Source code for xmipptomo.protocols.protocol_flexalign

# **************************************************************************
# *
# * Authors:     David Strelak (davidstrelak@gmail.com)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from tomo.protocols import ProtTsCorrectMotion
from xmipp3.protocols import XmippProtMovieCorr
from pathlib import Path

[docs]class XmippProtTsFlexAlign(ProtTsCorrectMotion, XmippProtMovieCorr): """ Simple protocol to average TiltSeries movies as basic motion correction. It is used mainly for testing purposes. """ _label = 'tiltseries FlexAlign' evenOddCapable = True def _defineParams(self, form): ProtTsCorrectMotion._defineParams(self, form) form.addSection(label="FlexAlign") XmippProtMovieCorr._defineAlignmentParams(self, form) def _getOutputMicName(self, movie): return self._getTiltImageMRoot(movie) + ".mrc" def _processTiltImageM(self, workingFolder, tiltImageM, *args): # XXX hack - create needed attributes and directories, so that we don't have to change the implementation of the FlexAlign dir = self._getOutputMovieFolder(tiltImageM) Path(dir).mkdir(parents=True, exist_ok=True) self.inputMovies = self.inputTiltSeriesM # Get actual user decision about keeping aligned movies doSaveMovie = self.doSaveMovie.get() # If need to do even/odd if self._doSplitEvenOdd(): self.doSaveMovie.set(True) self._processMovie(tiltImageM) # Restore user decision about saving movies self.doSaveMovie.set(doSaveMovie) self.inputMovies = None