# **************************************************************************
# *
# * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * 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
# * 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
# *
# * 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_flexalign import XmippProtFlexAlign
from xmipp3.protocols.protocol_movie_max_shift import XmippProtMovieMaxShift
from .viewer_ctf_consensus import getStringIfActive
[docs]class XmippMovieAlignViewer(Viewer):
_targets = [XmippProtOFAlignment, XmippProtFlexAlign]
_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