def soma(sm,
plane='xy',
new_fig=True,
subplot=False,
hadd=0.0,
vadd=0.0,
**kwargs):
'''Generates a 2d figure of the soma.
Parameters
----------
soma: Soma
neurom.Soma object
'''
treecolor = kwargs.get('treecolor', None)
outline = kwargs.get('outline', True)
if plane not in ('xy', 'yx', 'xz', 'zx', 'yz', 'zy'):
return None, 'No such plane found! Please select one of: xy, xz, yx, yz, zx, zy.'
# Initialization of matplotlib figure and axes.
fig, ax = _cm.get_figure(new_fig=new_fig, subplot=subplot)
# Definition of the tree color depending on the tree type.
treecolor = _cm.get_color(treecolor, tree_type='soma')
# Plot the outline of the soma as a circle, is outline is selected.
if not outline:
soma_circle = _cm.plt.Circle(sm.get_center() + [hadd, vadd, 0.0],
sm.get_diameter() / 2.,
color=treecolor,
alpha=_get_default('alpha', **kwargs))
ax.add_artist(soma_circle)
else:
horz = getattr(sm, plane[0]) + hadd
vert = getattr(sm, plane[1]) + vadd
horz = _np.append(
horz, horz[0]) + hadd # To close the loop for a soma viewer.
vert = _np.append(
vert, vert[0]) + vadd # To close the loop for a soma viewer.
_cm.plt.plot(horz,
vert,
color=treecolor,
alpha=_get_default('alpha', **kwargs),
linewidth=_get_default('linewidth', **kwargs))
kwargs['title'] = kwargs.get('title', 'Soma view')
kwargs['xlabel'] = kwargs.get('xlabel', plane[0])
kwargs['ylabel'] = kwargs.get('ylabel', plane[1])
return _cm.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
'''
treecolor = kwargs.get('treecolor', None)
# Initialization of matplotlib figure and axes.
fig, ax = _cm.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 = _cm.get_color(treecolor, tree_type='soma')
center = sm.get_center()
xs = center[0]
ys = center[1]
zs = center[2]
# Plot the soma as a circle.
fig, ax = _cm.plot_sphere(fig,
ax,
center=[xs, ys, zs],
radius=sm.get_diameter(),
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 _cm.plot_style(fig=fig, ax=ax, **kwargs)
def tree(tr,
plane='xy',
new_fig=True,
subplot=False,
hadd=0.0,
vadd=0.0,
**kwargs):
'''Generates a 2d figure of the tree.
Parameters
----------
tr: Tree
neurom.Tree object
'''
if plane not in ('xy', 'yx', 'xz', 'zx', 'yz', 'zy'):
return None, 'No such plane found! Please select one of: xy, xz, yx, yz, zx, zy.'
# Initialization of matplotlib figure and axes.
fig, ax = _cm.get_figure(new_fig=new_fig, subplot=subplot)
# Data needed for the viewer: x,y,z,r
bounding_box = tr.get_bounding_box()
def _seg_2d(seg, x_add=0.0, y_add=0.0):
"""2d coordinates required for the plotting of a segment"""
horz = _utils.term_dict[plane[0]]
vert = _utils.term_dict[plane[1]]
horz1 = seg[0][horz] + x_add
horz2 = seg[1][horz] + x_add
vert1 = seg[0][vert] + y_add
vert2 = seg[1][vert] + y_add
return ((horz1, vert1), (horz2, vert2))
segs = [_seg_2d(seg, hadd, vadd) for seg in tr.get_segments()]
linewidth = _get_default('linewidth', **kwargs)
# Definition of the linewidth according to diameter, if diameter is True.
if _get_default('diameter', **kwargs):
scale = _get_default('diameter_scale', **kwargs)
linewidth = [d * scale for d in tr.d]
if tr.get_type() not in _utils.tree_type:
treecolor = 'black'
else:
treecolor = _cm.get_color(_get_default('treecolor', **kwargs),
_utils.tree_type[tr.get_type()])
# Plot the collection of lines.
collection = _LC(segs,
color=treecolor,
linewidth=linewidth,
alpha=_get_default('alpha', **kwargs))
ax.add_collection(collection)
kwargs['title'] = kwargs.get('title', 'Tree view')
kwargs['xlabel'] = kwargs.get('xlabel', plane[0])
kwargs['ylabel'] = kwargs.get('ylabel', plane[1])
white_space = _get_default('white_space', **kwargs)
kwargs['xlim'] = kwargs.get('xlim', [
bounding_box[0][_utils.term_dict[plane[0]]] - white_space,
bounding_box[1][_utils.term_dict[plane[0]]] + white_space
])
kwargs['ylim'] = kwargs.get('ylim', [
bounding_box[0][_utils.term_dict[plane[1]]] - white_space,
bounding_box[1][_utils.term_dict[plane[1]]] + white_space
])
return _cm.plot_style(fig=fig, ax=ax, **kwargs)
def trunk3d(tr, new_fig=True, new_axes=True, subplot=False, N=10, **kwargs):
'''Generates a figure of the trunk in 3d.
Parameters
----------
tr: Tree
neurom.Tree object
'''
# pylint: disable=import-outside-toplevel
from mpl_toolkits.mplot3d.art3d import Line3DCollection
# Initialization of matplotlib figure and axes.
fig, ax = _cm.get_figure(new_fig=new_fig,
new_axes=new_axes,
subplot=subplot,
params={'projection': '3d'})
def _seg_3d(seg):
"""3d coordinates needed for the plotting of a segment"""
horz = _utils.term_dict['x']
vert = _utils.term_dict['y']
depth = _utils.term_dict['z']
horz1 = seg[0][horz]
horz2 = seg[1][horz]
vert1 = seg[0][vert]
vert2 = seg[1][vert]
depth1 = seg[0][depth]
depth2 = seg[1][depth]
return ((horz1, vert1, depth1), (horz2, vert2, depth2))
if len(tr.get_segments()) < N:
N = len(tr.get_segments())
segs = [_seg_3d(seg) for seg in tr.get_segments()[:N]]
linewidth = _get_default('linewidth', **kwargs)
# Definition of the linewidth according to diameter, if diameter is True.
if _get_default('diameter', **kwargs):
scale = _get_default('diameter_scale', **kwargs)
linewidth = [d * scale for d in tr.d]
treecolor = _cm.get_color(_get_default('treecolor', **kwargs),
_utils.tree_type[tr.get_type()])
# Plot the collection of lines.
collection = Line3DCollection(segs,
color=treecolor,
linewidth=linewidth,
alpha=_get_default('alpha', **kwargs))
ax.add_collection3d(collection)
kwargs['title'] = kwargs.get('title', 'Tree 3d-view')
kwargs['xlabel'] = kwargs.get('xlabel', 'X')
kwargs['ylabel'] = kwargs.get('ylabel', 'Y')
kwargs['zlabel'] = kwargs.get('zlabel', 'Z')
return _cm.plot_style(fig=fig, ax=ax, **kwargs)
