reliontomo.convert.convert40_tomo module

class reliontomo.convert.convert40_tomo.Reader(starFile, dataTable, **kwargs)[source]

Bases: reliontomo.convert.convertBase.ReaderTomo

ALIGNMENT_LABELS = ['rlnOriginXAngst', 'rlnOriginYAngst', 'rlnOriginZAngst', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi']
static gen3dCoordFromStarRow(row, sRate, precedentIdDict, factor=1)[source]
setParticleTransform(particle, row, sRate)[source]

Set the transform values from the row.

starFile2Coords3D(coordsSet, precedentsSet, scaleFactor)[source]
starFile2PseudoSubtomograms(outputSet)[source]
class reliontomo.convert.convert40_tomo.Writer(**kwargs)[source]

Bases: reliontomo.convert.convertBase.WriterTomo

Helper class to convert from Scipion SetOfTomograms and SetOfSubTomograms to star files .

coordinates2Star(coordSet, subtomosStar, sRate=1, coordsScale=1)[source]

Input coordsScale is used to scale the coordinates so they are expressed in bin 1, as expected by Relion 4

pseudoSubtomograms2Star(pSubtomoSet, subtomosStar)[source]
subtomograms2Star(subtomoSet, subtomosStar)[source]
tiltSeries2Star(tsSet, outStarFileName, prot=None, ctfPlotterParentDir=None, eTomoParentDir=None, whiteList=None)[source]

Writes the needed tomograms.star file for relion prepare

:param whiteList list with tilseriesIds to be filter by