Source code for gctf.protocols.protocol_ts_gctf

# **************************************************************************
# *
# * 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

try:
    from tomo.protocols import ProtTsEstimateCTF
except ImportError:
    raise ImportError(
        'To use a Tomography protocol scipion-em-tomo plugin is required.'
        ' See https://github.com/scipion-em/scipion-em-tomo for further details')

from .program_gctf import ProgramGctf
import gctf


[docs]class ProtTsGctf(ProtTsEstimateCTF): """ CTF estimation on Tilt-Series using GCTF. """ _label = 'tiltseries 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._getTmpPath()) except Exception as ex: print("ERROR: Gctf has failed for %s" % tiFn) # --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] return errors def _summary(self): return [self.summaryVar.get('')] # --------------------------- UTILS functions ---------------------------- def _getArgs(self): """ Return a list with parameters that will be passed to the process TiltSeries step. It can be redefined by subclasses. """ return []
[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') return self._gctfProgram.parseOutputAsCtf(outCtf, psdFile=psd)