Source code for relion.protocols.protocol_classify2d

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
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# * This program is free software; you can redistribute it and/or modify
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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 pwem.constants import ALIGN_2D
from pwem.objects import SetOfClasses2D
from pwem.protocols import ProtClassify2D

import relion.convert as convert
from .protocol_base import ProtRelionBase


[docs]class ProtRelionClassify2D(ProtRelionBase, ProtClassify2D): """ This protocol runs Relion 2D classification.""" _label = '2D classification' IS_2D = True OUTPUT_TYPE = SetOfClasses2D 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. """ if self.doImageAlignment: args['--offset_range'] = self.offsetSearchRangePix.get() args['--offset_step'] = self.offsetSearchStepPix.get() * self._getSamplingFactor() args['--psi_step'] = self.inplaneAngularSamplingDeg.get() * self._getSamplingFactor() if self.allowCoarserSampling: args['--allow_coarser_sampling'] = '' else: args['--skip_align'] = '' # --------------------------- STEPS functions ----------------------------- def _fillClassesFromIter(self, clsSet, iteration): """ Create the SetOfClasses2D from a given iteration. """ classLoader = convert.ClassesLoader(self, ALIGN_2D) classLoader.fillClassesFromIter(clsSet, iteration)
[docs] def createOutputStep(self): partSet = self.inputParticles.get() classes2D = self._createSetOfClasses2D(partSet) self._fillClassesFromIter(classes2D, self._lastIter()) self._defineOutputs(outputClasses=classes2D) self._defineSourceRelation(self.inputParticles, classes2D)
# --------------------------- INFO functions ------------------------------ def _validateNormal(self): return [] 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 = [ "Input Particles: %s" % self.getObjectTag('inputParticles'), "Classified into *%d* classes." % self.numberOfClasses, "Output set: %s" % self.getObjectTag('outputClasses') ] return summary def _summaryContinue(self): summary = ["Continue from iteration %01d" % self._getContinueIter()] return summary def _methods(self): methods = '' if hasattr(self, 'outputClasses'): methods += "We classified input particles %s (%d items) " % ( self.getObjectTag('inputParticles'), self.inputParticles.get().getSize()) methods += "into %d classes using Relion Classify2d. " % self.numberOfClasses methods += 'Output classes: %s' % self.getObjectTag('outputClasses') return [methods]