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_brain.py
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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import copy
import os
import os.path as op
import time
import traceback
import warnings
from functools import partial
from io import BytesIO
import numpy as np
from scipy.interpolate import interp1d
from scipy.sparse import csr_array
from scipy.spatial.distance import cdist
from ..._fiff.meas_info import Info
from ..._fiff.pick import pick_types
from ..._freesurfer import (
_estimate_talxfm_rigid,
_get_aseg,
_get_head_surface,
_get_skull_surface,
read_freesurfer_lut,
read_talxfm,
vertex_to_mni,
)
from ...defaults import DEFAULTS, _handle_default
from ...surface import _marching_cubes, _mesh_borders, mesh_edges
from ...transforms import (
Transform,
_frame_to_str,
_get_trans,
_get_transforms_to_coord_frame,
apply_trans,
)
from ...utils import (
Bunch,
_auto_weakref,
_check_fname,
_check_option,
_ensure_int,
_path_like,
_ReuseCycle,
_to_rgb,
_validate_type,
fill_doc,
get_subjects_dir,
logger,
use_log_level,
verbose,
warn,
)
from .._3d import (
_check_views,
_handle_sensor_types,
_handle_time,
_plot_forward,
_plot_helmet,
_plot_sensors_3d,
_process_clim,
)
from .._3d_overlay import _LayeredMesh
from ..ui_events import (
ColormapRange,
PlaybackSpeed,
TimeChange,
VertexSelect,
_get_event_channel,
disable_ui_events,
publish,
subscribe,
unsubscribe,
)
from ..utils import (
_generate_default_filename,
_get_color_list,
_save_ndarray_img,
_show_help_fig,
concatenate_images,
safe_event,
)
from .colormap import calculate_lut
from .surface import _Surface
from .view import _lh_views_dict, views_dicts
@fill_doc
class Brain:
"""Class for visualizing a brain.
.. warning::
The API for this class is not currently complete. We suggest using
:meth:`mne.viz.plot_source_estimates` with the PyVista backend
enabled to obtain a ``Brain`` instance.
Parameters
----------
subject : str
Subject name in Freesurfer subjects dir.
.. versionchanged:: 1.2
This parameter was renamed from ``subject_id`` to ``subject``.
hemi : str
Hemisphere id (ie 'lh', 'rh', 'both', or 'split'). In the case
of 'both', both hemispheres are shown in the same window.
In the case of 'split' hemispheres are displayed side-by-side
in different viewing panes.
surf : str
FreeSurfer surface mesh name (ie 'white', 'inflated', etc.).
title : str
Title for the window.
cortex : str, list, dict
Specifies how the cortical surface is rendered. Options:
1. The name of one of the preset cortex styles:
``'classic'`` (default), ``'high_contrast'``,
``'low_contrast'``, or ``'bone'``.
2. A single color-like argument to render the cortex as a single
color, e.g. ``'red'`` or ``(0.1, 0.4, 1.)``.
3. A list of two color-like used to render binarized curvature
values for gyral (first) and sulcal (second). regions, e.g.,
``['red', 'blue']`` or ``[(1, 0, 0), (0, 0, 1)]``.
4. A dict containing keys ``'vmin', 'vmax', 'colormap'`` with
values used to render the binarized curvature (where 0 is gyral,
1 is sulcal).
.. versionchanged:: 0.24
Add support for non-string arguments.
alpha : float in [0, 1]
Alpha level to control opacity of the cortical surface.
size : int | array-like, shape (2,)
The size of the window, in pixels. can be one number to specify
a square window, or a length-2 sequence to specify (width, height).
background : tuple(int, int, int)
The color definition of the background: (red, green, blue).
foreground : matplotlib color
Color of the foreground (will be used for colorbars and text).
None (default) will use black or white depending on the value
of ``background``.
figure : list of Figure | None
If None (default), a new window will be created with the appropriate
views.
subjects_dir : str | None
If not None, this directory will be used as the subjects directory
instead of the value set using the SUBJECTS_DIR environment
variable.
%(views)s
offset : bool | str
If True, shifts the right- or left-most x coordinate of the left and
right surfaces, respectively, to be at zero. This is useful for viewing
inflated surface where hemispheres typically overlap. Can be "auto"
(default) use True with inflated surfaces and False otherwise
(Default: 'auto'). Only used when ``hemi='both'``.
.. versionchanged:: 0.23
Default changed to "auto".
interaction : str
Can be "trackball" (default) or "terrain", i.e. a turntable-style
camera.
units : str
Can be 'm' or 'mm' (default).
%(view_layout)s
silhouette : dict | bool
As a dict, it contains the ``color``, ``linewidth``, ``alpha`` opacity
and ``decimate`` (level of decimation between 0 and 1 or None) of the
brain's silhouette to display. If True, the default values are used
and if False, no silhouette will be displayed. Defaults to False.
%(theme_3d)s
show : bool
Display the window as soon as it is ready. Defaults to True.
Attributes
----------
geo : dict
A dictionary of PyVista surface objects for each hemisphere.
overlays : dict
The overlays.
Notes
-----
The figure will publish and subscribe to the following UI events:
* :class:`~mne.viz.ui_events.TimeChange`
* :class:`~mne.viz.ui_events.PlaybackSpeed`
* :class:`~mne.viz.ui_events.ColormapRange`, ``kind="distributed_source_power"``
* :class:`~mne.viz.ui_events.VertexSelect`
This table shows the capabilities of each Brain backend ("✓" for full
support, and "-" for partial support):
.. table::
:widths: auto
+-------------------------------------+--------------+---------------+
| 3D function: | surfer.Brain | mne.viz.Brain |
+=====================================+==============+===============+
| :meth:`add_annotation` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_data` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_dipole` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_foci` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_forward` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_head` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_label` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_sensors` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_skull` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_text` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_volume_labels` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`close` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| data | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| foci | ✓ | |
+-------------------------------------+--------------+---------------+
| labels | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_data` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_dipole` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_forward` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_head` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_labels` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_annotations` | - | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_sensors` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_skull` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_text` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`remove_volume_labels` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`save_image` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`save_movie` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`screenshot` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`show_view` | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| TimeViewer | ✓ | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`get_picked_points` | | ✓ |
+-------------------------------------+--------------+---------------+
| :meth:`add_data(volume) <add_data>` | | ✓ |
+-------------------------------------+--------------+---------------+
| view_layout | | ✓ |
+-------------------------------------+--------------+---------------+
| flatmaps | | ✓ |
+-------------------------------------+--------------+---------------+
| vertex picking | | ✓ |
+-------------------------------------+--------------+---------------+
| label picking | | ✓ |
+-------------------------------------+--------------+---------------+
"""
def __init__(
self,
subject,
hemi="both",
surf="pial",
title=None,
cortex="classic",
alpha=1.0,
size=800,
background="black",
foreground=None,
figure=None,
subjects_dir=None,
views="auto",
*,
offset="auto",
interaction="trackball",
units="mm",
view_layout="vertical",
silhouette=False,
theme=None,
show=True,
):
from ..backends.renderer import _get_renderer, backend
_validate_type(subject, str, "subject")
self._surf = surf
if hemi is None:
hemi = "vol"
hemi = self._check_hemi(hemi, extras=("both", "split", "vol"))
if hemi in ("both", "split"):
self._hemis = ("lh", "rh")
else:
assert hemi in ("lh", "rh", "vol")
self._hemis = (hemi,)
self._view_layout = _check_option(
"view_layout", view_layout, ("vertical", "horizontal")
)
if figure is not None and not isinstance(figure, int):
backend._check_3d_figure(figure)
if title is None:
self._title = subject
else:
self._title = title
self._interaction = "trackball"
self._bg_color = _to_rgb(background, name="background")
if foreground is None:
foreground = "w" if sum(self._bg_color) < 2 else "k"
self._fg_color = _to_rgb(foreground, name="foreground")
del background, foreground
views = _check_views(surf, views, hemi)
col_dict = dict(lh=1, rh=1, both=1, split=2, vol=1)
shape = (len(views), col_dict[hemi])
if self._view_layout == "horizontal":
shape = shape[::-1]
self._subplot_shape = shape
size = tuple(np.atleast_1d(size).round(0).astype(int).flat)
if len(size) not in (1, 2):
raise ValueError(
'"size" parameter must be an int or length-2 sequence of ints.'
)
size = size if len(size) == 2 else size * 2 # 1-tuple to 2-tuple
subjects_dir = get_subjects_dir(subjects_dir)
if subjects_dir is not None:
subjects_dir = str(subjects_dir)
self.time_viewer = False
self._hash = time.time_ns()
self._hemi = hemi
self._units = units
self._alpha = float(alpha)
self._subject = subject
self._subjects_dir = subjects_dir
self._views = views
self._times = None
self._vertex_to_label_id = dict()
self._annotation_labels = dict()
self._labels = {"lh": list(), "rh": list()}
self._unnamed_label_id = 0 # can only grow
self._annots = {"lh": list(), "rh": list()}
self._layered_meshes = dict()
self._actors = dict()
self._cleaned = False
# default values for silhouette
self._silhouette = {
"color": self._bg_color,
"line_width": 2,
"alpha": alpha,
"decimate": 0.9,
}
_validate_type(silhouette, (dict, bool), "silhouette")
if isinstance(silhouette, dict):
self._silhouette.update(silhouette)
self.silhouette = True
else:
self.silhouette = silhouette
self._scalar_bar = None
# for now only one time label can be added
# since it is the same for all figures
self._time_label_added = False
# array of data used by TimeViewer
self._data = {}
self.geo = {}
self.set_time_interpolation("nearest")
geo_kwargs = self._cortex_colormap(cortex)
# evaluate at the midpoint of the used colormap
val = -geo_kwargs["vmin"] / (geo_kwargs["vmax"] - geo_kwargs["vmin"])
self._brain_color = geo_kwargs["colormap"](val)
# load geometry for one or both hemispheres as necessary
_validate_type(offset, (str, bool), "offset")
if isinstance(offset, str):
_check_option("offset", offset, ("auto",), extra="when str")
offset = surf in ("inflated", "flat")
offset = None if (not offset or hemi != "both") else 0.0
logger.debug(f"Hemi offset: {offset}")
_validate_type(theme, (str, None), "theme")
self._renderer = _get_renderer(
name=self._title, size=size, bgcolor=self._bg_color, shape=shape, fig=figure
)
self._renderer._window_close_connect(self._clean)
self._renderer._window_set_theme(theme)
self.plotter = self._renderer.plotter
self.widgets = dict()
self._setup_canonical_rotation()
# plot hemis
for h in ("lh", "rh"):
if h not in self._hemis:
continue # don't make surface if not chosen
# Initialize a Surface object as the geometry
geo = _Surface(
self._subject,
h,
surf,
self._subjects_dir,
offset,
units=self._units,
x_dir=self._rigid[0, :3],
)
# Load in the geometry and curvature
geo.load_geometry()
geo.load_curvature()
self.geo[h] = geo
for _, _, v in self._iter_views(h):
if self._layered_meshes.get(h) is None:
mesh = _LayeredMesh(
renderer=self._renderer,
vertices=self.geo[h].coords,
triangles=self.geo[h].faces,
normals=self.geo[h].nn,
)
mesh.map() # send to GPU
if self.geo[h].bin_curv is None:
scalars = mesh._default_scalars[:, 0]
else:
scalars = self.geo[h].bin_curv
mesh.add_overlay(
scalars=scalars,
colormap=geo_kwargs["colormap"],
rng=[geo_kwargs["vmin"], geo_kwargs["vmax"]],
opacity=alpha,
name="curv",
)
self._layered_meshes[h] = mesh
# add metadata to the mesh for picking
mesh._polydata._hemi = h
else:
actor = self._layered_meshes[h]._actor
self._renderer.plotter.add_actor(actor, render=False)
if self.silhouette:
mesh = self._layered_meshes[h]
self._renderer._silhouette(
mesh=mesh._polydata,
color=self._silhouette["color"],
line_width=self._silhouette["line_width"],
alpha=self._silhouette["alpha"],
decimate=self._silhouette["decimate"],
)
self._set_camera(**views_dicts[h][v])
self.interaction = interaction
self._closed = False
if show:
self.show()
# update the views once the geometry is all set
for h in self._hemis:
for ri, ci, v in self._iter_views(h):
self.show_view(v, row=ri, col=ci, hemi=h, update=False)
if surf == "flat":
self._renderer.set_interaction("rubber_band_2d")
self._renderer._update()
def _setup_canonical_rotation(self):
self._rigid = np.eye(4)
try:
xfm = _estimate_talxfm_rigid(self._subject, self._subjects_dir)
except Exception:
logger.info(
"Could not estimate rigid Talairach alignment, using identity matrix"
)
else:
self._rigid[:] = xfm
def setup_time_viewer(self, time_viewer=True, show_traces=True):
"""Configure the time viewer parameters.
Parameters
----------
time_viewer : bool
If True, enable widgets interaction. Defaults to True.
show_traces : bool
If True, enable visualization of time traces. Defaults to True.
Notes
-----
The keyboard shortcuts are the following:
'?': Display help window
'i': Toggle interface
's': Apply auto-scaling
'r': Restore original clim
'c': Clear all traces
'n': Shift the time forward by the playback speed
'b': Shift the time backward by the playback speed
'Space': Start/Pause playback
'Up': Decrease camera elevation angle
'Down': Increase camera elevation angle
'Left': Decrease camera azimuth angle
'Right': Increase camera azimuth angle
"""
if self.time_viewer:
return
if not self._data:
raise ValueError("No data to visualize. See ``add_data``.")
self.time_viewer = time_viewer
self.orientation = list(_lh_views_dict.keys())
self.default_smoothing_range = [-1, 15]
# Default configuration
self.visibility = False
self.default_playback_speed_range = [0.01, 1]
self.default_playback_speed_value = 0.01
self.default_status_bar_msg = "Press ? for help"
self.default_label_extract_modes = {
"stc": ["mean", "max"],
"src": ["mean_flip", "pca_flip", "auto"],
}
self.annot = None
self.label_extract_mode = None
all_keys = ("lh", "rh", "vol")
self.act_data_smooth = {key: (None, None) for key in all_keys}
self.color_list = _get_color_list()
# remove grey for better contrast on the brain
self.color_list.remove("#7f7f7f")
self.color_cycle = _ReuseCycle(self.color_list)
self.mpl_canvas = None
self.help_canvas = None
self.rms = None
self.picked_patches = {key: list() for key in all_keys}
self.picked_points = {key: list() for key in all_keys}
self.pick_table = dict()
self._spheres = list()
self._mouse_no_mvt = -1
# Derived parameters:
self.playback_speed = self.default_playback_speed_value
_validate_type(show_traces, (bool, str, "numeric"), "show_traces")
self.interactor_fraction = 0.25
if isinstance(show_traces, str):
self.show_traces = True
self.separate_canvas = False
self.traces_mode = "vertex"
if show_traces == "separate":
self.separate_canvas = True
elif show_traces == "label":
self.traces_mode = "label"
else:
assert show_traces == "vertex" # guaranteed above
else:
if isinstance(show_traces, bool):
self.show_traces = show_traces
else:
show_traces = float(show_traces)
if not 0 < show_traces < 1:
raise ValueError(
"show traces, if numeric, must be between 0 and 1, "
f"got {show_traces}"
)
self.show_traces = True
self.interactor_fraction = show_traces
self.traces_mode = "vertex"
self.separate_canvas = False
del show_traces
self._configure_time_label()
self._configure_scalar_bar()
self._configure_shortcuts()
self._configure_picking()
self._configure_dock()
self._configure_tool_bar()
self._configure_menu()
self._configure_status_bar()
self._configure_help()
# show everything at the end
self.toggle_interface()
self._renderer.show()
# sizes could change, update views
for hemi in ("lh", "rh"):
for ri, ci, v in self._iter_views(hemi):
self.show_view(view=v, row=ri, col=ci)
self._renderer._process_events()
self._renderer._update()
# finally, show the MplCanvas
if self.show_traces:
self.mpl_canvas.show()
@safe_event
def _clean(self):
# resolve the reference cycle
self._renderer._window_close_disconnect()
self.clear_glyphs()
self.remove_annotations()
# clear init actors
for hemi in self._layered_meshes:
self._layered_meshes[hemi]._clean()
self._clear_callbacks()
self._clear_widgets()
if getattr(self, "mpl_canvas", None) is not None:
self.mpl_canvas.clear()
if getattr(self, "act_data_smooth", None) is not None:
for key in list(self.act_data_smooth.keys()):
self.act_data_smooth[key] = None
# XXX this should be done in PyVista
for renderer in self._renderer._all_renderers:
renderer.RemoveAllLights()
# app_window cannot be set to None because it is used in __del__
for key in ("lighting", "interactor", "_RenderWindow"):
setattr(self.plotter, key, None)
# Qt LeaveEvent requires _Iren so we use _FakeIren instead of None
# to resolve the ref to vtkGenericRenderWindowInteractor
self.plotter._Iren = _FakeIren()
if getattr(self.plotter, "picker", None) is not None:
self.plotter.picker = None
# XXX end PyVista
for key in (
"plotter",
"window",
"dock",
"tool_bar",
"menu_bar",
"interactor",
"mpl_canvas",
"time_actor",
"picked_renderer",
"act_data_smooth",
"_scalar_bar",
"actions",
"widgets",
"geo",
"_data",
):
setattr(self, key, None)
self._cleaned = True
def toggle_interface(self, value=None):
"""Toggle the interface.
Parameters
----------
value : bool | None
If True, the widgets are shown and if False, they
are hidden. If None, the state of the widgets is
toggled. Defaults to None.
"""
if value is None:
self.visibility = not self.visibility
else:
self.visibility = value
# update tool bar and dock
with self._renderer._window_ensure_minimum_sizes():
if self.visibility:
self._renderer._dock_show()
self._renderer._tool_bar_update_button_icon(
name="visibility", icon_name="visibility_on"
)
else:
self._renderer._dock_hide()
self._renderer._tool_bar_update_button_icon(
name="visibility", icon_name="visibility_off"
)
self._renderer._update()
def apply_auto_scaling(self):
"""Detect automatically fitting scaling parameters."""
self._update_auto_scaling()
def restore_user_scaling(self):
"""Restore original scaling parameters."""
self._update_auto_scaling(restore=True)
def toggle_playback(self, value=None):
"""Toggle time playback.
Parameters
----------
value : bool | None
If True, automatic time playback is enabled and if False,
it's disabled. If None, the state of time playback is toggled.
Defaults to None.
"""
self._renderer._toggle_playback(value)
def reset(self):
"""Reset view, current time and time step."""
self.reset_view()
self._renderer._reset_time()
def set_playback_speed(self, speed):
"""Set the time playback speed.
Parameters
----------
speed : float
The speed of the playback.
"""
publish(self, PlaybackSpeed(speed=speed))
def _configure_time_label(self):
self.time_actor = self._data.get("time_actor")
if self.time_actor is not None:
self.time_actor.SetPosition(0.5, 0.03)
self.time_actor.GetTextProperty().SetJustificationToCentered()
self.time_actor.GetTextProperty().BoldOn()
def _configure_scalar_bar(self):
if self._scalar_bar is not None:
self._scalar_bar.SetOrientationToVertical()
self._scalar_bar.SetHeight(0.6)
self._scalar_bar.SetWidth(0.05)
self._scalar_bar.SetPosition(0.02, 0.2)
def _configure_dock_playback_widget(self, name):
len_time = len(self._data["time"]) - 1
# Time widget
if len_time < 1:
self.widgets["time"] = None
self.widgets["min_time"] = None
self.widgets["max_time"] = None
self.widgets["current_time"] = None
else:
@_auto_weakref
def current_time_func():
return self._current_time
self._renderer._enable_time_interaction(
self,
current_time_func,
self._data["time"],
self.default_playback_speed_value,
self.default_playback_speed_range,
)
# Time label
current_time = self._current_time
assert current_time is not None # should never be the case, float
time_label = self._data["time_label"]
if callable(time_label):
current_time = time_label(current_time)
else:
current_time = time_label
if self.time_actor is not None:
self.time_actor.SetInput(current_time)
del current_time
def _configure_dock_orientation_widget(self, name):
layout = self._renderer._dock_add_group_box(name)
# Renderer widget
rends = [str(i) for i in range(len(self._renderer._all_renderers))]
if len(rends) > 1:
@_auto_weakref
def select_renderer(idx):
idx = int(idx)
loc = self._renderer._index_to_loc(idx)
self.plotter.subplot(*loc)
self.widgets["renderer"] = self._renderer._dock_add_combo_box(
name="Renderer",
value="0",
rng=rends,
callback=select_renderer,
layout=layout,
)
# Use 'lh' as a reference for orientation for 'both'
if self._hemi == "both":
hemis_ref = ["lh"]
else:
hemis_ref = self._hemis
orientation_data = [None] * len(rends)
for hemi in hemis_ref:
for ri, ci, v in self._iter_views(hemi):
idx = self._renderer._loc_to_index((ri, ci))
if v == "flat":
_data = None
else:
_data = dict(default=v, hemi=hemi, row=ri, col=ci)
orientation_data[idx] = _data
@_auto_weakref
def set_orientation(value, orientation_data=orientation_data):
if "renderer" in self.widgets:
idx = int(self.widgets["renderer"].get_value())
else:
idx = 0
if orientation_data[idx] is not None:
self.show_view(
value,
row=orientation_data[idx]["row"],
col=orientation_data[idx]["col"],
hemi=orientation_data[idx]["hemi"],
)
self.widgets["orientation"] = self._renderer._dock_add_combo_box(
name=None,
value=self.orientation[0],
rng=self.orientation,
callback=set_orientation,
layout=layout,
)
def _configure_dock_colormap_widget(self, name):
fmax, fscale, fscale_power = _get_range(self)
rng = [0, fmax * fscale]
self._data["fscale"] = fscale
layout = self._renderer._dock_add_group_box(name)
text = "min / mid / max"
if fscale_power != 0:
text += f" (×1e{fscale_power:d})"
self._renderer._dock_add_label(
value=text,
align=True,
layout=layout,
)
@_auto_weakref
def update_single_lut_value(value, key):
# Called by the sliders and spin boxes.
self.update_lut(**{key: value / self._data["fscale"]})
keys = ("fmin", "fmid", "fmax")
for key in keys:
hlayout = self._renderer._dock_add_layout(vertical=False)
self.widgets[key] = self._renderer._dock_add_slider(
name=None,
value=self._data[key] * self._data["fscale"],
rng=rng,
callback=partial(update_single_lut_value, key=key),
double=True,
layout=hlayout,
)
self.widgets[f"entry_{key}"] = self._renderer._dock_add_spin_box(
name=None,
value=self._data[key] * self._data["fscale"],
callback=partial(update_single_lut_value, key=key),
rng=rng,
layout=hlayout,
)
self._renderer._layout_add_widget(layout, hlayout)
# reset / minus / plus
hlayout = self._renderer._dock_add_layout(vertical=False)
self._renderer._dock_add_label(
value="Rescale",
align=True,
layout=hlayout,
)
self.widgets["reset"] = self._renderer._dock_add_button(
name="↺",
callback=self.restore_user_scaling,
layout=hlayout,
style="toolbutton",
)
@_auto_weakref
def fminus():
self._update_fscale(1.2**-0.25)
self.widgets["fminus"] = self._renderer._dock_add_button(
name="➖",
callback=fminus,
layout=hlayout,
style="toolbutton",
)
@_auto_weakref
def fplus():
self._update_fscale(1.2**0.25)
self.widgets["fplus"] = self._renderer._dock_add_button(
name="➕",
callback=fplus,
layout=hlayout,
style="toolbutton",
)
self._renderer._layout_add_widget(layout, hlayout)
def _configure_dock_trace_widget(self, name):
if not self.show_traces:
return
# do not show trace mode for volumes
if (
self._data.get("src", None) is not None
and self._data["src"].kind == "volume"
):
self._configure_vertex_time_course()
return
layout = self._renderer._dock_add_group_box(name)
# setup candidate annots
@_auto_weakref
def _set_annot(annot):
self.clear_glyphs()
self.remove_labels()
self.remove_annotations()
self.annot = annot
if annot == "None":
self.traces_mode = "vertex"
self._configure_vertex_time_course()
else:
self.traces_mode = "label"
self._configure_label_time_course()
self._renderer._update()
# setup label extraction parameters
@_auto_weakref
def _set_label_mode(mode):
if self.traces_mode != "label":
return
glyphs = copy.deepcopy(self.picked_patches)
self.label_extract_mode = mode
self.clear_glyphs()
for hemi in self._hemis:
for label_id in glyphs[hemi]:
label = self._annotation_labels[hemi][label_id]
vertex_id = label.vertices[0]
self._add_label_glyph(hemi, None, vertex_id)
self.mpl_canvas.axes.relim()
self.mpl_canvas.axes.autoscale_view()
self.mpl_canvas.update_plot()
self._renderer._update()
from ...label import _read_annot_cands
from ...source_estimate import _get_allowed_label_modes
dir_name = op.join(self._subjects_dir, self._subject, "label")
cands = _read_annot_cands(dir_name, raise_error=False)
cands = cands + ["None"]
self.annot = cands[0]
stc = self._data["stc"]
modes = _get_allowed_label_modes(stc)
if self._data["src"] is None:
modes = [
m for m in modes if m not in self.default_label_extract_modes["src"]
]
self.label_extract_mode = modes[-1]
if self.traces_mode == "vertex":
_set_annot("None")
else:
_set_annot(self.annot)
self.widgets["annotation"] = self._renderer._dock_add_combo_box(
name="Annotation",
value=self.annot,
rng=cands,
callback=_set_annot,
layout=layout,
)
self.widgets["extract_mode"] = self._renderer._dock_add_combo_box(
name="Extract mode",
value=self.label_extract_mode,
rng=modes,
callback=_set_label_mode,
layout=layout,
)
def _configure_dock(self):
self._renderer._dock_initialize()
self._configure_dock_playback_widget(name="Playback")
self._configure_dock_orientation_widget(name="Orientation")
self._configure_dock_colormap_widget(name="Color Limits")
self._configure_dock_trace_widget(name="Trace")
# Smoothing widget
self.widgets["smoothing"] = self._renderer._dock_add_spin_box(
name="Smoothing",
value=self._data["smoothing_steps"],
rng=self.default_smoothing_range,
callback=self.set_data_smoothing,
double=False,
)
self._renderer._dock_finalize()
def _configure_mplcanvas(self):
# Get the fractional components for the brain and mpl
self.mpl_canvas = self._renderer._window_get_mplcanvas(
brain=self,
interactor_fraction=self.interactor_fraction,
show_traces=self.show_traces,