ProgCtfCreateCtfdat Class Reference

Inheritance diagram for ProgCtfCreateCtfdat:

Collaboration diagram for ProgCtfCreateCtfdat:

Public Member Functions
void	readParams ()
void	defineParams ()
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	fn_sel
FileName	fn_doc
FileName	fn_ctf
FileName	fn_param
FileName	oroot
bool	do_mode2
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 ctf_create_ctfdat.cpp.

Member Function Documentation

defineParams()

void ProgCtfCreateCtfdat::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 57 of file ctf_create_ctfdat.cpp.

    {
        addUsageLine("Create CTFdat files from a selfile that contains image selfiles for each micrograph.");
        addUsageLine("+This program is useful when interacting with other packages outputs. There are two ");
        addUsageLine("+main usage modes. In the first mode you should provide a ctfparam file with common");
        addUsageLine("+options of each micrograph and a metadata with defocus values for each one. ");
        addUsageLine("+In the second mode you should provide a metadata with filenames of the ctfparams for");
        addUsageLine("+each  micrograph.");

        addParamsLine("  -i <selfile>           : Input selfile of selfiles for each micrograph");
        addParamsLine("  --oroot <rootname=out>  : Root name for output files ");
        addParamsLine("  --defocus <metadata> <common_ctf> : CTFparam file with common parameters ");
        addParamsLine("                         : Metadata with defocus values for each micrograph ");
        addParamsLine("                         : this file may have either a single column (defocus)");
        addParamsLine("                         : or three columns (defocusU, defocusV, azimuth_angle)");
        addParamsLine("  or --ctfs <selfile>    : Selfile of CTF param files for each micrograph ");

        addExampleLine("Example of use: Sample at MODE 1", false);
        addExampleLine("   ctf_create_ctfdat -i input.sel --defocus defocus.doc input.ctfparam");
        addExampleLine("Example of use: Sample at MODE 2", false);
        addExampleLine("   ctf_create_ctfdat -i input.sel --ctfs ctfparams.sel");
    }

readParams()

void ProgCtfCreateCtfdat::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 41 of file ctf_create_ctfdat.cpp.

    {
        fn_sel = getParam("-i");
        oroot = getParam("--oroot");

        if ((do_mode2 = checkParam("--ctfs")))
        {
            fn_ctf = getParam("--ctfs");
        }
        else
        {
            fn_doc = getParam("--defocus", 0);
            fn_param = getParam("--defocus", 1);
        }
    }

run()

void ProgCtfCreateCtfdat::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 81 of file ctf_create_ctfdat.cpp.

    {
        MetaDataVec mdIn, SFind, mdCtf, ctfdat;
        FileName fnsel, fnimg, fnctf;

        mdIn.read(fn_sel);

        if (do_mode2)//Mode 2: read directly the ctf file
        {
            mdCtf.read(fn_ctf);
        }
        else //Mode 1: create ctf file from defocus file and a common ctfparam file
        {
            // Write param files for each micrograph to disc and make an internal SFctf
            CTFDescription ctf;
            MetaDataVec DFdef;
            double defU, defV, azi;
            int ii = 0;
            DFdef.read(fn_doc);
            ctf.read(fn_param);
            ctf.enable_CTF = true;
            ctf.enable_CTFnoise = false;

            if (mdIn.size() != DFdef.size())
                REPORT_ERROR(ERR_IO_SIZE, "Sizes between input images (-i) and docfile(-doc) should be the same!!! ");

            for (size_t objId : DFdef.ids())
            {
                ii++;
                DFdef.getValue(MDL_CTF_DEFOCUSU, defU, objId);
                if (!DFdef.getValue(MDL_CTF_DEFOCUSU, defV, objId))
                    defV=defU;
                if (!DFdef.getValue(MDL_CTF_DEFOCUS_ANGLE, azi, objId))
                    azi=0;

                ctf.DeltafU = defU;
                ctf.DeltafV = defV;
                ctf.azimuthal_angle = azi;
                fnctf.compose(oroot, ii, "ctfparam");
                ctf.write(fnctf);
                mdCtf.setValue(MDL_CTF_MODEL, fnctf, mdCtf.addObject());
                if (verbose)
                  std::cout << formatString(" Saved CTF parameter file %s for micrograph number %d", fnctf.c_str(), ii) << std::endl;
            }
        }

        // For both modes
        if (mdIn.size() != mdCtf.size())
            REPORT_ERROR(ERR_MD_OBJECTNUMBER, "Selfiles of options -i and -ctfs have unequal number of entries! ");

        size_t id;

        auto itIdIn = mdIn.ids().begin();
        auto itIdCtf = mdCtf.ids().begin();
        const auto totalSize = mdIn.ids().end();
        for (; itIdIn != totalSize; ++itIdIn, ++itIdCtf)
        {
            mdIn.getValue(MDL_SELFILE,fnsel, *itIdIn);
            mdCtf.getValue(MDL_CTF_MODEL,fnctf, *itIdCtf);
            SFind.read(fnsel);
            for (size_t objId : SFind.ids())
            {
                SFind.getValue(MDL_IMAGE,fnimg, objId);
                id = ctfdat.addObject();
                ctfdat.setValue(MDL_IMAGE,fnimg, id);
                ctfdat.setValue(MDL_CTF_MODEL,fnctf, id);
            }
        }

        FileName fn = oroot + ".ctfdat";
        ctfdat.write(fn);
        if (verbose)
          std::cout << " Saved CTFdat file as " << fn << std::endl << " Done! "<< std::endl;
    }

Member Data Documentation

do_mode2

bool ProgCtfCreateCtfdat::do_mode2

Definition at line 37 of file ctf_create_ctfdat.cpp.

fn_ctf

FileName ProgCtfCreateCtfdat::fn_ctf

Definition at line 36 of file ctf_create_ctfdat.cpp.

fn_doc

FileName ProgCtfCreateCtfdat::fn_doc

Definition at line 36 of file ctf_create_ctfdat.cpp.

fn_param

FileName ProgCtfCreateCtfdat::fn_param

Definition at line 36 of file ctf_create_ctfdat.cpp.

fn_sel

FileName ProgCtfCreateCtfdat::fn_sel

Definition at line 36 of file ctf_create_ctfdat.cpp.

oroot

FileName ProgCtfCreateCtfdat::oroot

Definition at line 36 of file ctf_create_ctfdat.cpp.

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

• xmipp/legacy/libraries/reconstruction/ctf_create_ctfdat.cpp