imod.protocols.protocol_base module

class imod.protocols.protocol_base.ProtImodBase(**args)

Bases: tomo.protocols.protocol_base.ProtTomoImportFiles, pwem.protocols.protocol.EMProtocol, tomo.protocols.protocol_base.ProtTomoBase

Base class with methods used in the rest of the imod protocols

addCTFTomoSeriesToSetFromDefocusFile(inputTs, defocusFilePath)

This method generates a CtfTomoSeries Scipion object from a CTF estimation IMOD .defocus file. :param inputTs: tilt series associated to the CTF tomo series to be added. :param defocusFilePath: Location of the input .defocus file.

convertInputStep(tsObjId, generateAngleFile=True, imodInterpolation=True)

defineExecutionPararell()

getOutputFailedSetOfTiltSeries(inputSet)

getOutputFiducialModelGaps()

getOutputFiducialModelNoGaps()

getOutputInterpolatedSetOfTiltSeries(inputSet)

Method to generate output interpolated classes of set of tilt-series

getOutputSetOfCTFTomoSeries(outputSetName)

getOutputSetOfCoordinates3Ds(inputSet=None, outputSet=None)

getOutputSetOfTiltSeries(inputSet, binning=1)

Method to generate output classes of set of tilt-series

getOutputSetOfTomograms(inputSet, binning=1)

iterFiles()

Iterate through the files matched with the pattern. Provide the fileName and fileId.