Source code for pwem.protocols.protocol_metadata_editor

# **************************************************************************
# *
# * Authors:     Pablo Conesa(pconesa@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pwem.protocols import EMProtocol


[docs]class ProtMetadataEditor(EMProtocol): """ Protocol to edit attributes of all the items of a set using a formula. This could be useful for corrupting your data for testing purposes or editing some values in the set that make sense to do it. Use this with extreme care, you can easily ruin your processing. """ _label = 'metadata editor' def _defineParams(self, form): """ Defines the parameters the protocol form will show and its behaviour :param form: """ form.addSection(label='Input') form.addParam('inputSet', params.PointerParam, pointerClass='EMSet', label='Set to edit', help='Set which items will be modified.') form.addParam('formula', params.StringParam, label="Formula", important=True, help='A python code compatible with eval, where item represents each of ' 'the elements of the set. E.g.: item._resolution.set(item._resolution.get() +1).' 'You could also use modules like "import numpy; item._resolution .... "') def _insertAllSteps(self): self._insertFunctionStep('editItemsStep')
[docs] def editItemsStep(self): """ Goes through all items in the input set and applies the formula to each of them using exec. Complex python code could be run separating lines with ; To use numpy you could do import numpy; item._resolution.set(numpy.random.randint(10)) """ inputSet = self.inputSet.get() modifiedSet = inputSet.create(self._getExtraPath()) modifiedSet.copyInfo(inputSet) for sourceItem in inputSet.iterItems(): item = sourceItem.clone() exec(self.formula.get()) modifiedSet.append(item) outputArgs = {self.inputSet.getExtended(): modifiedSet} self._defineOutputs(**outputArgs)