Source code for relion.viewers.viewer_motioncor

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# * Authors:     Grigory Sharov     (
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# * MRC Laboratory of Molecular Biology, MRC-LMB
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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 ProtRelionMotioncor

[docs]class RelionMotioncorrViewer(EmProtocolViewer): """ Visualization of relion motioncor results. """ _targets = [ProtRelionMotioncor] _environments = [DESKTOP_TKINTER, WEB_DJANGO] _label = 'viewer motioncor' 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', 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")]