gautomatch.convert module¶
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class
gautomatch.convert.
CoordStarWriter
(filename)[source]¶ Bases:
object
Helper class to write a star file containing coordinates.
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HEADER
= '\ndata_\n\nloop_\n_rlnCoordinateX #1\n_rlnCoordinateY #2\n_rlnAnglePsi #3\n_rlnClassNumber #4\n_rlnAutopickFigureOfMerit #5\n '¶
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gautomatch.convert.
readSetOfCoordinates
(workDir, micSet, coordSet, suffix=None)[source]¶ 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
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gautomatch.convert.
rowToObject
(row, obj, attrDict, extraLabels=[])[source]¶ 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
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gautomatch.convert.
writeCoordsConfig
(configFn, boxSize, state)[source]¶ 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
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gautomatch.convert.
writeDefectsFile
(coordSet, outputFn)[source]¶ Write all coordinates in coordSet as the defects.star file as expected by Gautomatch.
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gautomatch.convert.
writeMicCoords
(mic, coordSet, outputFn)[source]¶ Write all the coordinates in coordSet as star file for micrograph mic.
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gautomatch.convert.
writeSetOfCoordinates
(workDir, coordSet, isGlobal=False)[source]¶ 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.