relion.convert.convert_base module

New conversion functions dealing with Relion3.1 new star files format.

class relion.convert.convert_base.ReaderBase(**kwargs)

Bases: object

Helper class to grab information from star file rows and fill the required values in Scipion objects (e.g particles, micrographs, etc)

createExtraLabels(item, row, extraLabels)

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

readSetOfParticles(starFile, partsSet, **kwargs)

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:

setExtraLabels(item, row)

Set values for already computed extraLabels with self.createExtraLabels.

setParticleTransform(particle, row)

Set the transform values from the row.

class relion.convert.convert_base.WriterBase(**kwargs)

Bases: object

Helper class to convert from Scipion SetOfImages subclasses into Relion>3.1 star files (and binaries if conversion needed).

update(attrsList, **kwargs)

Update the some attributes with values from kwargs.

writeSetOfMicrographs(micsIterable, starFile, **kwargs)

writeSetOfMovies(moviesIterable, starFile, **kwargs)

writeSetOfParticles(partsSet, starFile, **kwargs)

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.