Source code for relion.protocols.protocol_refine3d

# **************************************************************************
# *
# * 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'
# *
# **************************************************************************
from emtable import Table

from pwem.constants import ALIGN_PROJ
from pwem.objects import Volume, FSC
from pwem.protocols import ProtRefine3D

import relion.convert as convert
from ..constants import PARTICLE_EXTRA_LABELS
from .protocol_base import ProtRelionBase


[docs]class ProtRelionRefine3D(ProtRefine3D, ProtRelionBase): """ Protocol to refine a 3D map using Relion. Relion employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). Many parameters of a statistical model are learned from the data,which leads to objective and high-quality results. """ _label = '3D auto-refine' IS_CLASSIFY = False CHANGE_LABELS = ['rlnChangesOptimalOrientations', 'rlnChangesOptimalOffsets', 'rlnOverallAccuracyRotations', 'rlnOverallAccuracyTranslationsAngst'] PREFIXES = ['half1_', 'half2_'] def __init__(self, **args): ProtRelionBase.__init__(self, **args) def _initialize(self): """ This function is mean to be called after the working dir for the protocol have been set. (maybe after recovery from mapper) """ ProtRelionBase._initialize(self) self.ClassFnTemplate = '%(ref)03d@%(rootDir)s/relion_it%(iter)03d_classes.mrcs' # -------------------------- INSERT steps functions ----------------------- def _setSamplingArgs(self, args): """ Set sampling related params""" args['--auto_local_healpix_order'] = self.localSearchAutoSamplingDeg.get() if not self.doContinue: args['--healpix_order'] = self.angularSamplingDeg.get() args['--offset_range'] = self.offsetSearchRangePix.get() f = self._getSamplingFactor() args['--offset_step'] = self.offsetSearchStepPix.get() * f args['--auto_refine'] = '' args['--split_random_halves'] = '' joinHalves = "--low_resol_join_halves" if joinHalves not in self.extraParams.get(): args['--low_resol_join_halves'] = 40 if self.useFinerSamplingFaster: args['--auto_ignore_angles'] = '' args['--auto_resol_angles'] = '' # -------------------------- STEPS functions ------------------------------
[docs] def createOutputStep(self): imgSet = self._getInputParticles() vol = Volume() vol.setFileName(self._getExtraPath('relion_class001.mrc')) vol.setSamplingRate(imgSet.getSamplingRate()) half1 = self._getFileName("final_half1_volume", ref3d=1) half2 = self._getFileName("final_half2_volume", ref3d=1) vol.setHalfMaps([half1, half2]) outImgSet = self._createSetOfParticles() outImgSet.copyInfo(imgSet) self._fillDataFromIter(outImgSet, self._lastIter()) self._defineOutputs(outputVolume=vol) self._defineSourceRelation(self.inputParticles, vol) self._defineOutputs(outputParticles=outImgSet) self._defineTransformRelation(self.inputParticles, outImgSet) fsc = FSC(objLabel=self.getRunName()) fn = self._getExtraPath("relion_model.star") table = Table(fileName=fn, tableName='model_class_1') resolution_inv = table.getColumnValues('rlnResolution') frc = table.getColumnValues('rlnGoldStandardFsc') fsc.setData(resolution_inv, frc) self._defineOutputs(outputFSC=fsc) self._defineSourceRelation(vol, fsc)
# -------------------------- INFO functions ------------------------------- def _validateNormal(self): errors = [] if self.IS_3D and self.solventFscMask and not self.referenceMask.get(): errors.append('When using solvent-corrected FSCs, ' 'please provide a reference mask.') return errors def _validateContinue(self): errors = [] continueRun = self.continueRun.get() continueRun._initialize() lastIter = continueRun._lastIter() if self.continueIter.get() == 'last': continueIter = lastIter else: continueIter = int(self.continueIter.get()) if continueIter > lastIter: errors += ["You can continue only from the iteration %01d or less" % lastIter] return errors def _summaryNormal(self): summary = [] if not hasattr(self, 'outputVolume'): summary.append("Output volume not ready yet.") it = self._lastIter() or -1 if it >= 1 and it > self._getContinueIter(): table = Table(fileName=self._getFileName('half1_model', iter=it), tableName='model_general') row = table[0] resol = float(row.rlnCurrentResolution) summary.append("Current resolution: *%0.2f A*" % resol) else: table = Table(fileName=self._getFileName('modelFinal'), tableName='model_general') row = table[0] resol = float(row.rlnCurrentResolution) summary.append("Final resolution: *%0.2f A*" % resol) return summary def _summaryContinue(self): return ["Continue from iteration %01d" % self._getContinueIter()] # -------------------------- UTILS functions ------------------------------ def _fillDataFromIter(self, imgSet, iteration): outImgsFn = self._getFileName('data', iter=iteration) imgSet.setAlignmentProj() self.reader = convert.createReader(alignType=ALIGN_PROJ, pixelSize=imgSet.getSamplingRate()) mdIter = Table.iterRows('particles@' + outImgsFn, key='rlnImageId') imgSet.copyItems(self._getInputParticles(), doClone=False, updateItemCallback=self._updateParticle, itemDataIterator=mdIter) def _updateParticle(self, particle, row): self.reader.setParticleTransform(particle, row) if getattr(self, '__updatingFirst', True): self.reader.createExtraLabels(particle, row, PARTICLE_EXTRA_LABELS) self.__updatingFirst = False else: self.reader.setExtraLabels(particle, row)