relion.convert package

Module contents

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).

fillClassesFromIter(clsSet, iteration)[source]

Create the SetOfClasses3D from a given iteration.

class relion.convert.DefocusGroups[source]

Bases: object

Helper class to create defocus groups for particles.

class Group(id)[source]

Bases: object

Single CTF group.

addDefocus(defocus)[source]
getGroup(defocus)[source]

Return the group that this defocus belong.

splitByDiff(inputParts, defocusDiff=1000, minGroupSize=10)[source]
relion.convert.createReader(**kwargs)[source]

Create a new Reader instance. By default it will create the version (3.1 or older) based on the current plugin binary. It can also be forced to use old format by passing the format=‘30’ argument.

relion.convert.createWriter(**kwargs)[source]

Create a new Writer instance. By default it will create the version (3.1 or older) based on the current plugin binary. It can also be forced to use old format by passing the format=‘30’ argument.

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, if not, it will depends on the binary version
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: fillRandomSubset: extraLabels: postprocessImageRow: format: string value to specify STAR format, if ‘30’ it will use

Relion3.0 format, if not, it will depends on the binary version