Source code for xmipp3.protocols.protocol_helical_parameters

# **************************************************************************
# *
# * Authors:     Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  e-mail address 'scipion@cnb.csic.es'
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import pyworkflow.object as pwobj
from pwem.objects import Volume
from pwem.emlib.image import ImageHandler
from pwem.protocols import ProtPreprocessVolumes
import pyworkflow.protocol.params as params
from pyworkflow.protocol.constants import LEVEL_ADVANCED

from pwem.emlib import MetaData, MDL_ANGLE_ROT, MDL_SHIFT_Z
from xmipp3.base import HelicalFinder
from xmipp3.convert import getImageLocation


[docs]class XmippProtHelicalParameters(ProtPreprocessVolumes, HelicalFinder): """ Estimate helical parameters and symmetrize. Helical symmetry is defined as V(r,rot,z)=V(r,rot+k*DeltaRot,z+k*Deltaz). """ _label = 'helical symmetry' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='General parameters') form.addParam('inputVolume', params.PointerParam, pointerClass="Volume", label='Input volume') form.addParam('cylinderInnerRadius', params.IntParam,label='Cylinder inner radius', default=-1, help="The helix is supposed to occupy this radius in voxels around the Z axis. Leave it as -1 for symmetrizing the whole volume") form.addParam('cylinderOuterRadius',params.IntParam,label='Cylinder outer radius', default=-1, help="The helix is supposed to occupy this radius in voxels around the Z axis. Leave it as -1 for symmetrizing the whole volume") form.addParam('dihedral',params.BooleanParam,default=False,label='Apply dihedral symmetry') form.addParam('forceDihedralX',params.BooleanParam,default=False,expertLevel=LEVEL_ADVANCED, label='Force the dihedral axis to be in X', help="If this option is chosen, then the dihedral axis is not searched and it is assumed that it is around X.") form.addParam('additionalCn',params.BooleanParam,default=False,label='Apply Cn symmetry') form.addParam('Cn',params.StringParam,default="C2",condition="additionalCn",label='Cn symmetry') form.addSection(label='Search limits') form.addParam('heightFraction',params.FloatParam,default=0.9,label='Height fraction', help="The helical parameters are only sought using the fraction indicated by this number. "\ "In this way, you can avoid including planes that are poorly resolved at the extremes of the volume. " \ "However, note that the algorithm can perfectly work with a fraction of 1.") form.addParam('rot0',params.FloatParam,default=0,label='Minimum rotational angle',help="In degrees") form.addParam('rotF',params.FloatParam,default=360,label='Maximum rotational angle',help="In degrees") form.addParam('rotStep',params.FloatParam,default=5,label='Angular step',help="In degrees") form.addParam('z0',params.FloatParam,default=1,label='Minimum shift Z',help="In Angstroms") form.addParam('zF',params.FloatParam,default=10,label='Maximum shift Z',help="In Angstroms") form.addParam('zStep',params.FloatParam,default=0.5,label='Shift step',help="In Angstroms") self.deltaZ= params.Float() self.deltaRot=params.Float() form.addParallelSection(threads=4, mpi=0) #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('copyInput') self._insertFunctionStep('coarseSearch') self._insertFunctionStep('fineSearch') self._insertFunctionStep('symmetrize') self._insertFunctionStep('createOutput') self.fnVol = getImageLocation(self.inputVolume.get()) self.fnVolSym=self._getPath('volume_symmetrized.vol') [self.height,_,_]=self.inputVolume.get().getDim() #--------------------------- STEPS functions --------------------------------------------
[docs] def copyInput(self): if self.dihedral: if not self.forceDihedralX: self.runJob("xmipp_transform_symmetrize","-i %s -o %s --sym dihedral --dont_wrap" % (self.fnVol, self.fnVolSym)) else: self.runJob("xmipp_transform_geometry","-i %s -o %s --rotate_volume axis 180 1 0 0" % (self.fnVol, self.fnVolSym)) self.runJob("xmipp_image_operate","-i %s --plus %s -o %s" % (self.fnVol, self.fnVolSym, self.fnVolSym)) self.runJob("xmipp_image_operate","-i %s --mult 0.5" % self.fnVolSym) else: ImageHandler().convert(self.inputVolume.get(), self.fnVolSym)
[docs] def coarseSearch(self): Cn = "c1" if self.additionalCn: Cn=self.Cn.get() self.runCoarseSearch(self.fnVolSym,self.dihedral.get(),float(self.heightFraction.get()), float(self.z0.get()),float(self.zF.get()),float(self.zStep.get()), float(self.rot0.get()),float(self.rotF.get()),float(self.rotStep.get()), self.numberOfThreads.get(),self._getExtraPath('coarseParams.xmd'), int(self.cylinderInnerRadius.get()),int(self.cylinderOuterRadius.get()),int(self.height), self.inputVolume.get().getSamplingRate(), Cn)
[docs] def fineSearch(self): Cn = "c1" if self.additionalCn: Cn=self.Cn.get() self.runFineSearch(self.fnVolSym, self.dihedral.get(), self._getExtraPath('coarseParams.xmd'), self._getExtraPath('fineParams.xmd'), float(self.heightFraction.get()),float(self.z0.get()),float(self.zF.get()), float(self.rot0.get()),float(self.rotF.get()), int(self.cylinderInnerRadius.get()),int(self.cylinderOuterRadius.get()),int(self.height), self.inputVolume.get().getSamplingRate(), Cn)
[docs] def symmetrize(self): Cn = "c1" if self.additionalCn: Cn=self.Cn.get() self.runSymmetrize(self.fnVolSym, self.dihedral.get(), self._getExtraPath('fineParams.xmd'), self.fnVolSym, float(self.heightFraction.get()), self.cylinderInnerRadius.get(), self.cylinderOuterRadius.get(), self.height, self.inputVolume.get().getSamplingRate(), Cn)
[docs] def createOutput(self): volume = Volume() volume.setFileName(self._getPath('volume_symmetrized.vol')) #volume.setSamplingRate(self.inputVolume.get().getSamplingRate()) volume.copyInfo(self.inputVolume.get()) self._defineOutputs(outputVolume=volume) self._defineTransformRelation(self.inputVolume, self.outputVolume) md = MetaData(self._getExtraPath('fineParams.xmd')) objId = md.firstObject() self._defineOutputs(deltaRot=pwobj.Float(md.getValue(MDL_ANGLE_ROT, objId)), deltaZ=pwobj.Float(md.getValue(MDL_SHIFT_Z, objId)))
#--------------------------- INFO functions -------------------------------------------- def _summary(self): messages = [] if self.deltaZ.hasValue(): messages.append('DeltaZ=%f (voxels) %f (Angstroms)'%(self.deltaZ.get()/self.inputVolume.get().getSamplingRate(),self.deltaZ.get())) messages.append('DeltaRot=%f (degrees)'%self.deltaRot.get()) return messages def _citations(self): papers=[] return papers def _validate(self): messages=[] if float(self.z0.get())<=0: messages.append("z0 should not be negative or zero") return messages def _methods(self): messages = [] messages.append('We looked for the helical symmetry parameters of the volume %s using Xmipp [delaRosaTrevin2013].' % self.getObjectTag('inputVolume')) if self.deltaZ.hasValue(): messages.append('We found them to be %f Angstroms and %f degrees.'%(self.deltaZ.get(),self.deltaRot.get())) messages.append('We symmetrized %s with these parameters and produced the volume %s.'%(self.getObjectTag('inputVolume'), self.getObjectTag('outputVolume'))) if self.dihedral.get(): messages.append('We applied dihedral symmetry.') return messages