Source code for xmipp3.viewers.viewer_movie_alignment

# **************************************************************************
# *
# * Authors:     J.M. de la Rosa Trevin (jmdelarosa@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
# * 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
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * 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
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

from pyworkflow.viewer import Viewer, DESKTOP_TKINTER, WEB_DJANGO
from pyworkflow.protocol.params import LabelParam
from pwem.viewers import showj, EmProtocolViewer, ObjectView
from pwem.objects import SetOfMicrographs, SetOfMovies

from xmipp3.protocols.protocol_movie_opticalflow import (XmippProtOFAlignment,
                                                 OBJCMD_MOVIE_ALIGNCARTESIAN)
from xmipp3.protocols.protocol_movie_correlation import XmippProtMovieCorr
from xmipp3.protocols.protocol_movie_max_shift import XmippProtMovieMaxShift
from .viewer_ctf_consensus import getStringIfActive

[docs]class XmippMovieAlignViewer(Viewer): _targets = [XmippProtOFAlignment, XmippProtMovieCorr] _environments = [DESKTOP_TKINTER, WEB_DJANGO] _label = 'viewer optical/correlation alignment' def _visualize(self, obj, **kwargs): views = [] if obj.hasAttribute('outputMicrographs'): views.append(ObjectView(self._project, obj.strId(), obj.outputMicrographs.getFileName(), viewParams=getViewParams())) elif obj.hasAttribute('outputMovies'): views.append(ObjectView(self._project, obj.strId(), obj.outputMovies.getFileName(), viewParams=getViewParams())) else: views.append(self.infoMessage("Output (micrographs or movies) has " "not been produced yet.")) return views
[docs]class XmippMovieMaxShiftViewer(EmProtocolViewer): """ This viewer is intendet to visualize the selection made by the Xmipp - Movie max shift protocol. """ _label = 'viewer Movie Max Shift' _environments = [DESKTOP_TKINTER, WEB_DJANGO] _targets = [XmippProtMovieMaxShift] _memory = False resolutionThresholdOLD = -1 # temporary metadata file with ctf that has some resolution greathan than X tmpMetadataFile = 'viewersTmp.sqlite' def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('visualizeMics', LabelParam, label="Visualize passed micrographs", help="Visualize those micrographs considered valid.") form.addParam('visualizeMicsDiscarded', LabelParam, label="Visualize discarded micrographs", help="Visualize discarded micrographs.") def _getVisualizeDict(self): return {'visualizeMics': self._visualizeMics, 'visualizeMicsDiscarded': self._visualizeMicsDiscarded} def _visualizeAny(self, outNameCondition): views = [] # to show micrographs is prior than movies objs = [x for x in self.protocol.iterOutputAttributes(SetOfMicrographs)] objs += [x for x in self.protocol.iterOutputAttributes(SetOfMovies)] for outName, outObj in objs: if outNameCondition(outName): views.append(self.objectView(outObj, viewParams=getViewParams())) break if not views: outputType = 'discarded' if outNameCondition('Discarded') else 'accepted' self.infoMessage('%s does not have %s outputs%s' % (self.protocol.getObjLabel(), outputType, getStringIfActive(self.protocol)), title='Info message').show() return views def _visualizeMics(self, e=None): return self._visualizeAny(lambda x: not x.endswith('Discarded')) def _visualizeMicsDiscarded(self, e=None): return self._visualizeAny(lambda x: x.endswith('Discarded'))
[docs]def getViewParams(): plotLabels = ('psdCorr._filename plotPolar._filename ' 'plotCart._filename plotGlobal._filename') labels = plotLabels + ' _filename ' viewParams = {showj.MODE: showj.MODE_MD, showj.ORDER: 'id ' + labels, showj.VISIBLE: 'id ' + labels, showj.RENDER: plotLabels, showj.ZOOM: 20, showj.OBJCMDS: "'%s'" % OBJCMD_MOVIE_ALIGNCARTESIAN } return viewParams