Source code for xmipp3.protocols.protocol_movie_opticalflow

# ******************************************************************************
# *
# * Authors:     Josue Gomez Blanco (
# *              Roberto Marabini (
# *              J.M. de la Rosa Trevin (
# *              Vahid Abrishami (
# *
# * 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.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
# *
# * 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
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address ''
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# ******************************************************************************

from os.path import join, exists

import pyworkflow.object as pwobj
import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
from pwem.objects import Image
from pyworkflow import VERSION_1_1
from pyworkflow.gui.project import ProjectWindow

import pwem.emlib.metadata as md
from pwem.protocols.protocol_align_movies import (ProtAlignMovies,

from xmipp3.convert import writeMovieMd
from xmipp3 import Plugin

OBJCMD_MOVIE_ALIGNCARTESIAN = "Display Cartesian Presentation"

[docs]class XmippProtOFAlignment(ProtAlignMovies): """ Wrapper protocol to Xmipp Movie Alignment by Optical Flow """ _label = 'optical alignment' _lastUpdateVersion = VERSION_1_1 CONVERT_TO_MRC = 'mrcs' #--------------------------- DEFINE param functions ------------------------ def _defineAlignmentParams(self, form): ProtAlignMovies._defineAlignmentParams(self, form) form.addSection("Aditional Parameters") # GROUP GPU PARAMETERS #group = form.addGroup('GPU') form.addHidden(params.USE_GPU, params.BooleanParam, default=False, label="Use GPU (vs CPU)", help="Set to true if you want the GPU implementation of " "Optical Flow") form.addHidden(params.GPU_LIST, params.StringParam, default=0, expertLevel=params.LEVEL_ADVANCED, label="Choose GPU core", help="GPU may have several cores. Set it to zero if you " "do not know what we are talking about. First core " "index is 0, second 1 and so on.") group = form.addGroup('OF Parameters') group.addParam('winSize', params.IntParam, default=150, expertLevel=params.LEVEL_ADVANCED, label="Window size", help="Window size (shifts are assumed to be constant " "within this window).") group.addParam('groupSize', params.IntParam, default=1, expertLevel=params.LEVEL_ADVANCED, label="Group Size", help="The number of frames in each group at the " "last step") group.addParam('useAlignment', params.BooleanParam, default=True, label="Use previous movie alignment to SUM frames?", help="Input movies could have alignment information from" "a previous protocol. If you select *Yes*, the " "previous alignment will be taken into account.") group.addParam('doComputePSD', params.BooleanParam, default=True, label="Compute PSD (before/after)?", help="If Yes, the protocol will compute for each movie " "the PSD of the average micrograph (without OF " "alignement) and after that, to compare each PSDs") group.addParam('memory', params.BooleanParam, default=False, label="Keep images in RAM ?", help="If True, the protocol will increase the demand of " "RAM, decreasing disc access") group = form.addGroup('Dose Compensation') group.addParam('doApplyDoseFilter', params.BooleanParam, default=False, label='Apply Dose filter', help='Apply a dose-dependent filter to frames before ' 'summing them. Pre-exposure and dose per frame ' 'should be specified during movies import.') group.addParam('doSaveUnweightedMic', params.BooleanParam, default=True, condition='doSaveAveMic and doApplyDoseFilter', label="Save unweighted micrographs?", help="Yes by default, if you have selected to apply a " "dose-dependent filter to the frames") group.addParam('applyDosePreAlign', params.BooleanParam, default=False, condition='doApplyDoseFilter', label="Apply Dose filter before alignment?", help="if *True*, you apply dose filter before perform " "the alignment; else will apply after alignment.") form.addParallelSection(threads=8, mpi=1) #--------------------------- STEPS functions ------------------------------- def _processMovie(self, movie): inputMovies = self.inputMovies.get() if self.doApplyDoseFilter: outMicFn = self._getExtraPath(self._getOutputMicWtName(movie)) else: outMicFn = self._getExtraPath(self._getOutputMicName(movie)) outMovieFn = self._getExtraPath(self._getOutputMovieName(movie)) aveMic = self._getFnInMovieFolder(movie, "uncorrected_mic.mrc") dark = inputMovies.getDark() gain = inputMovies.getGain() # Get the number of frames and the range # to be used for alignment and sum x, y, n = movie.getDim() a0, aN = self._getFrameRange(n, 'align') gpuId = self.gpuList.get() inputMd = self._getFnInMovieFolder(movie, 'input_movie.xmd') writeMovieMd(movie, inputMd, a0, aN, useAlignment=self.useAlignment) args = '-i %s ' % inputMd args += '-o "%s" ' % self._getOutputShifts(movie) args += ' --frameRange %d %d ' % (0, aN - a0) if dark: args += '--dark %s ' % dark if gain: args += '--gain %s ' % gain winSize = self.winSize.get() doSaveMovie = self.doSaveMovie.get() groupSize = self.groupSize.get() args += ' --winSize %(winSize)d --groupSize %(groupSize)d ' % locals() if self.useGpu: program = 'xmipp_movie_optical_alignment_gpu' args += '--gpu %s ' % gpuId else: program = 'xmipp_movie_optical_alignment_cpu' # We should save the movie either if the user selected it (default) # or if the PSD is going to be computed if self.doSaveAveMic or self.doComputePSD: args += '--oavg "%s" ' % outMicFn if self.doComputePSD: args += '--oavgInitial %s ' % aveMic if doSaveMovie: args += '--outMovie %s ' % outMovieFn roi = [self.cropOffsetX.get(), self.cropOffsetY.get(), self.cropDimX.get(), self.cropDimY.get()] args += '--cropULCorner %d %d ' % (roi[0], roi[1]) args += '--cropDRCorner %d %d ' % (roi[0] + roi[2] -1, roi[1] + roi[3] -1) if self.memory: args += ' --inmemory' toDelete=[] if self.doApplyDoseFilter: pxSize = movie.getSamplingRate() vol = movie.getAcquisition().getVoltage() preExp, dose = self._getCorrectedDose(inputMovies) args += ' --doseCorrection %f %f %f %f' %(dose, pxSize, vol, preExp) if self.applyDosePreAlign: args += ' pre' else: args += ' post' if self.doSaveUnweightedMic: outUnwtMicFn = self._getExtraPath(self._getOutputMicName(movie)) outUnwtMovieFn = self._getExtraPath(self._getOutputMovieUnWtName(movie)) args += ' --oUnc %s %s' % (outUnwtMicFn, outUnwtMovieFn) toDelete.append(outUnwtMovieFn) try: self.runJob(program, args) if self.doSaveAveMic: if not exists(outMicFn): raise Exception("Micrograph %s not produced after " "running %s " % (outMicFn, program)) if self.doSaveMovie: if not exists(outMovieFn): raise Exception("Movie %s not produced after running %s " % (outMovieFn, program)) if self.doComputePSD: self.computePSDImages(movie, aveMic, outMicFn, outputFnCorrected=outMicFn+'psd.png') # If the micrograph was only saved for computing the PSD # we can remove it if not self.doSaveAveMic: pwutils.cleanPath(outMicFn) for fn in toDelete: pwutils.cleanPath(fn) self._saveAlignmentPlots(movie) except Exception as e: print("ERROR: %s failed for movie %s.\n Exception: %s" % (program, movie.getFileName(), e)) #--------------------------- INFO functions ------------------------------- def _validate(self): errors = ProtAlignMovies._validate(self) # Although getFirstItem is not recommended in general, here it is # used only once, for validation purposes, so performance # problems not should be appear. if not self.inputMovies.get() is None: inputSet = self.inputMovies.get() movie = inputSet.getFirstItem() if (not movie.hasAlignment()) and self.useAlignment: errors.append("Your movies have no alignment. Please, set *No* " "the parameter _Use previous movie alignment to SUM" " frames?_") if self.doApplyDoseFilter: doseFrame = inputSet.getAcquisition().getDosePerFrame() if doseFrame == 0.0 or doseFrame is None: errors.append('Dose per frame for input movies is 0 or not ' 'set. You cannot apply dose filter.') if self.numberOfThreads > 1 and self.useGpu: errors.append("GPU and Parallelization can not be used together") ofCpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_cpu") ofGpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_gpu") if not (exists(ofGpu) or exists(ofCpu)): errors.append("It seems that Xmipp Optical Alignment is not installed. " "Please make sure that _scipion/config/scipion.config_ " "contains *OPENCV=True* and OpenCV is in your system.\n" "Then, re-install Xmipp by running " "'scipion installb xmippSrc'.") else: if self.useGpu and not exists(ofGpu): errors.append("It seems that Xmipp Optical Alignment has not been " "compiled with CUDA.\nPlease, try with *GPU=No*.\n" "Error: '%s' not found." % ofGpu) if not self.useGpu and not exists(ofCpu): errors.append("It seems that Xmipp Optical Alignment has been " "compiled with CUDA.\nPlease, try with *GPU=Yes*.\n" "Error: '%s' not found." % ofCpu) return errors def _citations(self): return ['Abrishami2015'] def _methods(self): methods = [] methods.append('Aligning method: Optical Flow') methods.append('- Used a window size of: *%d*' % self.winSize) methods.append('- Used a pyramid size of: *6*') if self.useGpu: methods.append('- Used GPU *%s* for processing' % self.gpuList) return methods def _summary(self): summary = [] inputSet = self.inputMovies.get() if inputSet: summary.append('Number of input movies: *%d*' % inputSet.getSize()) _, _, n = inputSet.getDim() a0, aN = self._getFrameRange(n, 'align') summary.append("Frames from *%d* to *%d* were aligned" % (a0, aN)) if self.doSaveMovie and self.doApplyDoseFilter: summary.append("Warning!!! *Your saved movies are dose weighted*.") return summary #--------------------------- UTILS functions ------------------------------- def _setAlignmentInfo(self, movie, obj): """ Set alignment info such as plot and psd filename, and the cumulative shifts values. Params: movie: Pass the reference movie obj: should pass either the created micrograph or movie """ obj.plotCart = Image() obj.plotCart.setFileName(self._getPlotCart(movie)) if self.doComputePSD: obj.psdCorr = Image() obj.psdCorr.setFileName(self._getPsdCorr(movie)) meanX, meanY = self._loadMeanShifts(movie) obj._xmipp_OFMeanX = pwobj.CsvList() obj._xmipp_OFMeanX.set(meanX) obj._xmipp_OFMeanY = pwobj.CsvList() obj._xmipp_OFMeanY.set(meanY) def _preprocessOutputMicrograph(self, mic, movie): self._setAlignmentInfo(movie, mic) def _createOutputMovie(self, movie): alignedMovie = ProtAlignMovies._createOutputMovie(self, movie) self._setAlignmentInfo(movie, alignedMovie) return alignedMovie def _getOutputMovieName(self, movie): """ Overrided to take into account that DW is append in the filename """ DWstr = '_DW' if self.doApplyDoseFilter.get() else '' return self._getMovieRoot(movie) + '_aligned_movie' + DWstr +'.mrcs' def _getNameExt(self, movie, postFix, ext, extra=False): fn = self._getMovieRoot(movie) + postFix + '.' + ext if extra: return self._getExtraPath(fn) else: return fn def _createOutputMovies(self): """ Returns True if an output set of movies will be generated. The most common case is to always generate output movies, either with alignment only or the binary aligned movie files. Subclasses can override this function to change this behavior. """ return self.doSaveMovie.get() def _getFnInMovieFolder(self, movie, filename): return join(self._getOutputMovieFolder(movie), filename) def _getShiftsFile(self, movie): shiftFile = self._getNameExt(movie, '_shifts', 'xmd', extra=False) return self._getFnInMovieFolder(movie, shiftFile) def _getOutputShifts(self, movie): return self._getNameExt(movie, '_aligned_mic', 'xmd', extra=True) def _getPlotCart(self, movie): return self._getNameExt(movie, '_plot_cart', 'png', extra=True) def _getPsdCorr(self, movie): return self._getNameExt(movie, '_aligned_corrected', 'psd', extra=True) def _loadMeanShifts(self, movie): alignMd = md.MetaData(self._getOutputShifts(movie)) meanX = alignMd.getColumnValues(md.MDL_OPTICALFLOW_MEANX) meanY = alignMd.getColumnValues(md.MDL_OPTICALFLOW_MEANY) return meanX, meanY def _saveAlignmentPlots(self, movie): """ Compute alignment shifts plot and save to file as a png image. """ meanX, meanY = self._loadMeanShifts(movie) plotter = createAlignmentPlot(meanX, meanY) plotter.savefig(self._getPlotCart(movie)) plotter.close() def _createOutputMicrographs(self): createWeighted = self._createOutputWeightedMicrographs() # To create the unweighted average micrographs # we only consider the 'doSaveUnweightedMic' flag if the # weighted ones should be created. return (self.doSaveAveMic and self.doSaveUnweightedMic) def _createOutputWeightedMicrographs(self): return (self.doSaveAveMic and self.doApplyDoseFilter) def _getOutputMovieUnWtName(self, movie): """ Returns the name of the output dose-weighted movie. (relative to micFolder) """ return self._getMovieRoot(movie) + '_aligned_movie.mrcs'
[docs]def showCartesianShiftsPlot(inputSet, itemId): item = inputSet[itemId] if item.hasAttribute('_xmipp_OFMeanX'): meanX = [float(x) for x in item._xmipp_OFMeanX] meanY = [float(y) for y in item._xmipp_OFMeanY] plotter = createAlignmentPlot(meanX, meanY) else: print("These items do not have OF alignment set. ")
ProjectWindow.registerObjectCommand(OBJCMD_MOVIE_ALIGNCARTESIAN, showCartesianShiftsPlot) # Just for backwards compatibility ProtMovieAlignment = XmippProtOFAlignment