Source code for gautomatch.viewers

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# * Authors:     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'
# *
# **************************************************************************
"""
This module implements the viewer for Gautomatch program
"""

from pwem.objects import SetOfCoordinates
from pyworkflow.protocol.params import *
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO
from pwem.viewers import ObjectView
import pyworkflow.utils as pwutils

from gautomatch.protocols import ProtGautomatch


[docs]class GautomatchViewer(ProtocolViewer): """ Visualization of Gautomatch results. """ _environments = [DESKTOP_TKINTER, WEB_DJANGO] _targets = [ProtGautomatch] _label = 'viewer Gautomatch' def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('doShowAutopick', LabelParam, label="Show auto-picked particles?", default=True, help="Show the auto-picked particles") form.addParam('doShowRejected', LabelParam, label="Show rejected particles?", default=True, help="Rejected particles may be useful for adjusting " "picking parameters.") form.addSection(label='Debug output') form.addParam('doShowCC', LabelParam, label="Show cross-correlation files?", default=True, condition='_writeCC') form.addParam('doShowFilt', LabelParam, label="Show pre-filtered micrographs?", default=True, condition='_writeFilt') form.addParam('doShowBgEst', LabelParam, label="Show background estimation?", default=True, condition='_writeBg') form.addParam('doShowBgSub', LabelParam, label="Show background-subtracted micrographs?", default=True, condition='_writeBgSub') form.addParam('doShowSigma', LabelParam, label="Show local sigma micrographs?", default=True, condition='_writeSigma') form.addParam('doShowMask', LabelParam, label="Show auto-detected mask?", default=True, condition='_writeMsk') def _writeCC(self): return True if self.protocol.writeCC.get() else False def _writeFilt(self): return True if self.protocol.writeFilt.get() else False def _writeBg(self): return True if self.protocol.writeBg.get() else False def _writeBgSub(self): return True if self.protocol.writeBgSub.get() else False def _writeSigma(self): return True if self.protocol.writeSigma.get() else False def _writeMsk(self): return True if self.protocol.writeMsk.get() else False def _getVisualizeDict(self): return {'doShowAutopick': self._viewParam, 'doShowRejected': self._viewParam, 'doShowCC': self._viewParam, 'doShowFilt': self._viewParam, 'doShowBgEst': self._viewParam, 'doShowBgSub': self._viewParam, 'doShowSigma': self._viewParam, 'doShowMask': self._viewParam } def _viewParam(self, param=None): micSet = self.protocol.getInputMicrographs() tmpDir = self.protocol._getTmpPath() pwutils.cleanPath(tmpDir) pwutils.makePath(tmpDir) # FIXME: (JMRT) We are always writing the SetOfCoordinates and removing # the tmpDir, we need to take into account if the user has picked # some particles in the tmpDir and has not saved them, that now he # will lose all picked particles. # A possible solution could be to alert that changes have not been # written during modification of tmpDir or create a new Xmipp picking # protocol to continue picking later without losing the coordinates. if micSet is None: raise Exception('visualize: SetOfCoordinates has no micrographs set.') micsFn = pwutils.join(tmpDir, micSet.getName() + '_micrographs.xmd') from .convert import writeSetOfMicrographs from pwem.viewers.showj import launchSupervisedPickerGUI writeSetOfMicrographs(micSet, micsFn) inTmpFolder = True view = [] if param == 'doShowAutopick': self._convertCoords(micSet, tmpDir, coordsType='autopick') launchSupervisedPickerGUI(micsFn, tmpDir, self.protocol, mode='review', inTmpFolder=inTmpFolder) elif param == 'doShowRejected': self._convertCoords(micSet, tmpDir, coordsType='rejected') launchSupervisedPickerGUI(micsFn, tmpDir, self.protocol, mode='review', inTmpFolder=inTmpFolder) elif param == 'doShowCC': fn = self.protocol._getPath('micrographs_ccmax.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view elif param == 'doShowFilt': fn = self.protocol._getPath('micrographs_pref.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view elif param == 'doShowBgEst': fn = self.protocol._getPath('micrographs_bg.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view elif param == 'doShowBgSub': fn = self.protocol._getPath('micrographs_bgfree.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view elif param == 'doShowSigma': fn = self.protocol._getPath('micrographs_lsigma.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view elif param == 'doShowMask': fn = self.protocol._getPath('micrographs_mask.sqlite') view.append(ObjectView(self._project, self.protocol.strId(), fn)) return view def _convertCoords(self, micSet, tmpDir, coordsType): """ Link specified coord set to tmpDir folder and convert it to .pos files""" coordTypes = {'autopick': 'coordinates.sqlite', 'rejected': 'coordinates_rejected.sqlite'} coordsFnIn = self.protocol._getPath(coordTypes[coordsType]) coordsFnOut = pwutils.join(tmpDir, 'coordinates.sqlite') pwutils.createLink(coordsFnIn, coordsFnOut) coordSet = SetOfCoordinates(filename=coordsFnOut) coordSet.setMicrographs(micSet) from .convert import writeSetOfCoordinatesXmipp writeSetOfCoordinatesXmipp(tmpDir, coordSet, ismanual=False)