# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# * Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk) [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * 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 3 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.utils import cleanPath
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO
from pyworkflow.protocol.params import LabelParam
from pwem.viewers import MicrographsView, EmProtocolViewer, EmPlotter
import pwem.viewers.showj as showj
from pwem.objects import SetOfMovies
from .protocols import ProtMotionCorr
[docs]class ProtMotioncorrViewer(EmProtocolViewer):
""" Visualization of Motioncor2 results. """
_targets = [ProtMotionCorr]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_label = 'viewer'
def _defineParams(self, form):
form.addSection(label='Visualization')
if self.hasMics():
form.addParam('doShowMics', LabelParam,
label="Show aligned micrographs?", default=True,
help="Show the output aligned micrographs.")
if self.hasDWMics():
form.addParam('doShowMicsDW', LabelParam,
label="Show aligned DOSE-WEIGHTED micrographs?",
default=True,
help="Show the output aligned dose-weighted "
"micrographs.")
form.addParam('doShowMovies', LabelParam,
label="Show output movies?", default=True,
help="Show the output movies with alignment "
"information.")
form.addParam('doShowFailedMovies', LabelParam,
label="Show FAILED movies?", default=True,
help="Create a set of failed movies "
"and display it.")
form.addParam('doShowMotion', LabelParam,
label="Plot motion per frame", default=True,
help="Show accumulated motion for all micrographs. "
"Early motion default cut-off is 4 e/A2.")
def _getVisualizeDict(self):
self._errors = []
visualizeDict = {'doShowMovies': self._viewParam,
'doShowFailedMovies': self._viewParam,
'doShowMotion': self._plotMotion,
}
if self.hasMics():
visualizeDict.update({'doShowMics': self._viewParam})
if self.hasDWMics():
visualizeDict.update({'doShowMicsDW': self._viewParam})
return visualizeDict
[docs] def hasMics(self):
return hasattr(self.protocol, 'outputMicrographs')
[docs] def hasDWMics(self):
return hasattr(self.protocol, 'outputMicrographsDoseWeighted')
def _viewParam(self, param=None):
labelsDef = 'enabled id _filename _samplingRate '
labelsDef += '_acquisition._dosePerFrame _acquisition._doseInitial '
viewParamsDef = {showj.MODE: showj.MODE_MD,
showj.ORDER: labelsDef,
showj.VISIBLE: labelsDef,
showj.RENDER: None
}
if param == 'doShowMics':
return [MicrographsView(self.getProject(),
self.protocol.outputMicrographs)]
elif param == 'doShowMicsDW':
return [MicrographsView(self.getProject(),
self.protocol.outputMicrographsDoseWeighted)]
elif param == 'doShowMovies':
if getattr(self.protocol, 'outputMovies', None) is not None:
output = self.protocol.outputMovies
return [self.objectView(output, viewParams=viewParamsDef)]
else:
return [self.errorMessage('No output movies found!',
title="Visualization error")]
elif param == 'doShowFailedMovies':
self.failedList = self.protocol._readFailedList()
if not self.failedList:
return [self.errorMessage('No failed movies found!',
title="Visualization error")]
else:
sqliteFn = self.protocol._getPath('movies_failed.sqlite')
self.createFailedMoviesSqlite(sqliteFn)
return [self.objectView(sqliteFn, viewParams=viewParamsDef)]
[docs] def createFailedMoviesSqlite(self, path):
inputMovies = self.protocol.inputMovies.get()
cleanPath(path)
movieSet = SetOfMovies(filename=path)
movieSet.copyInfo(inputMovies)
movieSet.copyItems(inputMovies,
updateItemCallback=self._findFailedMovies)
movieSet.write()
movieSet.close()
return movieSet
def _findFailedMovies(self, item, row):
if item.getObjId() not in self.failedList:
setattr(item, "_appendItem", False)
def _plotMotion(self, param=None):
if self.hasDWMics():
output = self.protocol.outputMicrographsDoseWeighted
columns = '_rlnAccumMotionTotal _rlnAccumMotionEarly _rlnAccumMotionLate'
xplotter = EmPlotter.createFromFile(output.getFileName(), '',
plotType='Plot',
columnsStr=columns,
colorsStr='r g b',
linesStr='- - -',
markersStr='. . .',
xcolumn='id',
ylabel='Motion per frame (A)',
xlabel='Micrograph id',
title='Accumulated motion per frame',
bins=False,
orderColumn='id',
orderDirection='ASC')
return [xplotter]
else:
return [self.errorMessage('Plot is available only when dose weighting is ON',
title="Visualization error")]