def __init__(self, source, start, stop, morphology, name=None):
self.morphology = morphology
if isinstance(source, SpatialSubgroup):
source = source.source
start += source.start
stop += source.start
Subgroup.__init__(self, source, start, stop, name)
def spatialneuron_segment(neuron, x):
'''
Selects a segment from `SpatialNeuron` neuron, where x is a slice of
either compartment indexes or distances.
Note a: segment is not a `SpatialNeuron`, only a `Group`.
'''
if not isinstance(x, slice):
raise TypeError(
'Subgroups can only be constructed using slicing syntax')
start, stop, step = x.start, x.stop, x.step
if step is None:
step = 1
if step != 1:
raise IndexError('Subgroups have to be contiguous')
if type(start) == type(1 * cm): # e.g. 10*um:20*um
# Convert to integers (compartment numbers)
morpho = neuron.morphology[x]
start = morpho._origin
stop = morpho._origin + len(morpho)
if start >= stop:
raise IndexError('Illegal start/end values for subgroup, %d>=%d' %
(start, stop))
return Subgroup(neuron, start, stop)
def spatialneuron_segment(neuron, item):
'''
Selects a segment from `SpatialNeuron` neuron, where item is a slice of
either compartment indexes or distances.
Note a: segment is not a `SpatialNeuron`, only a `Group`.
'''
if not isinstance(item, slice):
raise TypeError(
'Subgroups can only be constructed using slicing syntax')
start, stop, step = item.start, item.stop, item.step
if step is None:
step = 1
if step != 1:
raise IndexError('Subgroups have to be contiguous')
if isinstance(start, Quantity):
if not have_same_dimensions(
start, meter) or not have_same_dimensions(stop, meter):
raise DimensionMismatchError(
'Start and stop should have units of meter', start, stop)
# Convert to integers (compartment numbers)
indices = neuron.morphology.indices[item]
start, stop = indices[0], indices[-1] + 1
if start >= stop:
raise IndexError('Illegal start/end values for subgroup, %d>=%d' %
(start, stop))
return Subgroup(neuron, start, stop)
def spatialneuron_segment(neuron, item):
'''
Selects a segment from `SpatialNeuron` neuron, where item is a slice of
either compartment indexes or distances.
Note a: segment is not a `SpatialNeuron`, only a `Group`.
'''
if isinstance(item, slice) and isinstance(item.start, Quantity):
if item.step is not None:
raise ValueError('Cannot specify a step size for slicing based'
'on length.')
start, stop = item.start, item.stop
if (not have_same_dimensions(start, meter) or
not have_same_dimensions(stop, meter)):
raise DimensionMismatchError('Start and stop should have units '
'of meter', start, stop)
# Convert to integers (compartment numbers)
indices = neuron.morphology.indices[item]
start, stop = indices[0], indices[-1] + 1
elif not isinstance(item, slice) and hasattr(item, 'indices'):
start, stop = to_start_stop(item.indices[:], neuron._N)
else:
start, stop = to_start_stop(item, neuron._N)
if start >= stop:
raise IndexError('Illegal start/end values for subgroup, %d>=%d' %
(start, stop))
return Subgroup(neuron, start, stop)
def spatialneuron_segment(neuron, item):
"""
Selects a segment from `SpatialNeuron` neuron, where item is a slice of
either compartment indexes or distances.
Note a: segment is not a `SpatialNeuron`, only a `Group`.
"""
if isinstance(item, slice) and isinstance(item.start, Quantity):
if item.step is not None:
raise ValueError("Cannot specify a step size for slicing based"
"on length.")
start, stop = item.start, item.stop
if (not have_same_dimensions(start, meter) or
not have_same_dimensions(stop, meter)):
raise DimensionMismatchError("Start and stop should have units "
"of meter", start, stop)
# Convert to integers (compartment numbers)
indices = neuron.morphology.indices[item]
start, stop = indices[0], indices[-1] + 1
elif not isinstance(item, slice) and hasattr(item, 'indices'):
start, stop = to_start_stop(item.indices[:], neuron._N)
else:
start, stop = to_start_stop(item, neuron._N)
if isinstance(neuron, SpatialSubgroup):
start += neuron.start
stop += neuron.start
if start >= stop:
raise IndexError(f'Illegal start/end values for subgroup, {int(start)}>={int(stop)}')
if isinstance(neuron, SpatialSubgroup):
# Note that the start/stop values calculated above are always
# absolute values, even for subgroups
neuron = neuron.source
return Subgroup(neuron, start, stop)
def __getitem__(self, item):
if not isinstance(item, slice):
raise TypeError('Subgroups can only be constructed using slicing syntax')
start, stop, step = item.indices(self._N)
if step != 1:
raise IndexError('Subgroups have to be contiguous')
if start >= stop:
raise IndexError('Illegal start/end values for subgroup, %d>=%d' %
(start, stop))
return Subgroup(self, start, stop)
def __getitem__(self, item):
if not isinstance(item, slice):
raise TypeError(
"Subgroups can only be constructed using slicing syntax")
start, stop, step = item.indices(self._N)
if step != 1:
raise IndexError("Subgroups have to be contiguous")
if start >= stop:
raise IndexError(
f"Illegal start/end values for subgroup, {int(start)}>={int(stop)}"
)
return Subgroup(self, start, stop)
def spatialneuron_attribute(neuron, x):
'''
Selects a subtree from `SpatialNeuron` neuron and returns a `SpatialSubgroup`.
If it does not exist, returns the `Group` attribute.
'''
if x == 'main': # Main segment, without the subtrees
origin = neuron.morphology._origin
return Subgroup(neuron, origin, origin + len(neuron.morphology.x))
elif (x != 'morphology') and ((x in neuron.morphology._namedkid)
or all([c in 'LR123456789'
for c in x])): # subtree
morpho = neuron.morphology[x]
return SpatialSubgroup(neuron,
morpho._origin,
morpho._origin + len(morpho),
morphology=morpho)
else:
return Group.__getattr__(neuron, x)
def __init__(self, source, start, stop, morphology, name=None):
self.morphology = morphology
Subgroup.__init__(self, source, start, stop, name)
def __init__(self, source, start, stop, morphology, name=None):
self.morphology = morphology
Subgroup.__init__(self, source, start, stop, name)
