Source code for xmipp3.protocols.protocol_split_volume

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# * Authors:     Carlos Oscar Sorzano (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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Protocol to split a volume in two volumes based on a set of images

from pyworkflow.protocol.constants import LEVEL_ADVANCED
from pyworkflow.protocol.params import PointerParam, FloatParam, IntParam, StringParam
from pyworkflow.utils.path import cleanPath
from pyworkflow import BETA, UPDATED, NEW, PROD
from pwem.protocols import ProtClassify3D
from pwem.objects import Volume
from pwem.emlib.image import ImageHandler
from xmipp3.convert import writeSetOfParticles

[docs]class XmippProtSplitvolume(ProtClassify3D): """Split volume in two""" _label = 'split volume' _devStatus = BETA def __init__(self, **args): ProtClassify3D.__init__(self, **args) #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('directionalClasses', PointerParam, label="Directional classes", important=True, pointerClass='SetOfAverages', pointerCondition='hasAlignmentProj', help='Select a set of particles with angles. Preferrably the output of a run of directional classes') form.addParam('symmetryGroup', StringParam, default='c1', label="Symmetry group", help='See [[Xmipp Symmetry][]] page ' 'for a description of the symmetry format accepted by Xmipp') form.addParam('mask', PointerParam, label="Mask", pointerClass='VolumeMask', allowsNull=True, help='The mask values must be binary: 0 (remove these voxels) and 1 (let them pass).') form.addParam('Nrec', IntParam, label="Number of reconstructions", default=5000, expertLevel=LEVEL_ADVANCED, help="Number of random reconstructions to perform"); form.addParam('Nsamples', IntParam, label="Number of images/reconstruction", default=15, expertLevel=LEVEL_ADVANCED, help="Number of images per reconstruction. Consider that reconstructions with symmetry c1 will be perfomed"); form.addParam('alpha', FloatParam, label="Confidence level", default=0.05, expertLevel=LEVEL_ADVANCED, help="This parameter is alpha. Two volumes, one at alpha/2 and another one at 1-alpha/2, will be generated"); #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('convertInputStep',self.directionalClasses.getObjId()) self._insertFunctionStep('generateSplittedVolumes') self._insertFunctionStep('createOutput') #--------------------------- STEPS functions ---------------------------------------------------
[docs] def convertInputStep(self, inputParticlesId): writeSetOfParticles(self.directionalClasses.get(),self._getExtraPath("directionalClasses.xmd"))
[docs] def createOutput(self): inputParticles = self.directionalClasses.get() Ts = inputParticles.getSamplingRate() volumesSet = self._createSetOfVolumes() volumesSet.setSamplingRate(Ts) for i in range(2): vol = Volume() fnVol = self._getExtraPath("split_v%d.vol"%(i+1)) fnMrc = self._getExtraPath("split_v%d.mrc"%(i+1)) self.runJob("xmipp_image_convert","-i %s -o %s -t vol"%(fnVol,fnMrc), numberOfMpi=1) self.runJob("xmipp_image_header","-i %s --sampling_rate %f"%(fnMrc, Ts), numberOfMpi=1) cleanPath(fnVol) vol.setLocation(1, fnMrc) volumesSet.append(vol) self._defineOutputs(outputVolumes=volumesSet) self._defineSourceRelation(inputParticles, volumesSet)
[docs] def generateSplittedVolumes(self): inputParticles = self.directionalClasses.get() Xdim = inputParticles.getDimensions()[0] fnMask = "" if self.mask.hasValue(): fnMask = self._getExtraPath("mask.vol") img=ImageHandler() img.convert(self.mask.get(), fnMask) self.runJob('xmipp_image_resize',"-i %s --dim %d"%(fnMask,Xdim),numberOfMpi=1) self.runJob('xmipp_transform_threshold',"-i %s --select below 0.5 --substitute binarize"%fnMask,numberOfMpi=1) args="-i %s --oroot %s --Nrec %d --Nsamples %d --sym %s --alpha %f"%\ (self._getExtraPath("directionalClasses.xmd"),self._getExtraPath("split"),self.Nrec.get(),self.Nsamples.get(), self.symmetryGroup.get(), self.alpha.get()) if fnMask!="": args+=" --mask binary_file %s"%fnMask self.runJob("xmipp_classify_first_split",args)