def test_draw_filter_neurite():
for mode in ['2d', '3d']:
viewer.draw(nrn, mode=mode, neurite_type=NeuriteType.basal_dendrite)
assert_allclose(common.plt.gca().get_ylim(),
[-30., 78], atol=5)
common.plt.close('all')
def test_draw_filter_neurite():
for mode in ['2d', '3d']:
viewer.draw(nrn, mode=mode, neurite_type=NeuriteType.basal_dendrite)
assert_allclose(common.plt.gca().get_ylim(),
[-30., 78], atol=5)
common.plt.close('all')
def test_draw_neuron3d():
viewer.draw(nrn, mode='3d')
common.plt.close('all')
nt.assert_raises(NotImplementedError,
viewer.draw,
nrn,
mode='3d',
realistic_diameters=True)
def visualize(file_path):
""" Code to visualize the neuron """
nrn = nm.load_neuron(file_path)
fig, ax = viewer.draw(nrn)
fig.show()
input()
fig, ax = viewer.draw(nrn, mode='3d')
fig.show()
input()
def test_writing_output():
fig_name = 'Figure.png'
tempdir = tempfile.mkdtemp('test_viewer')
try:
old_dir = os.getcwd()
os.chdir(tempdir)
viewer.draw(nrn, mode='2d', output_path='subdir')
nt.ok_(os.path.isfile(os.path.join(tempdir, 'subdir', fig_name)))
finally:
os.chdir(old_dir)
shutil.rmtree(tempdir)
common.plt.close('all')
def test_writing_output():
fig_name = 'Figure.png'
tempdir = tempfile.mkdtemp('test_viewer')
try:
old_dir = os.getcwd()
os.chdir(tempdir)
viewer.draw(nrn, mode='2d', output_path='subdir')
nt.ok_(os.path.isfile(os.path.join(tempdir, 'subdir', fig_name)))
finally:
os.chdir(old_dir)
shutil.rmtree(tempdir)
common.plt.close('all')
def draw_neuron(neuron, cut_plane_position, cut_leaves=None):
'''Draw the neuron in the xy, yz and xz planes.
Parameters:
neuron: a Neuron
cut_plane_position: a tuple (plane, position) like ('Z', 27)
that can be specified to add the cut plane on
the relevant plots
cut_leaves: leaves to be highlighted by blue circles
'''
figures = dict()
for draw_plane in ['yz', 'xy', 'xz']:
fig, axes = viewer.draw(neuron, plane=draw_plane)
figures[draw_plane] = (fig, axes)
if cut_leaves is not None:
import matplotlib
slice_index = {'yz': [1, 2], 'xy': [0, 1], 'xz': [0, 2]}
for point in cut_leaves:
point_2d = point[slice_index[draw_plane]]
axes.add_artist(matplotlib.patches.Circle(point_2d, radius=2))
if cut_plane_position:
cut_plane, position = cut_plane_position
for axis, line_func in zip(draw_plane, ['axvline', 'axhline']):
if axis == cut_plane.lower():
getattr(axes, line_func)(position)
return figures
def get_list_of_diff_section_types(morphology, apical_point_sections):
morph = morphology
_, ax = draw(morph)
apical_trunk_sections = []
for apical_point_section in apical_point_sections:
some_trunk_sections = list(apical_point_section.iupstream())
apical_trunk_sections = list(
set(apical_trunk_sections) | set(some_trunk_sections))
apical_trunk_ids = [section.id for section in apical_trunk_sections]
apical_trunk_points = [
section.points[-1, :2] for section in apical_trunk_sections
]
for point in apical_trunk_points:
ax.plot(point[0], point[1], 'bo', ms=5)
apical_tuft_sections = []
for apical_point_section in apical_point_sections:
some_tuft_sections = list(apical_point_section.ipreorder())
#print some_tuft_sections
apical_tuft_sections = apical_tuft_sections + some_tuft_sections
"""!!!!!!"""
apical_tuft_sections = [
sec for sec in apical_tuft_sections if sec not in apical_point_sections
]
"""!!!!!!"""
apical_tuft_ids = [section.id for section in apical_tuft_sections]
apical_tuft_points = [
section.points[-1, :2] for section in apical_tuft_sections
]
for point in apical_tuft_points:
ax.plot(point[0], point[1], 'go', ms=5)
filter1 = lambda n: n.type == nm.APICAL_DENDRITE
all_sections = list(nm.iter_sections(morph, neurite_filter=filter1))
all_ids = [section.id for section in all_sections]
oblique_ids = set(all_ids) - (set(apical_trunk_ids) | set(apical_tuft_ids))
oblique_sections = [
section for section in all_sections if section.id in oblique_ids
]
oblique_points = [section.points[-1, :2] for section in oblique_sections]
for point in oblique_points:
ax.plot(point[0], point[1], 'yo', ms=5)
plt.show()
section_types = {
'tuft': apical_tuft_sections,
'trunk': apical_trunk_sections,
'obliques': oblique_sections
}
return section_types
def view(input_file, plane, backend):
'''A simple neuron viewer'''
if backend == 'matplotlib':
from neurom.viewer import draw
kwargs = {
'mode': '3d' if plane == '3d' else '2d',
}
if plane != '3d':
kwargs['plane'] = plane
draw(load_neuron(input_file), **kwargs)
else:
from neurom.view.plotly import draw
draw(load_neuron(input_file), plane=plane)
if backend == 'matplotlib':
import matplotlib.pyplot as plt
plt.show()
def view(input_file, plane, backend):
'''A simple neuron viewer'''
if backend == 'matplotlib':
from neurom.viewer import draw
kwargs = {
'mode': '3d' if plane == '3d' else '2d',
}
if plane != '3d':
kwargs['plane'] = plane
draw(load_neuron(input_file), **kwargs)
else:
from neurom.view.plotly import draw
draw(load_neuron(input_file), plane=plane)
if backend == 'matplotlib':
import matplotlib.pyplot as plt
plt.show()
def show_nrn(neuron):
ds.save_to_swc(filename, gid=neuron)
import neurom as nm
from neurom import viewer
nrn = nm.load_neuron(filename)
fig, ax = viewer.draw(nrn)
plt.axis('off')
fig.suptitle("")
ax.set_title("")
plt.tight_layout()
plt.show()
def test_draw_dendrogram():
viewer.draw(pt_nrn, mode='dendrogram')
plt.close('all')
def test_draw_soma3d():
viewer.draw(pt_nrn.soma, mode='3d')
viewer.draw(nrn.soma, mode='3d')
plt.close('all')
def test_draw_dendrogram():
viewer.draw(nrn, mode='dendrogram')
common.plt.close('all')
def test_invalid_object_raises():
class Dummy(object):
pass
viewer.draw(Dummy())
def test_invalid_combo_raises():
with pytest.raises(viewer.NotDrawableError):
viewer.draw(nrn.soma, mode='dendrogram')
def test_draw_soma():
viewer.draw(nrn.soma)
common.plt.close('all')
def test_draw_tree():
viewer.draw(pt_nrn.neurites[0])
viewer.draw(nrn.neurites[0])
plt.close('all')
def test_invalid_draw_mode_raises():
with pytest.raises(viewer.InvalidDrawModeError):
viewer.draw(nrn, mode='4d')
def test_invalid_object_raises():
class Dummy(object):
pass
viewer.draw(Dummy())
def test_invalid_combo_raises():
viewer.draw(nrn.soma, mode='dendrogram')
def test_invalid_draw_mode_raises():
viewer.draw(nrn, mode='4d')
def test_draw_dendrogram():
viewer.draw(nrn, mode='dendrogram')
common.plt.close('all')
viewer.draw(nrn.neurites[0], mode='dendrogram')
common.plt.close('all')
def test_draw_soma3d():
viewer.draw(nrn.soma, mode='3d')
common.plt.close('all')
axon = " (axon) " if i == neurite and "starbust" not in filename else ""
print("Asymmetry{}:".format(axon), np.average(asyms) / max_asym(num_tips))
# Sholl analysis
sholl = nm.get("sholl_frequency", nrn, step_size=10.)
print(sholl)
x = np.arange(10., (len(sholl) + 1) * 10, 10)
fig, ax = plt.subplots()
ax.bar(x, sholl, width=10)
ax.set_xlim(x.min() - 5, x[np.where(sholl > 0)[0][-1]] + 5)
ax.set_xlabel("Sholl radius ($\mu$m)")
ax.set_ylabel("Intersections")
plt.tight_layout()
fig, _ = viewer.draw(nrn)
fig, _ = viewer.draw(nrn.neurites[neurite])
for ax in fig.axes:
ax.set_title("")
import matplotlib.pyplot as plt
plt.axis('off')
fig.suptitle("")
plt.tight_layout()
plt.show()
pca.fit(data)
return pca
pca = doPCA(PcaData)
files2 = glob.glob(os.curdir + '/*edit.swc') #load all Filenames of SWC files
for item in files2:
nrn = nm.load_neuron(item)
#nrn = nm.load_neuron(os.curdir + '/Image001-007-01.CNG.swc')
from neurom import viewer
fig, ax = viewer.draw(nrn)
fig.show()
fig, ax = viewer.draw(nrn, mode='3d') # valid modes '2d', '3d', 'dendrogram'
fig.show()
def sec_len(sec):
'''Return the length of a section'''
return mm.section_length(sec.points)
print('Total neurite length (sections):',
sum(sec_len(s) for s in nm.iter_sections(nrn)))
# Get length of all neurites in cell by iterating over segments,
# and summing the segment lengths.
def test_draw_neuron3d():
viewer.draw(nrn, mode='3d')
common.plt.close('all')
with pytest.raises(NotImplementedError):
viewer.draw(nrn, mode='3d', realistic_diameters=True)
def test_draw_dendrogram_empty_segment():
neuron = load_neuron(os.path.join(DATA_PATH, 'empty_segments.swc'))
viewer.draw(neuron, mode='dendrogram')
common.plt.close('all')
def test_invalid_object_raises():
with pytest.raises(viewer.NotDrawableError):
class Dummy:
pass
viewer.draw(Dummy())
def test_invalid_object_raises():
viewer.draw(Dummy())
def test_writing_output():
with tempfile.TemporaryDirectory() as folder:
output_dir = Path(folder, 'subdir')
viewer.draw(nrn, mode='2d', output_path=output_dir)
assert (output_dir / 'Figure.png').is_file()
common.plt.close('all')
def test_draw_tree3d():
viewer.draw(nrn.neurites[0], mode='3d')
common.plt.close('all')
def test_draw_neuron():
viewer.draw(nrn)
common.plt.close('all')
def test_draw_tree3d():
viewer.draw(pt_nrn.neurites[0], mode='3d')
viewer.draw(nrn.neurites[0], mode='3d')
plt.close('all')
def multiple_apical_points(morphology):
morph = morphology
apical = [
neurite for neurite in morph.neurites
if nm.NeuriteType.apical_dendrite == neurite.type
]
if not apical:
L.warning('No apical found')
return None
elif 1 < len(apical):
L.warning('Too many apical dendrites')
return None
apical = apical[0]
dist_apical_point = []
apical_points_and_distances = []
closer_apical_points = []
point = get_apical_point(apical, morph)
if point is not None:
dist = nm.morphmath.point_dist(morph.soma.center,
point.points[-1, COLS.XYZ])
apical_points_and_distances.append([point, dist])
while any(point[1] < 200 for point in apical_points_and_distances):
#point = get_apical_point(apical, morph)
#apical_point.append(point)
#dist_apical_point.append(nm.morphmath.point_dist(morph.soma.center, point.points[-1, COLS.XYZ]))
#a, b = min(point[1] for idx, point in enumerate(apical_points_and_distances))
mn, idx = min((apical_points_and_distances[i][1], i)
for i in range(len(apical_points_and_distances)))
#print mn, idx
#print apical_points_and_distances
new_apical_points = []
new_apical_point_added = []
for child in apical_points_and_distances[idx][0].children:
root_node = child
tree = nm.core._neuron.Neurite(root_node)
point = get_apical_point(tree, morph)
if point is not None:
dist = nm.morphmath.point_dist(morph.soma.center,
point.points[-1, COLS.XYZ])
new_apical_point_added.append(True)
apical_points_and_distances.append([point, dist])
else:
new_apical_point_added.append(False)
""" avoid infinite loop"""
#print new_apical_point_added
if any(added == True for added in new_apical_point_added):
del apical_points_and_distances[idx]
else:
closer_apical_points.append(apical_points_and_distances[idx])
del apical_points_and_distances[idx]
apical_points_and_distances = apical_points_and_distances + closer_apical_points
#print apical_points_and_distances
apical_points = []
for point in apical_points_and_distances:
apical_points.append(point[0])
_, ax = draw(morph)
for point in apical_points:
pos = point.points[-1, COLS.XYZ]
ax.scatter([
pos[0],
], [
pos[1],
])
plt.show()
return apical_points
def test_draw_neuron3d():
viewer.draw(nrn, mode='3d')
common.plt.close('all')
ds.set_object_properties(n, dendrites_params=dend_params, axon_params=vp_axon)
ds.simulate(70000 * minute)
print(ds.get_kernel_status()["time"])
ds.plot.plot_neurons(show=True)
n.to_swc("pyramidal-cell.swc")
n.to_neuroml("bipolar_cell.nml")
import neurom as nm
from neurom import viewer
nrn = nm.load_neuron("pyramidal-cell.swc")
fig, _ = viewer.draw(nrn)
for ax in fig.axes:
ax.set_title("")
tree = n[0].axon.get_tree()
import matplotlib.pyplot as plt
plt.axis('off')
fig.suptitle("")
plt.tight_layout()
plt.show()
#~ tree.show_dendrogram()
print("Asymmetry of axon:", ds.structure.tree_asymmetry(n[0].axon))
def test_draw_tree():
viewer.draw(nrn.neurites[0])
common.plt.close('all')
def test_draw_soma3d():
viewer.draw(nrn.soma, mode='3d')
common.plt.close('all')
def test_draw_neuron3d():
viewer.draw(nrn, mode='3d')
common.plt.close('all')
def test_invalid_draw_mode_raises():
viewer.draw(nrn, mode='4d')
def test_draw_tree3d():
viewer.draw(nrn.neurites[0], mode='3d')
common.plt.close('all')
def test_invalid_combo_raises():
viewer.draw(nrn.soma, mode='dendrogram')
def test_draw_neuron3d():
viewer.draw(pt_nrn, mode='3d')
viewer.draw(nrn, mode='3d')
plt.close('all')
def test_draw_neuron():
viewer.draw(nrn)
common.plt.close('all')
def test_draw_soma():
viewer.draw(pt_nrn.soma)
viewer.draw(nrn.soma)
plt.close('all')
def test_draw_tree():
viewer.draw(nrn.neurites[0])
common.plt.close('all')
import neurom as nm
from neurom import viewer
nrn = nm.load_neuron('test.swc')
print nrn
fig, ax = viewer.draw(nrn)
fig.show()
def test_draw_soma():
viewer.draw(nrn.soma)
common.plt.close('all')
def test_draw_neuron():
viewer.draw(pt_nrn)
viewer.draw(nrn)
plt.close('all')