Source code for xmipp3.protocols.protocol_rotational_symmetry

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# * Authors:     Carlos Oscar S. Sorzano (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import pyworkflow
import pyworkflow.object as pwobj
from pwem.emlib.image import ImageHandler
from pwem.objects import Volume

from pwem.protocols import (ProtPreprocessVolumes)
from pyworkflow.protocol import (PointerParam, IntParam, EnumParam, FloatParam)

from pwem.emlib import MetaData, MDL_ANGLE_ROT, MDL_ANGLE_TILT
from xmipp3.convert import getImageLocation

[docs]class XmippProtRotationalSymmetry(ProtPreprocessVolumes): """ Estimate the orientation of a rotational axis and symmetrize. The user should know the order of the axis (two-fold, three-fold, ...) If this is unknown you may try several and see the most consistent results. """ _label = 'rotational symmetry' _version = pyworkflow.VERSION_1_1 GLOBAL_SEARCH = 0 LOCAL_SEARCH = 1 GLOBAL_LOCAL_SEARCH = 2 #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='General parameters') form.addParam('inputVolume', PointerParam, pointerClass="Volume", label='Input volume') form.addParam('symOrder',IntParam, default=3, label='Symmetry order', help="3 for a three-fold symmetry axis, " "4 for a four-fold symmetry axis, ...") form.addParam('searchMode', EnumParam,label='Search mode', choices=['Global','Local','Global+Local'], default=self.GLOBAL_LOCAL_SEARCH) form.addParam('rot', FloatParam, default=0, condition='searchMode==%d' % self.LOCAL_SEARCH, label='Initial rotational angle', help="In degrees") form.addParam('tilt', FloatParam, default=0, condition='searchMode==%d' % self.LOCAL_SEARCH, label='Initial tilt angle', help="In degrees. tilt=0 is a top axis while " "tilt=90 defines a side axis") rot = form.addLine('Rotational angle', condition='searchMode!=%d' % self.LOCAL_SEARCH, help='Minimum, maximum and step values for ' 'rotational angle range, all in degrees.') rot.addParam('rot0', FloatParam, default=0, label='Min') rot.addParam('rotF', FloatParam, default=360, label='Max') rot.addParam('rotStep', FloatParam, default=5, label='Step') tilt = form.addLine('Tilt angle', condition='searchMode!=%d' % self.LOCAL_SEARCH, help='In degrees. tilt=0 is a top axis while ' 'tilt=90 defines a side axis') tilt.addParam('tilt0', FloatParam, default=0, label='Min') tilt.addParam('tiltF', FloatParam, default=180, label='Max') tilt.addParam('tiltStep', FloatParam, default=5, label='Step') self.rotSym = pwobj.Float() self.tiltSym = pwobj.Float() form.addParallelSection(threads=4, mpi=0) #--------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): self._insertFunctionStep('copyInput') if self.searchMode.get()!=self.LOCAL_SEARCH: self._insertFunctionStep('coarseSearch') if self.searchMode.get()!=self.GLOBAL_SEARCH: self._insertFunctionStep('fineSearch') self._insertFunctionStep('symmetrize') self._insertFunctionStep('createOutput') self.fnVol = getImageLocation(self.inputVolume.get()) self.fnVolSym=self._getPath('volume_symmetrized.mrc') [self.height,_,_]=self.inputVolume.get().getDim() #--------------------------- STEPS functions -------------------------------
[docs] def copyInput(self): ImageHandler().convert(self.inputVolume.get(), self.fnVolSym)
[docs] def coarseSearch(self): self.runJob("xmipp_volume_find_symmetry", "-i %s -o %s --rot %f %f %f --tilt %f %f %f --sym rot %d --thr %d" % (self.fnVolSym, self._getExtraPath('coarse.xmd'), self.rot0, self.rotF, self.rotStep, self.tilt0, self.tiltF, self.tiltStep, self.symOrder, self.numberOfThreads))
[docs] def getAngles(self, fnAngles=""): if fnAngles=="": if self.searchMode.get()==self.GLOBAL_SEARCH: fnAngles = self._getExtraPath("coarse.xmd") else: fnAngles = self._getExtraPath("fine.xmd") md = MetaData(fnAngles) objId = md.firstObject() rot0 = md.getValue(MDL_ANGLE_ROT, objId) tilt0 = md.getValue(MDL_ANGLE_TILT, objId) return (rot0,tilt0)
[docs] def fineSearch(self): if self.searchMode == self.LOCAL_SEARCH: rot0 = self.rot.get() tilt0 = self.tilt.get() else: rot0, tilt0 = self.getAngles(self._getExtraPath('coarse.xmd')) self.runJob("xmipp_volume_find_symmetry", "-i %s -o %s --localRot %f %f --sym rot %d"% (self.fnVolSym,self._getExtraPath('fine.xmd'), rot0, tilt0, self.symOrder.get()))
[docs] def symmetrize(self): rot0, tilt0 = self.getAngles() self.runJob("xmipp_transform_geometry", "-i %s --rotate_volume euler %f %f 0 --dont_wrap" % (self.fnVolSym,rot0,tilt0)) self.runJob("xmipp_transform_symmetrize", "-i %s --sym c%d --dont_wrap" % (self.fnVolSym,self.symOrder.get()))
[docs] def createOutput(self): Ts = self.inputVolume.get().getSamplingRate() self.runJob("xmipp_image_header","-i %s --sampling_rate %f" %(self.fnVolSym,Ts)) volume = Volume() volume.setFileName(self.fnVolSym) volume.copyInfo(self.inputVolume.get()) self._defineOutputs(outputVolume=volume) self._defineTransformRelation(self.inputVolume, self.outputVolume) rot0, tilt0 = self.getAngles() self._defineOutputs(rotSym=pwobj.Float(rot0), tiltSym=pwobj.Float(tilt0))
#--------------------------- INFO functions -------------------------------- def _summary(self): messages = [] if self.rotSym.hasValue(): messages.append('Rot. Angle of Symmetry axis=%0.2f (degrees)' % self.rotSym.get()) messages.append('Tilt.Angle of Symmetry axis=%0.2f (degrees)' % self.tiltSym.get()) return messages def _methods(self): messages = [] messages.append('We looked for the %d-fold rotational axis of the ' 'volume %s using Xmipp [delaRosaTrevin2013]. ' 'We found it to be with an orientation given by a ' 'rotational angle of %f and a tilt angle of %f degrees.' % (self.symOrder, self.getObjectTag('inputVolume'), self.rotSym, self.tiltSym)) return messages