Source code for xmipp3.protocols.protocol_metaprotocol_create_subset

# **************************************************************************
# *
# * Authors:     Amaya Jimenez (ajimenez@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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from pyworkflow import VERSION_2_0
from pyworkflow.protocol.params import PointerParam, IntParam
from pwem.protocols import EMProtocol
from pwem.objects import Volume


[docs]class XmippMetaProtCreateSubset(EMProtocol): """ Metaprotocol to select a set of particles from a 3DClasses and a Volume from a SetOfVolumes """ _label = 'metaprotocol heterogeneity subset' _lastUpdateVersion = VERSION_2_0 #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') # form.addParam('inputSetOfVolumes', PointerParam, pointerClass='SetOfVolumes', # label="Input set of volumes", # help='Select the set of volumes to select an specific volume.') form.addParam('inputSetOfClasses3D', PointerParam, pointerClass='SetOfClasses3D', label="Input set of 3D classes", help='Select the set of 3D classes to select an specific set of particles.') form.addParam('idx', IntParam, label="Input Idx", default=0, help='Identifier of the volume and particles selected') #--------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions -------------------------------
[docs] def createOutputStep(self): id = self.idx.get() # inputSetOfVolumes=self.inputSetOfVolumes.get() inputSetOfClasses3D=self.inputSetOfClasses3D.get() newVolume = Volume() #newVolume.setFileName(inputSetOfVolumes[id].getFileName()) #newVolume.setSamplingRate(inputSetOfVolumes[id].getSamplingRate()) newVolume.setFileName(inputSetOfClasses3D[id].getRepresentative().getFileName()) newVolume.setSamplingRate(inputSetOfClasses3D[id].getSamplingRate()) newParticles = self._createSetOfParticles() newParticles.setSamplingRate(inputSetOfClasses3D[id].getSamplingRate()) if inputSetOfClasses3D[id].hasAlignmentProj(): newParticles.setAlignmentProj() newParticles.copyItems(inputSetOfClasses3D[id]) self._defineOutputs(**{'outputAuxVolumes': newVolume}) self._store(newVolume) self._defineOutputs(**{'outputAuxParticles': newParticles}) self._store(newParticles)
#--------------------------- INFO functions -------------------------------- def _validate(self): errors = [] return errors def _summary(self): summary = [] return summary