def plot_somas(somas):
"""Plot set of somas on same figure as spheres, each with different color."""
_, ax = common.get_figure(new_fig=True, subplot=111,
params={'projection': '3d', 'aspect': 'equal'})
for s in somas:
common.plot_sphere(ax, s.center, s.radius, color=random_color(), alpha=1)
plt.show()
def plot_somas(somas):
'''Plot set of somas on same figure as spheres, each with different color'''
_, ax = common.get_figure(new_fig=True, subplot=111,
params={'projection': '3d', 'aspect': 'equal'})
for s in somas:
common.plot_sphere(ax, s.center, s.radius, color=random_color(), alpha=1)
plt.show()
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 plot_somas(somas):
"""Plot set of somas on same figure as spheres, each with different color"""
fig, ax = common.get_figure(new_fig=True, subplot=111, params={"projection": "3d", "aspect": "equal"})
for s in somas:
center = s.center
radius = s.radius
common.plot_sphere(fig, ax, center, radius, color=random_color(), alpha=1)
plt.show()
def soma3d(sm, new_fig=True, new_axes=True, subplot=False, **kwargs):
'''Generates a 3d figure of the soma.
Parameters:
soma: Soma
neurom.Soma object
Options:
alpha: float \
Defines throughe transparency of the tree. \
0.0 transparent through 1.0 opaque. \
Default value is 0.8.
treecolor: str or None \
Defines the color of the soma. \
Soma : "black". \
Default value is None.
new_fig: boolean \
Defines if the tree will be plotted \
in the current figure (False) \
or in a new figure (True) \
Default value is True.
subplot: matplotlib subplot value or False \
If False the default subplot 111 will be used. \
For any other value a matplotlib subplot \
will be generated. \
Default value is False.
Returns:
A 3D matplotlib figure with a soma view.
'''
treecolor = kwargs.get('treecolor', None)
# Initialization of matplotlib figure and axes.
fig, ax = common.get_figure(new_fig=new_fig, new_axes=new_axes,
subplot=subplot, params={'projection': '3d'})
# Definition of the tree color depending on the tree type.
treecolor = common.get_color(treecolor, tree_type=TreeType.soma)
xs = sm.center[0]
ys = sm.center[1]
zs = sm.center[2]
# Plot the soma as a circle.
fig, ax = common.plot_sphere(fig, ax, center=[xs, ys, zs], radius=sm.radius, color=treecolor,
alpha=get_default('alpha', **kwargs))
kwargs['title'] = kwargs.get('title', 'Soma view')
kwargs['xlabel'] = kwargs.get('xlabel', 'X')
kwargs['ylabel'] = kwargs.get('ylabel', 'Y')
kwargs['zlabel'] = kwargs.get('zlabel', 'Z')
return common.plot_style(fig=fig, ax=ax, **kwargs)
def soma3d(sm, new_fig=True, new_axes=True, subplot=False, **kwargs):
"""Generates a 3d figure of the soma.
Parameters:
soma: Soma
neurom.Soma object
Options:
alpha: float \
Defines throughe transparency of the tree. \
0.0 transparent through 1.0 opaque. \
Default value is 0.8.
treecolor: str or None \
Defines the color of the soma. \
Soma : "black". \
Default value is None.
new_fig: boolean \
Defines if the tree will be plotted \
in the current figure (False) \
or in a new figure (True) \
Default value is True.
subplot: matplotlib subplot value or False \
If False the default subplot 111 will be used. \
For any other value a matplotlib subplot \
will be generated. \
Default value is False.
Returns:
A 3D matplotlib figure with a soma view.
"""
treecolor = kwargs.get("treecolor", None)
# Initialization of matplotlib figure and axes.
fig, ax = common.get_figure(new_fig=new_fig, new_axes=new_axes, subplot=subplot, params={"projection": "3d"})
# Definition of the tree color depending on the tree type.
treecolor = common.get_color(treecolor, tree_type=TreeType.soma)
xs = sm.center[0]
ys = sm.center[1]
zs = sm.center[2]
# Plot the soma as a circle.
fig, ax = common.plot_sphere(
fig, ax, center=[xs, ys, zs], radius=sm.radius, color=treecolor, alpha=get_default("alpha", **kwargs)
)
kwargs["title"] = kwargs.get("title", "Soma view")
kwargs["xlabel"] = kwargs.get("xlabel", "X")
kwargs["ylabel"] = kwargs.get("ylabel", "Y")
kwargs["zlabel"] = kwargs.get("zlabel", "Z")
return common.plot_style(fig=fig, ax=ax, **kwargs)
def test_plot_sphere():
fig0, ax0 = get_figure(params={'projection': '3d'})
fig1, ax1 = plot_sphere(fig0, ax0, [0, 0, 0], 10., color='black', alpha=1.)
nt.ok_(ax1.has_data() == True)
def test_plot_sphere():
fig0, ax0 = get_figure(params={'projection':'3d'})
fig1, ax1 = plot_sphere(fig0, ax0, [0,0,0], 10., color='black', alpha=1.)
nt.ok_(ax1.has_data() == True)
def test_plot_sphere():
fig0, ax0 = get_figure(params={'projection': '3d'})
plot_sphere(ax0, [0, 0, 0], 10., color='black', alpha=1.)
assert ax0.has_data()
