# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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'
# *
# **************************************************************************
import os
import pyworkflow.utils as pwutils
from pwem.objects import CTFModel, SetOfParticles
from .convert import readCtfModel, readSetOfParticles
[docs]class GrigorieffLabImportCTF:
""" Import CTF estimated with CTFFIND4. """
def __init__(self, protocol):
self.protocol = protocol
self.copyOrLink = self.protocol.getCopyOrLink()
[docs] def importCTF(self, mic, fileName):
""" Create a CTF model and populate its values.
:param mic: input micrograph object
:param fileName: input file to be parsed
:return: CTFModel object
"""
ctf = CTFModel()
ctf.setMicrograph(mic)
readCtfModel(ctf, fileName)
# Try to find the given PSD file associated with the cttfind log file
# we handle special cases of .ctf extension and _ctffind4 prefix for Relion runs
fnBase = pwutils.removeExt(fileName)
for suffix in ['_psd.mrc', '.mrc', '.ctf']:
psdPrefixes = [fnBase,
fnBase.replace('_ctffind4', '')]
for prefix in psdPrefixes:
psdFile = prefix + suffix
if os.path.exists(psdFile):
if psdFile.endswith('.ctf'):
psdFile += ':mrc'
ctf.setPsdFile(psdFile)
return ctf
return ctf
[docs]class GrigorieffLabImportParticles:
""" Import particles from a Frealign refinement.
:param parFile: the filename of the parameter file with the alignment
:param stackFile: single stack file with the images
"""
def __init__(self, protocol, parFile, stackFile):
self.protocol = protocol
self.copyOrLink = self.protocol.getCopyOrLink()
self.parFile = parFile
self.stackFile = stackFile
def _setupSet(self, partSet):
self.protocol.setSamplingRate(partSet)
partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol.fillAcquisition(partSet.getAcquisition())
[docs] def importParticles(self):
partSet = self.protocol._createSetOfParticles()
partSet.setObjComment('Particles imported from Frealign parfile:\n%s' % self.parFile)
# Create a local link to the input stack file
localStack = self.protocol._getExtraPath(os.path.basename(self.stackFile))
pwutils.createLink(self.stackFile, localStack)
# Create a temporary set only with location
tmpSet = SetOfParticles(filename=':memory:')
tmpSet.readStack(localStack)
self._setupSet(tmpSet)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self._setupSet(partSet)
# Now read the alignment parameters from par file
readSetOfParticles(tmpSet, partSet, self.parFile)
partSet.setHasCTF(True)
# Register the output set of particles
self.protocol._defineOutputs(outputParticles=partSet)
[docs] def validateParticles(self):
""" Overwrite the base class. """
errors = []
return errors