Source code for pwem.protocols.protocol_3d

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# * Authors:     Airen Zaldivar Peraza (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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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 filters, 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