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 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' 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() volumesSet = self._createSetOfVolumes() volumesSet.setSamplingRate(inputParticles.getSamplingRate()) for i in range(2): vol = Volume() vol.setLocation(1, self._getExtraPath("split_v%d.vol"%(i+1))) 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)