imod.protocols.protocol_base module

class imod.protocols.protocol_base.ProtImodBase(**args)[source]

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)[source]

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, generateExtraLink=False, imodInterpolation=True)[source]
defineExecutionPararell()[source]
getOutputFailedSetOfTiltSeries(inputSet)[source]
getOutputFiducialModelGaps()[source]
getOutputFiducialModelNoGaps()[source]
getOutputInterpolatedSetOfTiltSeries(inputSet)[source]

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

getOutputSetOfCTFTomoSeries(outputSetName)[source]
getOutputSetOfCoordinates3Ds(inputSet=None, outputSet=None)[source]
getOutputSetOfTiltSeries(inputSet, binning=1)[source]

Method to generate output classes of set of tilt-series

getOutputSetOfTomograms(inputSet, binning=1)[source]
iterFiles()[source]

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