relion.convert.convert_base module¶
New conversion functions dealing with Relion3.1 new star files format.
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class
relion.convert.convert_base.
ReaderBase
(**kwargs)[source]¶ Bases:
object
Helper class to grab information from star file rows and fill the required values in Scipion objects (e.g particles, micrographs, etc)
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createExtraLabels
(item, row, extraLabels)[source]¶ Create new Objects for each extra label if contained in the columnObj. It will set the self._extraLabels property. Args:
item: Object item that will have new extra labels objects row: column object that should have a method hasColumn extraLabels: list of label names that will be set if present
in columnObj
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readSetOfParticles
(starFile, partsSet, **kwargs)[source]¶ Convert a star file into a set of particles.
- Params:
- starFile: the filename of the star file partsSet: output particles set
- Keyword Arguments:
- blockName: The name of the data block (default particles) alignType: removeDisabled:
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-
class
relion.convert.convert_base.
WriterBase
(**kwargs)[source]¶ Bases:
object
Helper class to convert from Scipion SetOfImages subclasses into Relion>3.1 star files (and binaries if conversion needed).
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writeSetOfParticles
(partsSet, starFile, **kwargs)[source]¶ Convert a set of particles into a star file and maybe binary files.
- Params:
- partsSet: input particles set starFile: the filename of the star file that will be written.
- Keyword Arguments:
blockName: The name of the data block (default particles) fillMagnification: If True set magnification values (default False)
- outputStack: A file name to write all particles. If this option is
- passed, then the outputDir will be ignored.
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