# **************************************************************************
# *
# * 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
from pwem.protocols import EMProtocol, pwutils
from pyworkflow.protocol import STEPS_PARALLEL
from pyworkflow.constants import BETA
import pyworkflow.protocol.params as params
from tomo.objects import CTFTomo
from tomo.protocols import ProtTsEstimateCTF
from .program_gctf import ProgramGctf
import gctf
[docs]class ProtTsGctf(ProtTsEstimateCTF):
""" CTF estimation on a set of tilt series using GCTF. """
_label = 'tilt-series gctf'
_devStatus = BETA
def __init__(self, **kwargs):
EMProtocol.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL
# -------------------------- DEFINE param functions -----------------------
def _initialize(self):
ProtTsEstimateCTF._initialize(self)
self._gctfProgram = ProgramGctf(self)
def _defineProcessParams(self, form):
form.addParam('recalculate', params.BooleanParam, default=False,
condition='recalculate',
label="Do recalculate ctf?")
form.addParam('continueRun', params.PointerParam, allowsNull=True,
condition='recalculate', label="Input previous run",
pointerClass='ProtTsCtffind')
form.addHidden('sqliteFile', params.FileParam,
condition='recalculate',
allowsNull=True)
form.addParam('ctfDownFactor', params.FloatParam, default=1.,
label='CTF Downsampling factor',
help='Set to 1 for no downsampling. Non-integer downsample '
'factors are possible. This downsampling is only used '
'for estimating the CTF and it does not affect any '
'further calculation. Ideally the estimation of the '
'CTF is optimal when the Thon rings are not too '
'concentrated at the origin (too small to be seen) '
'and not occupying the whole power spectrum (since '
'this downsampling might entail aliasing).')
ProgramGctf.defineProcessParams(form)
# --------------------------- STEPS functions ----------------------------
def _estimateCtf(self, workingDir, tiFn, ti):
try:
program, args = self._gctfProgram.getCommand(
scannedPixelSize=self._params['scannedPixelSize'])
args += ' %s/*.mrc' % workingDir
self.runJob(program, args, env=gctf.Plugin.getEnviron())
ext = self._gctfProgram.getExt()
# Move files we want to keep
micBase = pwutils.removeBaseExt(tiFn)
def _getFile(suffix):
print("File: %s" % os.path.join(workingDir, micBase + suffix))
return os.path.join(workingDir, micBase + suffix)
# move output from tmp to extra
pwutils.moveFile(_getFile(ext),
self._getExtraPath(micBase + '_ctf.mrc'))
pwutils.moveFile(_getFile('_gctf.log'), self._getTmpPath())
pwutils.moveFile(_getFile('_EPA.log'),
self._getExtraPath())
except Exception as ex:
print("ERROR: Gctf has failed for %s" % tiFn)
# --------------------------- INFO functions ------------------------------
def _validate(self):
errors = []
return errors
# --------------------------- UTILS functions ----------------------------
[docs] def getCtf(self, ti):
""" Parse the CTF object estimated for this Tilt-Image. """
prefix = self.getTiPrefix(ti)
psd = self._getExtraPath(prefix + '_ctf.mrc')
outCtf = self._getTmpPath(prefix + '_gctf.log')
ctfModel = self._gctfProgram.parseOutputAsCtf(outCtf, psdFile=psd)
ctfTomo = CTFTomo.ctfModelToCtfTomo(ctfModel)
return ctfTomo