Source code for relion.protocols.protocol_expand_symmetry

# **************************************************************************
# *
# * Authors:     Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology, MRC-LMB
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from emtable import Table

from pyworkflow.protocol.params import StringParam
from pyworkflow.object import String
from pwem.constants import ALIGN_PROJ
from pwem.protocols import ProtProcessParticles

import relion.convert as convert

 
[docs]class ProtRelionExpandSymmetry(ProtProcessParticles): """ This protocols wraps relion_particle_symmetry_expand program. Given an input set of particles with angular assignment, expand the set by applying a pseudo-symmetry. """ _label = 'expand symmetry' # -------------------------- DEFINE param functions ----------------------- def _defineProcessParams(self, form): form.addParam('symmetryGroup', StringParam, default="c1", label='Symmetry group', help='See [[Relion Symmetry][http://www2.mrc-lmb.cam.ac.uk/' 'relion/index.php/Conventions_%26_File_formats#Symmetry]] ' 'page for a description of the symmetry format ' 'accepted by Relion') form.addParallelSection(threads=0, mpi=0) # -------------------------- INSERT steps functions ----------------------- def _insertAllSteps(self): imgsFn = self._getPath('input_particles.star') self._insertFunctionStep('convertInputStep', imgsFn) self._insertFunctionStep('expandSymmetryStep', imgsFn) self._insertFunctionStep('createOutputStep') # -------------------------- STEPS functions ------------------------------
[docs] def convertInputStep(self, outputFn): """ Create a metadata with the images and geometrical information. """ convert.writeSetOfParticles( self.inputParticles.get(), outputFn, outputDir=self._getPath())
[docs] def expandSymmetryStep(self, imgsFn): outImagesMd = self._getExtraPath('expanded_particles.star') args = " --i %s --sym %s --o %s" % (imgsFn, self.symmetryGroup.get(), outImagesMd) self.runJob("relion_particle_symmetry_expand", args)
[docs] def createOutputStep(self): imgSet = self.inputParticles.get() partSet = self._createSetOfParticles() partSet.copyInfo(imgSet) outImagesMd = self._getExtraPath('expanded_particles.star') # remove repeating rlnImageId column mdOptics = Table(fileName=outImagesMd, tableName='optics') mdOut = Table(fileName=outImagesMd, tableName='particles') mdOut.removeColumns("rlnImageId") with open(outImagesMd, "w") as f: mdOut.writeStar(f, tableName='particles') mdOptics.writeStar(f, tableName='optics') reader = convert.createReader() reader.readSetOfParticles( outImagesMd, partSet, alignType=ALIGN_PROJ, postprocessImageRow=self._postprocessImageRow) self._defineOutputs(outputParticles=partSet) self._defineSourceRelation(imgSet, partSet)
# -------------------------- INFO functions ------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputParticles'): summary.append("Output particles not ready yet.") else: summary.append("Symmetry used: %s" % self.symmetryGroup.get()) return summary def _validate(self): errors = [] if not self.inputParticles.get().hasAlignmentProj(): errors.append('Input particles must have angular assignment.') return errors def _citations(self): return [] def _methods(self): methods = ['Input particle dataset was artificially expanded according' ' to pseudo-symmetric %s point group' % self.symmetryGroup.get()] return methods # -------------------------- Utils functions ------------------------------ def _postprocessImageRow(self, item, row): if hasattr(row, 'rlnGroupName'): item._rlnGroupName = String(row.rlnGroupName)