relion.convert package¶
Submodules¶
Module contents¶
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class
relion.convert.
ClassesLoader
(protocol, alignType)[source]¶ Bases:
object
Helper class to read classes information from star files produced by Relion classification runs (2D or 3D).
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class
relion.convert.
DefocusGroups
[source]¶ Bases:
object
Helper class to create defocus groups for particles.
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relion.convert.
createReader
(**kwargs)[source]¶ Create a new Reader instance. By default it will create the new version (3.1 or newer) of STAR file. It can also be forced to use old format by passing the format=‘30’ argument
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relion.convert.
createWriter
(**kwargs)[source]¶ Create a new Writer instance. By default it will create the new version (3.1 or newer) of STAR file.
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relion.convert.
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: format: string value to specify STAR format, if ‘30’ it will use
Relion3.0 format
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relion.convert.
writeSetOfParticles
(imgSet, starFile, **kwargs)[source]¶ Convenience function to a SetOfImages as Relion metadata using a Writer.
- Params:
- imgSet: the SetOfImages instance. starFile: the filename where to write the meta
- Keyword Arguments:
- outputDir: where binary files will be converted or linked. blockName: The name of the data block (default particles) fillMagnification: If True set magnification values (default False) alignType: extraLabels: postprocessImageRow: