# **************************************************************************
# *
# * Authors: David Strelak (davidstrelak@gmail.com)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
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# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
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# **************************************************************************
from pyworkflow import BETA
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'
_devStatus = BETA
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