"""Functions to make simple plots with M/EEG data.""" # Authors: The MNE-Python contributors. # License: BSD-3-Clause # Copyright the MNE-Python contributors. import copy import io import os import os.path as op import warnings from collections import defaultdict from glob import glob from itertools import cycle from pathlib import Path import numpy as np from scipy.signal import filtfilt, freqz, group_delay, lfilter, sosfilt, sosfiltfilt from .._fiff.constants import FIFF from .._fiff.pick import ( _DATA_CH_TYPES_SPLIT, _picks_by_type, pick_channels, pick_info, pick_types, ) from .._fiff.proj import make_projector from .._freesurfer import _check_mri, _mri_orientation, _read_mri_info, _reorient_image from ..defaults import DEFAULTS from ..filter import estimate_ringing_samples from ..fixes import _safe_svd from ..rank import compute_rank from ..surface import read_surface from ..transforms import _frame_to_str, apply_trans from ..utils import ( _check_option, _mask_to_onsets_offsets, _on_missing, _pl, fill_doc, get_subjects_dir, logger, verbose, warn, ) from .utils import ( _figure_agg, _get_color_list, _prepare_trellis, _validate_type, plt_show, ) def _index_info_cov(info, cov, exclude): if exclude == "bads": exclude = info["bads"] info = pick_info(info, pick_channels(info["ch_names"], cov["names"], exclude)) del exclude picks_list = _picks_by_type(info, meg_combined=False, ref_meg=False, exclude=()) picks_by_type = dict(picks_list) ch_names = [n for n in cov.ch_names if n in info["ch_names"]] ch_idx = [cov.ch_names.index(n) for n in ch_names] info_ch_names = info["ch_names"] idx_by_type = defaultdict(list) for ch_type, sel in picks_by_type.items(): idx_by_type[ch_type] = [ ch_names.index(info_ch_names[c]) for c in sel if info_ch_names[c] in ch_names ] idx_names = [ ( idx_by_type[key], f"{DEFAULTS['titles'][key]} covariance", DEFAULTS["units"][key], DEFAULTS["scalings"][key], key, ) for key in _DATA_CH_TYPES_SPLIT if len(idx_by_type[key]) > 0 ] C = cov.data[ch_idx][:, ch_idx] return info, C, ch_names, idx_names @verbose def plot_cov( cov, info, exclude=(), colorbar=True, proj=False, show_svd=True, show=True, verbose=None, ): """Plot Covariance data. Parameters ---------- cov : instance of Covariance The covariance matrix. %(info_not_none)s exclude : list of str | str List of channels to exclude. If empty do not exclude any channel. If 'bads', exclude info['bads']. colorbar : bool Show colorbar or not. proj : bool Apply projections or not. show_svd : bool Plot also singular values of the noise covariance for each sensor type. We show square roots ie. standard deviations. show : bool Show figure if True. %(verbose)s Returns ------- fig_cov : instance of matplotlib.figure.Figure The covariance plot. fig_svd : instance of matplotlib.figure.Figure | None The SVD plot of the covariance (i.e., the eigenvalues or "matrix spectrum"). See Also -------- mne.compute_rank Notes ----- For each channel type, the rank is estimated using :func:`mne.compute_rank`. .. versionchanged:: 0.19 Approximate ranks for each channel type are shown with red dashed lines. """ import matplotlib.pyplot as plt from matplotlib.colors import Normalize from ..cov import Covariance info, C, ch_names, idx_names = _index_info_cov(info, cov, exclude) del cov, exclude projs = [] if proj: projs = copy.deepcopy(info["projs"]) # Activate the projection items for p in projs: p["active"] = True P, ncomp, _ = make_projector(projs, ch_names) if ncomp > 0: logger.info(f" Created an SSP operator (subspace dimension = {ncomp:d})") C = np.dot(P, np.dot(C, P.T)) else: logger.info(" The projection vectors do not apply to these channels.") if np.iscomplexobj(C): C = np.sqrt((C * C.conj()).real) fig_cov, axes = plt.subplots( 1, len(idx_names), squeeze=False, figsize=(3.8 * len(idx_names), 3.7), layout="constrained", ) for k, (idx, name, _, _, _) in enumerate(idx_names): vlim = np.max(np.abs(C[idx][:, idx])) im = axes[0, k].imshow( C[idx][:, idx], interpolation="nearest", norm=Normalize(vmin=-vlim, vmax=vlim), cmap="RdBu_r", ) axes[0, k].set(title=name) if colorbar: from mpl_toolkits.axes_grid1 import make_axes_locatable divider = make_axes_locatable(axes[0, k]) cax = divider.append_axes("right", size="5.5%", pad=0.05) cax.grid(False) # avoid mpl warning about auto-removal plt.colorbar(im, cax=cax, format="%.0e") fig_svd = None if show_svd: fig_svd, axes = plt.subplots( 1, len(idx_names), squeeze=False, figsize=(3.8 * len(idx_names), 3.7), layout="constrained", ) for k, (idx, name, unit, scaling, key) in enumerate(idx_names): this_C = C[idx][:, idx] s = _safe_svd(this_C, compute_uv=False) this_C = Covariance(this_C, [info["ch_names"][ii] for ii in idx], [], [], 0) this_info = pick_info(info, idx) with this_info._unlock(): this_info["projs"] = [] this_rank = compute_rank(this_C, info=this_info) # Protect against true zero singular values s[s <= 0] = 1e-10 * s[s > 0].min() s = np.sqrt(s) * scaling axes[0, k].plot(s, color="k", zorder=3) this_rank = this_rank[key] axes[0, k].axvline( this_rank - 1, ls="--", color="r", alpha=0.5, zorder=4, clip_on=False ) axes[0, k].text( this_rank - 1, axes[0, k].get_ylim()[1], f"rank ≈ {this_rank:d}", ha="right", va="top", color="r", alpha=0.5, zorder=4, ) axes[0, k].set( ylabel=f"Noise σ ({unit})", yscale="log", xlabel="Eigenvalue index", title=name, xlim=[0, len(s) - 1], ) plt_show(show) return fig_cov, fig_svd def plot_source_spectrogram( stcs, freq_bins, tmin=None, tmax=None, source_index=None, colorbar=False, show=True ): """Plot source power in time-freqency grid. Parameters ---------- stcs : list of SourceEstimate Source power for consecutive time windows, one SourceEstimate object should be provided for each frequency bin. freq_bins : list of tuples of float Start and end points of frequency bins of interest. tmin : float Minimum time instant to show. tmax : float Maximum time instant to show. source_index : int | None Index of source for which the spectrogram will be plotted. If None, the source with the largest activation will be selected. colorbar : bool If true, a colorbar will be added to the plot. show : bool Show figure if True. Returns ------- fig : instance of Figure The figure. """ import matplotlib.pyplot as plt # Input checks if len(stcs) == 0: raise ValueError("cannot plot spectrogram if len(stcs) == 0") stc = stcs[0] if tmin is not None and tmin < stc.times[0]: raise ValueError( "tmin cannot be smaller than the first time point provided in stcs" ) if tmax is not None and tmax > stc.times[-1] + stc.tstep: raise ValueError( "tmax cannot be larger than the sum of the last time " "point and the time step, which are provided in stcs" ) # Preparing time-frequency cell boundaries for plotting if tmin is None: tmin = stc.times[0] if tmax is None: tmax = stc.times[-1] + stc.tstep time_bounds = np.arange(tmin, tmax + stc.tstep, stc.tstep) freq_bounds = sorted(set(np.ravel(freq_bins))) freq_ticks = copy.deepcopy(freq_bounds) # Reject time points that will not be plotted and gather results source_power = [] for stc in stcs: stc = stc.copy() # copy since crop modifies inplace stc.crop(tmin, tmax - stc.tstep) source_power.append(stc.data) source_power = np.array(source_power) # Finding the source with maximum source power if source_index is None: source_index = np.unravel_index(source_power.argmax(), source_power.shape)[1] # If there is a gap in the frequency bins record its locations so that it # can be covered with a gray horizontal bar gap_bounds = [] for i in range(len(freq_bins) - 1): lower_bound = freq_bins[i][1] upper_bound = freq_bins[i + 1][0] if lower_bound != upper_bound: freq_bounds.remove(lower_bound) gap_bounds.append((lower_bound, upper_bound)) # Preparing time-frequency grid for plotting time_grid, freq_grid = np.meshgrid(time_bounds, freq_bounds) # Plotting the results fig = plt.figure(figsize=(9, 6), layout="constrained") plt.pcolor(time_grid, freq_grid, source_power[:, source_index, :], cmap="Reds") ax = plt.gca() ax.set(title="Source power", xlabel="Time (s)", ylabel="Frequency (Hz)") time_tick_labels = [str(np.round(t, 2)) for t in time_bounds] n_skip = 1 + len(time_bounds) // 10 for i in range(len(time_bounds)): if i % n_skip != 0: time_tick_labels[i] = "" ax.set_xticks(time_bounds) ax.set_xticklabels(time_tick_labels) plt.xlim(time_bounds[0], time_bounds[-1]) plt.yscale("log") ax.set_yticks(freq_ticks) ax.set_yticklabels([np.round(freq, 2) for freq in freq_ticks]) plt.ylim(freq_bounds[0], freq_bounds[-1]) plt.grid(True, ls="-") if colorbar: plt.colorbar() # Covering frequency gaps with horizontal bars for lower_bound, upper_bound in gap_bounds: plt.barh( lower_bound, time_bounds[-1] - time_bounds[0], upper_bound - lower_bound, time_bounds[0], color="#666666", ) plt_show(show) return fig def _plot_mri_contours( *, mri_fname, surfaces, src, orientation="coronal", slices=None, show=True, show_indices=False, show_orientation=False, width=512, slices_as_subplots=True, ): """Plot BEM contours on anatomical MRI slices. Parameters ---------- slices_as_subplots : bool Whether to add all slices as subplots to a single figure, or to create a new figure for each slice. If ``False``, return NumPy arrays instead of Matplotlib figures. Returns ------- matplotlib.figure.Figure | list of array The plotted slices. """ import matplotlib.pyplot as plt from matplotlib import patheffects from ..source_space._source_space import _ensure_src # For ease of plotting, we will do everything in voxel coordinates. _validate_type(show_orientation, (bool, str), "show_orientation") if isinstance(show_orientation, str): _check_option( "show_orientation", show_orientation, ("always",), extra="when str" ) _check_option("orientation", orientation, ("coronal", "axial", "sagittal")) # Load the T1 data _, _, _, _, _, nim = _read_mri_info(mri_fname, units="mm", return_img=True) data, rasvox_mri_t = _reorient_image(nim) mri_rasvox_t = np.linalg.inv(rasvox_mri_t) axis, x, y = _mri_orientation(orientation) n_slices = data.shape[axis] # if no slices were specified, pick some equally-spaced ones automatically if slices is None: slices = np.round(np.linspace(start=0, stop=n_slices - 1, num=14)).astype(int) # omit first and last one (not much brain visible there anyway…) slices = slices[1:-1] slices = np.atleast_1d(slices).copy() slices[slices < 0] += n_slices # allow negative indexing if ( not np.array_equal(np.sort(slices), slices) or slices.ndim != 1 or slices.size < 1 or slices[0] < 0 or slices[-1] >= n_slices or slices.dtype.kind not in "iu" ): raise ValueError( "slices must be a sorted 1D array of int with unique " "elements, at least one element, and no elements " f"greater than {n_slices - 1:d}, got {slices}" ) # create of list of surfaces surfs = list() for file_name, color in surfaces: surf = dict() surf["rr"], surf["tris"] = read_surface(file_name) # move surface to voxel coordinate system surf["rr"] = apply_trans(mri_rasvox_t, surf["rr"]) surfs.append((surf, color)) sources = list() if src is not None: _ensure_src(src, extra=" or None") # Eventually we can relax this by allowing ``trans`` if need be if src[0]["coord_frame"] != FIFF.FIFFV_COORD_MRI: raise ValueError( "Source space must be in MRI coordinates, got " f'{_frame_to_str[src[0]["coord_frame"]]}' ) for src_ in src: points = src_["rr"][src_["inuse"].astype(bool)] sources.append(apply_trans(mri_rasvox_t, points * 1e3)) sources = np.concatenate(sources, axis=0) # get the figure dimensions right if slices_as_subplots: n_col = 4 fig, axs, _, _ = _prepare_trellis(len(slices), n_col) fig.set_facecolor("k") dpi = fig.get_dpi() n_axes = len(axs) else: n_col = n_axes = 1 dpi = 96 # 2x standard MRI resolution is probably good enough for the # traces w = width / dpi figsize = (w, w / data.shape[x] * data.shape[y]) bounds = np.concatenate( [[-np.inf], slices[:-1] + np.diff(slices) / 2.0, [np.inf]] ) # float slicer = [slice(None)] * 3 ori_labels = dict(R="LR", A="PA", S="IS") xlabels, ylabels = ori_labels["RAS"[x]], ori_labels["RAS"[y]] path_effects = [patheffects.withStroke(linewidth=4, foreground="k", alpha=0.75)] figs = [] for ai, (sl, lower, upper) in enumerate(zip(slices, bounds[:-1], bounds[1:])): if slices_as_subplots: ax = axs[ai] else: # No need for constrained layout here because we make our axes fill the # entire figure fig = _figure_agg(figsize=figsize, dpi=dpi, facecolor="k") ax = fig.add_axes([0, 0, 1, 1], frame_on=False, facecolor="k") # adjust the orientations for good view slicer[axis] = sl dat = data[tuple(slicer)].T # First plot the anatomical data ax.imshow(dat, cmap=plt.cm.gray, origin="lower") ax.set_autoscale_on(False) ax.axis("off") ax.set_aspect("equal") # XXX eventually could deal with zooms # and then plot the contours on top for surf, color in surfs: with warnings.catch_warnings(record=True): # ignore contour warn warnings.simplefilter("ignore") ax.tricontour( surf["rr"][:, x], surf["rr"][:, y], surf["tris"], surf["rr"][:, axis], levels=[sl], colors=color, linewidths=1.0, zorder=1, ) if len(sources): in_slice = (sources[:, axis] >= lower) & (sources[:, axis] < upper) ax.scatter( sources[in_slice, x], sources[in_slice, y], marker=".", color="#FF00FF", s=1, zorder=2, ) if show_indices: ax.text( dat.shape[1] // 8 + 0.5, 0.5, str(sl), color="w", fontsize="x-small", va="bottom", ha="left", ) # label the axes kwargs = dict( color="#66CCEE", fontsize="medium", path_effects=path_effects, family="monospace", clip_on=False, zorder=5, weight="bold", ) always = show_orientation == "always" if show_orientation: if ai % n_col == 0 or always: # left ax.text( 0, dat.shape[0] / 2.0, xlabels[0], va="center", ha="left", **kwargs ) if ai % n_col == n_col - 1 or ai == n_axes - 1 or always: # right ax.text( dat.shape[1] - 1, dat.shape[0] / 2.0, xlabels[1], va="center", ha="right", **kwargs, ) if ai >= n_axes - n_col or always: # bottom ax.text( dat.shape[1] / 2.0, 0, ylabels[0], ha="center", va="bottom", **kwargs, ) if ai < n_col or n_col == 1 or always: # top ax.text( dat.shape[1] / 2.0, dat.shape[0] - 1, ylabels[1], ha="center", va="top", **kwargs, ) if not slices_as_subplots: # convert to NumPy array with io.BytesIO() as buff: fig.savefig( buff, format="raw", bbox_inches="tight", pad_inches=0, dpi=dpi ) w_, h_ = fig.canvas.get_width_height() plt.close(fig) buff.seek(0) fig_array = np.frombuffer(buff.getvalue(), dtype=np.uint8) fig = fig_array.reshape((int(h_), int(w_), -1)) figs.append(fig) if slices_as_subplots: plt_show(show, fig=fig) return fig else: return figs @fill_doc def plot_bem( subject, subjects_dir=None, orientation="coronal", slices=None, brain_surfaces=None, src=None, show=True, show_indices=True, mri="T1.mgz", show_orientation=True, ): """Plot BEM contours on anatomical MRI slices. Parameters ---------- %(subject)s %(subjects_dir)s orientation : str 'coronal' or 'axial' or 'sagittal'. slices : list of int | None The indices of the MRI slices to plot. If ``None``, automatically pick 12 equally-spaced slices. brain_surfaces : str | list of str | None One or more brain surface to plot (optional). Entries should correspond to files in the subject's ``surf`` directory (e.g. ``"white"``). src : SourceSpaces | path-like | None SourceSpaces instance or path to a source space to plot individual sources as scatter-plot. Sources will be shown on exactly one slice (whichever slice is closest to each source in the given orientation plane). Path can be absolute or relative to the subject's ``bem`` folder. .. versionchanged:: 0.20 All sources are shown on the nearest slice rather than some being omitted. show : bool Show figure if True. show_indices : bool Show slice indices if True. .. versionadded:: 0.20 mri : str The name of the MRI to use. Can be a standard FreeSurfer MRI such as ``'T1.mgz'``, or a full path to a custom MRI file. .. versionadded:: 0.21 show_orientation : bool | str Show the orientation (L/R, P/A, I/S) of the data slices. True (default) will only show it on the outside most edges of the figure, False will never show labels, and "always" will label each plot. .. versionadded:: 0.21 .. versionchanged:: 0.24 Added support for "always". Returns ------- fig : instance of matplotlib.figure.Figure The figure. See Also -------- mne.viz.plot_alignment Notes ----- Images are plotted in MRI voxel coordinates. If ``src`` is not None, for a given slice index, all source points are shown that are halfway between the previous slice and the given slice, and halfway between the given slice and the next slice. For large slice decimations, this can make some source points appear outside the BEM contour, which is shown for the given slice index. For example, in the case where the single midpoint slice is used ``slices=[128]``, all source points will be shown on top of the midpoint MRI slice with the BEM boundary drawn for that slice. """ from ..source_space import SourceSpaces, read_source_spaces subjects_dir = get_subjects_dir(subjects_dir, raise_error=True) mri_fname = _check_mri(mri, subject, subjects_dir) # Get the BEM surface filenames bem_path = subjects_dir / subject / "bem" if not bem_path.is_dir(): raise OSError(f'Subject bem directory "{bem_path}" does not exist') surfaces = _get_bem_plotting_surfaces(bem_path) if brain_surfaces is not None: if isinstance(brain_surfaces, str): brain_surfaces = (brain_surfaces,) for surf_name in brain_surfaces: for hemi in ("lh", "rh"): surf_fname = subjects_dir / subject / "surf" / f"{hemi}.{surf_name}" if surf_fname.exists(): surfaces.append((surf_fname, "#00DD00")) else: raise OSError(f"Surface {surf_fname} does not exist.") # TODO: Refactor with / improve _ensure_src to do this if isinstance(src, (str, Path, os.PathLike)): src = Path(src) if not src.exists(): # convert to Path until get_subjects_dir returns a Path object src_ = Path(subjects_dir) / subject / "bem" / src if not src_.exists(): raise OSError(f"{src} does not exist") src = src_ src = read_source_spaces(src) elif src is not None and not isinstance(src, SourceSpaces): raise TypeError( "src needs to be None, path-like or SourceSpaces instance, " f"not {repr(src)}" ) if len(surfaces) == 0: raise OSError( "No surface files found. Surface files must end with " "inner_skull.surf, outer_skull.surf or outer_skin.surf" ) # Plot the contours fig = _plot_mri_contours( mri_fname=mri_fname, surfaces=surfaces, src=src, orientation=orientation, slices=slices, show=show, show_indices=show_indices, show_orientation=show_orientation, slices_as_subplots=True, ) return fig def _get_bem_plotting_surfaces(bem_path): surfaces = [] for surf_name, color in ( ("*inner_skull", "#FF0000"), ("*outer_skull", "#FFFF00"), ("*outer_skin", "#FFAA80"), ): surf_fname = glob(op.join(bem_path, surf_name + ".surf")) if len(surf_fname) > 0: surf_fname = surf_fname[0] logger.info(f"Using surface: {surf_fname}") surfaces.append((surf_fname, color)) return surfaces @verbose def plot_events( events, sfreq=None, first_samp=0, color=None, event_id=None, axes=None, equal_spacing=True, show=True, on_missing="raise", verbose=None, ): """Plot :term:`events` to get a visual display of the paradigm. Parameters ---------- %(events)s sfreq : float | None The sample frequency. If None, data will be displayed in samples (not seconds). first_samp : int The index of the first sample. Recordings made on Neuromag systems number samples relative to the system start (not relative to the beginning of the recording). In such cases the ``raw.first_samp`` attribute can be passed here. Default is 0. color : dict | None Dictionary of event_id integers as keys and colors as values. If None, colors are automatically drawn from a default list (cycled through if number of events longer than list of default colors). Color can be any valid :ref:`matplotlib color `. event_id : dict | None Dictionary of event labels (e.g. 'aud_l') as keys and their associated event_id values. Labels are used to plot a legend. If None, no legend is drawn. axes : instance of Axes The subplot handle. equal_spacing : bool Use equal spacing between events in y-axis. show : bool Show figure if True. %(on_missing_events)s %(verbose)s Returns ------- fig : matplotlib.figure.Figure The figure object containing the plot. Notes ----- .. versionadded:: 0.9.0 """ if sfreq is None: sfreq = 1.0 xlabel = "Samples" else: xlabel = "Time (s)" events = np.asarray(events) if len(events) == 0: raise ValueError("No events in events array, cannot plot.") unique_events = np.unique(events[:, 2]) if event_id is not None: # get labels and unique event ids from event_id dict, # sorted by value event_id_rev = {v: k for k, v in event_id.items()} conditions, unique_events_id = zip( *sorted(event_id.items(), key=lambda x: x[1]) ) keep = np.ones(len(unique_events_id), bool) for ii, this_event in enumerate(unique_events_id): if this_event not in unique_events: msg = f"{this_event} from event_id is not present in events." _on_missing(on_missing, msg) keep[ii] = False conditions = [cond for cond, k in zip(conditions, keep) if k] unique_events_id = [id_ for id_, k in zip(unique_events_id, keep) if k] if len(unique_events_id) == 0: raise RuntimeError("No usable event IDs found") for this_event in unique_events: if this_event not in unique_events_id: warn(f"event {this_event} missing from event_id will be ignored") else: unique_events_id = unique_events color = _handle_event_colors(color, unique_events, event_id) import matplotlib.pyplot as plt fig = None if axes is None: fig = plt.figure(layout="constrained") ax = axes if axes else plt.gca() unique_events_id = np.array(unique_events_id) min_event = np.min(unique_events_id) max_event = np.max(unique_events_id) max_x = ( events[np.isin(events[:, 2], unique_events_id), 0].max() - first_samp ) / sfreq handles, labels = list(), list() for idx, ev in enumerate(unique_events_id): ev_mask = events[:, 2] == ev count = ev_mask.sum() if count == 0: continue y = np.full(count, idx + 1 if equal_spacing else events[ev_mask, 2][0]) if event_id is not None: event_label = f"{event_id_rev[ev]} ({count})" else: event_label = f"N={count:d}" labels.append(event_label) kwargs = {} if ev in color: kwargs["color"] = color[ev] handles.append( ax.plot( (events[ev_mask, 0] - first_samp) / sfreq, y, ".", clip_on=False, **kwargs, )[0] ) if equal_spacing: ax.set_ylim(0, unique_events_id.size + 1) ax.set_yticks(1 + np.arange(unique_events_id.size)) ax.set_yticklabels(unique_events_id) else: ax.set_ylim([min_event - 1, max_event + 1]) ax.set(xlabel=xlabel, ylabel="Event id", xlim=[0, max_x]) ax.grid(True) fig = fig if fig is not None else plt.gcf() # reverse order so that the highest numbers are at the top # (match plot order) handles, labels = handles[::-1], labels[::-1] box = ax.get_position() factor = 0.8 if event_id is not None else 0.9 ax.set_position([box.x0, box.y0, box.width * factor, box.height]) ax.legend( handles, labels, loc="center left", bbox_to_anchor=(1, 0.5), fontsize="small" ) fig.canvas.draw() plt_show(show) return fig def _get_presser(fig): """Get our press callback.""" callbacks = fig.canvas.callbacks.callbacks["button_press_event"] func = None for key, val in callbacks.items(): func = val() if func.__class__.__name__ == "partial": break else: func = None assert func is not None return func def plot_dipole_amplitudes(dipoles, colors=None, show=True): """Plot the amplitude traces of a set of dipoles. Parameters ---------- dipoles : list of instance of Dipole The dipoles whose amplitudes should be shown. colors : list of color | None Color to plot with each dipole. If None default colors are used. show : bool Show figure if True. Returns ------- fig : matplotlib.figure.Figure The figure object containing the plot. Notes ----- .. versionadded:: 0.9.0 """ import matplotlib.pyplot as plt if colors is None: colors = cycle(_get_color_list()) fig, ax = plt.subplots(1, 1, layout="constrained") xlim = [np.inf, -np.inf] for dip, color in zip(dipoles, colors): ax.plot(dip.times, dip.amplitude * 1e9, color=color, linewidth=1.5) xlim[0] = min(xlim[0], dip.times[0]) xlim[1] = max(xlim[1], dip.times[-1]) ax.set(xlim=xlim, xlabel="Time (s)", ylabel="Amplitude (nAm)") if show: fig.show(warn=False) return fig def adjust_axes(axes, remove_spines=("top", "right"), grid=True): """Adjust some properties of axes. Parameters ---------- axes : list List of axes to process. remove_spines : list of str Which axis spines to remove. grid : bool Turn grid on (True) or off (False). """ axes = [axes] if not isinstance(axes, (list, tuple, np.ndarray)) else axes for ax in axes: if grid: ax.grid(zorder=0) for key in remove_spines: ax.spines[key].set_visible(False) def _filter_ticks(lims, fscale): """Create approximately spaced ticks between lims.""" if fscale == "linear": return None, None # let matplotlib handle it lims = np.array(lims) ticks = list() if lims[1] > 20 * lims[0]: base = np.array([1, 2, 4]) else: base = np.arange(1, 11) for exp in range( int(np.floor(np.log10(lims[0]))), int(np.floor(np.log10(lims[1]))) + 1 ): ticks += (base * (10**exp)).tolist() ticks = np.array(ticks) ticks = ticks[(ticks >= lims[0]) & (ticks <= lims[1])] ticklabels = [(f"{t:g}" if t < 1 else f"{t}") for t in ticks] return ticks, ticklabels def _get_flim(flim, fscale, freq, sfreq=None): """Get reasonable frequency limits.""" if flim is None: if freq is None: flim = [0.1 if fscale == "log" else 0.0, sfreq / 2.0] else: if fscale == "linear": flim = [freq[0]] else: flim = [freq[0] if freq[0] > 0 else 0.1 * freq[1]] flim += [freq[-1]] if fscale == "log": if flim[0] <= 0: raise ValueError(f"flim[0] must be positive, got {flim[0]}") elif flim[0] < 0: raise ValueError(f"flim[0] must be non-negative, got {flim[0]}") return flim _DEFAULT_ALIM = (-80, 10) def plot_filter( h, sfreq, freq=None, gain=None, title=None, color="#1f77b4", flim=None, fscale="log", alim=_DEFAULT_ALIM, show=True, compensate=False, plot=("time", "magnitude", "delay"), axes=None, *, dlim=None, ): """Plot properties of a filter. Parameters ---------- h : dict or ndarray An IIR dict or 1D ndarray of coefficients (for FIR filter). sfreq : float Sample rate of the data (Hz). freq : array-like or None The ideal response frequencies to plot (must be in ascending order). If None (default), do not plot the ideal response. gain : array-like or None The ideal response gains to plot. If None (default), do not plot the ideal response. title : str | None The title to use. If None (default), determine the title based on the type of the system. color : color object The color to use (default '#1f77b4'). flim : tuple or None If not None, the x-axis frequency limits (Hz) to use. If None, freq will be used. If None (default) and freq is None, ``(0.1, sfreq / 2.)`` will be used. fscale : str Frequency scaling to use, can be "log" (default) or "linear". alim : tuple The y-axis amplitude limits (dB) to use (default: (-60, 10)). show : bool Show figure if True (default). compensate : bool If True, compensate for the filter delay (phase will not be shown). - For linear-phase FIR filters, this visualizes the filter coefficients assuming that the output will be shifted by ``N // 2``. - For IIR filters, this changes the filter coefficient display by filtering backward and forward, and the frequency response by squaring it. .. versionadded:: 0.18 plot : list | tuple | str A list of the requested plots from ``time``, ``magnitude`` and ``delay``. Default is to plot all three filter properties ('time', 'magnitude', 'delay'). .. versionadded:: 0.21.0 axes : instance of Axes | list | None The axes to plot to. If list, the list must be a list of Axes of the same length as the number of requested plot types. If instance of Axes, there must be only one filter property plotted. Defaults to ``None``. .. versionadded:: 0.21.0 dlim : None | tuple The y-axis delay limits (s) to use (default: ``(-tmax / 2., tmax / 2.)``). .. versionadded:: 1.1.0 Returns ------- fig : matplotlib.figure.Figure The figure containing the plots. See Also -------- mne.filter.create_filter plot_ideal_filter Notes ----- .. versionadded:: 0.14 """ import matplotlib.pyplot as plt sfreq = float(sfreq) _check_option("fscale", fscale, ["log", "linear"]) if isinstance(plot, str): plot = [plot] for xi, x in enumerate(plot): _check_option(f"plot[{xi}]", x, ("magnitude", "delay", "time")) flim = _get_flim(flim, fscale, freq, sfreq) if fscale == "log": omega = np.logspace(np.log10(flim[0]), np.log10(flim[1]), 1000) else: omega = np.linspace(flim[0], flim[1], 1000) xticks, xticklabels = _filter_ticks(flim, fscale) omega /= sfreq / (2 * np.pi) if isinstance(h, dict): # IIR h.ndim == 2: # second-order sections if "sos" in h: H = np.ones(len(omega), np.complex128) gd = np.zeros(len(omega)) for section in h["sos"]: this_H = freqz(section[:3], section[3:], omega)[1] H *= this_H if compensate: H *= this_H.conj() # time reversal is freq conj else: # Assume the forward-backward delay zeros out, which it # mostly should with warnings.catch_warnings(record=True): # singular GD warnings.simplefilter("ignore") gd += group_delay((section[:3], section[3:]), omega)[1] n = estimate_ringing_samples(h["sos"]) delta = np.zeros(n) delta[0] = 1 if compensate: delta = np.pad(delta, [(n - 1, 0)], "constant") func = sosfiltfilt gd += (len(delta) - 1) // 2 else: func = sosfilt h = func(h["sos"], delta) else: H = freqz(h["b"], h["a"], omega)[1] if compensate: H *= H.conj() with warnings.catch_warnings(record=True): # singular GD warnings.simplefilter("ignore") gd = group_delay((h["b"], h["a"]), omega)[1] if compensate: gd += group_delay((h["b"].conj(), h["a"].conj()), omega)[1] n = estimate_ringing_samples((h["b"], h["a"])) delta = np.zeros(n) delta[0] = 1 if compensate: delta = np.pad(delta, [(n - 1, 0)], "constant") func = filtfilt else: func = lfilter h = func(h["b"], h["a"], delta) if title is None: title = "SOS (IIR) filter" if compensate: title += " (forward-backward)" else: H = freqz(h, worN=omega)[1] with warnings.catch_warnings(record=True): # singular GD warnings.simplefilter("ignore") gd = group_delay((h, [1.0]), omega)[1] title = "FIR filter" if title is None else title if compensate: title += " (delay-compensated)" fig = None if axes is None: fig, axes = plt.subplots(len(plot), 1, layout="constrained") if isinstance(axes, plt.Axes): axes = [axes] elif isinstance(axes, np.ndarray): axes = list(axes) if fig is None: fig = axes[0].get_figure() if len(axes) != len(plot): raise ValueError( f"Length of axes ({len(axes)}) must be the same as number of " f"requested filter properties ({len(plot)})" ) t = np.arange(len(h)) if dlim is None: dlim = np.abs(t).max() / 2.0 dlim = [-dlim, dlim] if compensate: n_shift = (len(h) - 1) // 2 t -= n_shift assert t[0] == -t[-1] gd -= n_shift t = t / sfreq gd = gd / sfreq f = omega * sfreq / (2 * np.pi) sl = slice(0 if fscale == "linear" else 1, None, None) mag = 10 * np.log10(np.maximum((H * H.conj()).real, 1e-20)) if "time" in plot: ax_time_idx = np.where([p == "time" for p in plot])[0][0] axes[ax_time_idx].plot(t, h, color=color, linewidth=1.2) axes[ax_time_idx].grid(visible=True, which="major", axis="both", linewidth=0.15) axes[ax_time_idx].set( xlim=t[[0, -1]], xlabel="Time (s)", ylabel="Amplitude", title=title ) # Magnitude if "magnitude" in plot: ax_mag_idx = np.where([p == "magnitude" for p in plot])[0][0] axes[ax_mag_idx].plot(f[sl], mag[sl], color=color, linewidth=1.2, zorder=4) axes[ax_mag_idx].grid(visible=True, which="major", axis="both", linewidth=0.15) if freq is not None and gain is not None: plot_ideal_filter(freq, gain, axes[ax_mag_idx], fscale=fscale, show=False) axes[ax_mag_idx].set(ylabel="Magnitude (dB)", xlabel="", xscale=fscale) if xticks is not None: axes[ax_mag_idx].set(xticks=xticks) axes[ax_mag_idx].set(xticklabels=xticklabels) axes[ax_mag_idx].set( xlim=flim, ylim=alim, xlabel="Frequency (Hz)", ylabel="Amplitude (dB)" ) # Delay if "delay" in plot: ax_delay_idx = np.where([p == "delay" for p in plot])[0][0] axes[ax_delay_idx].plot(f[sl], gd[sl], color=color, linewidth=1.2, zorder=4) axes[ax_delay_idx].grid( visible=True, which="major", axis="both", linewidth=0.15 ) # shade nulled regions for start, stop in zip(*_mask_to_onsets_offsets(mag <= -39.9)): axes[ax_delay_idx].axvspan( f[start], f[stop - 1], facecolor="k", alpha=0.05, zorder=5 ) axes[ax_delay_idx].set( xlim=flim, ylabel="Group delay (s)", xlabel="Frequency (Hz)", xscale=fscale ) if xticks is not None: axes[ax_delay_idx].set(xticks=xticks) axes[ax_delay_idx].set(xticklabels=xticklabels) axes[ax_delay_idx].set( xlim=flim, ylim=dlim, xlabel="Frequency (Hz)", ylabel="Delay (s)" ) adjust_axes(axes) plt_show(show) return fig def plot_ideal_filter( freq, gain, axes=None, title="", flim=None, fscale="log", alim=_DEFAULT_ALIM, color="r", alpha=0.5, linestyle="--", show=True, ): """Plot an ideal filter response. Parameters ---------- freq : array-like The ideal response frequencies to plot (must be in ascending order). gain : array-like or None The ideal response gains to plot. axes : instance of Axes | None The subplot handle. With None (default), axes are created. title : str The title to use, (default: ''). flim : tuple or None If not None, the x-axis frequency limits (Hz) to use. If None (default), freq used. fscale : str Frequency scaling to use, can be "log" (default) or "linear". alim : tuple If not None (default), the y-axis limits (dB) to use. color : color object The color to use (default: 'r'). alpha : float The alpha to use (default: 0.5). linestyle : str The line style to use (default: '--'). show : bool Show figure if True (default). Returns ------- fig : instance of matplotlib.figure.Figure The figure. See Also -------- plot_filter Notes ----- .. versionadded:: 0.14 Examples -------- Plot a simple ideal band-pass filter:: >>> from mne.viz import plot_ideal_filter >>> freq = [0, 1, 40, 50] >>> gain = [0, 1, 1, 0] >>> plot_ideal_filter(freq, gain, flim=(0.1, 100)) #doctest: +SKIP <...Figure...> """ import matplotlib.pyplot as plt my_freq, my_gain = list(), list() if freq[0] != 0: raise ValueError( "freq should start with DC (zero) and end with " f"Nyquist, but got {freq[0]} for DC" ) freq = np.array(freq) # deal with semilogx problems @ x=0 _check_option("fscale", fscale, ["log", "linear"]) if fscale == "log": freq[0] = 0.1 * freq[1] if flim is None else min(flim[0], freq[1]) flim = _get_flim(flim, fscale, freq) transitions = list() for ii in range(len(freq)): if ii < len(freq) - 1 and gain[ii] != gain[ii + 1]: transitions += [[freq[ii], freq[ii + 1]]] my_freq += np.linspace(freq[ii], freq[ii + 1], 20, endpoint=False).tolist() my_gain += np.linspace(gain[ii], gain[ii + 1], 20, endpoint=False).tolist() else: my_freq.append(freq[ii]) my_gain.append(gain[ii]) my_gain = 10 * np.log10(np.maximum(my_gain, 10 ** (alim[0] / 10.0))) if axes is None: axes = plt.subplots(1, layout="constrained")[1] for transition in transitions: axes.axvspan(*transition, color=color, alpha=0.1) axes.plot( my_freq, my_gain, color=color, linestyle=linestyle, alpha=alpha, linewidth=2, zorder=3, ) xticks, xticklabels = _filter_ticks(flim, fscale) axes.set(ylim=alim, xlabel="Frequency (Hz)", ylabel="Amplitude (dB)", xscale=fscale) if xticks is not None: axes.set(xticks=xticks) axes.set(xticklabels=xticklabels) axes.set(xlim=flim) if title: axes.set(title=title) adjust_axes(axes) plt_show(show) return axes.figure def _handle_event_colors(color_dict, unique_events, event_id): """Create event-integer-to-color mapping, assigning defaults as needed.""" default_colors = dict(zip(sorted(unique_events), cycle(_get_color_list()))) # warn if not enough colors if color_dict is None: if len(unique_events) > len(_get_color_list()): warn( "More events than default colors available. You should pass " "a list of unique colors." ) else: custom_colors = dict() for key, color in color_dict.items(): if key in unique_events: # key was a valid event integer custom_colors[key] = color elif key in event_id: # key was an event label custom_colors[event_id[key]] = color else: # key not a valid event, warn and ignore warn( f"Event ID {key} is in the color dict but is not " "present in events or event_id." ) # warn if color_dict is missing any entries unassigned = sorted(set(unique_events) - set(custom_colors)) if len(unassigned): unassigned_str = ", ".join(str(e) for e in unassigned) warn( f"Color was not assigned for event{_pl(unassigned)} {unassigned_str}. " "Default colors will be used." ) default_colors.update(custom_colors) return default_colors @fill_doc def plot_csd( csd, info=None, mode="csd", colorbar=True, cmap=None, n_cols=None, show=True ): """Plot CSD matrices. A sub-plot is created for each frequency. If an info object is passed to the function, different channel types are plotted in different figures. Parameters ---------- csd : instance of CrossSpectralDensity The CSD matrix to plot. %(info)s Used to split the figure by channel-type, if provided. By default, the CSD matrix is plotted as a whole. mode : 'csd' | 'coh' Whether to plot the cross-spectral density ('csd', the default), or the coherence ('coh') between the channels. colorbar : bool Whether to show a colorbar. Defaults to ``True``. cmap : str | None The matplotlib colormap to use. Defaults to None, which means the colormap will default to matplotlib's default. n_cols : int | None CSD matrices are plotted in a grid. This parameter controls how many matrix to plot side by side before starting a new row. By default, a number will be chosen to make the grid as square as possible. show : bool Whether to show the figure. Defaults to ``True``. Returns ------- fig : list of Figure The figures created by this function. """ import matplotlib.pyplot as plt if mode not in ["csd", "coh"]: raise ValueError('"mode" should be either "csd" or "coh".') if info is not None: info_ch_names = info["ch_names"] sel_eeg = pick_types(info, meg=False, eeg=True, ref_meg=False, exclude=[]) sel_mag = pick_types(info, meg="mag", eeg=False, ref_meg=False, exclude=[]) sel_grad = pick_types(info, meg="grad", eeg=False, ref_meg=False, exclude=[]) idx_eeg = [ csd.ch_names.index(info_ch_names[c]) for c in sel_eeg if info_ch_names[c] in csd.ch_names ] idx_mag = [ csd.ch_names.index(info_ch_names[c]) for c in sel_mag if info_ch_names[c] in csd.ch_names ] idx_grad = [ csd.ch_names.index(info_ch_names[c]) for c in sel_grad if info_ch_names[c] in csd.ch_names ] indices = [idx_eeg, idx_mag, idx_grad] titles = ["EEG", "Magnetometers", "Gradiometers"] if mode == "csd": # The units in which to plot the CSD units = dict(eeg="µV²", grad="fT²/cm²", mag="fT²") scalings = dict(eeg=1e12, grad=1e26, mag=1e30) else: indices = [np.arange(len(csd.ch_names))] if mode == "csd": titles = ["Cross-spectral density"] # Units and scaling unknown units = dict() scalings = dict() elif mode == "coh": titles = ["Coherence"] n_freqs = len(csd.frequencies) if n_cols is None: n_cols = int(np.ceil(np.sqrt(n_freqs))) n_rows = int(np.ceil(n_freqs / float(n_cols))) figs = [] for ind, title, ch_type in zip(indices, titles, ["eeg", "mag", "grad"]): if len(ind) == 0: continue fig, axes = plt.subplots( n_rows, n_cols, squeeze=False, figsize=(2 * n_cols + 1, 2.2 * n_rows), layout="constrained", ) csd_mats = [] for i in range(len(csd.frequencies)): cm = csd.get_data(index=i)[ind][:, ind] if mode == "csd": cm = np.abs(cm) * scalings.get(ch_type, 1) elif mode == "coh": # Compute coherence from the CSD matrix psd = np.diag(cm).real cm = np.abs(cm) ** 2 / psd[np.newaxis, :] / psd[:, np.newaxis] csd_mats.append(cm) vmax = np.max(csd_mats) for i, (freq, mat) in enumerate(zip(csd.frequencies, csd_mats)): ax = axes[i // n_cols][i % n_cols] im = ax.imshow(mat, interpolation="nearest", cmap=cmap, vmin=0, vmax=vmax) ax.set_xticks([]) ax.set_yticks([]) if csd._is_sum: ax.set_title(f"{np.min(freq):.1f}-{np.max(freq):.1f} Hz.") else: ax.set_title(f"{freq:.1f} Hz.") plt.suptitle(title) if colorbar: cb = plt.colorbar(im, ax=[a for ax_ in axes for a in ax_]) if mode == "csd": label = "CSD" if ch_type in units: label += f" ({units[ch_type]})" cb.set_label(label) elif mode == "coh": cb.set_label("Coherence") figs.append(fig) plt_show(show) return figs def plot_chpi_snr(snr_dict, axes=None): """Plot time-varying SNR estimates of the HPI coils. Parameters ---------- snr_dict : dict The dictionary returned by `~mne.chpi.compute_chpi_snr`. Must have keys ``times``, ``freqs``, ``TYPE_snr``, ``TYPE_power``, and ``TYPE_resid`` (where ``TYPE`` can be ``mag`` or ``grad`` or both). axes : None | list of matplotlib.axes.Axes Figure axes in which to draw the SNR, power, and residual plots. The number of axes should be 3× the number of MEG sensor types present in ``snr_dict``. If ``None`` (the default), a new `~matplotlib.figure.Figure` is created with the required number of axes. Returns ------- fig : instance of matplotlib.figure.Figure A figure with subplots for SNR, power, and residual variance, separately for magnetometers and/or gradiometers (depending on what is present in ``snr_dict``). Notes ----- If you supply a list of existing `~matplotlib.axes.Axes`, then the figure legend will not be drawn automatically. If you still want it, running ``fig.legend(loc='right', title='cHPI frequencies')`` will recreate it. .. versionadded:: 0.24 """ import matplotlib.pyplot as plt valid_keys = list(snr_dict)[2:] titles = dict(snr="SNR", power="cHPI power", resid="Residual variance") full_names = dict(mag="magnetometers", grad="gradiometers") axes_was_none = axes is None if axes_was_none: fig, axes = plt.subplots(len(valid_keys), 1, sharex=True, layout="constrained") else: fig = axes[0].get_figure() if len(axes) != len(valid_keys): raise ValueError( f"axes must be a list of {len(valid_keys)} axes, got " f"length {len(axes)} ({axes})." ) fig.set_size_inches(10, 10) legend_labels_exist = False for key, ax in zip(valid_keys, axes): ch_type, kind = key.split("_") scaling = 1 if kind == "snr" else DEFAULTS["scalings"][ch_type] plot_kwargs = dict(color="k") if kind == "resid" else dict() lines = ax.plot(snr_dict["times"], snr_dict[key] * scaling**2, **plot_kwargs) # the freqs should be the same for all sensor types (and for SNR and # power subplots), so we only need to label the lines on one axes # (otherwise we get duplicate legend entries). if not legend_labels_exist: for line, freq in zip(lines, snr_dict["freqs"]): line.set_label(f"{freq} Hz") legend_labels_exist = True unit = DEFAULTS["units"][ch_type] unit = f"({unit})" if "/" in unit else unit set_kwargs = dict( title=f"{titles[kind]}, {full_names[ch_type]}", ylabel="dB" if kind == "snr" else f"{unit}²", ) if not axes_was_none: set_kwargs.update(xlabel="Time (s)") ax.set(**set_kwargs) if axes_was_none: ax.set(xlabel="Time (s)") fig.align_ylabels() fig.legend(loc="right", title="cHPI frequencies") return fig