# **************************************************************************
# *
# * Authors: Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * 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'
# *
# **************************************************************************
import os
import pyworkflow.utils as pwutils
from pwem.objects import CTFModel
from .convert import readCtfModel
[docs]class GctfImportCTF:
""" Import CTF estimated with GCTF. """
def __init__(self, protocol):
self.protocol = protocol
self.copyOrLink = self.protocol.getCopyOrLink()
[docs] def importCTF(self, mic, fileName):
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 _ctffindX prefix for Relion runs
fnBase = pwutils.removeExt(fileName)
for suffix in ['_psd.mrc', '.mrc', '.ctf']:
psdPrefixes = [fnBase,
fnBase.replace('_ctffind3', ''),
fnBase.replace('_gctf', '')]
for prefix in psdPrefixes:
psdFile = prefix + suffix
if os.path.exists(psdFile):
if psdFile.endswith('.ctf'):
psdFile += ':mrc'
ctf.setPsdFile(psdFile)
return ctf