relion.convert.convert31 module

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

class relion.convert.convert31.OpticsGroups(opticsTable)[source]

Bases: object

Store information about optics groups in an indexable way. Existing groups can be accessed by number of name.


Add new columns with default values (type inferred from it).

static create(**kwargs)[source]

Return first optics group.

static fromImages(imageSet)[source]
static fromStar(starFilePath)[source]

Create an OpticsGroups from a given STAR file.

static fromString(stringValue)[source]

Create an OpticsGroups from string content (STAR format)


Store the optics groups information in the image acquisition.


Write current optics groups to a given file.


Return a string (STAR format) with the current optics groups.

update(ogId, **kwargs)[source]

Update all Optics Groups with these values.

class relion.convert.convert31.Reader(**kwargs)[source]

Bases: relion.convert.convert_base.ReaderBase

ALIGNMENT_LABELS = ['rlnOriginXAngst', 'rlnOriginYAngst', 'rlnOriginZAngst', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi']
COORD_LABELS = ['rlnCoordinateX', 'rlnCoordinateY', 'rlnMicrographName', 'rlnAutopickFigureOfMerit', 'rlnClassNumber', 'rlnAnglePsi']
CTF_LABELS = ['rlnDefocusU', 'rlnDefocusV', 'rlnDefocusAngle', 'rlnCtfAstigmatism', 'rlnCtfFigureOfMerit', 'rlnCtfMaxResolution']
readSetOfParticles(starFile, partSet, **kwargs)[source]

Convert a star file into a set of particles.


starFile: the filename of the star file partsSet: output particles set

Keyword Arguments:

blockName: The name of the data block (default particles) alignType: alignment type removeDisabled: Remove disabled items

static rowToAcquisition(optics, acq)[source]
static rowToCoord(row)[source]

Create a Coordinate from the row.

static rowToCtf(row, ctf)[source]

Create a CTFModel from the row.

setParticleTransform(particle, row)[source]

Set the transform values from the row.

class relion.convert.convert31.Writer(**kwargs)[source]

Bases: relion.convert.convert_base.WriterBase

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

writeSetOfMicrographs(micsIterable, starFile, **kwargs)[source]
writeSetOfMovies(moviesIterable, starFile, **kwargs)[source]
writeSetOfParticles(partsSet, starFile, **kwargs)[source]

Convert a set of particles into a star file and maybe binary files.


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.


Return the proper label for pixel size.