[074d3d]: / mne / viz / tests / test_topo.py

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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from collections import namedtuple
from pathlib import Path
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pytest
from mne import Epochs, compute_proj_evoked, read_cov, read_events
from mne.channels import read_layout
from mne.io import read_raw_fif
from mne.time_frequency.tfr import AverageTFRArray
from mne.utils import _record_warnings
from mne.viz import (
_get_presser,
mne_analyze_colormap,
plot_evoked_topo,
plot_topo_image_epochs,
)
from mne.viz.evoked import _line_plot_onselect
from mne.viz.topo import _imshow_tfr, _plot_update_evoked_topo_proj, iter_topography
from mne.viz.utils import _fake_click, _fake_keypress
base_dir = Path(__file__).parents[2] / "io" / "tests" / "data"
evoked_fname = base_dir / "test-ave.fif"
raw_fname = base_dir / "test_raw.fif"
event_name = base_dir / "test-eve.fif"
cov_fname = base_dir / "test-cov.fif"
event_id, tmin, tmax = 1, -0.2, 0.2
layout = read_layout("Vectorview-all")
def _get_events():
"""Get events."""
return read_events(event_name)
def _get_picks(raw):
"""Get picks."""
return [0, 1, 2, 6, 7, 8, 306, 340, 341, 342] # take a only few channels
def _get_epochs():
"""Get epochs."""
raw = read_raw_fif(raw_fname)
raw.add_proj([], remove_existing=True)
events = _get_events()
picks = _get_picks(raw)
# bad proj warning
epochs = Epochs(raw, events[:10], event_id, tmin, tmax, picks=picks)
return epochs
def _get_epochs_delayed_ssp():
"""Get epochs with delayed SSP."""
raw = read_raw_fif(raw_fname)
events = _get_events()
picks = _get_picks(raw)
reject = dict(mag=4e-12)
with pytest.warns(RuntimeWarning, match="projection"):
epochs_delayed_ssp = Epochs(
raw,
events[:10],
event_id,
tmin,
tmax,
picks=picks,
proj="delayed",
reject=reject,
)
return epochs_delayed_ssp
def test_plot_joint():
"""Test joint plot."""
evoked = _get_epochs().average()
evoked.plot_joint(ts_args=dict(time_unit="s"), topomap_args=dict(time_unit="s"))
def return_inds(d): # to test function kwarg to zorder arg of evoked.plot
return list(range(d.shape[0]))
evoked.plot_joint(
title="test",
topomap_args=dict(contours=0, res=8, time_unit="ms"),
ts_args=dict(spatial_colors=True, zorder=return_inds, time_unit="s"),
)
with pytest.raises(ValueError, match="If one of `ts_args` and"):
evoked.plot_joint(ts_args=dict(axes=True, time_unit="s"))
axes = plt.subplots(nrows=3)[-1].flatten().tolist()
evoked.plot_joint(
times=[0],
picks=[6, 7, 8],
ts_args=dict(axes=axes[0]),
topomap_args={"axes": axes[1:], "time_unit": "s"},
)
with pytest.raises(ValueError, match="of length 4"):
evoked.plot_joint(
picks=[6, 7, 8],
ts_args=dict(axes=axes[0]),
topomap_args=dict(axes=axes[2:]),
)
plt.close("all")
# test proj options
assert len(evoked.info["projs"]) == 0
evoked.pick(picks="meg")
evoked.add_proj(compute_proj_evoked(evoked, n_mag=1, n_grad=1, meg="combined"))
assert len(evoked.info["projs"]) == 1
with pytest.raises(ValueError, match="must match ts_args"):
evoked.plot_joint(ts_args=dict(proj=True), topomap_args=dict(proj=False))
evoked.plot_joint(
ts_args=dict(proj="reconstruct"), topomap_args=dict(proj="reconstruct")
)
plt.close("all")
# test sEEG (gh:8733)
evoked.del_proj().pick("mag") # avoid overlapping positions error
mapping = {ch_name: "seeg" for ch_name in evoked.ch_names}
evoked.set_channel_types(mapping, on_unit_change="ignore")
evoked.plot_joint()
# test DBS (gh:8739)
evoked = _get_epochs().average().pick("mag")
mapping = {ch_name: "dbs" for ch_name in evoked.ch_names}
evoked.set_channel_types(mapping, on_unit_change="ignore")
evoked.plot_joint()
plt.close("all")
def test_plot_topo():
"""Test plotting of ERP topography."""
# Show topography
evoked = _get_epochs().average()
# should auto-find layout
plot_evoked_topo([evoked, evoked], merge_grads=True, background_color="w")
plot_evoked_topo(
[evoked, evoked], merge_grads=True, background_color="w", color="blue"
)
# test legend colors
colors = ["red", "blue"]
fig = plot_evoked_topo([evoked, evoked], merge_grads=True, color=colors)
legend = fig.axes[0].get_legend()
legend_colors = [
line.properties()["markeredgecolor"] for line in legend.get_lines()
]
assert legend_colors == colors
with pytest.raises(ValueError, match="must be .*tuple, list, str,.*"):
plot_evoked_topo(
[evoked, evoked], merge_grads=True, color=np.array(["blue", "red"])
)
picked_evoked = evoked.copy().pick(evoked.ch_names[:3])
picked_evoked_eeg = evoked.copy().pick(picks="eeg")
picked_evoked_eeg.pick(picked_evoked_eeg.ch_names[:3])
# test scaling
for ylim in [dict(mag=[-600, 600]), None]:
plot_evoked_topo([picked_evoked] * 2, layout, ylim=ylim)
for evo in [evoked, [evoked, picked_evoked]]:
pytest.raises(ValueError, plot_evoked_topo, evo, layout, color=["y", "b"])
evoked_delayed_ssp = _get_epochs_delayed_ssp().average()
ch_names = evoked_delayed_ssp.ch_names[:3] # make it faster
picked_evoked_delayed_ssp = evoked_delayed_ssp.pick(ch_names)
fig = plot_evoked_topo(picked_evoked_delayed_ssp, layout, proj="interactive")
func = _get_presser(fig)
event = namedtuple("Event", ["inaxes", "xdata", "ydata"])
func(
event(
inaxes=fig.axes[0],
xdata=fig.axes[0]._mne_axs[0].pos[0],
ydata=fig.axes[0]._mne_axs[0].pos[1],
)
)
func(event(inaxes=fig.axes[0], xdata=0, ydata=0))
params = dict(
evokeds=[picked_evoked_delayed_ssp],
times=picked_evoked_delayed_ssp.times,
fig=fig,
projs=picked_evoked_delayed_ssp.info["projs"],
)
bools = [True] * len(params["projs"])
with pytest.warns(RuntimeWarning, match="projection"):
_plot_update_evoked_topo_proj(params, bools)
# should auto-generate layout
plot_evoked_topo(
picked_evoked_eeg.copy(),
fig_background=np.zeros((4, 3, 3)),
proj=True,
background_color="k",
)
# Test RMS plot of grad pairs
picked_evoked.plot_topo(merge_grads=True, background_color="w")
plt.close("all")
for ax, idx in iter_topography(evoked.info, legend=True):
ax.plot(evoked.data[idx], color="red")
# test status bar message
if idx != -1:
assert evoked.ch_names[idx] in ax.format_coord(0.5, 0.5)
assert idx == -1
plt.close("all")
cov = read_cov(cov_fname)
cov["projs"] = []
evoked.pick(picks="meg").plot_topo(noise_cov=cov)
plt.close("all")
# Test exclude parameter
exclude = ["MEG 0112"]
fig = picked_evoked.plot_topo(exclude=exclude)
n_axes_expected = len(picked_evoked.info["ch_names"]) - len(exclude)
n_axes_found = len(fig.axes[0].lines)
assert n_axes_found == n_axes_expected
# test plot_topo
evoked.plot_topo() # should auto-find layout
_line_plot_onselect(0, 200, ["mag", "grad"], evoked.info, evoked.data, evoked.times)
plt.close("all")
for ax, idx in iter_topography(evoked.info): # brief test with false
ax.plot([0, 1, 2])
break
plt.close("all")
# Test plot_topo with selection of channels enabled.
fig = evoked.plot_topo(select=True)
ax = fig.axes[0]
_fake_click(fig, ax, (0.05, 0.62), xform="data")
_fake_click(fig, ax, (0.2, 0.62), xform="data", kind="motion")
_fake_click(fig, ax, (0.2, 0.7), xform="data", kind="motion")
_fake_click(fig, ax, (0.05, 0.7), xform="data", kind="motion")
_fake_click(fig, ax, (0.05, 0.7), xform="data", kind="release")
assert fig.lasso.selection == ["MEG 0113", "MEG 0112", "MEG 0111"]
def test_plot_topo_nirs(fnirs_evoked):
"""Test plotting of ERP topography for nirs data."""
fnirs_evoked.pick(picks="hbo")
fig = plot_evoked_topo(fnirs_evoked)
assert len(fig.axes) == 1
plt.close("all")
def test_plot_topo_single_ch():
"""Test single channel topoplot with time cursor."""
evoked = _get_epochs().average()
evoked2 = evoked.copy()
# test plotting several evokeds on different time grids
evoked.crop(-0.19, 0)
evoked2.crop(0.05, 0.19)
fig = plot_evoked_topo([evoked, evoked2], background_color="w")
# test status bar message
ax = plt.gca()
assert "MEG 0113" in ax.format_coord(0.065, 0.63)
num_figures_before = len(plt.get_fignums())
_fake_click(fig, fig.axes[0], (0.08, 0.65))
assert num_figures_before + 1 == len(plt.get_fignums())
fig = plt.gcf()
ax = plt.gca()
_fake_click(fig, ax, (0.5, 0.5), kind="motion") # cursor should appear
assert isinstance(ax._cursorline, matplotlib.lines.Line2D)
_fake_click(fig, ax, (1.5, 1.5), kind="motion") # cursor should disappear
assert ax._cursorline is None
plt.close("all")
def test_plot_topo_image_epochs():
"""Test plotting of epochs image topography."""
title = "ERF images - MNE sample data"
epochs = _get_epochs()
epochs.load_data()
cmap = mne_analyze_colormap(format="matplotlib")
data_min = epochs._data.min()
plt.close("all")
fig = plot_topo_image_epochs(
epochs, sigma=0.5, vmin=-200, vmax=200, colorbar=True, title=title, cmap=cmap
)
assert epochs._data.min() == data_min
num_figures_before = len(plt.get_fignums())
_fake_click(fig, fig.axes[0], (0.08, 0.64))
assert num_figures_before + 1 == len(plt.get_fignums())
# test for auto-showing a colorbar when only 1 sensor type
ep = epochs.copy().pick(picks="eeg")
fig = plot_topo_image_epochs(ep, vmin=None, vmax=None, colorbar=None, cmap=cmap)
ax = [x for x in fig.get_children() if isinstance(x, matplotlib.axes.Axes)]
# include inset axes (newer MPL)
ax.extend(
y for x in ax for y in x.get_children() if isinstance(y, matplotlib.axes.Axes)
)
qm_cmap = [
y.cmap
for x in ax
for y in x.get_children()
if isinstance(y, matplotlib.collections.QuadMesh)
]
assert len(qm_cmap) >= 1
assert qm_cmap[0] is cmap
def test_plot_topo_select():
"""Test selecting sensors in an ERP topography plot."""
# Show topography
evoked = _get_epochs().average()
fig = plot_evoked_topo(evoked, select=True)
ax = fig.axes[0]
# Lasso select 3 out of the 6 sensors.
_fake_click(fig, ax, (0.05, 0.5), xform="data")
_fake_click(fig, ax, (0.2, 0.5), xform="data", kind="motion")
_fake_click(fig, ax, (0.2, 0.6), xform="data", kind="motion")
_fake_click(fig, ax, (0.05, 0.6), xform="data", kind="motion")
_fake_click(fig, ax, (0.05, 0.5), xform="data", kind="motion")
_fake_click(fig, ax, (0.05, 0.5), xform="data", kind="release")
assert fig.lasso.selection == ["MEG 0132", "MEG 0133", "MEG 0131"]
# Add another sensor with a single click.
_fake_keypress(fig, "control")
_fake_click(fig, ax, (0.11, 0.65), xform="data")
_fake_click(fig, ax, (0.21, 0.65), xform="data", kind="release")
_fake_keypress(fig, "control", kind="release")
assert fig.lasso.selection == ["MEG 0111", "MEG 0132", "MEG 0133", "MEG 0131"]
def test_plot_tfr_topo():
"""Test plotting of TFR data."""
epochs = _get_epochs()
n_freqs = 3
nave = 1
data = np.random.RandomState(0).randn(
len(epochs.ch_names), n_freqs, len(epochs.times)
)
tfr = AverageTFRArray(
info=epochs.info,
data=data,
times=epochs.times,
freqs=np.arange(n_freqs),
nave=nave,
)
plt.close("all")
fig = tfr.plot_topo(baseline=(None, 0), mode="ratio", vmin=0.0, vmax=14.0)
# test complex
tfr.data = tfr.data * (1 + 1j)
plt.close("all")
fig = tfr.plot_topo(baseline=(None, 0), mode="ratio", vmin=0.0, vmax=14.0)
# test opening tfr by clicking
num_figures_before = len(plt.get_fignums())
# could use np.reshape(fig.axes[-1].images[0].get_extent(), (2, 2)).mean(1)
with _record_warnings(), pytest.warns(RuntimeWarning, match="not masking"):
_fake_click(fig, fig.axes[0], (0.08, 0.65))
assert num_figures_before + 1 == len(plt.get_fignums())
plt.close("all")
tfr.plot([4], baseline=(None, 0), mode="ratio", show=False, title="foo")
pytest.raises(ValueError, tfr.plot, [4], yscale="lin", show=False)
# nonuniform freqs
freqs = np.logspace(*np.log10([3, 10]), num=3)
tfr = AverageTFRArray(
info=epochs.info, data=data, times=epochs.times, freqs=freqs, nave=nave
)
fig = tfr.plot([4], baseline=(None, 0), mode="mean", vlim=(None, 14.0), show=False)
assert fig[0].axes[0].get_yaxis().get_scale() == "log"
# one timesample
tfr = AverageTFRArray(
info=epochs.info,
data=data[:, :, [0]],
times=epochs.times[[1]],
freqs=freqs,
nave=nave,
)
with _record_warnings(): # matplotlib equal left/right
tfr.plot([4], baseline=None, vlim=(None, 14.0), show=False, yscale="linear")
# one frequency bin, log scale required: as it doesn't make sense
# to plot log scale for one value, we test whether yscale is set to linear
vmin, vmax = 0.0, 2.0
fig, ax = plt.subplots()
tmin, tmax = epochs.times[0], epochs.times[-1]
with _record_warnings(), pytest.warns(RuntimeWarning, match="not masking"):
_imshow_tfr(
ax,
3,
tmin,
tmax,
vmin,
vmax,
None,
tfr=data[:, [0], :],
freq=freqs[[-1]],
x_label=None,
y_label=None,
colorbar=False,
cmap=("RdBu_r", True),
yscale="log",
)
fig = plt.gcf()
assert fig.axes[0].get_yaxis().get_scale() == "linear"
# ValueError when freq[0] == 0 and yscale == 'log'
these_freqs = freqs[:3].copy()
these_freqs[0] = 0
with _record_warnings(), pytest.warns(RuntimeWarning, match="not masking"):
pytest.raises(
ValueError,
_imshow_tfr,
ax,
3,
tmin,
tmax,
vmin,
vmax,
None,
tfr=data[:, :3, :],
freq=these_freqs,
x_label=None,
y_label=None,
colorbar=False,
cmap=("RdBu_r", True),
yscale="log",
)