tomo.protocols.protocol_ts_correct_motion module

class tomo.protocols.protocol_ts_correct_motion.ProtTsAverage(**kwargs)

Bases: ProtTsCorrectMotion

Simple protocol to average TiltSeries movies as basic motion correction. It is used mainly for testing purposes.

class tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion(**kwargs)

Bases: ProtTsProcess

Base class for movie alignment protocols such as: motioncorr, crosscorrelation and optical flow

Alignment parameters are defined in common. For example, the frames range used for alignment and final sum, the binning factor or the cropping options (region of interest)

convertInputStep(inputId)

To be implemented in subclasses.

createOutputStep()

” Overwrites the parent method to allow the creation of odd and even outputs

evenAvgFrameList = []

evenOddCapable = False

getGainAndDark()

Return temporary paths of gain and dark if relevant.

oddAvgFrameList = []

outputSetEven = None

outputSetOdd = None

processTiltImageStep(tsId, tiltImageId, *args)

To be implemented in subclasses.

processTiltSeriesStep(tsId)

Create a single stack with the tiltseries.

tsMList = []