Source code for tomo.protocols.protocol_assign_tomo2subtomo

# **************************************************************************
# *
# * Authors:     Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from pyworkflow.protocol.params import PointerParam
from pyworkflow.utils import removeExt
from pwem.protocols import EMProtocol

[docs]class ProtAssignTomo2Subtomo(EMProtocol): """ This protocol assign tomograms to subtomograms that have been imported before without tomograms. Subtomograms should contain the name of the original tomogram in their own file name. """ _label = 'assign tomos to subtomos' def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputSubtomos', PointerParam, pointerClass='SetOfSubTomograms', label='Subtomograms', help='Select the subtomograms that you want to update with original tomograms as precedents.' 'The subtomograms should contain the original tomogram name in their own filename.') form.addParam('inputTomos', PointerParam, pointerClass='SetOfTomograms', label='Tomograms', help='Select the tomograms to be assigned to the subtomograms.') # --------------------------- INSERT steps functions -------------------------- def _insertAllSteps(self): self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------------------------
[docs] def createOutputStep(self): self.tomoDict = {} inputTomos = self.inputTomos.get() for tomo in inputTomos: self.tomoDict[tomo.getBaseName()] = tomo.getObjId() inputSubtomos = self.inputSubtomos.get() outputSubtomos = inputSubtomos.create(self._getPath()) outputSubtomos.copyInfo(inputSubtomos) outputSubtomos.copyItems(inputSubtomos, updateItemCallback=self._updateItem) self._defineOutputs(outputSubtomograms=outputSubtomos) self._defineSourceRelation(self.inputSubtomos, outputSubtomos) self._defineSourceRelation(self.inputTomos, outputSubtomos)
# --------------------------- UTILS functions -------------------------------------------- def _updateItem(self, item, row): for tomoName in self.tomoDict: if removeExt(tomoName) in item.getFileName(): item.setVolName(tomoName) item.setVolId(self.tomoDict.get(tomoName)) break # --------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputSubtomograms'): summary.append("Output subtomograms not ready yet.") else: summary.append("%s tomograms assigned to %s subtomograms." % (self.getObjectTag('inputTomos'), self.getObjectTag('inputSubtomos'))) return summary def _methods(self): methods = [] if not hasattr(self, 'outputSubtomograms'): methods.append("Output subtomograms not ready yet.") else: methods.append("%d %s tomograms assigned to %d %s subtomograms." % (self.inputTomos.get().getSize(), self.getObjectTag('inputTomos'), self.inputSubtomos.get().getSize(), self.getObjectTag('inputSubtomos'))) return methods