"""Visualization functions."""
# Authors: Mainak Jas <mjas@mgh.harvard.edu>
# Sam Neymotin <samnemo@gmail.com>
# Christopher Bailey <cjb@cfin.au.dk>
import numpy as np
from itertools import cycle
import colorsys
import warnings
from .externals.mne import _validate_type
def _lighten_color(color, amount=0.5):
import matplotlib.colors as mc
try:
c = mc.cnames[color]
except:
c = color
c = colorsys.rgb_to_hls(*mc.to_rgb(c))
return colorsys.hls_to_rgb(c[0], 1 - amount * (1 - c[1]), c[2])
def _get_plot_data_trange(times, data, tmin=None, tmax=None):
"""Get slices of times and data based on tmin and tmax"""
if isinstance(times, list):
times = np.array(times)
if isinstance(data, list):
data = np.array(data)
plot_tmin = times[0]
if tmin is not None:
plot_tmin = max(tmin, plot_tmin)
plot_tmax = times[-1]
if tmax is not None:
plot_tmax = min(tmax, plot_tmax)
mask = np.logical_and(times >= plot_tmin, times < plot_tmax)
return data[mask], times[mask]
def _decimate_plot_data(decim, data, times, sfreq=None):
from scipy.signal import decimate
if not isinstance(decim, list):
decim = [decim]
for dec in decim:
if not isinstance(dec, int) or dec < 1:
raise ValueError(
"each decimation factor must be a positive int, "
f"but {dec} is a {type(dec)}"
)
data = decimate(data, dec)
times = times[::dec]
if sfreq is None:
return data, times
else:
sfreq /= np.prod(decim)
return data, times, sfreq
def plt_show(show=True, fig=None, **kwargs):
"""Show a figure while suppressing warnings.
NB copied from :func:`mne.viz.utils.plt_show`.
Parameters
----------
show : bool
Show the figure.
fig : instance of Figure | None
If non-None, use fig.show().
**kwargs : dict
Extra arguments for :func:`matplotlib.pyplot.show`.
"""
from matplotlib import get_backend
import matplotlib.pyplot as plt
if show and get_backend() != "agg":
(fig or plt).show(**kwargs)
[docs]
def plot_laminar_lfp(
times,
data,
contact_labels,
tmin=None,
tmax=None,
ax=None,
decim=None,
color="cividis",
voltage_offset=50,
voltage_scalebar=200,
show=True,
):
"""Plot laminar extracellular electrode array voltage time series.
Parameters
----------
times : array-like, shape (n_times,)
Sampling times (in ms).
data : Two-dimensional Numpy array
The extracellular voltages as an (n_contacts, n_times) array.
ax : instance of matplotlib figure | None
The matplotlib axis
decim : int | list of int | None (default)
Optional (integer) factor by which to decimate the raw dipole traces.
The SciPy function :func:`~scipy.signal.decimate` is used, which
recommends values <13. To achieve higher decimation factors, a list of
ints can be provided. These are applied successively.
color : str | array of floats | ``matplotlib.colors.ListedColormap``
The colormap to use for plotting. The usual Matplotlib standard
colormap strings may be used (e.g., 'jetblue'). A color can also be
defined as an RGBA-quadruplet, or an array of RGBA-values (one for each
electrode contact trace to plot). An instance of
:class:`~matplotlib.colors.ListedColormap` may also be provided.
voltage_offset : float | None (optional)
Amount to offset traces by on the voltage-axis. Useful for plotting
laminar arrays.
voltage_scalebar : float | None (optional)
Height, in units of uV, of a scale bar to plot in the top-left corner
of the plot.
contact_labels : list
Labels associated with the contacts to plot. Passed as-is to
:func:`~matplotlib.axes.Axes.set_yticklabels`.
show : bool
If True, show the figure
Returns
-------
fig : instance of plt.fig
The matplotlib figure handle into which time series were plotted.
"""
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
_validate_type(times, (list, np.ndarray), "times")
_validate_type(data, (list, np.ndarray), "data")
if isinstance(times, list):
times = np.array(times)
if isinstance(data, list):
data = np.array(data)
if data.ndim != 2:
raise ValueError(f"data must be 2D, got shape {data.shape}")
if len(times) != data.shape[1]:
raise ValueError(
f"length of times ({len(times)}) and data ({len(data)}) do not match"
)
n_contacts = data.shape[0]
if color is not None:
_validate_type(color, (str, tuple, list, np.ndarray, ListedColormap), "color")
if isinstance(color, (tuple, list)):
if (
not np.all([isinstance(c, float) for c in color])
or len(color) < 3
or len(color) > 4
):
raise ValueError(f"color must be length 3 or 4, got {color}")
elif isinstance(color, np.ndarray):
if color.shape[0] != n_contacts or (
color.shape[1] < 3 or color.shape[1] > 4
):
raise ValueError(f"color must be n_contacts x (3 or 4), got {color}")
elif isinstance(color, ListedColormap):
if color.N != n_contacts:
raise ValueError(
f"ListedColormap has N={color.N}, but "
f"there are {n_contacts} contacts"
)
elif isinstance(color, str):
color = plt.get_cmap(color, len(contact_labels))
if ax is None:
_, ax = plt.subplots(1, 1)
n_offsets = data.shape[0]
trace_offsets = np.zeros((n_offsets, 1))
if voltage_offset is not None:
trace_offsets = np.arange(n_offsets)[:, np.newaxis] * voltage_offset
for contact_no, trace in enumerate(np.atleast_2d(data)):
plot_data = trace
plot_times = times
if decim is not None:
plot_data, plot_times = _decimate_plot_data(decim, plot_data, plot_times)
if isinstance(color, np.ndarray):
col = color[contact_no]
elif isinstance(color, ListedColormap):
col = color(contact_no)
else:
col = color
ax.plot(
plot_times,
plot_data + trace_offsets[contact_no],
label=f"C{contact_no}",
color=col,
)
# To be removed after deprecation cycle
if tmin is not None or tmax is not None:
ax.set_xlim(left=tmin, right=tmax)
warnings.warn(
"tmin and tmax are deprecated and will be "
"removed in future releases of hnn-core. Please"
"use matplotlib plt.xlim to set tmin and tmax.",
DeprecationWarning,
)
else:
ax.set_xlim(left=times[0], right=times[-1])
if voltage_offset is not None:
ax.set_ylim(-voltage_offset, n_offsets * voltage_offset)
ylabel = "Individual contact traces"
if len(contact_labels) != n_offsets:
raise ValueError(
f"contact_labels is length {len(contact_labels)},"
f" but {n_offsets} contacts to be plotted"
)
else:
trace_ticks = np.arange(
0, len(contact_labels) * voltage_offset, voltage_offset
)
ax.set_yticks(trace_ticks)
ax.set_yticklabels(contact_labels)
if voltage_scalebar is None:
voltage_scalebar = voltage_offset
if voltage_scalebar is not None:
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
scalebar = AnchoredSizeBar(
ax.transData,
1,
f"{voltage_scalebar:.0f} " + r"$\mu V$",
"upper left",
size_vertical=voltage_scalebar,
pad=0.1,
color="black",
label_top=False,
frameon=False,
)
ax.add_artist(scalebar)
else:
ylabel = r"Electric potential ($\mu V$)"
ax.ticklabel_format(axis="both", scilimits=(-2, 3))
ax.set_ylabel(ylabel, multialignment="center")
ax.set_xlabel("Time (ms)")
plt_show(show)
return ax.get_figure()
[docs]
def plot_dipole(
dpl,
tmin=None,
tmax=None,
ax=None,
layer="agg",
decim=None,
color="k",
label="average",
average=False,
show=True,
):
"""Simple layer-specific plot function.
Parameters
----------
dpl : instance of Dipole | list of Dipole instances
The Dipole object.
ax : instance of matplotlib figure | None
The matplotlib axis
layer : str
The layer to plot. Can be one of
'agg', 'L2', and 'L5'
decim : int or list of int or None (default)
Optional (integer) factor by which to decimate the raw dipole traces.
The SciPy function :func:`~scipy.signal.decimate` is used, which
recommends values <13. To achieve higher decimation factors, a list of
ints can be provided. These are applied successively.
color : tuple of float | str
RGBA value to use for plotting. By default, 'k' (black)
label : str
Dipole label. Enabled when average=True
average : bool
If True, render the average across all dpls.
show : bool
If True, show the figure
Returns
-------
fig : instance of plt.fig
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from .dipole import Dipole, average_dipoles
layers = layer if isinstance(layer, list) else [layer]
if ax is None:
_, ax = plt.subplots(
len(layers), 1, constrained_layout=True, sharex=True, sharey=True
)
axes = ax if isinstance(ax, (list, np.ndarray)) else [ax]
if isinstance(dpl, Dipole):
dpl = [dpl]
for this_dpl in dpl:
_validate_type(this_dpl, Dipole, "dpl", "Dipole, list of Dipole")
if average:
dpl.append(average_dipoles(dpl))
scale_applied = dpl[0].scale_applied
assert len(layers) == len(axes), "ax and layer should have the same size"
for layer, ax in zip(layers, axes):
for idx, dpl_trial in enumerate(dpl):
if dpl_trial.scale_applied != scale_applied:
raise RuntimeError("All dipoles must be scaled equally!")
if layer in dpl_trial.data.keys():
# extract scaled data and times
data = dpl_trial.data[layer]
times = dpl_trial.times
if decim is not None:
data, times = _decimate_plot_data(decim, data, times)
if idx == len(dpl) - 1 and average:
# the average dpl
ax.plot(times, data, color=color, label=label, lw=1.5)
else:
alpha = 0.5 if average else 1.0
ax.plot(
times,
data,
color=_lighten_color(color, 0.5),
alpha=alpha,
lw=1.0,
)
# To be removed after deprecation cycle
if tmin is not None or tmax is not None:
if tmin is not None or tmax is not None:
warnings.warn(
"tmin and tmax are deprecated and will be "
"removed in future releases of hnn-core. "
"Please use matplotlib plt.xlim to set tmin"
" and tmax.",
DeprecationWarning,
)
ax.set_xlim(left=tmin, right=tmax)
else:
ax.set_xlim(left=0, right=times[-1])
if average:
ax.legend()
ax.ticklabel_format(axis="both", scilimits=(-2, 3))
ax.set_xlabel("Time (ms)")
if scale_applied == 1:
ylabel = "Dipole moment (nAm)"
else:
ylabel = "Dipole moment\n(nAm " + r"$\times$ {:.0f})".format(scale_applied)
ax.set_ylabel(ylabel, multialignment="center")
if layer == "agg":
title_str = "Aggregate (L2/3 + L5)"
elif layer == "L2":
title_str = "L2/3"
else:
title_str = layer
ax.set_title(title_str)
plt_show(show)
return axes[0].get_figure()
[docs]
def plot_spikes_hist(
cell_response,
trial_idx=None,
ax=None,
spike_types=None,
color=None,
invert_spike_types=None,
show=True,
**kwargs_hist,
):
"""Plot the histogram of spiking activity across trials.
Parameters
----------
cell_response : instance of CellResponse
The CellResponse object from net.cell_response
trial_idx : int | list of int | None
Index of trials to be plotted. If None, all trials plotted.
ax : instance of matplotlib axis | None
An axis object from matplotlib. If None,
a new figure is created.
spike_types: string | list | dictionary | None
String input of a valid spike type is plotted individually.
| Ex: ``'poisson'``, ``'evdist'``, ``'evprox'``, ...
List of valid string inputs will plot each spike type individually.
| Ex: ``['poisson', 'evdist']``
Dictionary of valid lists will plot list elements as a group.
| Ex: ``{'Evoked': ['evdist', 'evprox'], 'Tonic': ['poisson']}``
If None, all input spike types are plotted individually if any
are present. Otherwise spikes from all cells are plotted.
Valid strings also include leading characters of spike types
| Ex: ``'ev'`` is equivalent to ``['evdist', 'evprox']``
invert_spike_types: string | list | None
String input of a valid spike type to be mirrored about the y axis
| Ex: ``'evdist'``, ``'evprox'``, ...
List of valid spike types to be mirrored about the y axis
| Ex: ``['evdist', 'evprox']``
If None, all input spike types are plotted on the same y axis
color : str | list of str | dict | None
Input defining colors of plotted histograms. If str, all
histograms plotted with same color. If list of str provided,
histograms for each spike type will be plotted by cycling
through colors in the list.
If dict, colors must be specified for all spike_types as a key.
If a group of spike types is defined by the `spike_types`
parameter (see dictionary example for `spike_types`),
the name of this group must be used to specify the colors.
| Ex: ``{'evdist': 'g', 'evprox': 'r'}``, ``{'Tonic': 'b'}``
If None, default color cycle used.
show : bool
If True, show the figure.
**kwargs_hist : dict
Additional keyword arguments to pass to ax.hist.
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
n_trials = len(cell_response.spike_times)
if trial_idx is None:
trial_idx = list(range(n_trials))
if isinstance(trial_idx, int):
trial_idx = [trial_idx]
_validate_type(trial_idx, list, "trial_idx", "int, list of int")
# Extract desired trials
if len(cell_response._spike_times[0]) > 0:
spike_times = np.concatenate(
np.array(cell_response._spike_times, dtype=object)[trial_idx]
)
spike_types_data = np.concatenate(
np.array(cell_response._spike_types, dtype=object)[trial_idx]
)
else:
spike_times = np.array([])
spike_types_data = np.array([])
unique_types = np.unique(spike_types_data)
spike_types_mask = {
s_type: np.isin(spike_types_data, s_type) for s_type in unique_types
}
cell_types = ["L5_pyramidal", "L5_basket", "L2_pyramidal", "L2_basket"]
input_types = np.setdiff1d(unique_types, cell_types)
if isinstance(spike_types, str):
spike_types = {spike_types: [spike_types]}
if spike_types is None:
if any(input_types):
spike_types = input_types.tolist()
else:
spike_types = unique_types.tolist()
if isinstance(spike_types, list):
spike_types = {s_type: [s_type] for s_type in spike_types}
if isinstance(spike_types, dict):
for spike_label in spike_types:
if not isinstance(spike_types[spike_label], list):
raise TypeError(
f"spike_types[{spike_label}] must be a list. "
f"Got "
f"{type(spike_types[spike_label]).__name__}."
)
if not isinstance(spike_types, dict):
raise TypeError("spike_types should be str, list, dict, or None")
spike_labels = dict()
for spike_label, spike_type_list in spike_types.items():
for spike_type in spike_type_list:
n_found = 0
for unique_type in unique_types:
if unique_type.startswith(spike_type):
if unique_type in spike_labels:
raise ValueError(
f"Elements of spike_types must map to"
f" mutually exclusive input types."
f" {unique_type} is found more than"
f" once."
)
spike_labels[unique_type] = spike_label
n_found += 1
if n_found == 0:
raise ValueError(f"No input types found for {spike_type}")
if ax is None:
_, ax = plt.subplots(1, 1, constrained_layout=True)
_validate_type(color, (str, list, dict, None), "color", "str, list of str, or dict")
if color is None:
color_cycle = cycle(["r", "g", "b", "y", "m", "c"])
elif isinstance(color, str):
color_cycle = cycle([color])
elif isinstance(color, list):
color_cycle = cycle(color)
if len(cell_response.times) > 0:
bins = np.linspace(0, cell_response.times[-1], 50)
else:
bins = np.linspace(0, spike_times[-1], 50)
# Create dictionary to aggregate spike times that have the same spike_label
spike_type_times = {
spike_label: list() for spike_label in np.unique(list(spike_labels.values()))
}
spike_color = dict() # Store colors specified for each spike_label
for spike_type, spike_label in spike_labels.items():
if spike_label not in spike_color:
if isinstance(color, dict):
if spike_label not in color:
raise ValueError(
f"'{spike_label}' must be defined in color dictionary"
)
_validate_type(
color[spike_label], str, "Dictionary values of color", "str"
)
spike_color[spike_label] = color[spike_label]
else:
spike_color[spike_label] = next(color_cycle)
spike_type_times[spike_label].extend(spike_times[spike_types_mask[spike_type]])
if invert_spike_types is None:
invert_spike_types = list()
else:
if not isinstance(invert_spike_types, (str, list)):
raise TypeError(
"'invert_spike_types' must be a string or a list of strings"
)
if isinstance(invert_spike_types, str):
invert_spike_types = [invert_spike_types]
# Check that spike types to invert are correctly specified
unique_inputs = set(spike_labels.values())
unique_invert_inputs = set(invert_spike_types)
check_intersection = unique_invert_inputs.intersection(unique_inputs)
if not check_intersection == unique_invert_inputs:
raise ValueError(
"Elements of 'invert_spike_types' mustmap to valid input types"
)
# Initialize secondary axis
ax1 = None
# Plot aggregated spike_times
for spike_label, plot_data in spike_type_times.items():
hist_color = spike_color[spike_label]
# Plot on the primary y-axis
if spike_label not in invert_spike_types:
ax.hist(plot_data, bins, label=spike_label, color=hist_color, **kwargs_hist)
# Plot on secondary y-axis
else:
if ax1 is None:
ax1 = ax.twinx()
ax1.hist(
plot_data, bins, label=spike_label, color=hist_color, **kwargs_hist
)
# Need to add label for easy removal later
# Set the y-limits based on the maximum across both axes
if ax1 is not None:
ax_ylim = ax.get_ylim()[1]
ax1_ylim = ax1.get_ylim()[1]
y_max = max(ax_ylim, ax1_ylim)
ax.set_ylim(0, y_max)
ax1.set_ylim(0, y_max)
ax1.invert_yaxis()
ax1.set_label("Inverted spike histogram")
if len(cell_response.times) > 0:
ax.set_xlim(left=0, right=cell_response.times[-1])
else:
ax.set_xlim(left=0)
ax.set_ylabel("Counts")
ax.set_label("Spike histogram")
if ax1 is not None:
# Combine legends
handles, labels = ax.get_legend_handles_labels()
handles1, labels1 = ax1.get_legend_handles_labels()
handles.extend(handles1)
labels.extend(labels1)
ax1.legend(handles, labels, loc="upper left")
else:
ax.legend()
plt_show(show)
return ax.get_figure()
[docs]
def plot_spikes_raster(
cell_response,
trial_idx=None,
ax=None,
show=True,
cell_types=None,
colors=None,
show_legend=True,
marker_size=1.0,
dpl=None,
overlay_dipoles=False,
):
"""Plot the aggregate spiking activity according to cell type.
Parameters
----------
cell_response : instance of CellResponse
The CellResponse object from net.cell_response
trial_idx : int | list of int | None
Index of trials to be plotted. If None, all trials plotted
ax : instance of matplotlib axis | None
An axis object from matplotlib. If None, a new figure is created.
show : bool
If True, show the figure.
cell_types : list of str
List of cell types to plot
colors : list of str | None
Optional custom colors to plot. Default will use the color cycler.
show_legend : bool
If True, show the legend with colors for cell types
marker_size : float
Optional marker size to use when plotting spikes. Uses
"linelengths" argument of ax.eventplot, which accepts positive
numeric values only
dpl : instance of Dipole | list
The Dipole object containing layer-specific dipole data
to overlay on the raster plot
overlay_dipoles : bool
If True, overlay the layer-specific dipole data on the
raster plot
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure object.
"""
import matplotlib.pyplot as plt
from .dipole import Dipole, average_dipoles
n_trials = len(cell_response.spike_times)
if trial_idx is None:
trial_idx = list(range(n_trials))
# Get spike types from cell response
unique_spike_types = cell_response.cell_types
# validate trial argument
if isinstance(trial_idx, int):
trial_idx = [trial_idx]
_validate_type(trial_idx, list, "trial_idx", "int, list of int")
# validate cell types
if cell_types:
_validate_type(cell_types, list, "cell_types", "list of str")
if not set(cell_types).issubset(set(unique_spike_types)):
raise ValueError(
"Invalid cell types provided. "
f"Must be of set {unique_spike_types}. "
f"Got {cell_types}"
)
else:
# Use default cell types
cell_types = ["L2_basket", "L2_pyramidal", "L5_basket", "L5_pyramidal"]
# Set default colors
default_colors = plt.rcParams["axes.prop_cycle"].by_key()["color"][
: len(cell_types)
]
cell_colors = {cell: color for cell, color in zip(cell_types, default_colors)}
# validate colors argument
_validate_type(colors, (list, dict, None), "color", "list of str, or dict")
if colors:
if isinstance(colors, list):
if len(colors) != len(cell_types):
raise ValueError(
f"Number of colors must be equal to number of "
f"cell types. {len(colors)} colors provided "
f"for {len(cell_types)} cell types."
)
cell_colors = {cell: color for cell, color in zip(cell_types, colors)}
if isinstance(colors, dict):
# Check valid cell types
if not set(colors.keys()).issubset(set(unique_spike_types)):
raise ValueError(
"Invalid cell types provided. "
f"Must be of set {unique_spike_types}. "
f"Got {colors.keys()}"
)
cell_colors.update(colors)
# validate show_legend argument
_validate_type(show_legend, bool, "show_legend", "bool")
# validate marker_size
_validate_type(marker_size, (float, int), "marker_size", "float or int")
# if marker_size is <= 0, set it to the default value of 1.0
if marker_size <= 0:
marker_size = 1.0
# Extract desired trials
spike_times = np.concatenate(
np.array(cell_response._spike_times, dtype=object)[trial_idx]
)
spike_types = np.concatenate(
np.array(cell_response._spike_types, dtype=object)[trial_idx]
)
spike_gids = np.concatenate(
np.array(cell_response._spike_gids, dtype=object)[trial_idx]
)
if ax is None:
_, ax = plt.subplots(1, 1, constrained_layout=True)
events = []
for cell_type, color in cell_colors.items():
cell_type_gids = np.unique(spike_gids[spike_types == cell_type])
cell_type_times, cell_type_ypos = [], []
for gid in cell_type_gids:
gid_time = spike_times[spike_gids == gid]
cell_type_times.append(gid_time)
cell_type_ypos.append(-gid)
if cell_type_times:
events.append(
ax.eventplot(
cell_type_times,
lineoffsets=cell_type_ypos,
color=color,
label=cell_type,
linelengths=marker_size,
)
)
else:
# Blank plot for no spiking
events.append(
ax.eventplot(
[-1], lineoffsets=[-1], color=color, label=cell_type, linelengths=1
)
)
# Overlay dipoles on raster plot
if overlay_dipoles:
# Confirm that the dpl is not None
if dpl is None:
raise ValueError("Dipole object must be provided to overlay dipoles")
# In the case that a single Dipole object is provided, cast to a list
if isinstance(dpl, Dipole):
dpl = [dpl]
# Validate that all list elements are Dipole objects
for trial in dpl:
_validate_type(trial, Dipole, "dpl", "Dipole, list of Dipole")
# Get (average) layer-sepcific dipole data
avgs = []
avgs.append(average_dipoles(dpl))
l2_dipole = avgs[0].data["L2"]
l5_dipole = avgs[0].data["L5"]
dipole_times = dpl[0].times
# Scale dipole to fit the spike raster plot
raster_yrange = ax.get_yticks()
raster_min = min(raster_yrange)
raster_midpoint = round((raster_min / 2), 0)
raster_quarterpoint = round((raster_min / 4), 0)
# Scale down by .95 until the dipoles fit within the appropriate area
while (
max(max(l5_dipole), max(l2_dipole)) - min(min(l5_dipole), min(l2_dipole))
) > abs(raster_midpoint):
l5_dipole = l5_dipole * 0.95
l2_dipole = l2_dipole * 0.95
# Shift the dipole positions to overlay the correct cell types
l2_dipole = l2_dipole - abs(raster_midpoint) + abs(raster_quarterpoint)
l5_dipole = l5_dipole - abs(raster_midpoint) - abs(raster_quarterpoint)
# Draw the dipole plots
(l2_line,) = ax.plot(
dipole_times,
l2_dipole,
color="grey",
linewidth=1,
linestyle="--",
label="L2 Dipole",
)
(l5_line,) = ax.plot(
dipole_times,
l5_dipole,
color="grey",
linewidth=1,
linestyle="-",
label="L5 Dipole",
)
# set legend
handles = [e[0] for e in events]
# Add labels for the spike events
for handle in handles:
handle.set_label(handle.get_label() + " Spikes")
if overlay_dipoles:
handles.append(l2_line)
handles.append(l5_line)
spike_legend = ax.legend(
handles=handles,
loc="lower left",
framealpha=0.25,
)
if not show_legend:
ax.get_legend().remove()
else:
ax.add_artist(spike_legend)
# set axis labels
ax.set_xlabel("Time (ms)")
ax.set_ylabel("Cell ID")
# hide y-axis ticks and tick labels
ax.set_yticklabels([])
ax.tick_params(axis="y", length=0)
# add title
if overlay_dipoles:
ax.set_title("Raster Plot with Layer-Specific Dipole Overlays")
else:
ax.set_title("Raster Plot")
if len(cell_response.times) > 0:
ax.set_xlim(left=0, right=cell_response.times[-1])
else:
ax.set_xlim(left=0)
ax.set_xlim(left=0)
plt_show(show)
return ax.get_figure()
[docs]
def plot_cells(net, ax=None, show=True):
"""Plot the cells using Network.pos_dict.
Parameters
----------
net : instance of Network
The Network object.
ax : instance of matplotlib Axes3D | None
An axis object from matplotlib. If None,
a new figure is created.
show : bool
If True, show the figure.
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
if ax is None:
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
elif not isinstance(ax, Axes3D):
raise TypeError(
f"Expected 'ax' to be an instance of Axes3D, but got {type(ax).__name__}"
)
colors = {
"L5_pyramidal": "b",
"L2_pyramidal": "c",
"L5_basket": "r",
"L2_basket": "m",
}
markers = {
"L5_pyramidal": "^",
"L2_pyramidal": "^",
"L5_basket": "x",
"L2_basket": "x",
}
for cell_type in net.cell_types:
x = [pos[0] for pos in net.pos_dict[cell_type]]
y = [pos[1] for pos in net.pos_dict[cell_type]]
z = [pos[2] for pos in net.pos_dict[cell_type]]
if cell_type in colors:
color = colors[cell_type]
marker = markers[cell_type]
ax.scatter(x, y, z, c=color, s=50, marker=marker, label=cell_type)
if net.rec_arrays:
cols = plt.get_cmap("inferno", len(net.rec_arrays) + 2)
for ii, (arr_name, arr) in enumerate(net.rec_arrays.items()):
x = [p[0] for p in arr.positions]
y = [p[1] for p in arr.positions]
z = [p[2] for p in arr.positions]
ax.scatter(x, y, z, color=cols(ii + 1), s=25, marker="o", label=arr_name)
plt.legend(bbox_to_anchor=(-0.15, 1.025), loc="upper left")
plt_show(show)
return ax.get_figure()
[docs]
def plot_tfr_morlet(
dpl,
freqs,
*,
n_cycles=7.0,
tmin=None,
tmax=None,
layer="agg",
decim=None,
padding="zeros",
ax=None,
colormap="inferno",
colorbar=True,
colorbar_inside=False,
show=True,
):
"""Plot Morlet time-frequency representation of dipole time course
Parameters
----------
dpl : instance of Dipole | list of Dipole instances
The Dipole object. If a list of dipoles is given, the power is
calculated separately for each trial, then averaged.
freqs : array
Frequency range of interest.
n_cycles : float or array of float, default 7.0
Number of cycles. Fixed number or one per frequency.
tmin : float or None
Start time of plot in milliseconds. If None, plot entire simulation.
tmax : float or None
End time of plot in milliseconds. If None, plot entire simulation.
layer : str, default 'agg'
The layer to plot. Can be one of 'agg', 'L2', and 'L5'
decim : int or list of int or None (default)
Optional (integer) factor by which to decimate the raw dipole traces.
The SciPy function :func:`~scipy.signal.decimate` is used, which
recommends values <13. To achieve higher decimation factors, a list of
ints can be provided. These are applied successively.
padding : str or None
Optional padding of the dipole time course beyond the plotting limits.
Possible values are: 'zeros' for padding with 0's (default), 'mirror'
for mirror-image padding.
ax : instance of matplotlib figure | None
The matplotlib axis
colormap : str
The name of a matplotlib colormap, e.g., 'viridis'. Default: 'inferno'
colorbar : bool
If True (default), adjust figure to include colorbar.
colorbar_inside: bool, default False
Put the color inside the heatmap if True.
show : bool
If True, show the figure
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from matplotlib.ticker import ScalarFormatter
from .externals.mne import tfr_array_morlet
from .dipole import Dipole
if isinstance(dpl, Dipole):
dpl = [dpl]
if ax is None:
fig, ax = plt.subplots(1, 1, constrained_layout=True)
scale_applied = dpl[0].scale_applied
sfreq = dpl[0].sfreq
trial_power = []
for dpl_trial in dpl:
if dpl_trial.scale_applied != scale_applied:
raise RuntimeError("All dipoles must be scaled equally!")
if dpl_trial.sfreq != sfreq:
raise RuntimeError("All dipoles must be sampled equally!")
data, times = _get_plot_data_trange(
dpl_trial.times, dpl_trial.data[layer], tmin, tmax
)
sfreq = dpl_trial.sfreq
if decim is not None:
data, times, sfreq = _decimate_plot_data(decim, data, times, sfreq=sfreq)
if padding is not None:
if not isinstance(padding, str):
raise ValueError("padding must be a string (or None)")
if padding == "zeros":
data = np.r_[
np.zeros((len(data) - 1,)), data.ravel(), np.zeros((len(data) - 1,))
]
elif padding == "mirror":
data = np.r_[data[-1:0:-1], data, data[-2::-1]]
# MNE expects an array of shape (n_trials, n_channels, n_times)
data = data[None, None, :]
power = tfr_array_morlet(
data, sfreq=sfreq, freqs=freqs, n_cycles=n_cycles, output="power"
)
if padding is not None:
# get the middle portion after padding
power = power[:, :, :, times.shape[0] - 1 : 2 * times.shape[0] - 1]
trial_power.append(power)
power = np.mean(trial_power, axis=0)
im = ax.pcolormesh(times, freqs, power[0, 0, ...], cmap=colormap, shading="auto")
if freqs[0] > freqs[-1]:
freqs = freqs[::-1]
ax.invert_yaxis()
ax.set_xlabel("Time (ms)")
ax.set_ylabel("Frequency (Hz)")
if colorbar:
fig = ax.get_figure()
xfmt = ScalarFormatter()
xfmt.set_powerlimits((-2, 2))
# default colorbar
if colorbar_inside is False:
cbar = fig.colorbar(im, ax=ax, format=xfmt, shrink=0.8, pad=0)
cbar.ax.yaxis.set_ticks_position("left")
cbar.ax.set_ylabel(
r"Power ([nAm $\times$ {:.0f}]$^2$)".format(scale_applied),
rotation=-90,
va="bottom",
)
# put colorbar inside the heatmap.
else:
cbar_color = "white"
cbar_fontsize = 6
ax_pos = ax.get_position()
ax_width = ax_pos.x1 - ax_pos.x0
ax_height = ax_pos.y1 - ax_pos.y0
cbar_L = ax_pos.x0 + 0.9 * ax_width
cbar_B = ax_pos.y0 + 0.8 * ax_height
cbar_W = ax_width * 0.04
cbar_H = ax_height * 0.15
cax = fig.add_axes([cbar_L, cbar_B, cbar_W, cbar_H])
cbar = fig.colorbar(im, cax=cax, format=xfmt, shrink=0.8, pad=0)
cbar.ax.yaxis.set_ticks_position("left")
cbar.ax.yaxis.offsetText.set_fontsize(cbar_fontsize)
cbar.ax.set_ylabel(
r"Power ([nAm $\times$ {:.0f}]$^2$)".format(scale_applied),
rotation=-90,
va="bottom",
fontsize=cbar_fontsize,
color=cbar_color,
)
cbar.ax.tick_params(
direction="in",
labelsize=cbar_fontsize,
labelcolor=cbar_color,
colors=cbar_color,
)
plt.setp(cbar.ax.spines.values(), color=cbar_color)
setattr(fig, f"_cbar-ax-{id(ax)}", cbar)
plt_show(show)
return ax.get_figure()
[docs]
def plot_psd(
dpl,
*,
fmin=0,
fmax=None,
tmin=None,
tmax=None,
layer="agg",
color=None,
label=None,
ax=None,
show=True,
):
"""Plot power spectral density (PSD) of dipole time course
Applies `~scipy.signal.periodogram` from SciPy with ``window='hamming'``.
Note that no spectral averaging is applied across time, as most
``hnn_core`` simulations are short-duration. However, passing a list of
`Dipole` instances will plot their average (Hamming-windowed) power, which
resembles the `Welch`-method applied over time.
Parameters
----------
dpl : instance of Dipole | list of Dipole instances
The Dipole object.
fmin : float
Minimum frequency to plot (in Hz). Default: 0 Hz
fmax : float
Maximum frequency to plot (in Hz). Default: None (plot up to Nyquist)
tmin : float or None
Start time of data to include (in ms). If None, use entire simulation.
tmax : float or None
End time of data to include (in ms). If None, use entire simulation.
layer : str, default 'agg'
The layer to plot. Can be one of 'agg', 'L2', and 'L5'
color : str or tuple or None
The line color of PSD
label : str or None
Line label for PSD
ax : instance of matplotlib figure | None
The matplotlib axis.
show : bool
If True, show the figure
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from scipy.signal import periodogram
from .dipole import Dipole
if ax is None:
_, ax = plt.subplots(1, 1, constrained_layout=True)
if isinstance(dpl, Dipole):
dpl = [dpl]
scale_applied = dpl[0].scale_applied
sfreq = dpl[0].sfreq
trial_power = []
for dpl_trial in dpl:
if dpl_trial.scale_applied != scale_applied:
raise RuntimeError("All dipoles must be scaled equally!")
if dpl_trial.sfreq != sfreq:
raise RuntimeError("All dipoles must be sampled equally!")
data, _ = _get_plot_data_trange(
dpl_trial.times, dpl_trial.data[layer], tmin, tmax
)
freqs, Pxx = periodogram(data, sfreq, window="hamming", nfft=len(data))
trial_power.append(Pxx)
ax.plot(freqs, np.mean(np.array(Pxx, ndmin=2), axis=0), color=color, label=label)
if label:
ax.legend()
if fmax is not None:
ax.set_xlim((fmin, fmax))
ax.ticklabel_format(axis="both", scilimits=(-2, 3))
ax.set_xlabel("Frequency (Hz)")
if scale_applied == 1:
ylabel = "Power spectral density\n(nAm" + r"$^2 \ Hz^{-1}$)"
else:
ylabel = (
"Power spectral density\n"
+ r"([nAm$\times$ {:.0f}]".format(scale_applied)
+ r"$^2 \ Hz^{-1}$)"
)
ax.set_ylabel(ylabel, multialignment="center")
plt_show(show)
return ax.get_figure()
def _linewidth_from_data_units(ax, linewidth):
# see: https://stackoverflow.com/a/35501485
fig = ax.get_figure()
length = fig.bbox_inches.width * ax.get_position().width
value_range = np.diff(ax.get_xlim())[0]
length *= 72 # Convert length to points
# Scale linewidth to value range
return linewidth * (length / value_range)
[docs]
def plot_cell_morphology(
cell,
ax,
color=None,
pos=(0, 0, 0),
xlim=(-250, 150),
ylim=(-100, 100),
zlim=(-100, 1200),
show=True,
):
"""Plot the cell morphology.
Parameters
----------
cell : instance of Cell
The cell object
ax : instance of Axes3D
Matplotlib 3D axis
show : bool
If True, show the plot
color : str | dict | None
Color of cell. If str, entire cell plotted with
color indicated by str. If dict, colors of individual sections
can be specified. Must have a key for every section in cell as
defined in the `Cell.sections` attribute.
| Ex: ``{'apical_trunk': 'r', 'soma': 'b', ...}``
pos : tuple of int or float | None
Position of cell soma. Must be a tuple of 3 elements for the
(x, y, z) position of the soma in 3D space. Default: (0, 0, 0)
xlim : tuple of int | tuple of float
x limits of plot window. Default (-250, 150)
ylim : tuple of int | tuple of float
y limits of plot window. Default (-100, 100)
zlim : tuple of int | tuple of float
z limits of plot window. Default (-100, 1200)
show : bool
If True, show the plot
Returns
-------
axes : list of instance of Axes3D
The matplotlib 3D axis handle.
"""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # noqa
if ax is None:
plt.figure()
ax = plt.axes(projection="3d")
_validate_type(color, (str, dict, None), "color")
if color is None:
section_colors = {section: "b" for section in cell.sections.keys()}
if isinstance(color, str):
section_colors = {section: color for section in cell.sections.keys()}
if isinstance(color, dict):
section_colors = color
_validate_type(pos, tuple, "pos")
if isinstance(pos, tuple):
if len(pos) != 3:
raise ValueError("pos must be a tuple of 3 elements")
for pos_idx in pos:
_validate_type(pos_idx, (float, int), "pos[idx]")
# Cell is in XZ plane
ax.set_xlim((pos[0] + xlim[0], pos[0] + xlim[1]))
ax.set_zlim((pos[1] + zlim[0], pos[1] + zlim[1]))
ax.set_ylim((pos[2] + ylim[0], pos[2] + ylim[1]))
for sec_name, section in cell.sections.items():
linewidth = _linewidth_from_data_units(ax, section.diam)
end_pts = section.end_pts
dx = pos[0] - cell.sections["soma"].end_pts[0][0]
dy = pos[1] - cell.sections["soma"].end_pts[0][1]
dz = pos[2] - cell.sections["soma"].end_pts[0][2]
xs, ys, zs = list(), list(), list()
for pt in end_pts:
xs.append(pt[0] + dx)
ys.append(pt[1] + dz)
zs.append(pt[2] + dy)
ax.plot(xs, ys, zs, "-", linewidth=linewidth, color=section_colors[sec_name])
ax.view_init(0, -90)
ax.axis("off")
plt.tight_layout()
plt_show(show)
return ax
[docs]
def plot_connectivity_matrix(
net, conn_idx, ax=None, show_weight=True, colorbar=True, colormap="Greys", show=True
):
"""Plot connectivity matrix with color bar for synaptic weights
Parameters
----------
net : Instance of Network object
The Network object
conn_idx : int
Index of connection to be visualized
from `net.connectivity`
ax : instance of Axes3D
Matplotlib 3D axis
show_weight : bool
If True, visualize connectivity weights as gradient.
If False, all weights set to constant value.
colormap : str
The name of a matplotlib colormap. Default: 'Greys'
colorbar : bool
If True (default), adjust figure to include colorbar.
show : bool
If True, show the plot
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from matplotlib.ticker import ScalarFormatter
from .network import Network
from .cell import _get_gaussian_connection
_validate_type(net, Network, "net", "Network")
_validate_type(conn_idx, int, "conn_idx", "int")
_validate_type(show_weight, bool, "show_weight", "bool")
if ax is None:
_, ax = plt.subplots(1, 1)
# Load objects for distance calculation
conn = net.connectivity[conn_idx]
nc_dict = conn["nc_dict"]
src_type = conn["src_type"]
target_type = conn["target_type"]
src_type_pos = net.pos_dict[src_type]
target_type_pos = net.pos_dict[target_type]
src_range = np.array(net.gid_ranges[conn["src_type"]])
target_range = np.array(net.gid_ranges[conn["target_type"]])
connectivity_matrix = np.zeros((len(src_range), len(target_range)))
for src_gid, target_src_pair in conn["gid_pairs"].items():
src_idx = np.where(src_range == src_gid)[0][0]
target_indeces = np.where(np.isin(target_range, target_src_pair))[0]
for target_idx in target_indeces:
src_pos = src_type_pos[src_idx]
target_pos = target_type_pos[target_idx]
# Identical calculation used in Cell.par_connect_from_src()
if show_weight:
weight, _ = _get_gaussian_connection(
src_pos, target_pos, nc_dict, inplane_distance=net._inplane_distance
)
else:
weight = 1.0
connectivity_matrix[src_idx, target_idx] = weight
im = ax.imshow(connectivity_matrix, cmap=colormap, interpolation="none")
ax.set_xlabel("Time (ms)")
ax.set_ylabel("Frequency (Hz)")
if colorbar:
fig = ax.get_figure()
xfmt = ScalarFormatter()
xfmt.set_powerlimits((-2, 2))
cbar = fig.colorbar(im, ax=ax, format=xfmt)
cbar.ax.yaxis.set_ticks_position("right")
cbar.ax.set_ylabel("Weight", rotation=-90, va="bottom")
ax.set_xlabel(
f"{conn['target_type']} target gids ({target_range[0]}-{target_range[-1]})"
)
ax.set_xticklabels(list())
ax.set_ylabel(f"{conn['src_type']} source gids ({src_range[0]}-{src_range[-1]})")
ax.set_yticklabels(list())
ax.set_title(
f"{conn['src_type']} -> {conn['target_type']} "
f"({conn['loc']}, {conn['receptor']})"
)
plt.tight_layout()
plt_show(show)
return ax.get_figure()
[docs]
def plot_drive_strength(
net,
show_weight=True,
ax=None,
colorbar=True,
color_scale="linear",
normalize=True,
show=True,
):
"""Plot the relative strength of drives to cell types.
Parameters
----------
net : Network
Instance of a Network object.
show_weight : bool, default=True
If True, visualize connectivity weights as gradient.
If False, all weights set to constant value.
ax : matplotlib.Axes, optional
Matplotlib axes. If None, create a new figure.
colorbar : bool, default=True
If True (default), adjust figure to include colorbar.
color_scale : {'linear', 'log'}, default='linear'
Color scaling for drive strength.
normalize : bool, default=True
If True, normalize the strength values to be between 0 and 1.
show : bool, default=True
If True, show the plot immediately.
Returns
-------
fig : matplotlib.figure.Figure
The figure handle.
"""
import numpy as np
import matplotlib.pyplot as plt
from .network import Network
from .cell import _get_gaussian_connection
_validate_type(net, Network, "net", "Network")
_validate_type(show_weight, bool, "show_weight", "bool")
# Get drive and cell type information
drive_names = list(net.external_drives.keys())
cell_types = list(net.cell_types.keys())
strength_matrix = np.zeros((len(drive_names), len(cell_types)))
for conn in net.connectivity:
src_type = conn["src_type"]
target_type = conn["target_type"]
if src_type in drive_names and target_type in cell_types:
nc_dict = conn["nc_dict"]
drive_idx = drive_names.index(src_type)
cell_idx = cell_types.index(target_type)
src_type_pos = net.pos_dict[src_type]
target_type_pos = net.pos_dict[target_type]
src_range = np.array(net.gid_ranges[src_type])
target_range = np.array(net.gid_ranges[target_type])
total_weight = 0
for src_gid, target_src_pair in conn["gid_pairs"].items():
src_idx = np.where(src_range == src_gid)[0][0]
target_indeces = np.where(np.isin(target_range, target_src_pair))[0]
for target_idx in target_indeces:
src_pos = src_type_pos[src_idx]
target_pos = target_type_pos[target_idx]
if show_weight:
weight = _get_gaussian_connection(
src_pos,
target_pos,
nc_dict,
inplane_distance=net._inplane_distance,
)
else:
weight = 1.0
total_weight += sum(weight)
strength_matrix[drive_idx, cell_idx] = total_weight
if normalize:
min_val = np.min(strength_matrix)
max_val = np.max(strength_matrix)
if max_val > min_val:
strength_matrix = (strength_matrix - min_val) / (max_val - min_val)
if color_scale == "log":
strength_matrix = np.log1p(strength_matrix)
if ax is None:
fig, ax = plt.subplots(figsize=(12, 6))
else:
fig = ax.figure
cax = ax.imshow(
strength_matrix, cmap="viridis", aspect="auto", interpolation="nearest"
)
if colorbar:
cbar = fig.colorbar(cax, ax=ax)
cbar.ax.yaxis.set_ticks_position("right")
ax.set_xticks(np.arange(len(cell_types)))
ax.set_yticks(np.arange(len(drive_names)))
ax.set_xticklabels(cell_types)
ax.set_yticklabels(drive_names)
ax.set_xlabel("Cell Types")
ax.set_ylabel("Drive Names")
ax.set_title("External Drive Strengths")
# For addition of units information
unit_text = (
"Units: µS (microsiemens)"
if not normalize
else "Units: Relative Strength (0-1)"
)
ax.text(
0.98,
0.02,
unit_text,
transform=ax.transAxes,
fontsize=12,
verticalalignment="bottom",
horizontalalignment="right",
bbox=dict(facecolor="white", alpha=0.6, edgecolor="black"),
)
plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor")
for i in range(len(drive_names)):
for j in range(len(cell_types)):
value = strength_matrix[i, j]
color = "black" if value > strength_matrix.max() * 0.7 else "white"
ax.text(
j,
i,
f"{value:.2f}",
ha="center",
va="center",
color=color,
fontsize=12,
weight="bold",
)
plt.tight_layout()
if show:
plt.show()
return fig
def _update_target_plot(
ax,
conn,
src_gid,
src_type_pos,
target_type_pos,
src_range,
target_range,
nc_dict,
colormap,
inplane_distance,
):
from .cell import _get_gaussian_connection
# Extract indices to get position in network
# Index in gid range aligns with net.pos_dict
target_src_pair = conn["gid_pairs"][src_gid]
target_indeces = np.where(np.isin(target_range, target_src_pair))[0]
src_idx = np.where(src_range == src_gid)[0][0]
src_pos = src_type_pos[src_idx]
# Aggregate positions and weight of each connected target
weights, target_x_pos, target_y_pos = list(), list(), list()
for target_idx in target_indeces:
target_pos = target_type_pos[target_idx]
target_x_pos.append(target_pos[0])
target_y_pos.append(target_pos[1])
weight, _ = _get_gaussian_connection(
src_pos, target_pos, nc_dict, inplane_distance
)
weights.append(weight)
ax.clear()
im = ax.scatter(target_x_pos, target_y_pos, c=weights, s=50, cmap=colormap)
x_pos = target_type_pos[:, 0]
y_pos = target_type_pos[:, 1]
ax.scatter(x_pos, y_pos, color="k", marker="x", zorder=-1, s=20)
ax.scatter(src_pos[0], src_pos[1], marker="s", color="red", s=150)
ax.set_ylabel("Y Position")
ax.set_xlabel("X Position")
return im
[docs]
def plot_cell_connectivity(
net, conn_idx, src_gid=None, axes=None, colorbar=True, colormap="viridis", show=True
):
"""Plot synaptic weight of connections.
This is an interactive plot with source cells shown in the left
subplot and connectivity from a source cell to all the target cells
in the right subplot. Click on the cells in the left subplot to
explore how the connectivity pattern changes for different source cells.
Parameters
----------
net : Instance of Network object
The Network object
conn_idx : int
Index of connection to be visualized from net.connectivity
src_gid : int | None
The cell ID of the source cell. It must be an element of
net.connectivity[conn_idx]['gid_pairs'].keys()
If None, the first cell from the list of valid src_gids is selected.
axes : instance of Axes3D
Matplotlib 3D axis
colormap : str
The name of a matplotlib colormap. Default: 'viridis'
colorbar : bool
If True (default), adjust figure to include colorbar.
show : bool
If True, show the plot
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
Notes
-----
Target cells will be determined by the connections in
net.connectivity[conn_idx].
If the target cell is not connected to the source cell,
it will appear as a smaller black cross.
Source cell is plotted as a red square. Source cell will not be plotted if
the connection corresponds to a drive, ex: poisson, bursty, etc.
"""
import matplotlib.pyplot as plt
from .network import Network
from matplotlib.ticker import ScalarFormatter
_validate_type(net, Network, "net", "Network")
_validate_type(conn_idx, int, "conn_idx", "int")
# Load objects for distance calculation
conn = net.connectivity[conn_idx]
nc_dict = conn["nc_dict"]
src_type = conn["src_type"]
target_type = conn["target_type"]
src_type_pos = np.array(net.pos_dict[src_type])
target_type_pos = np.array(net.pos_dict[target_type])
src_range = np.array(net.gid_ranges[conn["src_type"]])
valid_src_gids = list(net.connectivity[conn_idx]["gid_pairs"].keys())
src_pos_valid = src_type_pos[np.isin(src_range, valid_src_gids)]
if src_gid is None:
src_gid = valid_src_gids[0]
_validate_type(src_gid, int, "src_gid", "int")
if src_gid not in valid_src_gids:
raise ValueError(
f"src_gid {src_gid} not a valid cell ID for this "
f"connection. Please select one of {valid_src_gids}"
)
target_range = np.array(net.gid_ranges[conn["target_type"]])
if axes is None:
if src_type in net.cell_types:
fig, axes = plt.subplots(1, 2, sharex=True, sharey=True)
else:
fig, axes = plt.subplots(1, 1, sharex=True, sharey=True)
axes = [axes]
if len(axes) == 2:
ax_src, ax = axes
else:
ax = axes[0]
im = _update_target_plot(
ax,
conn,
src_gid,
src_type_pos,
target_type_pos,
src_range,
target_range,
nc_dict,
colormap,
net._inplane_distance,
)
x_src = src_type_pos[:, 0]
y_src = src_type_pos[:, 1]
x_src_valid = src_pos_valid[:, 0]
y_src_valid = src_pos_valid[:, 1]
if src_type in net.cell_types:
ax_src.scatter(x_src, y_src, marker="s", color="red", s=50, alpha=0.2)
ax_src.scatter(x_src_valid, y_src_valid, marker="s", color="red", s=50)
plt.suptitle(
f"{conn['src_type']}-> {conn['target_type']}"
f" ({conn['loc']}, {conn['receptor']})"
)
def _onclick(event):
if event.inaxes in [ax] or event.inaxes is None:
return
dist = np.linalg.norm(
src_type_pos[:, :2] - np.array([event.xdata, event.ydata]), axis=1
)
src_idx = np.argmin(dist)
src_gid = src_range[src_idx]
if src_gid not in valid_src_gids:
return
_update_target_plot(
ax,
conn,
src_gid,
src_type_pos,
target_type_pos,
src_range,
target_range,
nc_dict,
colormap,
net._inplane_distance,
)
fig.canvas.draw()
if colorbar:
fig = ax.get_figure()
xfmt = ScalarFormatter()
xfmt.set_powerlimits((-2, 2))
cbar = fig.colorbar(im, ax=ax, format=xfmt)
cbar.ax.yaxis.set_ticks_position("right")
cbar.ax.set_ylabel("Weight", rotation=-90, va="bottom")
plt.tight_layout()
fig.canvas.mpl_connect("button_press_event", _onclick)
plt_show(show)
return ax.get_figure()
[docs]
def plot_laminar_csd(
times,
data,
contact_labels,
ax=None,
colorbar=True,
vmin=None,
vmax=None,
sink="b",
interpolation="spline",
show=True,
):
"""Plot laminar current source density (CSD) estimation from LFP array.
Parameters
----------
times : Numpy array, shape (n_times,)
Sampling times (in ms).
data : array-like, shape (n_channels, n_times)
CSD data, channels x time.
ax : instance of matplotlib figure | None
The matplotlib axis.
colorbar : bool
If True (default), adjust figure to include colorbar.
contact_labels : list
Labels associated with the contacts to plot. Passed as-is to
:func:`~matplotlib.axes.Axes.set_yticklabels`.
vmin: float, optional
lower bound of the color axis.
Will be set automatically of None.
vmax: float, optional
upper bound of the color axis.
Will be set automatically of None.
sink : str
If set to 'blue' or 'b', plots sinks in blue and sources in red,
if set to 'red' or 'r', sinks plotted in red and sources blue.
interpolation : str | None
If 'spline', will smoothen the CSD using spline method,
if None, no smoothing will be applied.
show : bool
If True, show the plot.
Returns
-------
fig : instance of matplotlib Figure
The matplotlib figure handle.
"""
import matplotlib.pyplot as plt
from scipy.interpolate import RectBivariateSpline
if ax is None:
_, ax = plt.subplots(1, 1, constrained_layout=True)
if sink[0].lower() == "b":
cmap = "jet"
elif sink[0].lower() == "r":
cmap = "jet_r"
elif sink[0].lower() != "b" or sink[0].lower() != "r":
raise RuntimeError(
'Please use sink = "b" or sink = "r".'
' Only colormap "jet" is supported for CSD.'
)
if interpolation == "spline":
# create interpolation function
interp_data = RectBivariateSpline(times, contact_labels, data.T)
# increase number of contacts
new_depths = np.linspace(
contact_labels[0],
contact_labels[-1],
contact_labels[-1] - contact_labels[0],
)
# interpolate
data = interp_data(times, new_depths).T
elif interpolation is None:
data = data
new_depths = contact_labels
# if vmin and vmax are both None, set colormap such that green = zero
if vmin is None and vmax is None:
vmin = -np.max(np.abs(data))
vmax = np.max(np.abs(data))
im = ax.pcolormesh(
times, new_depths, data, cmap=cmap, shading="auto", vmin=vmin, vmax=vmax
)
ax.set_xlabel("time (s)")
ax.set_ylabel("electrode depth")
if colorbar:
color_axis = ax.inset_axes([1.05, 0, 0.02, 1], transform=ax.transAxes)
plt.colorbar(im, ax=ax, cax=color_axis).set_label(r"$CSD (uV/um^{2})$")
plt.tight_layout()
plt_show(show)
return ax.get_figure()
[docs]
class NetworkPlotter:
"""Helper class to visualize full morphology of HNN model.
Parameters
----------
net : Instance of Network object
The Network object
ax : instance of matplotlib Axes3D | None
An axis object from matplotlib. If None,
a new figure is created.
vmin : int | float
Lower limit of colormap for plotting voltage
Default: -100 mV
vmax : int | float
Upper limit of colormap for plotting voltage
Default: 50 mV
bg_color : str
Background color of ax. Default: 'black'
colorbar : bool
If True (default), adjust figure to include colorbar.
voltage_colormap : str
Colormap used for plotting voltages
Default: 'viridis'
elev : int | float
Elevation 3D plot viewpoint, default: 10
azim : int | float
Azimuth of 3D plot view point, default: 20
xlim : tuple of int | tuple of float
x limits of plot window. Default (-200, 3100)
ylim : tuple of int | tuple of float
y limits of plot window. Default (-200, 3100)
zlim : tuple of int | tuple of float
z limits of plot window. Default (-300, 2200)
trial_idx : int
Index of simulation trial plotted. Default: 0
time_idx : int
Index of time point plotted. Default: 0
"""
def __init__(
self,
net,
ax=None,
vmin=-100,
vmax=50,
bg_color="black",
colorbar=True,
voltage_colormap="viridis",
elev=10,
azim=-500,
xlim=(-200, 3100),
ylim=(-200, 3100),
zlim=(-300, 2200),
trial_idx=0,
time_idx=0,
):
from matplotlib import colormaps
self._validate_parameters(
vmin,
vmax,
bg_color,
voltage_colormap,
colorbar,
elev,
azim,
xlim,
ylim,
zlim,
trial_idx,
time_idx,
)
# Set init arguments
self.net = net
self.ax = ax
self._vmin = vmin
self._vmax = vmax
self._bg_color = bg_color
self._colorbar = colorbar
self._voltage_colormap = voltage_colormap
self._colormaps = colormaps
self._xlim = xlim
self._ylim = ylim
self._zlim = zlim
self._elev = elev
self._azim = azim
self._trial_idx = trial_idx
self._time_idx = time_idx
# Check if Network object is simulated
self.times, self._vsec_recorded = self._check_network_simulation()
# Initialize plots and colormap
self.fig = None
self._colormap = colormaps[voltage_colormap]
self.vsec_array = self._get_voltages()
self.color_array = self._colormap(self.vsec_array)
self._initialize_plots()
if self._colorbar:
self._update_colorbar()
else:
self._cbar = None
def _validate_parameters(
self,
vmin,
vmax,
bg_color,
voltage_colormap,
colorbar,
elev,
azim,
xlim,
ylim,
zlim,
trial_idx,
time_idx,
):
_validate_type(vmin, (int, float), "vmin")
_validate_type(vmax, (int, float), "vmax")
_validate_type(bg_color, str, "bg_color")
_validate_type(voltage_colormap, str, "voltage_colormap")
_validate_type(colorbar, bool, "colorbar")
_validate_type(xlim, tuple, "xlim")
_validate_type(ylim, tuple, "ylim")
_validate_type(zlim, tuple, "zlim")
_validate_type(elev, (int, float), "elev")
_validate_type(azim, (int, float), "azim")
_validate_type(trial_idx, int, "trial_idx")
_validate_type(time_idx, int, "time_idx")
def _check_network_simulation(self):
times = None
vsec_recorded = False
# Check if network simulated
if self.net.cell_response is not None:
times = self.net.cell_response.times
# Check if voltage recorded
if self.net._params["record_vsec"] == "all":
vsec_recorded = True
return times, vsec_recorded
def _initialize_plots(self):
import matplotlib.pyplot as plt
# Create figure
if self.ax is None:
self.fig = plt.figure()
self.ax = self.fig.add_subplot(projection="3d")
self.ax.set_facecolor(self._bg_color)
self._init_network_plot()
self._update_axes()
def _get_voltages(self):
vsec_list = list()
for cell_type in self.net.cell_types:
gid_range = self.net.gid_ranges[cell_type]
for gid in gid_range:
cell = self.net.cell_types[cell_type]["cell_object"]
for sec_name in cell.sections.keys():
if self._vsec_recorded is True:
vsec = np.array(
self.net.cell_response.vsec[self.trial_idx][gid][sec_name]
)
vsec_list.append(vsec)
else: # Populate with zeros if no voltage recording
vsec_list.append([0.0])
vsec_array = np.vstack(vsec_list)
vsec_array = (vsec_array - self.vmin) / (self.vmax - self.vmin)
return vsec_array
def _update_section_voltages(self, t_idx):
if not self._vsec_recorded:
raise RuntimeError(
"Network must be simulated with"
"`simulate_dipole(record_vsec='all')` before"
"plotting voltages."
)
color_list = self.color_array[:, t_idx]
for line, color in zip(self.ax.lines, color_list):
line.set_color(color)
def _init_network_plot(self):
for cell_type in self.net.cell_types:
gid_range = self.net.gid_ranges[cell_type]
for gid_idx, gid in enumerate(gid_range):
cell = self.net.cell_types[cell_type]
pos = self.net.pos_dict[cell_type][gid_idx]
pos = (float(pos[0]), float(pos[2]), float(pos[1]))
cell["cell_object"].plot_morphology(
ax=self.ax,
show=False,
pos=pos,
xlim=self.xlim,
ylim=self.ylim,
zlim=self.zlim,
)
def _update_axes(self):
self.ax.set_xlim(self._xlim)
self.ax.set_ylim(self._ylim)
self.ax.set_zlim(self._zlim)
self.ax.view_init(self._elev, self._azim)
def _update_colorbar(self):
import matplotlib.pyplot as plt
import matplotlib.colors as mc
fig = self.ax.get_figure()
sm = plt.cm.ScalarMappable(
cmap=self.voltage_colormap,
norm=mc.Normalize(vmin=self.vmin, vmax=self.vmax),
)
self._cbar = fig.colorbar(sm, ax=self.ax)
[docs]
def export_movie(
self,
fname,
fps=30,
dpi=300,
decim=10,
interval=30,
frame_start=0,
frame_stop=None,
writer="pillow",
):
"""Export movie of network activity
Parameters
----------
fname : str
Filename of exported movie
fps : int
Frames per second, default: 30
dpi : int
Dots per inch, default: 300
decim : int
Decimation factor for frames, default: 10
interval : int
Delay between frames, default: 30
frame_start : int
Index of first frame, default: 0
frame_stop : int | None
Index of last frame, default: None
If None, entire simulation is animated
writer : str
Movie writer, default: 'pillow'.
Alternative movie writers can be found at
https://matplotlib.org/stable/api/animation_api.html
"""
import matplotlib.animation as animation
if not self._vsec_recorded:
raise RuntimeError(
"Network must be simulated with"
"`simulate_dipole(record_vsec='all')` before"
"plotting voltages."
)
if frame_stop is None:
frame_stop = len(self.times) - 1
frames = np.arange(frame_start, frame_stop, decim)
ani = animation.FuncAnimation(
self.fig, self._set_time_idx, frames, interval=interval
)
writer = animation.writers[writer](fps=fps)
ani.save(fname, writer=writer, dpi=dpi)
return ani
# Axis limits
@property
def xlim(self):
return self._xlim
@xlim.setter
def xlim(self, xlim):
_validate_type(xlim, tuple, "xlim")
self._xlim = xlim
self.ax.set_xlim(self._xlim)
@property
def ylim(self):
return self._ylim
@ylim.setter
def ylim(self, ylim):
_validate_type(ylim, tuple, "ylim")
self._ylim = ylim
self.ax.set_ylim(self._ylim)
@property
def zlim(self):
return self._zlim
@zlim.setter
def zlim(self, zlim):
_validate_type(zlim, tuple, "zlim")
self._zlim = zlim
self.ax.set_zlim(self._zlim)
# Elevation and azimuth of 3D viewpoint
@property
def elev(self):
return self._elev
@elev.setter
def elev(self, elev):
_validate_type(elev, (int, float), "elev")
self._elev = elev
self.ax.view_init(self._elev, self._azim)
@property
def azim(self):
return self._azim
@azim.setter
def azim(self, azim):
_validate_type(azim, (int, float), "azim")
self._azim = azim
self.ax.view_init(self._elev, self._azim)
# Minimum and maximum voltages
@property
def vmin(self):
return self._vmin
@vmin.setter
def vmin(self, vmin):
_validate_type(vmin, (int, float), "vmin")
self._vmin = vmin
self.vsec_array = self._get_voltages()
self.color_array = self._colormap(self.vsec_array)
if self._colorbar:
self._cbar.remove()
self._update_colorbar()
@property
def vmax(self):
return self._vmax
@vmax.setter
def vmax(self, vmax):
_validate_type(vmax, (int, float), "vmax")
self._vmax = vmax
self.vsec_array = self._get_voltages()
self.color_array = self._colormap(self.vsec_array)
if self._colorbar:
self._cbar.remove()
self._update_colorbar()
# Time and trial indices
@property
def trial_idx(self):
return self._trial_idx
@trial_idx.setter
def trial_idx(self, trial_idx):
_validate_type(trial_idx, int, "trial_idx")
if not self._vsec_recorded:
raise RuntimeError(
"Network must be simulated with"
"`simulate_dipole(record_vsec='all')` before"
"setting `trial_idx`."
)
self._trial_idx = trial_idx
self.vsec_array = self._get_voltages()
self.color_array = self._colormap(self.vsec_array)
self._update_section_voltages(self._time_idx)
@property
def time_idx(self):
return self._time_idx
@time_idx.setter
def time_idx(self, time_idx):
_validate_type(time_idx, (int, np.integer), "time_idx")
if not self._vsec_recorded:
raise RuntimeError(
"Network must be simulated with"
"`simulate_dipole(record_vsec='all')` before"
"setting `time_idx`."
)
self._time_idx = time_idx
self._update_section_voltages(self._time_idx)
# Callable update function for making animations
def _set_time_idx(self, time_idx):
self.time_idx = time_idx
# Background color and voltage colormaps
@property
def bg_color(self):
return self._bg_color
@bg_color.setter
def bg_color(self, bg_color):
self._bg_color = bg_color
self.ax.set_facecolor(self._bg_color)
@property
def voltage_colormap(self):
return self._voltage_colormap
@voltage_colormap.setter
def voltage_colormap(self, voltage_colormap):
self._voltage_colormap = voltage_colormap
self._colormap = self._colormaps[self._voltage_colormap]
self.color_array = self._colormap(self.vsec_array)
if self._colorbar:
self._cbar.remove()
self._update_colorbar()
@property
def colorbar(self):
return self._colorbar
@colorbar.setter
def colorbar(self, colorbar):
_validate_type(colorbar, bool, "colorbar")
self._colorbar = colorbar
if self._colorbar:
# Remove old colorbar if already exists
if self._cbar is not None:
self._cbar.remove()
self._update_colorbar()
else:
self._cbar.remove()
self._cbar = None
