def test_register_neurite_feature_nrns():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(NRNS)]
n_points = fst.get('foo', NRNS)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_points = fst.get('foo', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(NRNS)]
n_volume = fst.get('bar', NRNS)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_volume = fst.get('bar', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_pop():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(POP)]
n_points = fst.get('foo', POP)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(POP,
filt=_is_type(NeuriteType.basal_dendrite))]
n_points = fst.get('foo', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(POP)]
n_volume = fst.get('bar', POP)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(POP, filt=_is_type(NeuriteType.basal_dendrite))]
n_volume = fst.get('bar', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_pop():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(POP)]
n_points = fst.get('foo', POP)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(POP,
filt=_is_type(NeuriteType.basal_dendrite))]
n_points = fst.get('foo', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(POP)]
n_volume = fst.get('bar', POP)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(POP, filt=_is_type(NeuriteType.basal_dendrite))]
n_volume = fst.get('bar', POP, neurite_type=NeuriteType.basal_dendrite)
assert_items_equal(n_volume, n_volume_ref)
def test_register_neurite_feature_nrns():
def npts(neurite):
return len(neurite.points)
def vol(neurite):
return neurite.volume
fst.register_neurite_feature('foo', npts)
n_points_ref = [len(n.points) for n in iter_neurites(NRNS)]
n_points = fst.get('foo', NRNS)
assert_items_equal(n_points, n_points_ref)
# test neurite type filtering
n_points_ref = [len(n.points) for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_points = fst.get('foo', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_points, n_points_ref)
fst.register_neurite_feature('bar', vol)
n_volume_ref = [n.volume for n in iter_neurites(NRNS)]
n_volume = fst.get('bar', NRNS)
assert_items_equal(n_volume, n_volume_ref)
# test neurite type filtering
n_volume_ref = [n.volume for n in iter_neurites(NRNS, filt=_is_type(NeuriteType.axon))]
n_volume = fst.get('bar', NRNS, neurite_type=NeuriteType.axon)
assert_items_equal(n_volume, n_volume_ref)
def test_get_section_path_distances_endpoint(self):
ref_sec_path_len_start = list(iter_neurites(self.neuron, sec.start_point_path_length))
ref_sec_path_len = list(iter_neurites(self.neuron, sec.end_point_path_length))
path_lengths = self.neuron.get_section_path_distances()
nt.assert_true(ref_sec_path_len != ref_sec_path_len_start)
nt.assert_equal(len(path_lengths), 84)
nt.assert_true(np.all(path_lengths == ref_sec_path_len))
def test_section_path_distances_endpoint():
ref_sec_path_len_start = list(iter_neurites(NEURON, sec.start_point_path_length))
ref_sec_path_len = list(iter_neurites(NEURON, sec.end_point_path_length))
path_lengths = fst_get('section_path_distances', NEURON)
nt.ok_(ref_sec_path_len != ref_sec_path_len_start)
nt.eq_(len(path_lengths), 84)
nt.ok_(np.all(path_lengths == ref_sec_path_len))
def test_section_path_distances_endpoint():
ref_sec_path_len_start = list(iter_neurites(NEURON, sec.start_point_path_length))
ref_sec_path_len = list(iter_neurites(NEURON, sec.end_point_path_length))
path_lengths = fst_get('section_path_distances', NEURON)
nt.ok_(ref_sec_path_len != ref_sec_path_len_start)
nt.eq_(len(path_lengths), 84)
nt.ok_(np.all(path_lengths == ref_sec_path_len))
def test_section_path_distances_endpoint():
ref_sec_path_len_start = list(
iter_neurites(NEURON, sec.start_point_path_length))
ref_sec_path_len = list(iter_neurites(NEURON, sec.end_point_path_length))
path_lengths = get_feature('section_path_distances', NEURON)
assert ref_sec_path_len != ref_sec_path_len_start
assert len(path_lengths) == 84
assert np.all(path_lengths == ref_sec_path_len)
def _check_volume(obj):
sec_vol = [l for l in iter_neurites(obj, sec.volume)]
seg_vol = [l for l in iter_neurites(obj, seg.volume)]
sum_sec_vol = sum(sec_vol)
sum_seg_vol = sum(seg_vol)
# check that sum of section volumes is same as sum of segment lengths
nt.assert_almost_equal(sum_sec_vol, sum_seg_vol)
nt.assert_almost_equal(sum_sec_vol, 307.68010178856395)
def _check_area(obj):
sec_area = [l for l in iter_neurites(obj, sec.area)]
seg_area = [l for l in iter_neurites(obj, seg.area)]
sum_sec_area = sum(sec_area)
sum_seg_area = sum(seg_area)
# check that sum of section areas is same as sum of segment lengths
nt.assert_almost_equal(sum_sec_area, sum_seg_area)
nt.assert_almost_equal(sum_sec_area, 349.75070138106133)
def _check_length(obj):
sec_len = [l for l in iter_neurites(obj, sec.length)]
seg_len = [l for l in iter_neurites(obj, seg.length)]
sum_sec_len = sum(sec_len)
sum_seg_len = sum(seg_len)
# check that sum of section lengths is same as sum of segment lengths
nt.eq_(sum_sec_len, sum_seg_len)
nt.assert_almost_equal(sum_sec_len, 33.0330776588)
def TMD(neuron_handle):
"""
Compute the TMD of a neuron i.e. its dimension 0 persistence
using path distance as a filtration
:param neuron_handle:
:return:
"""
nrn = nm.load_neuron(neuron_handle)
diag = []
roots = []
f = {None: 0}
nodes = [neurite.root_node for neurite in nm.iter_neurites(nrn)]
while len(nodes) > 0:
n = nodes.pop()
f[n] = f[n.parent] + n.length
nodes.extend(n.children)
for neurite in nm.iter_neurites(nrn):
R = neurite.root_node # the root of the neuron tree
A = {} # A set of active nodes, initialized to the set of tree leaves
for l in R.ileaf():
A[l] = f[l]
while not R in A:
for l in A:
p = l.parent
# break if a child of p is not active, might need to improve this to avoid quadratic complexity
stop = False
m = 0
c0 = None
for c in p.children:
if not c in A:
stop = True
break
elif A[c] > m:
m = A[c]
c0 = c
if not stop:
A[p] = m
for c in p.children:
if not c == c0:
diag.append((min(A[c], f[p]), max(A[c], f[p])))
A.pop(c)
break
roots.append((min(A[R], f[R]), max(A[R], f[R])))
# merge root of dendrites
i = np.argmax(map(lambda a, b: b, roots))
a, b = roots.pop(i)
diag.extend(roots)
diag.append((b, ))
return diag
def test_get_section_radial_distances_endpoint(self):
ref_sec_rad_dist_start = []
for t in self.neuron.neurites:
ref_sec_rad_dist_start.extend(
ll for ll in iter_neurites(t, sec.radial_dist(t.value, use_start_point=True)))
ref_sec_rad_dist = []
for t in self.neuron.neurites:
ref_sec_rad_dist.extend(ll for ll in iter_neurites(t, sec.radial_dist(t.value)))
rad_dists = self.neuron.get_section_radial_distances()
nt.assert_true(ref_sec_rad_dist != ref_sec_rad_dist_start)
nt.assert_equal(len(rad_dists), 84)
nt.assert_true(np.all(rad_dists == ref_sec_rad_dist))
def _check_segment_radial_dists(obj):
origin = [0.0, 0.0, 0.0]
rd = [d for d in iter_neurites(SIMPLE_NEURON, seg.radial_dist(origin))]
nt.eq_(rd, [1.0, 3.0, 5.0, 7.0, 1.0, 3.0, 5.0, 7.0])
def _check_section_radial_dists_start_point(obj):
origin = [0.0, 0.0, 0.0]
rd = [d for d in iter_neurites(obj, sec.radial_dist(origin, True))]
nt.eq_(rd, [0.0, 0.0])
def _check_section_radial_dists_end_point(obj):
origin = [0.0, 0.0, 0.0]
rd = [d for d in iter_neurites(obj, sec.radial_dist(origin))]
nt.eq_(rd, [8.0, 8.0])
def test_section_path_distances_start_point():
ref_sec_path_len_start = list(
iter_neurites(NEURON, sec.start_point_path_length))
path_lengths = get_feature('section_path_distances',
NEURON,
use_start_point=True)
assert len(path_lengths) == 84
assert np.all(path_lengths == ref_sec_path_len_start)
def _check_points(obj):
@bif.bifurcation_point_function(as_tree=False)
def point(bif):
return bif[:4]
bif_points = [p for p in iter_neurites(obj, point)]
nt.eq_(bif_points,
[[0.0, 4.0, 0.0, 2.0], [0.0, 5.0, 0.0, 2.0], [0.0, 5.0, 3.0, 0.75]])
def test_load_trees_good_neuron():
'''Check trees in good neuron are the same as trees from loaded neuron'''
filepath = os.path.join(SWC_PATH, 'Neuron.swc')
nrn = utils.load_neuron(filepath)
trees = utils.load_trees(filepath)
nt.eq_(len(nrn.neurites), 4)
nt.eq_(len(nrn.neurites), len(trees))
nrn2 = MockNeuron(trees)
@pts.point_function(as_tree=False)
def elem(point):
return point
# Check data are the same in tree collection and neuron's neurites
for a, b in izip(iter_neurites(nrn, elem), iter_neurites(nrn2, elem)):
nt.ok_(np.all(a == b))
def test_get_remote_bifurcation_angles(self):
ref_remote_bifangles = list(iter_neurites(self.neuron, bifs.remote_angle))
remote_bifangles = self.neuron.get_remote_bifurcation_angles()
nt.assert_equal(len(remote_bifangles), 40)
nt.assert_true(np.all(remote_bifangles == ref_remote_bifangles))
remote_bifangles = self.neuron.get_remote_bifurcation_angles(TreeType.all)
nt.assert_equal(len(remote_bifangles), 40)
nt.assert_true(np.all(remote_bifangles == ref_remote_bifangles))
def _pkg(self, magic_iter, neurite_type=TreeType.all):
'''Return an iterable built from magic_iter'''
stuff = list(
iter_neurites(self,
magic_iter,
tree_type_checker(neurite_type))
)
return self._iterable_type(stuff)
def test_section_path_distances_start_point():
ref_sec_path_len_start = list(
iter_neurites(NEURON, sec.start_point_path_length))
path_lengths = get_feature('section_path_distances',
NEURON,
use_start_point=True)
nt.eq_(len(path_lengths), 84)
nt.ok_(np.all(path_lengths == ref_sec_path_len_start))
def _check_segment_areas(obj):
sa = (l/math.pi for l in iter_neurites(obj, seg.area))
ref = (2.0, 2.0, 6.7082039, 4.0, 6.7082039, 1.8038587,
1.5, 6.7082039, 1.8038587, 1.5)
for a, b in izip(sa, ref):
nt.assert_almost_equal(a, b)
def test_get_section_lengths(self):
ref_seclen = list(iter_neurites(self.neuron, sec.length))
seclen = self.neuron.get_section_lengths()
nt.assert_equal(len(seclen), 84)
nt.assert_true(np.all(seclen == ref_seclen))
seclen = self.neuron.get_section_lengths(TreeType.all)
nt.assert_equal(len(seclen), 84)
nt.assert_true(np.all(seclen == ref_seclen))
def _check_segment_volumes(obj):
sv = (l/math.pi for l in iter_neurites(obj, seg.volume))
ref = (1.0, 1.0, 4.6666667, 4.0, 4.6666667, 0.7708333,
0.5625, 4.6666667, 0.7708333, 0.5625)
for a, b in izip(sv, ref):
nt.assert_almost_equal(a, b)
def test_volume_density_per_neurite():
vol = np.array(_nf.total_volume_per_neurite(NRN))
hull_vol = np.array([convex_hull(n).volume for n in nm.iter_neurites(NRN)])
vol_density = _nf.volume_density_per_neurite(NRN)
nt.eq_(len(vol_density), 4)
nt.ok_(np.allclose(vol_density, vol / hull_vol))
ref_density = [0.43756606998299519, 0.52464681266899216,
0.24068543213643726, 0.26289304906104355]
nt.ok_(np.allclose(vol_density, ref_density))
def _make_trace(neuron,
plane,
prefix='',
opacity=1.,
visible=True,
style=None,
line_width=2):
'''Create the trace to be plotted'''
names = defaultdict(int)
lines = list()
for neurite in iter_neurites(neuron):
names[neurite.type] += 1
coords = dict(x=list(), y=list(), z=list())
colors = list()
try:
default_color = style[neurite]['color']
except KeyError:
default_color = TREE_COLOR.get(neurite.root_node.type, 'black')
for section in iter_sections(neurite):
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ])
for s in iter_segments(section)]
section_style = style.get(section, {
'range': slice(0, len(segs)),
'color': default_color
})
range_ = section_style['range']
colors += list(repeat(default_color, 3 * range_.start))
colors += list(
repeat(section_style['color'],
3 * (range_.stop - range_.start)))
colors += list(repeat(default_color,
3 * (len(segs) - range_.stop)))
for i, coord in enumerate('xyz'):
coords[coord] += list(
chain.from_iterable(
(p1[i], p2[i], None) for p1, p2 in segs) if coord in
plane else chain.from_iterable((0, 0, None) for _ in segs))
lines.append(
go.Scatter3d(name=_neurite_name(neurite, prefix, names),
showlegend=False,
visible=visible,
opacity=opacity,
line=dict(color=colors, width=line_width),
mode='lines',
**coords))
return lines
def test_neurite_volume_density():
vol = np.array(_nf.total_volume_per_neurite(NRN))
hull_vol = np.array([convex_hull(n).volume for n in nm.iter_neurites(NRN)])
vol_density = _nf.neurite_volume_density(NRN)
nt.eq_(len(vol_density), 4)
nt.ok_(np.allclose(vol_density, vol / hull_vol))
ref_density = [
0.43756606998299519, 0.52464681266899216, 0.24068543213643726,
0.26289304906104355
]
assert_allclose(vol_density, ref_density)
def _find_intact_sub_trees(self):
'''Returns intact neurites
There is a fallback mechanism in case there are no intact basals:
https://bbpcode.epfl.ch/source/xref/platform/BlueRepairSDK/BlueRepairSDK/src/repair.cpp#658
'''
basals = [
neurite.root_node for neurite in iter_neurites(self.neuron)
if (neurite.type == NeuriteType.basal_dendrite
and is_branch_intact(neurite.root_node, self.cut_leaves))
]
if not basals:
L.warning(
"No intact basals found. Falling back on less strict selection."
)
basals = [
section for section in iter_sections(self.neuron)
if (section.type == NeuriteType.basal_dendrite
and not is_cut_section(section, self.cut_leaves))
]
axons = [
neurite.root_node for neurite in iter_neurites(self.neuron)
if (neurite.type == NeuriteType.axon
and is_branch_intact(neurite.root_node, self.cut_leaves))
]
obliques = self._find_intact_obliques()
tufts = [
section for section in iter_sections(self.neuron)
if (self.repair_type_map[section] == RepairType.tuft
and not is_cut_section(section, self.cut_leaves))
]
return basals + obliques + axons + tufts
def _make_trace2d(neuron,
plane,
prefix='',
opacity=1.,
visible=True,
style=None,
line_width=2):
'''Create the trace to be plotted'''
names = defaultdict(int)
lines = list()
for neurite in iter_neurites(neuron):
names[neurite.type] += 1
try:
neurite_color = style[neurite]['color']
except KeyError:
neurite_color = TREE_COLOR.get(neurite.root_node.type, 'black')
name = _neurite_name(neurite, prefix, names)
for section in iter_sections(neurite):
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ])
for s in iter_segments(section)]
try:
colors = style[section]['color']
except KeyError:
colors = neurite_color
coords = dict()
for i, coord in enumerate('xyz'):
coords[coord] = list(
chain.from_iterable(
(p1[i], p2[i], None) for p1, p2 in segs))
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
lines.append(
go.Scattergl(name=name,
visible=visible,
opacity=opacity,
showlegend=False,
line=dict(color=colors, width=line_width),
mode='lines',
**coords))
return lines
def _make_trace(neuron, plane):
'''Create the trace to be plotted'''
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(x=list(chain.from_iterable((p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable((p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable((p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(
line=dict(color=color, width=2),
mode='lines',
**coords
)
def _make_trace(neuron, plane):
"""Create the trace to be plotted."""
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(
x=list(chain.from_iterable(
(p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable(
(p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable(
(p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(line=dict(color=color, width=2), mode='lines', **coords)
def count(neuron):
"""
Return number of bifurcation points in neuron or population
"""
return sum(1 for _ in iter_neurites(neuron, identity))
def count(neuron, tree_filter=None):
"""
Return number of segments in neuron or population
"""
return sum(1 for _ in iter_neurites(neuron, identity, tree_filter))
def _check_segment_taper_rate(obj):
tp = [t for t in iter_neurites(obj, seg.taper_rate)]
nt.eq_(tp,
[0.0, 0.0, 1.0, 0.0, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0])
def _check_path_length_start_point(obj, ref):
pl = [l for l in iter_neurites(obj, sec.start_point_path_length)]
nt.eq_(pl, ref)
def _check_segment_radius(obj):
rad = [r for r in iter_neurites(obj, seg.radius)]
nt.eq_(rad,
[1.0, 1.0, 1.5, 2.0, 1.5, 0.875, 0.75, 1.5, 0.875, 0.75])
def count(neuron):
"""
Return number of triplets in neuron or population
"""
return sum(1 for _ in iter_neurites(neuron, identity))
def _check_segment_lengths(obj):
lg = [l for l in iter_neurites(obj, seg.length)]
nt.eq_(lg, [1.0, 1.0, 2.0, 1.0, 2.0, 1.0, 1.0, 2.0, 1.0, 1.0])
def test_section_branch_order():
sec_bo = [bo for bo in iter_neurites(MOCK_TREE, sec.branch_order)]
nt.eq_(sec_bo, [0, 1, 1, 0, 1, 2, 2, 1])
def complete_morph_feature_info(self, neuroM_extra_config_path=None):
"""Adding more features by means of other NeuroM's functionalities
to the prediction generated by function 'set_morph_feature_info',
which uses just NeuroM's API for morph_stats
Example of features added: field diameter, bounding-box -X,Y,Z- extents
and -largest,shortest- principal extents"""
extra_file_exists = os.path.isfile(neuroM_extra_config_path)
if not extra_file_exists:
return
with open(neuroM_extra_config_path, 'r') as fp:
morph_extra_dict = json.load(fp)
# Adding more neurite's features, if requested:
# field diameter, bounding-box -X,Y,Z- extents and -largest,shortest- principal extents
with open(self.output_pred_file, 'r') as fp:
mod_prediction = json.load(fp)
if os.path.isdir(self.morph_path):
morph_files = nm.io.utils.get_morph_files(self.morph_path)
mapping = lambda section: section.points
for neurite_name, extra_feat_list in list(
morph_extra_dict.items()): # Dict. with neurite names and
# extra features to be computed
for cell_ID, dict0 in list(mod_prediction.items(
)): # Dict. with cell's morph_path-features dict. pairs
# for each cell
if os.path.isdir(self.morph_path):
morph_file_name = [
morph_file for morph_file in morph_files
if cell_ID in morph_file
]
neuron_path = os.path.join(
self.morph_path, os.path.basename(morph_file_name[0]))
else:
neuron_path = self.morph_path
neuron_model = nm.load_neuron(neuron_path)
for cell_part, dict1 in list(dict0.items()):
if cell_part == neurite_name:
neurite_filter = lambda neurite: neurite.type == getattr(
nm.NeuriteType, cell_part)
neurite_points = [
neurite_points
for neurite_points in nm.iter_neurites(
neuron_model, mapping, neurite_filter)
]
neurite_points = np.concatenate(neurite_points)
neurite_cloud = neurite_points[:, 0:3]
for feat_name in extra_feat_list:
# Compute the neurite's bounding-box -X,Y,Z- extents
if feat_name == 'neurite_X_extent':
neurite_X_extent = np.max(neurite_cloud[:, 0], axis=0) - \
np.min(neurite_cloud[:, 0], axis=0)
dict1.update(
{"neurite_X_extent": neurite_X_extent})
elif feat_name == 'neurite_Y_extent':
neurite_Y_extent = np.max(neurite_cloud[:, 1], axis=0) - \
np.min(neurite_cloud[:, 1], axis=0)
dict1.update(
{"neurite_Y_extent": neurite_Y_extent})
elif feat_name == 'neurite_Z_extent':
neurite_Z_extent = np.max(neurite_cloud[:, 2], axis=0) - \
np.min(neurite_cloud[:, 2], axis=0)
dict1.update(
{"neurite_Z_extent": neurite_Z_extent})
# Compute the neurite's principal extents
elif feat_name == 'neurite_shortest_extent':
# Compute the neurite's shortest principal extents
principal_extents = sorted(
nm.morphmath.principal_direction_extent(
neurite_cloud))
dict1.update({
"neurite_shortest_extent":
principal_extents[0]
})
elif feat_name == 'neurite_largest_extent':
# Compute the neurite's largest principal extents
principal_extents = sorted(
nm.morphmath.principal_direction_extent(
neurite_cloud))
dict1.update({
"neurite_largest_extent":
principal_extents[-1]
})
# Compute the neurite-field diameter
elif feat_name == 'neurite_field_diameter':
neurite_field_diameter = nm.morphmath.polygon_diameter(
neurite_cloud)
dict1.update({
"neurite_field_diameter":
neurite_field_diameter
})
# Saving NeuroM's output in a formatted json-file
# with open(self.output_pred_file, 'w') as fp:
# json.dump(mod_prediction, fp, sort_keys=True, indent=3)
return mod_prediction
def _check_local_bifurcation_angles(obj):
angles = [a for a in iter_neurites(obj, bif.local_angle)]
nt.eq_(angles, [math.pi / 4, math.pi / 2, math.pi / 4])
def _check_remote_bifurcation_angles(obj):
angles = [a for a in iter_neurites(obj, bif.remote_angle)]
nt.eq_(angles,
[0.9380474917927135, math.pi / 2, math.pi / 4])
view.plot_neuron(ax, neuron)
# draw circles
center = neuron.soma.center[:2]
_dist = np.linalg.norm(neuron.points[:,:2]-center, axis=1).max()
radii = np.arange(step_size, _dist, step_size)
patches = []
for rad in radii:
circle = mpatches.Circle(center, rad, fill=False, edgecolor='dimgray')
patches.append(circle)
p = PatchCollection(patches, match_original=True)
ax.add_collection(p)
# add labels
if label_dict is None:
apical_points = np.concatenate([x.points for x in nm.iter_neurites(neuron, filt=lambda t: t.type==nm.APICAL_DENDRITE)])
apical_label_pos_xs = [apical_points[:,0].min()-center[0], apical_points[:,0].max()-center[0]]
apical_label_pos_x = apical_label_pos_xs[0] if np.abs(apical_label_pos_xs[0])>np.abs(apical_label_pos_xs[1]) else apical_label_pos_xs[1]
apical_label_pos_y = center[1]+(apical_points[:,1].max()-center[1])/2
basal_points = np.concatenate([x.points for x in nm.iter_neurites(neuron, filt=lambda t: t.type==nm.BASAL_DENDRITE)])
basal_label_pos_xs = [basal_points[:,0].min()-center[0],basal_points[:,0].max()-center[0]]
basal_label_pos_x = basal_label_pos_xs[0] if np.abs(basal_label_pos_xs[0])>np.abs(basal_label_pos_xs[1]) else basal_label_pos_xs[1]
basal_label_pos_y = center[1]+(basal_points[:,1].min()-center[1])/2
label_dict = {'Apical':(apical_label_pos_x, apical_label_pos_y), 'Basal': (basal_label_pos_x, basal_label_pos_y)}
for name,pos in label_dict.items():
plt.annotate(name, pos)
ax.autoscale()
ax.set_axis_off()
plt.title(None)
