# **************************************************************************
# *
# * Authors: Airen Zaldivar Peraza (azaldivar@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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'
# *
# **************************************************************************
"""
In this module are protocol base classes related to 2D processing
"""
import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pwem.protocols import EMProtocol
[docs]class Prot3D(EMProtocol):
pass
[docs]class ProtPreprocessVolumes(Prot3D):
""" This class will serve as a base for all protocol
that performs some operation on Volumes (i.e. filters, mask, resize, etc)
It is mainly defined by an inputVolumes and outputVolumes.
"""
def _defineParams(self, form):
form.addSection(label=pwutils.Message.LABEL_INPUT)
form.addParam('inputVolumes', params.PointerParam, important=True,
label=pwutils.Message.LABEL_INPUT_VOLS, pointerClass='Volume, SetOfVolumes',
help='Can be a density volume or a SetOfVolumes.')
# Hook that should be implemented in subclasses
self._defineProcessParams(form)
form.addParallelSection(threads=2, mpi=1)
def _defineProcessParams(self, form):
""" This method should be implemented by subclasses
to add other parameter relatives to the specific operation."""
pass
[docs]class ProtFilterVolumes(ProtPreprocessVolumes):
""" This is the base for the branch of filters,
between the ProtPreprocessVolumes """
pass
[docs]class ProtOperateVolumes(ProtPreprocessVolumes):
""" This is the base for the branch of operations,
between the ProtPreprocessParticles """
def __init__(self, **args):
ProtPreprocessVolumes.__init__(self, **args)
[docs]class ProtMaskVolumes(ProtPreprocessVolumes):
""" This is the base for the branch of mask,
between the ProtPreprocessVolumes """
pass
[docs]class ProtCreateMask3D(ProtPreprocessVolumes):
pass
[docs]class ProtAlignVolume(ProtPreprocessVolumes):
"""Protocol base for Align volumes protocols"""
pass
[docs]class ProtReconstruct3D(Prot3D):
pass
[docs]class ProtRefine3D(Prot3D):
pass
[docs]class ProtClassify3D(Prot3D):
pass
[docs]class ProtInitialVolume(Prot3D):
"""Protocol base for Initial volumes protocols"""
pass
[docs]class ProtAnalysis3D(Prot3D):
pass
[docs]class ProtFitting3D(Prot3D):
pass