Source code for reliontomo.protocols.protocol_refine_3d_tomo

# *
# * Authors:     Scipion Team
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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This module contains the protocol for 3d refinement with Relion.
import glob
from os import remove
from os.path import abspath, exists, getmtime

from pwem import ALIGN_PROJ
from pwem.objects import FSC, Integer
from pwem.protocols import ProtRefine3D
from pyworkflow import BETA
from relion.convert import Table, convert31
from reliontomo import Plugin

from tomo.objects import AverageSubTomogram
from tomo.protocols import ProtTomoBase

from reliontomo.protocols.protocol_base_tomo import ProtRelionBaseTomo

[docs]class ProtRelionSubtomoRefine3D(ProtRefine3D, ProtRelionBaseTomo, ProtTomoBase): """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 subtomogram auto-refine' _devStatus = BETA IS_CLASSIFY = False PREFIXES = ['half1_', 'half2_'] def __init__(self, **args): ProtRelionBaseTomo.__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) """ ProtRelionBaseTomo._initialize(self) self.ClassFnTemplate = '%(ref)03d@%(rootDir)s/relion_it%(iter)03d_classes.mrcs' self.numberOfClasses.set(1) # For refinement we only need just one "class" # --------------------------- INSERT steps functions -------------------------------------------- def _setSamplingArgs(self, args): """ Set sampling related params""" # Sampling stuff args['--auto_local_healpix_order'] = self.localSearchAutoSamplingDeg.get() if not self.doContinue: args['--healpix_order'] = self.angularSamplingDeg.get() args['--offset_range'] = self.offsetSearchRangePix.get() args['--offset_step'] = self.offsetSearchStepPix.get() * 2 args['--auto_refine'] = '' args['--split_random_halves'] = '' joinHalves = "--low_resol_join_halves" if not joinHalves in self.extraParams.get(): args['--low_resol_join_halves'] = 40 if not Plugin.IS_30() and self.useFinerSamplingFaster: args['--auto_ignore_angles'] = '' args['--auto_resol_angles'] = '' # --------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self): subtomoSet = self._getInputParticles() vol = AverageSubTomogram() vol.setFileName(self._getExtraPath('relion_class001.mrc')) vol.setSamplingRate(subtomoSet.getSamplingRate()) pattern = '*it*half%s_class*.mrc' half1 = self._getLastFileName(self._getExtraPath(pattern % 1)) half2 = self._getLastFileName(self._getExtraPath(pattern % 2)) vol.setHalfMaps([half1, half2]) outSubtomoSet = self._createSetOfSubTomograms() outSubtomoSet.copyInfo(subtomoSet) self._fillDataFromIter(outSubtomoSet, self._lastIter()) self._defineOutputs(outputVolume=vol) self._defineSourceRelation(subtomoSet, vol) self._defineOutputs(outputParticles=outSubtomoSet) self._defineTransformRelation(subtomoSet, outSubtomoSet) fsc = FSC(objLabel=self.getRunName()) fn = self._getExtraPath("") 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): """ Should be overriden in subclasses to return summary message for NORMAL EXECUTION. """ errors = [] if self.referenceVolume.get() is not None: particlesDim = self._getInputParticles().getDim() volumeDim = self.referenceVolume.get().getDim() if particlesDim is None: errors.append('Can not get dimensions from input particles!!!') elif volumeDim is None: errors.append('Can not get dimensions from reference volume!!!') elif particlesDim[0] != volumeDim[0]: errors.append('Volume and particles dimensions must be equal!!!') return errors def _validateContinue(self): """ Should be overriden in subclasses to return summary messages for CONTINUE EXECUTION. """ 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 += ["The iteration from you want to continue must be %01d or less" % lastIter] return errors def _summaryNormal(self): """ Should be overriden in subclasses to return summary message for NORMAL EXECUTION. """ summary = [] it = self._lastIter() if it: if it >= 1: modelStar = self._getFileName('half1_model', iter=it) summary.append("Current resolution %s: *%0.2f* Å" % self._getRlnCurrentResolution(modelStar)) return summary def _summaryContinue(self): """ Should be overriden in subclasses to return summary messages for CONTINUE EXECUTION. """ summary = ["Continue from iteration %01d" % self._getContinueIter()] return summary # --------------------------- UTILS functions -------------------------------------------- def _createItemMatrix(self, item, row): self.reader.setParticleTransform(item, row) def _cleanUndesiredFiles(self): """Remove all files generated by relion_refine 3d excepting the ones which correspond to the last iteration. Example for iteration 12: relion_it012_half1_class001.mrc relion_it012_half2_class001_angdist.bild relion_it012_half2_class001.mrc relion_it012_half1_class001_angdist.bild """ itPref = 'relion_it' clPref = 'class' starExt = '.star' mrcExt = '.mrc' bildExt = '_angdist.bild' halfPref = 'half' # Refine calculations related files calcFiles = ['data', '%s1_model' % halfPref, '%s2_model' % halfPref, 'optimiser', 'sampling'] for i in range(self._lastIter()): for calcFile in calcFiles: fn = abspath(self._getExtraPath('{}{:03d}_{}{}'.format( itPref, i, calcFile, starExt))) if exists(fn): remove(fn) # Classes related files for itr in range(1, self.nClasses + 1): for h in range(1, 3): # Two halves fn = abspath(self._getExtraPath('{}{:03d}_{}{}_{}{:03d}'.format( itPref, i, halfPref, h, clPref, itr))) mrcFile = fn + mrcExt bildFile = fn + bildExt if exists(mrcFile): remove(mrcFile) if exists(bildFile): remove(bildFile) def _fillDataFromIter(self, subtomoClassesSet, iteration): # tableName = 'particles@' if self.IS_GT30() else '' dataStar = self._getFileName('data', iter=iteration) # imgSet.setAlignmentProj() for item in subtomoClassesSet: item.setAlignmentProj() # with open(dataStar) as fid: # self.dataTable.readStar(fid) self.reader = convert31.Reader(alignType=ALIGN_PROJ, pixelSize=subtomoClassesSet.getSamplingRate()) mdIter = Table.iterRows(dataStar, key='rlnImageName') subtomoClassesSet.copyItems(self._getInputParticles(), doClone=False, updateItemCallback=self._updateParticle, itemDataIterator=mdIter) def _updateParticle(self, particle, row): self.reader.setParticleTransform(particle, row) if not hasattr(particle, '_rlnRandomSubset'): particle._rlnRandomSubset = Integer() particle._rlnRandomSubset.set(row.rlnRandomSubset) @staticmethod def _getLastFileName(pattern): files = glob.glob(pattern) files.sort(key=getmtime) return files[-1]