Source code for xmipp3.protocols.protocol_movie_split_frames

# **************************************************************************
# *
# * Authors:     Jose Luis Vilas Prieto (jlvilas@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * This program is distributed in the hope that it will be useful,
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# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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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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import os, shutil
from os.path import basename
import pyworkflow.utils as pwutils
from pyworkflow import VERSION_1_1
from pyworkflow.protocol.params import (PointerParam, BooleanParam)

from pwem.protocols import ProtPreprocessMicrographs

from pwem.objects import Movie, Micrograph, SetOfMovies


[docs]class XmippProtSplitFrames(ProtPreprocessMicrographs): """ Wrapper protocol to Xmipp split Odd Even. Applies the possibility of creating 2 different outputs of movies with a quantity of frames related to their odd or even nature (that is, if each frame represents an odd or even number). """ _label = 'split frames' _lastUpdateVersion = VERSION_1_1 #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputMovies', PointerParam, pointerClass='SetOfMovies', label="Input movies", important=True, help='Select a set of movies to be split into two sets (odd and even).' 'It means, the set of frames is split in two subsets.') form.addParam('sumFrames', BooleanParam, label="Sum Frames", important=False, help='Set yes to get a set of micrograms, or no to get a set of movies.') #--------------------------- STEPS functions ------------------------------- def _insertAllSteps(self): self._insertFunctionStep(self.splittingStep) self._insertFunctionStep(self.convertXmdToStackStep) self._insertFunctionStep(self.separateOddEvenOutputs) self._insertFunctionStep(self.createOutputStep)
[docs] def splittingStep(self): for movie in self.inputMovies.get(): fnMovie = movie.getFileName() if fnMovie.endswith(".mrc"): fnMovie+=":mrcs" fnMovieOdd = pwutils.removeExt(basename(fnMovie)) + "_odd.xmd" fnMovieEven = pwutils.removeExt(basename(fnMovie)) + "_even.xmd" args = '--img "%s" ' % fnMovie args += '-o "%s" ' % self._getTmpPath(fnMovieOdd) args += '-e %s ' % self._getTmpPath(fnMovieEven) args += '--type frames ' if self.sumFrames.get() is True: args += '--sum_frames' self.runJob('xmipp_image_odd_even', args)
[docs] def convertXmdToStackStep(self): for movie in self.inputMovies.get(): fnMovie = movie.getFileName() fnMovieOdd = pwutils.removeExt(basename(fnMovie)) + "_odd.xmd" fnMovieEven = pwutils.removeExt(basename(fnMovie)) + "_even.xmd" fnMovieOddMrcs = pwutils.removeExt(basename(fnMovieOdd)) + ".mrcs" fnMovieEvenMrcs = pwutils.removeExt(basename(fnMovieEven)) + ".mrcs" args = '-i "%s" ' % self._getTmpPath(fnMovieOdd) args += '-o "%s" ' % self._getExtraPath(fnMovieOddMrcs) self.runJob('xmipp_image_convert', args) args = '-i "%s" ' % self._getTmpPath(fnMovieEven) args += '-o "%s" ' % self._getExtraPath(fnMovieEvenMrcs) self.runJob('xmipp_image_convert', args)
[docs] def separateOddEvenOutputs(self): oddDir = os.path.join(self._getExtraPath(), 'oddFrames') evenDir = os.path.join(self._getExtraPath(), 'evenFrames') os.makedirs(oddDir, exist_ok=True) os.makedirs(evenDir, exist_ok=True) for movie in self.inputMovies.get(): fnMovie = movie.getFileName() fnMovieOddMrcs = self._getExtraPath(pwutils.removeExt(basename(fnMovie)) + "_odd.mrcs") shutil.move(fnMovieOddMrcs, os.path.join(oddDir,pwutils.removeExt(basename(fnMovie)) + ".mrcs")) fnMovieEvenMrcs = self._getExtraPath(pwutils.removeExt(basename(fnMovie)) + "_even.mrcs") shutil.move(fnMovieEvenMrcs, os.path.join(evenDir, pwutils.removeExt(basename(fnMovie)) + ".mrcs"))
[docs] def createOutputStep(self): inSet = self.inputMovies.get() oddSet = self._createSetOfMovies(suffix='odd') evenSet = self._createSetOfMovies(suffix='even') oddSet.copyInfo(inSet) evenSet.copyInfo(inSet) oddDir = os.path.join(self._getExtraPath(), 'oddFrames') evenDir = os.path.join(self._getExtraPath(), 'evenFrames') for movie in inSet: fnMovie = movie.getFileName() fnMovieOddMrcs = os.path.join(oddDir,pwutils.removeExt(basename(fnMovie)) + ".mrcs") fnMovieEvenMrcs = os.path.join(evenDir,pwutils.removeExt(basename(fnMovie)) + ".mrcs") imgOutOdd = Movie() imgOutEven = Movie() imgOutOdd.copyInfo(movie) imgOutEven.copyInfo(movie) imgOutOdd.setFileName(fnMovieOddMrcs) imgOutEven.setFileName(fnMovieEvenMrcs) if movie.getNumberOfFrames() % 2 == 0: imgOutOdd.setFramesRange([1, imgOutOdd.getNumberOfFrames() / 2, 1]) imgOutEven.setFramesRange([1, imgOutEven.getNumberOfFrames() / 2, 1]) else: imgOutOdd.setFramesRange([1, round(imgOutOdd.getNumberOfFrames() / 2), 1]) imgOutEven.setFramesRange([1, round(imgOutEven.getNumberOfFrames() / 2) - 1, 1]) oddSet.append(imgOutOdd) evenSet.append(imgOutEven) oddSet.setFramesRange([1,oddSet.getFirstItem().getNumberOfFrames(),1]) evenSet.setFramesRange([1,evenSet.getFirstItem().getNumberOfFrames(),1]) self._defineOutputs(oddMovie=oddSet) self._defineOutputs(evenMovie=evenSet) self._defineSourceRelation(inSet, oddSet) self._defineSourceRelation(inSet, evenSet) '''for movie in inSet: self._defineSourceRelation(movie, oddSet) self._defineSourceRelation(movie, evenSet)''' ''' if self.sumFrames.get() is True: oddSetAligned = self._createSetOfMicrographs(suffix='oddMic') evenSetAligned = self._createSetOfMicrographs(suffix='evenMic') for movie in self.inputMovies.get(): fnMovie = movie.getFileName() fnMicOdd = self._getExtraPath(pwutils.removeExt(basename(fnMovie)) + "_odd_aligned.mrcs") fnMicEven = self._getExtraPath(pwutils.removeExt(basename(fnMovie)) + "_even_aligned.mrcs") imgOutOdd = Micrograph() imgOutEven = Micrograph() imgOutOdd.setFileName(fnMicOdd) imgOutEven.setFileName(fnMicEven) imgOutOdd.setSamplingRate(movie.getSamplingRate()) imgOutEven.setSamplingRate(movie.getSamplingRate()) oddSetAligned.append(imgOutOdd) evenSetAligned.append(imgOutEven) oddSetAligned.copyInfo(self.inputMovies.get()) evenSetAligned.copyInfo(self.inputMovies.get()) oddSetAligned.setSamplingRate(self.inputMovies.get().getSamplingRate()) evenSetAligned.setSamplingRate(self.inputMovies.get().getSamplingRate()) self._defineOutputs(oddMicrographs=oddSetAligned) self._defineOutputs(evenMicrographs=evenSetAligned) self._defineSourceRelation(self.inputMovies.get(), oddSetAligned) self._defineSourceRelation(self.inputMovies.get(), evenSetAligned) '''
# --------------------------- INFO functions ------------------------------ def _methods(self): messages = [] if hasattr(self, 'resolution_Volume'): messages.append( 'Information about the method/article in ') return messages def _summary(self): summary = [] return summary def _citations(self): return ['']