def check_cloned_neuron(nrn1, nrn2):
# check if two neurons are identical
# soma
nt.ok_(isinstance(nrn2.soma, type(nrn1.soma)))
nt.eq_(nrn1.soma.radius, nrn2.soma.radius)
for v1, v2 in zip(nrn1.soma.iter(), nrn2.soma.iter()):
nt.ok_(np.allclose(v1, v2))
# neurites
for v1, v2 in zip(iter_segments(nrn1), iter_segments(nrn2)):
(v1_start, v1_end), (v2_start, v2_end) = v1, v2
nt.ok_(np.allclose(v1_start, v2_start))
nt.ok_(np.allclose(v1_end, v2_end))
# check if the ids are different
# somata
nt.ok_(nrn1.soma is not nrn2.soma)
# neurites
for neu1, neu2 in zip(nrn1.neurites, nrn2.neurites):
nt.ok_(neu1 is not neu2)
# check if changes are propagated between neurons
nrn2.soma.radius = 10.
nt.ok_(nrn1.soma.radius != nrn2.soma.radius)
nrn2._data.data_block[0, :] = np.zeros_like(nrn2._data.data_block[0, :])
nt.ok_(not np.allclose(nrn1._data.data_block[0, :],
nrn2._data.data_block[0, :]))
def check_cloned_neuron(nrn1, nrn2):
# check if two neurons are identical
# soma
nt.ok_(isinstance(nrn2.soma, type(nrn1.soma)))
nt.eq_(nrn1.soma.radius, nrn2.soma.radius)
for v1, v2 in zip(nrn1.soma.iter(), nrn2.soma.iter()):
nt.ok_(np.allclose(v1, v2))
# neurites
for v1, v2 in zip(iter_segments(nrn1), iter_segments(nrn2)):
(v1_start, v1_end), (v2_start, v2_end) = v1, v2
nt.ok_(np.allclose(v1_start, v2_start))
nt.ok_(np.allclose(v1_end, v2_end))
# check if the ids are different
# somata
nt.ok_(nrn1.soma is not nrn2.soma)
# neurites
for neu1, neu2 in zip(nrn1.neurites, nrn2.neurites):
nt.ok_(neu1 is not neu2)
# check if changes are propagated between neurons
nrn2.soma.radius = 10.
nt.ok_(nrn1.soma.radius != nrn2.soma.radius)
nrn2._data.data_block[0, :] = np.zeros_like(nrn2._data.data_block[0, :])
nt.ok_(not np.allclose(nrn1._data.data_block[0, :], nrn2._data.data_block[
0, :]))
def plot_soma3d(ax, soma, color=None, alpha=_ALPHA):
'''Generates a 3d figure of the soma.
Args:
ax(matplotlib axes): on what to plot
soma(neurom.core.Soma): plotted soma
color(str or None): Color of plotted values, None corresponds to default choice
alpha(float): Transparency of plotted values
'''
color = _get_color(color, tree_type=NeuriteType.soma)
if isinstance(soma, SomaCylinders):
for start, end in zip(soma.points, soma.points[1:]):
common.plot_cylinder(ax,
start=start[COLS.XYZ],
end=end[COLS.XYZ],
start_radius=start[COLS.R],
end_radius=end[COLS.R],
color=color,
alpha=alpha)
else:
common.plot_sphere(ax,
center=soma.center[COLS.XYZ],
radius=soma.radius,
color=color,
alpha=alpha)
# unlike w/ 2d Axes, the dataLim isn't set by collections, so it has to be updated manually
_update_3d_datalim(ax, soma)
def _render_dendrogram(dnd, ax, displacement):
'''Renders dendrogram'''
# set of unique colors that reflect the set of types of the neurites
colors = set()
for n, (indices, ctype) in enumerate(zip(dnd.groups, dnd.types)):
# slice rectangles array for the current neurite
group = dnd.data[indices[0]:indices[1]]
if n > 0:
# displace the neurites by half of their maximum x dimension
# plus half of the previous neurite's maxmimum x dimension
displacement += 0.5 * (dnd.dims[n - 1][0] + dnd.dims[n][0])
# arrange the trees without overlapping with each other
group += (displacement, 0.)
# create the polygonal collection of the dendrogram
# segments
_generate_collection(group, ax, ctype, colors)
soma_square = dnd.soma
if soma_square is not None:
_generate_collection((soma_square + (displacement / 2., 0.), ), ax,
NeuriteType.soma, colors)
ax.plot((displacement / 2., displacement), (0., 0.), color='k')
ax.plot((0., displacement / 2.), (0., 0.), color='k')
return displacement
def _render_dendrogram(dnd, ax, displacement):
'''Renders dendrogram'''
# set of unique colors that reflect the set of types of the neurites
colors = set()
for n, (indices, ctype) in enumerate(zip(dnd.groups, dnd.types)):
# slice rectangles array for the current neurite
group = dnd.data[indices[0]:indices[1]]
if n > 0:
# displace the neurites by half of their maximum x dimension
# plus half of the previous neurite's maxmimum x dimension
displacement += 0.5 * (dnd.dims[n - 1][0] + dnd.dims[n][0])
# arrange the trees without overlapping with each other
group += (displacement, 0.)
# create the polygonal collection of the dendrogram
# segments
_generate_collection(group, ax, ctype, colors)
soma_square = dnd.soma
if soma_square is not None:
_generate_collection((soma_square + (displacement / 2., 0.),), ax, NeuriteType.soma, colors)
ax.plot((displacement / 2., displacement), (0., 0.), color='k')
ax.plot((0., displacement / 2.), (0., 0.), color='k')
return displacement
def plot_soma(ax,
soma,
plane='xy',
soma_outline=True,
linewidth=_LINEWIDTH,
color=None,
alpha=_ALPHA):
'''Generates a 2d figure of the soma.
Args:
ax(matplotlib axes): on what to plot
soma(neurom.core.Soma): plotted soma
plane(str): Any pair of 'xyz'
diameter_scale(float): Scale factor multiplied with segment diameters before plotting
linewidth(float): all segments are plotted with this width, but only if diameter_scale=None
color(str or None): Color of plotted values, None corresponds to default choice
alpha(float): Transparency of plotted values
'''
plane0, plane1 = _plane2col(plane)
color = _get_color(color, tree_type=NeuriteType.soma)
if isinstance(soma, SomaCylinders):
plane0, plane1 = _plane2col(plane)
for start, end in zip(soma.points, soma.points[1:]):
common.project_cylinder_onto_2d(ax, (plane0, plane1),
start=start[COLS.XYZ],
end=end[COLS.XYZ],
start_radius=start[COLS.R],
end_radius=end[COLS.R],
color=color,
alpha=alpha)
else:
if soma_outline:
ax.add_artist(
Circle(soma.center[[plane0, plane1]],
soma.radius,
color=color,
alpha=alpha))
else:
plane0, plane1 = _plane2col(plane)
points = [(p[plane0], p[plane1]) for p in soma.iter()]
if points:
points.append(points[0]) # close the loop
ax.plot(points, color=color, alpha=alpha, linewidth=linewidth)
ax.set_xlabel(plane[0])
ax.set_ylabel(plane[1])
bounding_box = geom.bounding_box(soma)
ax.dataLim.update_from_data_xy(np.vstack(
([bounding_box[0][plane0], bounding_box[0][plane1]],
[bounding_box[1][plane0], bounding_box[1][plane1]])),
ignore=False)
def iter_segments(obj, neurite_filter=None):
'''Return an iterator to the segments in a collection of neurites
Parameters:
obj: neuron, population, neurite, section, or iterable containing neurite objects
neurite_filter: optional top level filter on properties of neurite neurite objects
Note:
This is a convenience function provideded for generic access to
neuron segments. It may have a performance overhead WRT custom-made
segment analysis functions that leverage numpy and section-wise iteration.
'''
sections = iter((obj,) if isinstance(obj, Section) else
iter_sections(obj, neurite_filter=neurite_filter))
return chain.from_iterable(zip(sec.points[:-1], sec.points[1:])
for sec in sections)
def iter_segments(obj, neurite_filter=None):
'''Return an iterator to the segments in a collection of neurites
Parameters:
obj: neuron, population, neurite, section, or iterable containing neurite objects
neurite_filter: optional top level filter on properties of neurite neurite objects
Note:
This is a convenience function provideded for generic access to
neuron segments. It may have a performance overhead WRT custom-made
segment analysis functions that leverage numpy and section-wise iteration.
'''
sections = iter((obj, ) if isinstance(obj, Section) else iter_sections(
obj, neurite_filter=neurite_filter))
return chain.from_iterable(
zip(sec.points[:-1], sec.points[1:]) for sec in sections)
def plot_soma(ax, soma, plane='xy',
soma_outline=True,
linewidth=_LINEWIDTH,
color=None, alpha=_ALPHA):
'''Generates a 2d figure of the soma.
Args:
ax(matplotlib axes): on what to plot
soma(neurom.core.Soma): plotted soma
plane(str): Any pair of 'xyz'
diameter_scale(float): Scale factor multiplied with segment diameters before plotting
linewidth(float): all segments are plotted with this width, but only if diameter_scale=None
color(str or None): Color of plotted values, None corresponds to default choice
alpha(float): Transparency of plotted values
'''
plane0, plane1 = _plane2col(plane)
color = _get_color(color, tree_type=NeuriteType.soma)
if isinstance(soma, SomaCylinders):
plane0, plane1 = _plane2col(plane)
for start, end in zip(soma.points, soma.points[1:]):
common.project_cylinder_onto_2d(ax, (plane0, plane1),
start=start[COLS.XYZ], end=end[COLS.XYZ],
start_radius=start[COLS.R], end_radius=end[COLS.R],
color=color, alpha=alpha)
else:
if soma_outline:
ax.add_artist(Circle(soma.center[[plane0, plane1]], soma.radius,
color=color, alpha=alpha))
else:
plane0, plane1 = _plane2col(plane)
points = [(p[plane0], p[plane1]) for p in soma.iter()]
if points:
points.append(points[0]) # close the loop
ax.plot(points, color=color, alpha=alpha, linewidth=linewidth)
ax.set_xlabel(plane[0])
ax.set_ylabel(plane[1])
bounding_box = geom.bounding_box(soma)
ax.dataLim.update_from_data_xy(np.vstack(([bounding_box[0][plane0], bounding_box[0][plane1]],
[bounding_box[1][plane0], bounding_box[1][plane1]])),
ignore=False)
def has_all_nonzero_segment_lengths(neuron, threshold=0.0):
'''Check presence of neuron segments with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a segment length is considered to
be non-zero
Returns:
CheckResult with result including list of (section_id, segment_id)
of zero length segments
'''
bad_ids = []
for sec in _nf.iter_sections(neuron):
p = sec.points
for i, s in enumerate(zip(p[:-1], p[1:])):
if segment_length(s) <= threshold:
bad_ids.append((sec.id, i))
return CheckResult(len(bad_ids) == 0, bad_ids)
def has_all_nonzero_segment_lengths(neuron, threshold=0.0):
'''Check presence of neuron segments with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a segment length is considered to
be non-zero
Returns:
CheckResult with result including list of (section_id, segment_id)
of zero length segments
'''
bad_ids = []
for sec in _nf.iter_sections(neuron):
p = sec.points
for i, s in enumerate(zip(p[:-1], p[1:])):
if segment_length(s) <= threshold:
bad_ids.append((sec.id, i))
return CheckResult(len(bad_ids) == 0, bad_ids)
def iter_segments(obj, neurite_filter=None, neurite_order=NeuriteIter.FileOrder):
'''Return an iterator to the segments in a collection of neurites
Parameters:
obj: neuron, population, neurite, section, or iterable containing neurite objects
neurite_filter: optional top level filter on properties of neurite neurite objects
neurite_order: order upon which neurite should be iterated. Values:
- NeuriteIter.FileOrder: order of appearance in the file
- NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical
Note:
This is a convenience function provided for generic access to
neuron segments. It may have a performance overhead WRT custom-made
segment analysis functions that leverage numpy and section-wise iteration.
'''
sections = iter((obj,) if isinstance(obj, Section) else
iter_sections(obj,
neurite_filter=neurite_filter,
neurite_order=neurite_order))
return chain.from_iterable(zip(sec.points[:-1], sec.points[1:])
for sec in sections)
def iter_segments(obj, neurite_filter=None, neurite_order=NeuriteIter.FileOrder):
"""Return an iterator to the segments in a collection of neurites.
Arguments:
obj: neuron, population, neurite, section, or iterable containing neurite objects
neurite_filter: optional top level filter on properties of neurite neurite objects
neurite_order: order upon which neurite should be iterated. Values:
- NeuriteIter.FileOrder: order of appearance in the file
- NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical
Note:
This is a convenience function provided for generic access to
neuron segments. It may have a performance overhead WRT custom-made
segment analysis functions that leverage numpy and section-wise iteration.
"""
sections = iter((obj,) if isinstance(obj, Section) else
iter_sections(obj,
neurite_filter=neurite_filter,
neurite_order=neurite_order))
return chain.from_iterable(zip(sec.points[:-1], sec.points[1:])
for sec in sections)
def plot_soma3d(ax, soma, color=None, alpha=_ALPHA):
'''Generates a 3d figure of the soma.
Args:
ax(matplotlib axes): on what to plot
soma(neurom.core.Soma): plotted soma
color(str or None): Color of plotted values, None corresponds to default choice
alpha(float): Transparency of plotted values
'''
color = _get_color(color, tree_type=NeuriteType.soma)
if isinstance(soma, SomaCylinders):
for start, end in zip(soma.points, soma.points[1:]):
common.plot_cylinder(ax,
start=start[COLS.XYZ], end=end[COLS.XYZ],
start_radius=start[COLS.R], end_radius=end[COLS.R],
color=color, alpha=alpha)
else:
common.plot_sphere(ax, center=soma.center[COLS.XYZ], radius=soma.radius,
color=color, alpha=alpha)
# unlike w/ 2d Axes, the dataLim isn't set by collections, so it has to be updated manually
_update_3d_datalim(ax, soma)
def _check_fst_neurite_rotate(nrt_a, nrt_b, rot_mat):
for sa, sb in zip(_nf.iter_sections(nrt_a),
_nf.iter_sections(nrt_b)):
nt.assert_true(np.allclose(sb.points[:, 0:3],
_apply_rot(sa.points[:, 0:3], rot_mat)))
def _check_fst_neurite_translate(nrts_a, nrts_b, t):
# neurite sections
for sa, sb in zip(_nf.iter_sections(nrts_a),
_nf.iter_sections(nrts_b)):
nt.assert_true(np.allclose((sb.points[:, 0:3] - sa.points[:, 0:3]), t))
def map_segments(fun, section):
'''Map a function to segments in a section'''
pts = section.points
return list(fun(s) for s in zip(pts[:-1], pts[1:]))