Source code for xmipp3.protocols.protocol_local_ctf

# coding=utf-8
# **************************************************************************
# *
# * Authors:     Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
# *              Carlos Oscar Sanchez Sorzano
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia, CSIC
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# * 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 2 of the License, or
# * (at your option) any later version.
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# * 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.
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# * 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 math import floor
import os

from pyworkflow import VERSION_2_0
from pyworkflow.protocol.params import PointerParam, FloatParam
from pyworkflow.protocol.constants import LEVEL_ADVANCED
from pyworkflow.utils.path import cleanPattern
from pwem.protocols import ProtAnalysis3D
from pwem import emlib

from xmipp3.convert import readSetOfParticles, writeSetOfParticles


[docs]class XmippProtLocalCTF(ProtAnalysis3D): """Compares a set of particles with the corresponding projections of a reference volume. The set of particles must have a 3D angular assignment. This protocol refines the CTF, computing local defocus change. The maximun allowed defocus is a parameter introduced by the user (advanced). The protocol gives back the input set of particles with the refine local defocus and the defocus change with relation to the global defocus.""" _label = 'estimate local defocus' _lastUpdateVersion = VERSION_2_0 def __init__(self, **args): ProtAnalysis3D.__init__(self, **args) #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputSet', PointerParam, label="Input images", pointerClass='SetOfParticles', pointerCondition='hasAlignmentProj') form.addParam('inputVolume', PointerParam, label="Volume to compare images to", pointerClass='Volume', help='Volume to be used for class comparison') form.addParam('maxDefocusChange', FloatParam, label="Maximum defocus change (A)", default=10000, expertLevel=LEVEL_ADVANCED) form.addParam('maxGrayScaleChange', FloatParam, label="Maximum gray scale change", default=1, expertLevel=LEVEL_ADVANCED, help="The reprojection is modified as a*P+b, a is restricted to the interval [1-maxGrayScale,1+maxGrayScale]") form.addParam('maxGrayShiftChange', FloatParam, label="Maximum gray shift change", default=1, expertLevel=LEVEL_ADVANCED, help = "The reprojection is modified as a*P+b, b is restricted to the interval [-maxGrayShift,maxGrayShift]") form.addParallelSection(threads=0, mpi=8) #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep("convertStep") self._insertFunctionStep("refineDefocus") self._insertFunctionStep("createOutputStep") #--------------------------- STEPS functions ---------------------------------------------------
[docs] def convertStep(self): """convert input to proper format and dimensions if necessary""" imgSet = self.inputSet.get() writeSetOfParticles(imgSet, self._getExtraPath('input_imgs.xmd')) img = emlib.image.ImageHandler() fnVol = self._getExtraPath("volume.vol") img.convert(self.inputVolume.get(), fnVol) xDimVol=self.inputVolume.get().getDim()[0] xDimImg = imgSet.getDim()[0] if xDimVol!=xDimImg: self.runJob("xmipp_image_resize","-i %s --dim %d"%(fnVol,xDimImg),numberOfMpi=1)
[docs] def refineDefocus(self): """compute local defocus using Xmipp (xmipp_angular_continuous_assign2) and add to metadata columns related to defocus""" fnVol = self._getExtraPath("volume.vol") fnIn = self._getExtraPath('input_imgs.xmd') fnOut = self._getExtraPath('output_imgs.xmd') anglesOutFn=self._getExtraPath("anglesCont.stk") Ts=self.inputSet.get().getSamplingRate() args="-i %s -o %s --ref %s --optimizeDefocus --max_defocus_change %d --sampling %f "\ "--optimizeGray --max_gray_scale %f --max_gray_shift %f"%\ (fnIn,anglesOutFn,fnVol,self.maxDefocusChange.get(),Ts,self.maxGrayScaleChange.get(), self.maxGrayShiftChange.get()) if self.inputSet.get().isPhaseFlipped(): args += " --phaseFlipped" self.runJob("xmipp_angular_continuous_assign2", args) fnCont = self._getExtraPath('anglesCont.xmd') self.runJob("xmipp_metadata_utilities",'-i %s --operate keep_column "itemId ctfDefocusU ctfDefocusV ctfDefocusChange ctfDefocusAngle"'% fnCont,numberOfMpi=1) self.runJob("xmipp_metadata_utilities", '-i %s -o %s --operate drop_column "ctfDefocusU ctfDefocusV ctfDefocusChange ctfDefocusAngle"' % (fnIn,fnOut),numberOfMpi=1) self.runJob("xmipp_metadata_utilities", "-i %s --set join %s itemId itemId" % (fnOut, fnCont),numberOfMpi=1) cleanPattern(self._getExtraPath("anglesCont.*"))
[docs] def createOutputStep(self): """create scipion output data from metadata""" outputSet = self._createSetOfParticles() imgSet = self.inputSet.get() outputSet.copyInfo(imgSet) readSetOfParticles(self._getExtraPath('output_imgs.xmd'), outputSet, extraLabels=[emlib.MDL_CTF_DEFOCUS_CHANGE]) self._defineOutputs(outputParticles=outputSet) self._defineSourceRelation(self.inputSet, outputSet)
#--------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] summary.append("Refined defocus of %i particles" % self.inputSet.get().getSize()) summary.append("Volume: %s" % self.inputVolume.getNameId()) summary.append("Allowed defocus: %s" % self.maxDefocusChange.get()) return summary def _methods(self): methods = [] if hasattr(self, 'outputParticles'): methods.append("We refined the defocus %i input particles %s regarding to volume %s, allowing a maximun defocus of %s"\ %(self.inputSet.get().getSize(), self.getObjectTag('inputSet'), self.getObjectTag('inputVolume'), self.maxDefocusChange.get()) ) return methods