Source code for pwem.protocols.protocol_set_editor

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# *
# * Authors:     Pablo Conesa(
# *              Roberto Marabini(
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import pyworkflow.protocol.params as params
from pwem.protocols import EMProtocol
from import SetOfParticles

import numpy as np

[docs]class ProtSetEditor(EMProtocol): """ Protocol to edit attributes of all the items of a set using a formula. This could be useful for editing some values in the set. Use this protocol with extreme care, you can easily produce a set that is not consistent. """ _label = 'edit set' 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.') # formula form.addParam('formula', params.StringParam, label="Formula", 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('formulaStep')
[docs] def formulaStep(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.createCopy(self._getExtraPath(), copyInfo=True) for sourceItem in inputSet.iterItems(): item = sourceItem.clone() exec(self.formula.get()) modifiedSet.append(item) self.createOutput(self.inputSet, modifiedSet)
[docs] def createOutput(self, inputSet, modifiedSet): """ Save the output set.""" outputArgs = {inputSet.getExtended(): modifiedSet} self._defineOutputs(**outputArgs)
def _summary(self): return ["The this formula (%s) is/was applied to the items of the input set." % self.formula.get()]