gautomatch.convert module

class gautomatch.convert.CoordStarWriter(filename)

Bases: object

Helper class to write a star file containing coordinates.

HEADER = '\ndata_\n\nloop_\n_rlnCoordinateX #1\n_rlnCoordinateY #2\n_rlnAnglePsi #3\n_rlnClassNumber #4\n_rlnAutopickFigureOfMerit #5\n '

close()

writeRow(x, y, psi=0, classNumber=0, autopickFom=0)

gautomatch.convert.openMd(fn, state='Manual')

gautomatch.convert.readCoordinates(mic, fileName, coordsSet)

gautomatch.convert.readSetOfCoordinates(workDir, micSet, coordSet, suffix=None)

Read from coordinates from Gautomatch .star files. For a micrograph: mic1.mrc, the expected coordinate file is: mic1_automatch.star Params:

workDir: where the Gautomatch output files are located. micSet: the SetOfMicrographs. coordSet: the SetOfCoordinates that will be populated. suffix: input coord file suffix

gautomatch.convert.rowToCoordinate(coordRow)

Create a Coordinate from a row of a meta

gautomatch.convert.rowToObject(row, obj, attrDict, extraLabels=[])

This function will convert from a XmippMdRow to an EMObject. Params:

row: the XmippMdRow instance (input) obj: the EMObject instance (output) attrDict: dictionary with the map between obj attributes(keys) and

row MDLabels in Xmipp (values).

extraLabels: a list with extra labels that could be included

as properties with the label name such as: _rlnSomeThing

gautomatch.convert.writeCoordsConfig(configFn, boxSize, state)

Write the config.xmd file needed for Xmipp picker. Params:

configFn: The filename were to store the configuration. boxSize: the box size in pixels for extraction. state: picker state

gautomatch.convert.writeDefectsFile(coordSet, outputFn)

Write all coordinates in coordSet as the defects.star file as expected by Gautomatch.

gautomatch.convert.writeMicCoords(mic, coordSet, outputFn)

Write all the coordinates in coordSet as star file for micrograph mic.

gautomatch.convert.writeSetOfCoordinates(workDir, coordSet, isGlobal=False)

Write set of coordinates from md to star file. Used only for exclusive picking. Creates .star files with bad coordinates (for each mic) and/or a single .star file with global detector defects.

gautomatch.convert.writeSetOfCoordinatesXmipp(posDir, coordSet, ismanual=True, scale=1)

Write a pos file on metadata format for each micrograph on the coordSet. Params:

posDir: the directory where the .pos files will be written. coordSet: the SetOfCoordinates that will be read.

gautomatch.convert.writeSetOfMicrographs(micSet, filename)

Simplified function borrowed from xmipp.