Is there a way to programmatically mark/select cells for extraction?

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Oh, I like that. So, for instance, I would define a node/cell data array, assign integers to it (inlet pressure = 1, wall = 2, etc.) and then threshold:

(swiped from here):

    selector = vtkThreshold()
    selector.SetInputArrayToProcess(0, 0, 0, vtkDataObject().FIELD_ASSOCIATION_CELLS,
                                    vtkDataSetAttributes().SCALARS)
    selector.SetInputConnection(pad.GetOutputPort())
    selector.SetLowerThreshold(start_label)
    selector.SetUpperThreshold(end_label)
    selector.Update()