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import moose
def model(element):
"""Given model root element, extracts morphology
information about all neurons and compartments belonging
to that model
"""
if element.path.endswith("/") :
return morphology(moose.element(element.path + "cells"))
else:
return morphology(moose.element(element.path + "/cells"))
def morphology(element):
"""Given the element containing all neurons, extracts
morphology information from all child elements.
"""
return { "name" : element.name
, "id" : element.path
, "type" : etype(element)
, "neurons" : recurse(element, neuron, moose.Neuron)
}
def neuron(element):
"""Given a neuron element, extracts morphology
information from all child compartment elements.
"""
return element.path, { "name" : element.name
, "id" : element.path
, "object" : element
, "type" : etype(element)
, "compartments" : recurse(element, compartment, moose.CompartmentBase)
}
def compartment(element):
return element.path, { "name" : element.name
, "object" : element
, "id" : element.path
, "type" : etype(element)
, "proximal" : { "x" : element.x0
, "y" : element.y0
, "z" : element.z0
}
, "distal" : { "x" : element.x
, "y" : element.y
, "z" : element.z
}
, "diameter" : element.diameter
}
def etype(element):
element_type = element.name.rpartition("_")[0]
if element_type == '': return element.name
return element_type
def recurse(element, func, classType):
return dict( [ func(child[0]) for child in element.children
if isinstance(child, classType)
]
)