def _do_plot(self,
val_min,
val_max,
sections,
variable,
cmap=cm.cool,
**kwargs):
"""
Plots a 3D shapeplot
Args:
sections = list of h.Section() objects to be plotted
**kwargs passes on to matplotlib (e.g. linewidth=2 for thick lines)
Returns:
lines = list of line objects making up shapeplot
"""
# Adapted from
# https://github.com/ahwillia/PyNeuron-Toolbox/blob/master/PyNeuronToolbox/morphology.py
# Accessed 2019-04-11, which had an MIT license
# Default is to plot all sections.
if sections is None:
sections = list(h.allsec())
h.define_shape()
# default color is black
kwargs.setdefault('color', 'black')
# Plot each segement as a line
lines = {}
lines_list = []
vals = []
for sec in sections:
all_seg_pts = _segment_3d_pts(sec)
for seg, (xs, ys, zs, _, _) in zip(sec, all_seg_pts):
line, = self.plot(xs, ys, zs, '-', **kwargs)
if variable is not None:
try:
if '.' in variable:
mech, var = variable.split('.')
val = getattr(getattr(seg, mech), var)
else:
val = getattr(seg, variable)
except AttributeError:
# leave default color if no variable found
val = None
vals.append(val)
lines[line] = '%s at %s' % (val, seg)
lines_list.append(line)
if variable is not None:
val_range = val_max - val_min
if val_range:
for sec in sections:
for line, val in zip(lines_list, vals):
if val is not None:
col = cmap(
int(255 * (val - val_min) /
(val_range)))
line.set_color(col)
return lines
def _do_plot_on_plotly():
"""requires matplotlib for colormaps if not specified explicitly"""
import ctypes
import plotly.graph_objects as go
class FigureWidgetWithNEURON(go.FigureWidget):
def mark(self, segment, marker='or', **kwargs):
"""plot a marker on a segment
Args:
segment = the segment to mark
**kwargs = passed to go.Scatter3D plot
"""
x, y, z = _get_3d_pt(segment)
# approximately match the appearance of the matplotlib defaults
kwargs.setdefault('marker_size', 5)
kwargs.setdefault('marker_color', 'red')
kwargs.setdefault('marker_opacity', 1)
self.add_trace(
go.Scatter3d(
x=[x], y=[y], z=[z], name='', hovertemplate=str(segment), **kwargs
)
)
return self
get_plotshape_data = nrn_dll_sym('get_plotshape_data')
get_plotshape_data.restype = ctypes.py_object
variable, varobj, lo, hi, secs = get_plotshape_data(ctypes.py_object(self._data))
if varobj is not None:
variable = varobj
if secs is None:
secs = list(h.allsec())
if variable is None:
kwargs.setdefault('color', 'black')
data = []
for sec in secs:
xs = [sec.x3d(i) for i in range(sec.n3d())]
ys = [sec.y3d(i) for i in range(sec.n3d())]
zs = [sec.z3d(i) for i in range(sec.n3d())]
data.append(
go.Scatter3d(
x=xs,
y=ys,
z=zs,
name='',
hovertemplate=str(sec),
mode="lines",
line=go.scatter3d.Line(
color=kwargs['color'],
width=2
))
)
return FigureWidgetWithNEURON(data=data, layout={'showlegend': False})
else:
if 'cmap' not in kwargs:
# use same default colormap as the matplotlib version
from matplotlib.pyplot import cm
kwargs['cmap'] = cm.cool
cmap = kwargs['cmap']
show_diam = False
# calculate bounds
val_range = hi - lo
data = []
for sec in secs:
all_seg_pts = _segment_3d_pts(sec)
for seg, (xs, ys, zs, _, _) in zip(sec, all_seg_pts):
val = _get_variable_seg(seg, variable)
hover_template = str(seg)
if val is not None:
hover_template += '<br>' + ('%.3f' % val)
col = _get_color(variable, val, cmap, lo, hi, val_range)
if show_diam:
diam = seg.diam
else:
diam = 2
data.append(
go.Scatter3d(
x=xs,
y=ys,
z=zs,
name='',
hovertemplate=hover_template,
mode="lines",
line=go.scatter3d.Line(
color=col,
width=diam
))
)
return FigureWidgetWithNEURON(data=data, layout={'showlegend': False})
def _do_plot(self,
val_min,
val_max,
sections,
variable,
cmap=cm.cool,
**kwargs):
"""
Plots a 3D shapeplot
Args:
sections = list of h.Section() objects to be plotted
**kwargs passes on to matplotlib (e.g. linewidth=2 for thick lines)
Returns:
lines = list of line objects making up shapeplot
"""
# Adapted from
# https://github.com/ahwillia/PyNeuron-Toolbox/blob/master/PyNeuronToolbox/morphology.py
# Accessed 2019-04-11, which had an MIT license
# Default is to plot all sections.
if sections is None:
sections = list(h.allsec())
h.define_shape()
# default color is black
kwargs.setdefault("color", "black")
# Plot each segement as a line
lines = {}
lines_list = []
vals = []
for sec in sections:
all_seg_pts = _segment_3d_pts(sec)
for seg, (xs, ys, zs, _, _) in zip(sec, all_seg_pts):
(line, ) = self.plot(xs, ys, zs, "-", **kwargs)
if variable is not None:
val = _get_variable_seg(seg, variable)
vals.append(val)
if val is not None:
lines[line] = "%s at %s" % (val, seg)
else:
lines[line] = str(seg)
else:
lines[line] = str(seg)
lines_list.append(line)
if variable is not None:
val_range = val_max - val_min
if val_range:
for sec in sections:
for line, val in zip(lines_list, vals):
if val is not None:
col = _get_color(
variable,
val,
cmap,
val_min,
val_max,
val_range,
)
line.set_color(col)
return lines