
         fnStack = getParam("--stack");
         fnAngles = getParam("--tiltAngles");
         fnOut = getParam("-o");
     }

◆ run()

void ProgMrcCreateMetaData::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 60 of file mrc_create_metadata_main.cpp.

     {
         std::string extension=fnStack.getExtension();
         if (extension=="mrc")
             fnStack+=":mrcs";
         else if (extension=="ali")
             fnStack+=":mrcs";
 
         std::ifstream fhAngles;
         fhAngles.open(fnAngles.c_str());
         if (!fhAngles)
             REPORT_ERROR(ERR_IO_NOTOPEN,fnAngles);
 
         Image<double> stack;
         stack.read(fnStack, HEADER);
         size_t xdim, ydim, zdim, ndim;
         stack.getDimensions(xdim, ydim, zdim, ndim);
 
         MetaDataVec MD;
         FileName fnSlice;
         for (unsigned long slice = FIRST_IMAGE; slice <= ndim; slice++)
         {
             double angle;
             fhAngles >> angle;
             fnSlice.compose((int)slice,fnStack);
             size_t objId=MD.addObject();
             MD.setValue(MDL_IMAGE,fnSlice,objId);
             MD.setValue(MDL_ANGLE_TILT,angle,objId);
             MD.setValue(MDL_ENABLED,1,objId);
         }
         MD.write(fnOut);
     }

◆ show()

void ProgMrcCreateMetaData::show ( )

inline

Definition at line 51 of file mrc_create_metadata_main.cpp.

     {
         std::cout
         << "Stack   = " << fnStack  << std::endl
         << "Angles  = " << fnAngles << std::endl
         << "Output  = " << fnOut << std::endl
         ;
     }