def iter_neurites(self, iterator_type, mapping=None, neurite_type=TreeType.all):
'''Iterate over collection of neurites applying iterator_type
Parameters:
iterator_type: Type of iterator with which to perform the iteration.\
(e.g. isegment, isection, i_section_path_length)
mapping: mapping function to be applied to the target of iteration.\
(e.g. segment_length). Must be compatible with the iterator_type.
neurite_type: TreeType object. Neurites of incompatible type are\
filtered out.
Returns:
Iterator of mapped iteration targets.
Example:
Get the total volume of all neurites in the cell and the total\
length or neurites from their segments.
>>> from neurom import ezy
>>> from neurom.analysis import morphmath as mm
>>> from neurom.core import tree as tr
>>> nrn = ezy.load_neuron('test_data/swc/Neuron.swc')
>>> v = sum(nrn.iter_neurites(tr.isegment, mm.segment_volume))
>>> tl = sum(nrn.iter_neurites(tr.isegment, mm.segment_length)))
'''
return self.i_neurites(iterator_type,
mapping,
tree_filter=lambda t: checkTreeType(neurite_type,
t.type))
def _n_sections_per_neurite(self, **kwargs):
'''Get an iterable with the number of sections for a given neurite type'''
neurite_type = kwargs.get('neurite_type', TreeType.all)
return self._iterable_type(
[n_sections(n) for n in self.neurites
if checkTreeType(neurite_type, n.type)]
)
def _n_neurites(self, **kwargs):
'''Get the number of neurites of a given type in a neuron'''
neurite_type = kwargs.get('neurite_type', TreeType.all)
return sum(1 for n in self.neurites if checkTreeType(neurite_type, n.type))
def get_n_neurites(self, neurite_type=TreeType.all):
'''Get the number of neurites of a given type in a neuron'''
return sum(1 for n in self.neurites
if checkTreeType(neurite_type, n.type))
def _n_sections(self, **kwargs):
'''Get the number of sections of a given type'''
neurite_type = kwargs.get('neurite_type', TreeType.all)
return sum(n_sections(t) for t in self.neurites if checkTreeType(neurite_type, t.type))
def get_n_sections(self, neurite_type=TreeType.all):
'''Get the number of sections of a given type'''
return sum(n_sections(t) for t in self.neurites
if checkTreeType(neurite_type, t.type))
def get_n_sections_per_neurite(self, neurite_type=TreeType.all):
'''Get an iterable with the number of sections for a given neurite type'''
return self._iterable_type(
[n_sections(n) for n in self.neurites
if checkTreeType(neurite_type, n.type)]
)
def get_trunk_lengths(self, neurite_type=TreeType.all):
'''Get the trunk lengths of a given type in a neuron'''
return self._iterable_type(
[trunk_length(t) for t in self.neurites
if checkTreeType(neurite_type, t.type)]
)
def get_trunk_lengths(self, neurite_type=TreeType.all):
'''Get the trunk lengths of a given type in a neuron'''
return self._iterable_type([
trunk_length(t) for t in self.neurites
if checkTreeType(neurite_type, t.type)
])
def get_n_neurites(self, neurite_type=TreeType.all):
'''Get the number of neurites of a given type in a neuron'''
return sum(1 for n in self.neurites
if checkTreeType(neurite_type, n.type))
def get_n_sections_per_neurite(self, neurite_type=TreeType.all):
'''Get an iterable with the number of sections for a given neurite type'''
return self._iterable_type([
n_sections(n) for n in self.neurites
if checkTreeType(neurite_type, n.type)
])
def get_n_sections(self, neurite_type=TreeType.all):
'''Get the number of sections of a given type'''
return sum(
n_sections(t) for t in self.neurites
if checkTreeType(neurite_type, t.type))
