# **************************************************************************
# *
# * 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 pyworkflow.protocol.params as params
from pyworkflow.constants import PROD
from pwem.objects import Volume
from pwem.emlib.image import ImageHandler
from pwem.protocols import ProtAlignVolume
[docs]class ProtRelionSymmetrizeVolume(ProtAlignVolume):
"""
Symmetrize a volume using Relion programs:
*relion_align_symmetry* and *relion_image_handler*.
"""
_label = 'symmetrize volume'
_devStatus = PROD
# --------------------------- DEFINE param functions -----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputVolume', params.PointerParam,
pointerClass='Volume',
label="Input volume", important=True,
help='Select the input volume to be symmetrized. ')
form.addParam('symmetryGroup', params.StringParam, default='c1',
label="Symmetry",
help='Select which symmetry do you want to apply. ')
form.addParallelSection(threads=0, mpi=0)
# --------------------------- INSERT steps functions -----------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep', self.inputVolume.getObjId())
# --------------------------- STEPS functions ------------------------------
[docs] def createOutputStep(self, volId):
sym = self.symmetryGroup.get()
inFn = self._getPath('input_volume.mrc')
alignedFn = self._getPath('volume_aligned_sym%s.mrc' % sym)
symFn = self._getPath('volume_sym%s.mrc' % sym)
pixSize = self.inputVolume.get().getSamplingRate()
ImageHandler().convert(self.inputVolume.get(), inFn)
self.runJob("relion_align_symmetry",
"--i %s --o %s --sym %s --angpix %0.5f" % (
inFn, alignedFn, sym, pixSize))
self.runJob("relion_image_handler",
"--i %s --o %s --sym %s" % (alignedFn, symFn, sym))
def _defineOutputVol(name, fn):
vol = Volume()
vol.copyInfo(self.inputVolume.get())
vol.setLocation(fn)
self._defineOutputs(**{name: vol})
self._defineTransformRelation(self.inputVolume, vol)
_defineOutputVol('outputVolumeAligned', alignedFn)
_defineOutputVol('outputVolumeSymmetrized', symFn)