Source code for relion.protocols.protocol_classify3d

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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from emtable import Table

from pwem.constants import ALIGN_PROJ
from pwem.protocols import ProtClassify3D

import relion.convert as convert
from .protocol_base import ProtRelionBase


[docs]class ProtRelionClassify3D(ProtClassify3D, ProtRelionBase): """ Protocol to classify 3D using Relion Bayesian approach. Relion employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-EM. Many parameters of a statistical model are learned from the data, which leads to objective and high-quality results. """ _label = '3D classification' CHANGE_LABELS = ['rlnChangesOptimalOrientations', 'rlnChangesOptimalOffsets', 'rlnOverallAccuracyRotations', 'rlnOverallAccuracyTranslationsAngst', 'rlnChangesOptimalClasses'] 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) # -------------------------- INSERT steps functions ----------------------- def _setSamplingArgs(self, args): """ Set sampling related params. """ if self.doImageAlignment: args['--healpix_order'] = self.angularSamplingDeg.get() args['--offset_range'] = self.offsetSearchRangePix.get() args['--offset_step'] = self.offsetSearchStepPix.get() * self._getSamplingFactor() # check if sigma_ang is in extra params # before adding the default value if self.localAngularSearch: if self.extraParams.hasValue(): if self.extraParams.get().find("--sigma_ang") == -1: args['--sigma_ang'] = self.localAngularSearchRange.get() / 3. else: args['--sigma_ang'] = self.localAngularSearchRange.get() / 3. if self.allowCoarserSampling: args['--allow_coarser_sampling'] = '' else: args['--skip_align'] = '' # -------------------------- STEPS functions ------------------------------
[docs] def createOutputStep(self): partSet = self.inputParticles.get() classes3D = self._createSetOfClasses3D(partSet) self._fillClassesFromIter(classes3D, self._lastIter()) self._defineOutputs(outputClasses=classes3D) self._defineSourceRelation(self.inputParticles, classes3D) # create a SetOfVolumes and define its relations volumes = self._createSetOfVolumes() volumes.setSamplingRate(partSet.getSamplingRate()) for class3D in classes3D: vol = class3D.getRepresentative() vol.setObjId(class3D.getObjId()) volumes.append(vol) self._defineOutputs(outputVolumes=volumes) self._defineSourceRelation(self.inputParticles, volumes) if not self.doContinue: self._defineSourceRelation(self.referenceVolume, classes3D) self._defineSourceRelation(self.referenceVolume, volumes)
# -------------------------- INFO functions ------------------------------- def _validateNormal(self): errors = [] 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 = [] it = self._lastIter() or -1 if it >= 1: table = Table(fileName=self._getFileName('model', iter=it), tableName='model_general') row = table[0] resol = float(row.rlnCurrentResolution) summary.append("Current resolution: *%0.2f A*" % resol) inputParts = self.inputParticles.get() sizeStr = 'None' if inputParts is None else inputParts.getSize() summary.append("Input Particles: *%s*\n" "Classified into *%d* 3D classes\n" % (sizeStr, self.numberOfClasses)) return summary def _summaryContinue(self): summary = list() summary.append("Continue from iteration %01d" % self._getContinueIter()) return summary def _methods(self): strline = '' if hasattr(self, 'outputClasses'): strline += 'We classified %d particles into %d 3D classes using Relion Classify3d. ' %\ (self.inputParticles.get().getSize(), self.numberOfClasses.get()) return [strline] # -------------------------- UTILS functions ------------------------------ def _fillClassesFromIter(self, clsSet, iteration): """ Create the SetOfClasses3D from a given iteration. """ classLoader = convert.ClassesLoader(self, ALIGN_PROJ) classLoader.fillClassesFromIter(clsSet, iteration)