ProgMetadataSplit3D Class Reference

#include <metadata_split_3D.h>

Inheritance diagram for ProgMetadataSplit3D:

Collaboration diagram for ProgMetadataSplit3D:

Public Member Functions
void	readParams ()
	Read argument from command line. More...
void	show ()
	Show. More...
void	defineParams ()
	Usage. More...
void	run ()
	Run. 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)
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_in
FileName	fn_vol
FileName	fn_sym
FileName	fn_oroot
double	angularSampling
double	maxDist
MetaDataDb	mdRef
MetaDataDb	mdIn
Matrix1D< int >	correlatesWell
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

MetadataSplit3D parameters.

Definition at line 36 of file metadata_split_3D.h.

Member Function Documentation

defineParams()

void ProgMetadataSplit3D::defineParams ( )

virtual

Usage.

Reimplemented from XmippProgram.

Definition at line 60 of file metadata_split_3D.cpp.

{
    addUsageLine("Separate projections according to a volume");
    addParamsLine("   -i <metadata>               : Metadata with the images to separate. Make sure they have an angular assignment");
    addParamsLine("   --vol <volume>              : Reference volume");
    addParamsLine("  [--oroot <rootname=split>]   : Rootname for the output files");
    addParamsLine("  [--sym <symmetry_file=c1>]   : Symmetry file if any");
    addParamsLine("                               :+The definition of the symmetry is described at [[transform_symmetrize_v3][transform_symmetrize]]");
    addParamsLine("  [--angSampling <a=5>]        : Angular sampling in degrees");
    addParamsLine("  [--maxDist <a=10>]           : Maximum angular distance in degrees");
    addExampleLine("xmipp_metadata_split_3D -i projections.sel --vol volume.vol --oroot split");
}

readParams()

void ProgMetadataSplit3D::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 34 of file metadata_split_3D.cpp.

{
    fn_in    = getParam("-i");
    fn_vol   = getParam("--vol");
    fn_sym   = getParam("--sym");
    fn_oroot = getParam("--oroot");
    angularSampling = getDoubleParam("--angSampling");
    maxDist = getDoubleParam("--maxDist");
}

run()

void ProgMetadataSplit3D::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 127 of file metadata_split_3D.cpp.

{
    // Generate projections
    std::cerr << "Generating projections ..." << std::endl;
    String cmd=formatString("xmipp_angular_project_library -i %s -o %s_gallery.stk --sampling_rate %f --sym %s --method fourier 1 0.25 bspline --compute_neighbors --angular_distance -1 --experimental_images %s -v 0",
            fn_vol.c_str(),fn_oroot.c_str(),angularSampling,fn_sym.c_str(),fn_in.c_str());
    if (system(cmd.c_str())!=0)
        REPORT_ERROR(ERR_UNCLASSIFIED,"Error when generating projections");

    // Read reference and input metadatas
    mdIn.read(fn_in);
    if (!mdIn.containsLabel(MDL_IMAGE_IDX))
        REPORT_ERROR(ERR_MD_MISSINGLABEL,"Input metadata with images does not contain an imageIndex column");
    mdIn.removeDisabled();
    mdRef.read(fn_oroot+"_gallery.doc");
    deleteFile(fn_oroot+"_gallery.doc");
    deleteFile(fn_oroot+"_gallery.stk");
    deleteFile(fn_oroot+"_gallery_sampling.xmd");

    // Get the maximum reference number
    size_t maxRef=0, refno;
    for (size_t objId : mdIn.ids())
    {
        mdIn.getValue(MDL_IMAGE_IDX, refno, objId);
        if (refno>maxRef)
            maxRef=refno;
    }

    // Calculate coocurrence matrix
    correlatesWell.initZeros(maxRef+1);
    Matrix1D<double> projectionDir;
    std::vector<FileName> fnNeighbours;
    FileName fnImg;
    maxDist=DEG2RAD(maxDist);
    MetaDataDb mdNeighbours;
    std::vector<size_t> refs;
    std::vector<double> upperHalf;
    int i=0;
    std::cerr << "Classifying projections ...\n";
    init_progress_bar(mdRef.size());

    for (size_t objId : mdRef.ids())
    {
        // Get the projection direction of this image
        double rot, tilt;
        mdRef.getValue(MDL_ANGLE_ROT,rot, objId);
        mdRef.getValue(MDL_ANGLE_TILT,tilt, objId);
        Euler_direction(rot,tilt,0,projectionDir);

        // Get all images in the input metadata that are close to this one
        getNeighbours(mdIn,projectionDir,mdNeighbours,maxDist);

        // Check if it is upper or lower half
        if (mdNeighbours.size()>0)
        {
            mdRef.getValue(MDL_IMAGE,fnImg, objId);
            analyzeNeighbours(mdNeighbours,fnImg);
            mdNeighbours.getColumnValues(MDL_IMAGE_IDX,refs);
            mdNeighbours.getColumnValues(MDL_COST,upperHalf);

            size_t imax=refs.size();
            for (size_t i=0; i<imax; ++i)
                VEC_ELEM(correlatesWell,refs[i])+=upperHalf[i];
        }
        ++i;
        progress_bar(i);
    }
    progress_bar(mdRef.size());

    // Split in two metadatas
    MetaDataVec mdUpper, mdLower;
    for (auto& row : mdIn)
    {
        mdIn.getValue(MDL_IMAGE_IDX, refno, row.id());
        row.setValue(MDL_COST,(double)VEC_ELEM(correlatesWell,refno));

        if (VEC_ELEM(correlatesWell,refno)>0)
            mdUpper.addRow(row);
        else if (VEC_ELEM(correlatesWell,refno)<0)
            mdLower.addRow(row);
    }
    mdUpper.write(fn_oroot+"_upper.xmd");
    mdLower.write(fn_oroot+"_lower.xmd");
}

show()

void ProgMetadataSplit3D::show

(

)

Show.

Definition at line 45 of file metadata_split_3D.cpp.

{
    if (!verbose)
        return;
    std::cout
    << "Input images:     " << fn_in << std::endl
    << "Reference volume: " << fn_vol << std::endl
    << "Output rootname:  " << fn_oroot << std::endl
    << "Symmetry:         " << fn_sym << std::endl
    << "Angular sampling: " << angularSampling << std::endl
    << "Maximum distance: " << maxDist << std::endl
    ;
}

Member Data Documentation

angularSampling

double ProgMetadataSplit3D::angularSampling

Angular sampling rate

Definition at line 48 of file metadata_split_3D.h.

correlatesWell

Matrix1D<int> ProgMetadataSplit3D::correlatesWell

Definition at line 59 of file metadata_split_3D.h.

fn_in

FileName ProgMetadataSplit3D::fn_in

Input metadata with images

Definition at line 40 of file metadata_split_3D.h.

fn_oroot

FileName ProgMetadataSplit3D::fn_oroot

Rootname for output

Definition at line 46 of file metadata_split_3D.h.

fn_sym

FileName ProgMetadataSplit3D::fn_sym

Filename for the symmetry file

Definition at line 44 of file metadata_split_3D.h.

fn_vol

FileName ProgMetadataSplit3D::fn_vol

Reference volume

Definition at line 42 of file metadata_split_3D.h.

maxDist

double ProgMetadataSplit3D::maxDist

Maximum angular distance

Definition at line 50 of file metadata_split_3D.h.

mdIn

MetaDataDb ProgMetadataSplit3D::mdIn

Definition at line 56 of file metadata_split_3D.h.

mdRef

MetaDataDb ProgMetadataSplit3D::mdRef

Definition at line 53 of file metadata_split_3D.h.

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

• xmipp/libraries/reconstruction/metadata_split_3D.h
• xmipp/libraries/reconstruction/metadata_split_3D.cpp