Source code for xmipp3.protocols.protocol_cl2d_align

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# * Authors:     Josue Gomez Blanco (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import pyworkflow.protocol.params as params

import pwem.emlib.metadata as md
from pwem.objects import Particle
from pwem.protocols import ProtAlign2D
from pwem import ALIGN_NONE, ALIGN_2D

from xmipp3.convert import createItemMatrix, writeSetOfParticles, getImageLocation

[docs]class XmippProtCL2DAlign(ProtAlign2D): """ Aligns a set of particles using the CL2D algorithm. """ _label = 'align with cl2d' # --------------------------- DEFINE param functions ----------------------- def _defineAlignParams(self, form): form.addParam('useReferenceImage', params.BooleanParam, default=False, label='Use a Reference Image ?', help='If you set to *Yes*, you should provide a ' 'reference image.\n' 'If *No*, the default generation is done by ' 'averaging subsets of the input images.') form.addParam('referenceImage', params.PointerParam, condition='useReferenceImage', pointerClass='Particle', allowsNull=True, label="Reference image", help='Image that will serve as class reference') form.addParam('maximumShift', params.IntParam, default=10, label='Maximum shift (px):') form.addParam('numberOfIterations', params.IntParam, default=10, expertLevel=params.LEVEL_ADVANCED, label='Number of iterations:', help='Maximum number of iterations') form.addParallelSection(threads=0, mpi=4) # --------------------------- INSERT steps functions ----------------------- def _insertAllSteps(self): """ Mainly prepare the command line for call cl2d align program""" # Convert input images if necessary self.imgsFn = self._getExtraPath('images.xmd') self._insertFunctionStep('convertInputStep') # Prepare arguments to call program: xmipp_classify_CL2D self._params = {'imgsFn': self.imgsFn, 'extraDir': self._getExtraPath(), 'maxshift': self.maximumShift.get(), 'iter': self.numberOfIterations.get(), } args = ('-i %(imgsFn)s --odir %(extraDir)s --nref 1 --iter %(iter)d ' '--maxShift %(maxshift)d') if self.useReferenceImage: args += " --ref0 " + getImageLocation(self.referenceImage.get()) else: args += " --nref0 1" self._insertRunJobStep("xmipp_classify_CL2D", args % self._params) self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------
[docs] def convertInputStep(self): writeSetOfParticles(self.inputParticles.get(), self.imgsFn, alignType=ALIGN_NONE)
[docs] def createOutputStep(self): """ Store the setOfParticles object as result of the protocol. """ particles = self.inputParticles.get() # Define the output average avgFile = self._getExtraPath('level_00', 'class_classes.stk') avg = Particle() avg.setLocation(1, avgFile) avg.copyInfo(particles) self._defineOutputs(outputAverage=avg) self._defineSourceRelation(self.inputParticles, avg) # Generate the Set of Particles with alignment alignedSet = self._createSetOfParticles() alignedSet.copyInfo(particles) alignedSet.setRepresentative(avg) alignedSet.copyItems(particles, updateItemCallback=self._createItemMatrix, itemDataIterator=md.iterRows(self.imgsFn, sortByLabel=md.MDL_ITEM_ID)) alignedSet.setAlignment(ALIGN_2D) self._defineOutputs(outputParticles=alignedSet) self._defineSourceRelation(self.inputParticles, alignedSet)
# --------------------------- INFO functions ------------------------------- def _validate(self): errors = [] if self.numberOfMpi <= 1: errors.append('Mpi needs to be greater than 1.') if self.useReferenceImage: if self.referenceImage.hasValue(): refImage = self.referenceImage.get() [x1, y1, z1] = refImage.getDim() [x2, y2, z2] = self.inputParticles.get().getDim() if x1 != x2 or y1 != y2 or z1 != z2: errors.append('The input images and the reference image ' 'have different sizes') else: errors.append("Please, enter a reference image") return errors def _summary(self): summary = [] if not hasattr(self, 'outputParticles'): summary.append("Output alignment not ready yet.") else: summary.append("Input Particles: %s" % self.inputParticles.get().getSize()) if self.useReferenceImage: summary.append("Aligned with reference image: %s" % self.referenceImage.get().getNameId()) else: summary.append("Aligned with no reference image.") return summary def _citations(self): return ['Sorzano2010a'] def _methods(self): methods = [] if not hasattr(self, 'outputParticles'): methods.append("Output alignment not ready yet.") else: if self.useReferenceImage: methods.append( "We aligned images %s with respect to the reference image " "%s using CL2D [Sorzano2010a]" % (self.getObjectTag('inputParticles'), self.getObjectTag('referenceImage'))) else: methods.append( "We aligned images %s with no reference using CL2D " "[Sorzano2010a]" % self.getObjectTag('inputParticles')) methods.append(" and produced %s images." % self.getObjectTag('outputParticles')) return methods def _createItemMatrix(self, item, row): createItemMatrix(item, row, align=ALIGN_2D)