# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import inspect
import os
import os.path as op
import platform
import queue
import re
import threading
import time
from contextlib import contextmanager
from functools import partial
from pathlib import Path
import numpy as np
from traitlets import Bool, Float, HasTraits, Instance, Unicode, observe
from .._fiff.constants import FIFF
from .._fiff.meas_info import _empty_info, read_fiducials, read_info, write_fiducials
from .._fiff.open import dir_tree_find, fiff_open
from .._fiff.pick import pick_types
from ..bem import make_bem_solution, write_bem_solution
from ..channels import read_dig_fif
from ..coreg import (
Coregistration,
_find_head_bem,
_is_mri_subject,
_map_fid_name_to_idx,
_mri_subject_has_bem,
bem_fname,
fid_fname,
scale_mri,
)
from ..defaults import DEFAULTS
from ..io._read_raw import _get_supported, read_raw
from ..surface import _CheckInside, _DistanceQuery
from ..transforms import (
Transform,
_ensure_trans,
_get_trans,
_get_transforms_to_coord_frame,
read_trans,
rotation_angles,
write_trans,
)
from ..utils import (
_check_fname,
_validate_type,
check_fname,
fill_doc,
get_subjects_dir,
logger,
verbose,
)
from ..viz._3d import (
_plot_head_fiducials,
_plot_head_shape_points,
_plot_head_surface,
_plot_helmet,
_plot_hpi_coils,
_plot_mri_fiducials,
_plot_sensors_3d,
)
from ..viz.backends._utils import _qt_app_exec, _qt_safe_window
from ..viz.utils import safe_event
class _WorkerData:
def __init__(self, name, params=None):
self._name = name
self._params = params
def _get_subjects(sdir):
# XXX: would be nice to move this function to util
is_dir = sdir and op.isdir(sdir)
if is_dir:
dir_content = os.listdir(sdir)
subjects = [s for s in dir_content if _is_mri_subject(s, sdir)]
if len(subjects) == 0:
subjects.append("")
else:
subjects = [""]
return sorted(subjects)
@fill_doc
class CoregistrationUI(HasTraits):
"""Class for coregistration assisted by graphical interface.
Parameters
----------
info_file : None | path-like
The FIFF file with digitizer data for coregistration.
%(subject)s
%(subjects_dir)s
%(fiducials)s
head_resolution : bool
If ``True``, use a high-resolution head surface. Defaults to ``False``.
head_opacity : float
The opacity of the head surface. Defaults to ``0.8``.
hpi_coils : bool
If ``True``, display the HPI coils. Defaults to ``True``.
head_shape_points : bool
If ``True``, display the head shape points. Defaults to ``True``.
eeg_channels : bool
If ``True``, display the EEG channels. Defaults to ``True``.
meg_channels : bool
If ``True``, display the MEG channels. Defaults to ``False``.
fnirs_channels : bool
If ``True``, display the fNIRS channels. Defaults to ``True``.
orient_glyphs : bool
If ``True``, orient the sensors towards the head surface. Default to ``False``.
scale_by_distance : bool
If ``True``, scale the sensors based on their distance to the head surface.
Defaults to ``True``.
mark_inside : bool
If ``True``, mark the head shape points that are inside the head surface
with a different color. Defaults to ``True``.
sensor_opacity : float
The opacity of the sensors between ``0`` and ``1``. Defaults to ``1.``.
trans : path-like | Transform
The Head<->MRI transform or the path to its FIF file (``"-trans.fif"``).
size : tuple
The dimensions (width, height) of the rendering view. The default is
``(800, 600)``.
bgcolor : tuple of float | str
The background color as a tuple (red, green, blue) of float
values between ``0`` and ``1`` or a valid color name (i.e. ``'white'``
or ``'w'``). Defaults to ``'grey'``.
show : bool
Display the window as soon as it is ready. Defaults to ``True``.
block : bool
Whether to halt program execution until the GUI has been closed
(``True``) or not (``False``, default).
%(fullscreen)s
The default is ``False``.
.. versionadded:: 1.1
%(interaction_scene)s
Defaults to ``'terrain'``.
.. versionadded:: 1.0
%(verbose)s
Attributes
----------
coreg : mne.coreg.Coregistration
The coregistration instance used by the graphical interface.
"""
_subject = Unicode()
_subjects_dir = Unicode()
_lock_fids = Bool()
_current_fiducial = Unicode()
_info_file = Instance(Path, default_value=Path("."))
_orient_glyphs = Bool()
_scale_by_distance = Bool()
_mark_inside = Bool()
_hpi_coils = Bool()
_head_shape_points = Bool()
_eeg_channels = Bool()
_meg_channels = Bool()
_fnirs_channels = Bool()
_head_resolution = Bool()
_head_opacity = Float()
_helmet = Bool()
_grow_hair = Float()
_subject_to = Unicode()
_scale_mode = Unicode()
_icp_fid_match = Unicode()
@_qt_safe_window(
splash="_renderer.figure.splash", window="_renderer.figure.plotter"
)
@verbose
def __init__(
self,
info_file,
*,
subject=None,
subjects_dir=None,
fiducials="auto",
head_resolution=None,
head_opacity=None,
hpi_coils=None,
head_shape_points=None,
eeg_channels=None,
meg_channels=None,
fnirs_channels=None,
orient_glyphs=None,
scale_by_distance=None,
mark_inside=None,
sensor_opacity=None,
trans=None,
size=None,
bgcolor=None,
show=True,
block=False,
fullscreen=False,
interaction="terrain",
verbose=None,
):
from ..viz.backends.renderer import _get_renderer
def _get_default(var, val):
return var if var is not None else val
self._actors = dict()
self._surfaces = dict()
self._widgets = dict()
self._verbose = verbose
self._plot_locked = False
self._params_locked = False
self._refresh_rate_ms = max(int(round(1000.0 / 60.0)), 1)
self._redraws_pending = set()
self._parameter_mutex = threading.Lock()
self._redraw_mutex = threading.Lock()
self._job_queue = queue.Queue()
self._parameter_queue = queue.Queue()
self._head_geo = None
self._check_inside = None
self._nearest = None
self._coord_frame = "mri"
self._mouse_no_mvt = -1
self._to_cf_t = None
self._omit_hsp_distance = 0.0
self._fiducials_file = None
self._trans_modified = False
self._mri_fids_modified = False
self._mri_scale_modified = False
self._accept_close_event = True
self._fid_colors = tuple(
DEFAULTS["coreg"][f"{key}_color"] for key in ("lpa", "nasion", "rpa")
)
self._defaults = dict(
size=_get_default(size, (800, 600)),
bgcolor=_get_default(bgcolor, "grey"),
orient_glyphs=_get_default(orient_glyphs, True),
scale_by_distance=_get_default(scale_by_distance, True),
mark_inside=_get_default(mark_inside, True),
hpi_coils=_get_default(hpi_coils, True),
head_shape_points=_get_default(head_shape_points, True),
eeg_channels=_get_default(eeg_channels, True),
meg_channels=_get_default(meg_channels, False),
fnirs_channels=_get_default(fnirs_channels, True),
head_resolution=_get_default(head_resolution, True),
head_opacity=_get_default(head_opacity, 0.8),
helmet=False,
sensor_opacity=_get_default(sensor_opacity, 1.0),
fiducials=("LPA", "Nasion", "RPA"),
fiducial="LPA",
lock_fids=True,
grow_hair=0.0,
subject_to="",
scale_modes=["None", "uniform", "3-axis"],
scale_mode="None",
icp_fid_matches=("nearest", "matched"),
icp_fid_match="matched",
icp_n_iterations=20,
omit_hsp_distance=10.0,
lock_head_opacity=self._head_opacity < 1.0,
weights=dict(
lpa=1.0,
nasion=10.0,
rpa=1.0,
hsp=1.0,
eeg=1.0,
hpi=1.0,
),
)
# process requirements
info = None
subjects_dir = str(
get_subjects_dir(subjects_dir=subjects_dir, raise_error=True)
)
subject = _get_default(subject, _get_subjects(subjects_dir)[0])
# setup the window
splash = "Initializing coregistration GUI..." if show else False
self._renderer = _get_renderer(
size=self._defaults["size"],
bgcolor=self._defaults["bgcolor"],
splash=splash,
fullscreen=fullscreen,
)
self._renderer._window_close_connect(self._clean)
self._renderer._window_close_connect(self._close_callback, after=False)
self._renderer.set_interaction(interaction)
# coregistration model setup
self._immediate_redraw = self._renderer._kind != "qt"
self._info = info
self._fiducials = fiducials
self.coreg = Coregistration(
info=self._info,
subject=subject,
subjects_dir=subjects_dir,
fiducials=fiducials,
on_defects="ignore", # safe due to interactive visual inspection
)
fid_accurate = self.coreg._fid_accurate
for fid in self._defaults["weights"].keys():
setattr(self, f"_{fid}_weight", self._defaults["weights"][fid])
# set main traits
self._set_head_opacity(self._defaults["head_opacity"])
self._old_head_opacity = self._head_opacity
self._set_subjects_dir(subjects_dir)
self._set_subject(subject)
self._set_info_file(info_file)
self._set_orient_glyphs(self._defaults["orient_glyphs"])
self._set_scale_by_distance(self._defaults["scale_by_distance"])
self._set_mark_inside(self._defaults["mark_inside"])
self._set_hpi_coils(self._defaults["hpi_coils"])
self._set_head_shape_points(self._defaults["head_shape_points"])
self._set_eeg_channels(self._defaults["eeg_channels"])
self._set_meg_channels(self._defaults["meg_channels"])
self._set_fnirs_channels(self._defaults["fnirs_channels"])
self._set_head_resolution(self._defaults["head_resolution"])
self._set_helmet(self._defaults["helmet"])
self._set_grow_hair(self._defaults["grow_hair"])
self._set_omit_hsp_distance(self._defaults["omit_hsp_distance"])
self._set_icp_n_iterations(self._defaults["icp_n_iterations"])
self._set_icp_fid_match(self._defaults["icp_fid_match"])
# configure UI
self._reset_fitting_parameters()
self._configure_dialogs()
self._configure_status_bar()
self._configure_dock()
self._configure_picking()
self._configure_legend()
# once the docks are initialized
self._set_current_fiducial(self._defaults["fiducial"])
self._set_scale_mode(self._defaults["scale_mode"])
self._set_subject_to(self._defaults["subject_to"])
if trans is not None:
self._load_trans(trans)
self._redraw() # we need the elements to be present now
if fid_accurate:
assert self.coreg._fid_filename is not None
# _set_fiducials_file() calls _update_fiducials_label()
# internally
self._set_fiducials_file(self.coreg._fid_filename)
else:
self._set_head_resolution("high")
self._forward_widget_command("high_res_head", "set_value", True)
self._set_lock_fids(True) # hack to make the dig disappear
self._update_fiducials_label()
self._update_fiducials()
self._set_lock_fids(fid_accurate)
# configure worker
self._configure_worker()
# must be done last
if show:
self._renderer.show()
# update the view once shown
views = {
True: dict(azimuth=90, elevation=90), # front
False: dict(azimuth=180, elevation=90),
} # left
self._renderer.set_camera(distance="auto", **views[self._lock_fids])
self._redraw()
# XXX: internal plotter/renderer should not be exposed
if not self._immediate_redraw:
self._renderer.plotter.add_callback(self._redraw, self._refresh_rate_ms)
self._renderer.plotter.show_axes()
# initialization does not count as modification by the user
self._trans_modified = False
self._mri_fids_modified = False
self._mri_scale_modified = False
if block and self._renderer._kind != "notebook":
_qt_app_exec(self._renderer.figure.store["app"])
def _set_subjects_dir(self, subjects_dir):
if subjects_dir is None or not subjects_dir:
return
try:
subjects_dir = str(
_check_fname(
subjects_dir,
overwrite="read",
must_exist=True,
need_dir=True,
)
)
subjects = _get_subjects(subjects_dir)
low_res_path = _find_head_bem(subjects[0], subjects_dir, high_res=False)
high_res_path = _find_head_bem(subjects[0], subjects_dir, high_res=True)
valid = low_res_path is not None or high_res_path is not None
except Exception:
valid = False
if valid:
style = dict(border="initial")
self._subjects_dir = subjects_dir
else:
style = dict(border="2px solid #ff0000")
self._forward_widget_command("subjects_dir_field", "set_style", style)
def _set_subject(self, subject):
self._subject = subject
def _set_lock_fids(self, state):
self._lock_fids = bool(state)
def _set_fiducials_file(self, fname):
if fname is None:
fids = "auto"
else:
fname = str(
_check_fname(
fname,
overwrite="read",
must_exist=True,
need_dir=False,
)
)
fids, _ = read_fiducials(fname)
self._fiducials_file = fname
self.coreg._setup_fiducials(fids)
self._update_distance_estimation()
self._update_fiducials_label()
self._update_fiducials()
self._reset(keep_trans=True)
if fname is None:
self._set_lock_fids(False)
self._forward_widget_command("reload_mri_fids", "set_enabled", False)
else:
self._set_lock_fids(True)
self._forward_widget_command("reload_mri_fids", "set_enabled", True)
self._display_message(f"Loading MRI fiducials from {fname}... Done!")
def _set_current_fiducial(self, fid):
self._current_fiducial = fid.lower()
def _set_info_file(self, fname):
if fname is None:
return
# info file can be anything supported by read_raw
supported = _get_supported()
try:
check_fname(
fname,
"info",
tuple(supported),
endings_err=tuple(supported),
)
fname = Path(fname)
# ctf ds `files` are actually directories
if fname.suffix == ".ds":
info_file = _check_fname(
fname, overwrite="read", must_exist=True, need_dir=True
)
else:
info_file = _check_fname(
fname, overwrite="read", must_exist=True, need_dir=False
)
valid = True
except OSError:
valid = False
if valid:
style = dict(border="initial")
self._info_file = info_file
else:
style = dict(border="2px solid #ff0000")
self._forward_widget_command("info_file_field", "set_style", style)
def _set_omit_hsp_distance(self, distance):
self._omit_hsp_distance = distance
def _set_orient_glyphs(self, state):
self._orient_glyphs = bool(state)
def _set_scale_by_distance(self, state):
self._scale_by_distance = bool(state)
def _set_mark_inside(self, state):
self._mark_inside = bool(state)
def _set_hpi_coils(self, state):
self._hpi_coils = bool(state)
def _set_head_shape_points(self, state):
self._head_shape_points = bool(state)
def _set_eeg_channels(self, state):
self._eeg_channels = bool(state)
def _set_meg_channels(self, state):
self._meg_channels = bool(state)
def _set_fnirs_channels(self, state):
self._fnirs_channels = bool(state)
def _set_head_resolution(self, state):
self._head_resolution = bool(state)
def _set_head_opacity(self, value):
self._head_opacity = value
def _set_helmet(self, state):
self._helmet = bool(state)
def _set_grow_hair(self, value):
self._grow_hair = value
def _set_subject_to(self, value):
self._subject_to = value
self._forward_widget_command("save_subject", "set_enabled", len(value) > 0)
if self._check_subject_exists():
style = dict(border="2px solid #ff0000")
else:
style = dict(border="initial")
self._forward_widget_command("subject_to", "set_style", style)
def _set_scale_mode(self, mode):
self._scale_mode = mode
def _set_fiducial(self, value, coord):
self._mri_fids_modified = True
fid = self._current_fiducial
fid_idx = _map_fid_name_to_idx(name=fid)
coords = ["X", "Y", "Z"]
coord_idx = coords.index(coord)
self.coreg.fiducials.dig[fid_idx]["r"][coord_idx] = value / 1e3
self._update_plot("mri_fids")
def _set_parameter(self, value, mode_name, coord, plot_locked=False):
if mode_name == "scale":
self._mri_scale_modified = True
else:
self._trans_modified = True
if self._params_locked:
return
if mode_name == "scale" and self._scale_mode == "uniform":
with self._lock(params=True):
self._forward_widget_command(["sY", "sZ"], "set_value", value)
with self._parameter_mutex:
self._set_parameter_safe(value, mode_name, coord)
if not plot_locked:
self._update_plot("sensors")
def _set_parameter_safe(self, value, mode_name, coord):
params = dict(
rotation=self.coreg._rotation,
translation=self.coreg._translation,
scale=self.coreg._scale,
)
idx = ["X", "Y", "Z"].index(coord)
if mode_name == "rotation":
params[mode_name][idx] = np.deg2rad(value)
elif mode_name == "translation":
params[mode_name][idx] = value / 1e3
else:
assert mode_name == "scale"
if self._scale_mode == "uniform":
params[mode_name][:] = value / 1e2
else:
params[mode_name][idx] = value / 1e2
self._update_plot("head")
self.coreg._update_params(
rot=params["rotation"],
tra=params["translation"],
sca=params["scale"],
)
def _set_icp_n_iterations(self, n_iterations):
self._icp_n_iterations = n_iterations
def _set_icp_fid_match(self, method):
self._icp_fid_match = method
def _set_point_weight(self, weight, point):
funcs = {
"hpi": "_set_hpi_coils",
"hsp": "_set_head_shape_points",
"eeg": "_set_eeg_channels",
"meg": "_set_meg_channels",
"fnirs": "_set_fnirs_channels",
}
if point in funcs.keys():
getattr(self, funcs[point])(weight > 0)
setattr(self, f"_{point}_weight", weight)
setattr(self.coreg, f"_{point}_weight", weight)
self._update_distance_estimation()
@observe("_subjects_dir")
def _subjects_dir_changed(self, change=None):
# XXX: add coreg.set_subjects_dir
self.coreg._subjects_dir = self._subjects_dir
subjects = _get_subjects(self._subjects_dir)
if self._subject not in subjects: # Just pick the first available one
self._subject = subjects[0]
self._reset()
@observe("_subject")
def _subject_changed(self, change=None):
# XXX: add coreg.set_subject()
self.coreg._subject = self._subject
self.coreg._setup_bem()
self.coreg._setup_fiducials(self._fiducials)
self._reset()
default_fid_fname = fid_fname.format(
subjects_dir=self._subjects_dir, subject=self._subject
)
if Path(default_fid_fname).exists():
fname = default_fid_fname
else:
fname = None
self._set_fiducials_file(fname)
self._reset_fiducials()
@observe("_lock_fids")
def _lock_fids_changed(self, change=None):
locked_widgets = [
# MRI fiducials
"save_mri_fids",
# View options
"helmet",
"meg",
"head_opacity",
"high_res_head",
# Digitization source
"info_file",
"grow_hair",
"omit_distance",
"omit",
"reset_omit",
# Scaling
"scaling_mode",
"sX",
"sY",
"sZ",
# Transformation
"tX",
"tY",
"tZ",
"rX",
"rY",
"rZ",
# Fitting buttons
"fit_fiducials",
"fit_icp",
# Transformation I/O
"save_trans",
"load_trans",
"reset_trans",
# ICP
"icp_n_iterations",
"icp_fid_match",
"reset_fitting_options",
# Weights
"hsp_weight",
"eeg_weight",
"hpi_weight",
"lpa_weight",
"nasion_weight",
"rpa_weight",
]
fits_widgets = ["fits_fiducials", "fits_icp"]
fid_widgets = ["fid_X", "fid_Y", "fid_Z", "fids_file", "fids"]
if self._lock_fids:
self._forward_widget_command(locked_widgets, "set_enabled", True)
self._forward_widget_command(
"head_opacity", "set_value", self._old_head_opacity
)
self._scale_mode_changed()
self._display_message()
self._update_distance_estimation()
else:
self._old_head_opacity = self._head_opacity
self._forward_widget_command("head_opacity", "set_value", 1.0)
self._forward_widget_command(locked_widgets, "set_enabled", False)
self._forward_widget_command(fits_widgets, "set_enabled", False)
self._display_message(
f"Placing MRI fiducials - {self._current_fiducial.upper()}"
)
self._set_sensors_visibility(self._lock_fids)
self._forward_widget_command("lock_fids", "set_value", self._lock_fids)
self._forward_widget_command(fid_widgets, "set_enabled", not self._lock_fids)
@observe("_current_fiducial")
def _current_fiducial_changed(self, change=None):
self._update_fiducials()
self._follow_fiducial_view()
if not self._lock_fids:
self._display_message(
f"Placing MRI fiducials - {self._current_fiducial.upper()}"
)
@observe("_info_file")
def _info_file_changed(self, change=None):
if not self._info_file:
return
elif self._info_file.name.endswith((".fif", ".fif.gz")):
fid, tree, _ = fiff_open(self._info_file)
fid.close()
if len(dir_tree_find(tree, FIFF.FIFFB_MEAS_INFO)) > 0:
self._info = read_info(self._info_file, verbose=False)
elif len(dir_tree_find(tree, FIFF.FIFFB_ISOTRAK)) > 0:
self._info = _empty_info(1)
self._info["dig"] = read_dig_fif(fname=self._info_file).dig
self._info._unlocked = False
else:
self._info = read_raw(self._info_file).info
# XXX: add coreg.set_info()
self.coreg._info = self._info
self.coreg._setup_digs()
self._reset()
@observe("_orient_glyphs")
def _orient_glyphs_changed(self, change=None):
self._update_plot(["hpi", "hsp", "sensors"])
@observe("_scale_by_distance")
def _scale_by_distance_changed(self, change=None):
self._update_plot(["hpi", "hsp", "sensors"])
@observe("_mark_inside")
def _mark_inside_changed(self, change=None):
self._update_plot("hsp")
@observe("_hpi_coils")
def _hpi_coils_changed(self, change=None):
self._update_plot("hpi")
@observe("_head_shape_points")
def _head_shape_point_changed(self, change=None):
self._update_plot("hsp")
@observe("_eeg_channels")
def _eeg_channels_changed(self, change=None):
self._update_plot("sensors")
@observe("_meg_channels")
def _meg_channels_changed(self, change=None):
self._update_plot("sensors")
@observe("_fnirs_channels")
def _fnirs_channels_changed(self, change=None):
self._update_plot("sensors")
@observe("_head_resolution")
def _head_resolution_changed(self, change=None):
self._update_plot(["head", "hsp"])
@observe("_head_opacity")
def _head_opacity_changed(self, change=None):
if "head" in self._actors:
self._actors["head"].GetProperty().SetOpacity(self._head_opacity)
self._renderer._update()
@observe("_helmet")
def _helmet_changed(self, change=None):
self._update_plot("helmet")
@observe("_grow_hair")
def _grow_hair_changed(self, change=None):
self.coreg.set_grow_hair(self._grow_hair)
self._update_plot("head")
self._update_plot("hsp") # inside/outside could change
@observe("_scale_mode")
def _scale_mode_changed(self, change=None):
locked_widgets = ["sX", "sY", "sZ", "fits_icp", "subject_to"]
mode = None if self._scale_mode == "None" else self._scale_mode
self.coreg.set_scale_mode(mode)
if self._lock_fids:
self._forward_widget_command(
locked_widgets, "set_enabled", mode is not None
)
self._forward_widget_command(
"fits_fiducials", "set_enabled", mode not in (None, "3-axis")
)
if self._scale_mode == "uniform":
self._forward_widget_command(["sY", "sZ"], "set_enabled", False)
@observe("_icp_fid_match")
def _icp_fid_match_changed(self, change=None):
self.coreg.set_fid_match(self._icp_fid_match)
def _run_worker(self, queue, jobs):
while True:
data = queue.get()
func = jobs[data._name]
if data._params is not None:
func(**data._params)
else:
func()
queue.task_done()
def _configure_dialogs(self):
from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
for name, buttons in zip(
["overwrite_subject", "overwrite_subject_exit"],
[["Yes", "No"], ["Yes", "Discard", "Cancel"]],
):
self._widgets[name] = self._renderer._dialog_create(
title="CoregistrationUI",
text="The name of the output subject used to "
"save the scaled anatomy already exists.",
info_text="Do you want to overwrite?",
callback=self._overwrite_subject_callback,
buttons=buttons,
modal=not MNE_3D_BACKEND_TESTING,
)
def _configure_worker(self):
work_plan = {
"_job_queue": dict(save_subject=self._save_subject),
"_parameter_queue": dict(set_parameter=self._set_parameter),
}
for queue_name, jobs in work_plan.items():
t = threading.Thread(
target=partial(
self._run_worker,
queue=getattr(self, queue_name),
jobs=jobs,
)
)
t.daemon = True
t.start()
def _configure_picking(self):
self._renderer._update_picking_callback(
self._on_mouse_move,
self._on_button_press,
self._on_button_release,
self._on_pick,
)
def _configure_legend(self):
colors = [
np.array(DEFAULTS["coreg"][f"{fid.lower()}_color"]).astype(float)
for fid in self._defaults["fiducials"]
]
labels = list(zip(self._defaults["fiducials"], colors))
mri_fids_legend_actor = self._renderer.legend(labels=labels)
self._update_actor("mri_fids_legend", mri_fids_legend_actor)
@safe_event
@verbose
def _redraw(self, *, verbose=None):
if not self._redraws_pending:
return
draw_map = dict(
head=self._add_head_surface,
mri_fids=self._add_mri_fiducials,
hsp=self._add_head_shape_points,
hpi=self._add_hpi_coils,
sensors=self._add_channels,
head_fids=self._add_head_fiducials,
helmet=self._add_helmet,
)
with self._redraw_mutex:
# We need at least "head" before "hsp", because the grow_hair param
# for head sets the rr that are used for inside/outside hsp
redraws_ordered = sorted(
self._redraws_pending, key=lambda key: list(draw_map).index(key)
)
logger.debug(f"Redrawing {redraws_ordered}")
for ki, key in enumerate(redraws_ordered):
logger.debug(f"{ki}. Drawing {repr(key)}")
draw_map[key]()
self._redraws_pending.clear()
self._renderer._update()
# necessary for MacOS
if platform.system() == "Darwin":
self._renderer._process_events()
def _on_mouse_move(self, vtk_picker, event):
if self._mouse_no_mvt:
self._mouse_no_mvt -= 1
def _on_button_press(self, vtk_picker, event):
self._mouse_no_mvt = 2
def _on_button_release(self, vtk_picker, event):
if self._mouse_no_mvt > 0:
x, y = vtk_picker.GetEventPosition()
# XXX: internal plotter/renderer should not be exposed
plotter = self._renderer.figure.plotter
picked_renderer = self._renderer.figure.plotter.renderer
# trigger the pick
plotter.picker.Pick(x, y, 0, picked_renderer)
self._mouse_no_mvt = 0
def _on_pick(self, vtk_picker, event):
if self._lock_fids:
return
# XXX: taken from Brain, can be refactored
cell_id = vtk_picker.GetCellId()
mesh = vtk_picker.GetDataSet()
if mesh is None or cell_id == -1 or not self._mouse_no_mvt:
return
if not getattr(mesh, "_picking_target", False):
return
pos = np.array(vtk_picker.GetPickPosition())
vtk_cell = mesh.GetCell(cell_id)
cell = [
vtk_cell.GetPointId(point_id)
for point_id in range(vtk_cell.GetNumberOfPoints())
]
vertices = mesh.points[cell]
idx = np.argmin(abs(vertices - pos), axis=0)
vertex_id = cell[idx[0]]
fiducials = [s.lower() for s in self._defaults["fiducials"]]
idx = fiducials.index(self._current_fiducial.lower())
# XXX: add coreg.set_fids
self.coreg._fid_points[idx] = self._surfaces["head"].points[vertex_id]
self.coreg._reset_fiducials()
self._update_fiducials()
self._update_plot("mri_fids")
def _reset_fitting_parameters(self):
self._forward_widget_command(
"icp_n_iterations", "set_value", self._defaults["icp_n_iterations"]
)
self._forward_widget_command(
"icp_fid_match", "set_value", self._defaults["icp_fid_match"]
)
weights_widgets = [f"{w}_weight" for w in self._defaults["weights"].keys()]
self._forward_widget_command(
weights_widgets, "set_value", list(self._defaults["weights"].values())
)
def _reset_fiducials(self):
self._set_current_fiducial(self._defaults["fiducial"])
def _omit_hsp(self):
self.coreg.omit_head_shape_points(self._omit_hsp_distance / 1e3)
n_omitted = np.sum(~self.coreg._extra_points_filter)
n_remaining = len(self.coreg._dig_dict["hsp"]) - n_omitted
self._update_plot("hsp")
self._update_distance_estimation()
self._display_message(
f"{n_omitted} head shape points omitted, {n_remaining} remaining."
)
def _reset_omit_hsp_filter(self):
self.coreg._extra_points_filter = None
self.coreg._update_params(force_update=True)
self._update_plot("hsp")
self._update_distance_estimation()
n_total = len(self.coreg._dig_dict["hsp"])
self._display_message(
f"No head shape point is omitted, the total is {n_total}."
)
@verbose
def _update_plot(self, changes="all", verbose=None):
# Update list of things that need to be updated/plotted (and maybe
# draw them immediately)
try:
fun_name = inspect.currentframe().f_back.f_back.f_code.co_name
except Exception: # just in case one of these attrs is missing
fun_name = "unknown"
logger.debug(f"Updating plots based on {fun_name}: {repr(changes)}")
if self._plot_locked:
return
if self._info is None:
changes = ["head", "mri_fids"]
self._to_cf_t = dict(mri=dict(trans=np.eye(4)), head=None)
else:
self._to_cf_t = _get_transforms_to_coord_frame(
self._info, self.coreg.trans, coord_frame=self._coord_frame
)
all_keys = (
"head",
"mri_fids", # MRI first
"hsp",
"hpi",
"sensors",
"head_fids", # then dig
"helmet",
)
if changes == "all":
changes = list(all_keys)
elif changes == "sensors":
changes = all_keys[2:] # omit MRI ones
elif isinstance(changes, str):
changes = [changes]
changes = set(changes)
# ideally we would maybe have this in:
# with self._redraw_mutex:
# it would reduce "jerkiness" of the updates, but this should at least
# work okay
bad = changes.difference(set(all_keys))
assert len(bad) == 0, f"Unknown changes: {bad}"
self._redraws_pending.update(changes)
if self._immediate_redraw:
self._redraw()
@contextmanager
def _lock(self, plot=False, params=False, scale_mode=False, fitting=False):
"""Which part of the UI to temporarily disable."""
if plot:
old_plot_locked = self._plot_locked
self._plot_locked = True
if params:
old_params_locked = self._params_locked
self._params_locked = True
if scale_mode:
old_scale_mode = self.coreg._scale_mode
self.coreg._scale_mode = None
if fitting:
widgets = [
"sX",
"sY",
"sZ",
"tX",
"tY",
"tZ",
"rX",
"rY",
"rZ",
"fit_icp",
"fit_fiducials",
"fits_icp",
"fits_fiducials",
]
states = [
self._forward_widget_command(
w, "is_enabled", None, input_value=False, output_value=True
)
for w in widgets
]
self._forward_widget_command(widgets, "set_enabled", False)
try:
yield
finally:
if plot:
self._plot_locked = old_plot_locked
if params:
self._params_locked = old_params_locked
if scale_mode:
self.coreg._scale_mode = old_scale_mode
if fitting:
for idx, w in enumerate(widgets):
self._forward_widget_command(w, "set_enabled", states[idx])
def _display_message(self, msg=""):
self._forward_widget_command("status_message", "set_value", msg)
self._forward_widget_command("status_message", "show", None, input_value=False)
self._forward_widget_command(
"status_message", "update", None, input_value=False
)
if msg:
logger.info(msg)
def _follow_fiducial_view(self):
fid = self._current_fiducial.lower()
view = dict(lpa="left", rpa="right", nasion="front")
kwargs = dict(front=(90.0, 90.0), left=(180, 90), right=(0.0, 90))
kwargs = dict(zip(("azimuth", "elevation"), kwargs[view[fid]]))
if not self._lock_fids:
self._renderer.set_camera(distance="auto", **kwargs)
def _update_fiducials(self):
fid = self._current_fiducial
if not fid:
return
idx = _map_fid_name_to_idx(name=fid)
val = self.coreg.fiducials.dig[idx]["r"] * 1e3
with self._lock(plot=True):
self._forward_widget_command(["fid_X", "fid_Y", "fid_Z"], "set_value", val)
def _update_distance_estimation(self):
value = (
self.coreg._get_fiducials_distance_str()
+ "\n"
+ self.coreg._get_point_distance_str()
)
dists = self.coreg.compute_dig_mri_distances() * 1e3
if self._hsp_weight > 0:
if len(dists) == 0:
value += "\nNo head shape points found."
else:
value += (
"\nHSP <-> MRI (mean/min/max): "
f"{np.mean(dists):.2f} "
f"/ {np.min(dists):.2f} / {np.max(dists):.2f} mm"
)
self._forward_widget_command("fit_label", "set_value", value)
def _update_parameters(self):
with self._lock(plot=True, params=True):
# rotation
deg = np.rad2deg(self.coreg._rotation)
logger.debug(f" Rotation: {deg}")
self._forward_widget_command(["rX", "rY", "rZ"], "set_value", deg)
# translation
mm = self.coreg._translation * 1e3
logger.debug(f" Translation: {mm}")
self._forward_widget_command(["tX", "tY", "tZ"], "set_value", mm)
# scale
sc = self.coreg._scale * 1e2
logger.debug(f" Scale: {sc}")
self._forward_widget_command(["sX", "sY", "sZ"], "set_value", sc)
def _reset(self, keep_trans=False):
"""Refresh the scene, and optionally reset transformation & scaling.
Parameters
----------
keep_trans : bool
Whether to retain translation, rotation, and scaling; or reset them
to their default values (no translation, no rotation, no scaling).
"""
if not keep_trans:
self.coreg.set_scale(self.coreg._default_parameters[6:9])
self.coreg.set_rotation(self.coreg._default_parameters[:3])
self.coreg.set_translation(self.coreg._default_parameters[3:6])
self._update_plot()
self._update_parameters()
self._update_distance_estimation()
def _forward_widget_command(
self, names, command, value, input_value=True, output_value=False
):
"""Invoke a method of one or more widgets if the widgets exist.
Parameters
----------
names : str | array-like of str
The widget names to operate on.
command : str
The method to invoke.
value : object | array-like
The value(s) to pass to the method.
input_value : bool
Whether the ``command`` accepts a ``value``. If ``False``, no
``value`` will be passed to ``command``.
output_value : bool
Whether to return the return value of ``command``.
Returns
-------
ret : object | None
``None`` if ``output_value`` is ``False``, and the return value of
``command`` otherwise.
"""
_validate_type(item=names, types=(str, list), item_name="names")
if isinstance(names, str):
names = [names]
if not isinstance(value, str | float | int | dict | type(None)):
value = list(value)
assert len(names) == len(value)
for idx, name in enumerate(names):
val = value[idx] if isinstance(value, list) else value
if name in self._widgets and self._widgets[name] is not None:
if input_value:
ret = getattr(self._widgets[name], command)(val)
else:
ret = getattr(self._widgets[name], command)()
if output_value:
return ret
def _set_sensors_visibility(self, state):
sensors = [
"head_fiducials",
"hpi_coils",
"head_shape_points",
"sensors",
"helmet",
]
for sensor in sensors:
if sensor in self._actors and self._actors[sensor] is not None:
actors = self._actors[sensor]
actors = actors if isinstance(actors, list) else [actors]
for actor in actors:
actor.SetVisibility(state)
self._renderer._update()
def _update_actor(self, actor_name, actor):
# XXX: internal plotter/renderer should not be exposed
# Work around PyVista sequential update bug with iterable until > 0.42.3 is req
# https://github.com/pyvista/pyvista/pull/5046
actors = self._actors.get(actor_name) or [] # convert None to list
if not isinstance(actors, list):
actors = [actors]
for this_actor in actors:
self._renderer.plotter.remove_actor(this_actor, render=False)
self._actors[actor_name] = actor
def _add_mri_fiducials(self):
mri_fids_actors = _plot_mri_fiducials(
self._renderer,
self.coreg._fid_points,
self._subjects_dir,
self._subject,
self._to_cf_t,
self._fid_colors,
)
# disable picking on the markers
for actor in mri_fids_actors:
actor.SetPickable(False)
self._update_actor("mri_fiducials", mri_fids_actors)
def _add_head_fiducials(self):
head_fids_actors = _plot_head_fiducials(
self._renderer, self._info, self._to_cf_t, self._fid_colors
)
self._update_actor("head_fiducials", head_fids_actors)
def _add_hpi_coils(self):
if self._hpi_coils:
hpi_actors = _plot_hpi_coils(
self._renderer,
self._info,
self._to_cf_t,
opacity=self._defaults["sensor_opacity"],
scale=DEFAULTS["coreg"]["extra_scale"],
orient_glyphs=self._orient_glyphs,
scale_by_distance=self._scale_by_distance,
surf=self._head_geo,
check_inside=self._check_inside,
nearest=self._nearest,
)
else:
hpi_actors = None
self._update_actor("hpi_coils", hpi_actors)
def _add_head_shape_points(self):
if self._head_shape_points:
hsp_actors = _plot_head_shape_points(
self._renderer,
self._info,
self._to_cf_t,
opacity=self._defaults["sensor_opacity"],
orient_glyphs=self._orient_glyphs,
scale_by_distance=self._scale_by_distance,
mark_inside=self._mark_inside,
surf=self._head_geo,
mask=self.coreg._extra_points_filter,
check_inside=self._check_inside,
nearest=self._nearest,
)
else:
hsp_actors = None
self._update_actor("head_shape_points", hsp_actors)
def _add_channels(self):
plot_types = dict(eeg=False, meg=False, fnirs=False)
if self._eeg_channels:
plot_types["eeg"] = ["original"]
if self._meg_channels:
plot_types["meg"] = ["sensors"]
if self._fnirs_channels:
plot_types["fnirs"] = ["sources", "detectors"]
sensor_alpha = dict(
eeg=self._defaults["sensor_opacity"],
fnirs=self._defaults["sensor_opacity"],
meg=0.25,
)
picks = pick_types(
self._info,
ref_meg=False,
meg=True,
eeg=True,
fnirs=True,
exclude=(),
)
these_actors = _plot_sensors_3d(
self._renderer,
self._info,
self._to_cf_t,
picks=picks,
warn_meg=False,
head_surf=self._head_geo,
units="m",
sensor_alpha=sensor_alpha,
orient_glyphs=self._orient_glyphs,
scale_by_distance=self._scale_by_distance,
surf=self._head_geo,
check_inside=self._check_inside,
nearest=self._nearest,
**plot_types,
)
sens_actors = sum((these_actors or {}).values(), list())
self._update_actor("sensors", sens_actors)
def _add_head_surface(self):
bem = None
if self._head_resolution:
surface = "head-dense"
key = "high"
else:
surface = "head"
key = "low"
try:
head_actor, head_surf, _ = _plot_head_surface(
self._renderer,
surface,
self._subject,
self._subjects_dir,
bem,
self._coord_frame,
self._to_cf_t,
alpha=self._head_opacity,
)
except OSError:
head_actor, head_surf, _ = _plot_head_surface(
self._renderer,
"head",
self._subject,
self._subjects_dir,
bem,
self._coord_frame,
self._to_cf_t,
alpha=self._head_opacity,
)
key = "low"
self._update_actor("head", head_actor)
# mark head surface mesh to restrict picking
head_surf._picking_target = True
# We need to use _get_processed_mri_points to incorporate grow_hair
rr = self.coreg._get_processed_mri_points(key) * self.coreg._scale.T
head_surf.points = rr
head_surf.compute_normals()
self._surfaces["head"] = head_surf
tris = self._surfaces["head"].faces.reshape(-1, 4)[:, 1:]
assert tris.ndim == 2 and tris.shape[1] == 3, tris.shape
nn = self._surfaces["head"].point_normals
assert nn.shape == (len(rr), 3), nn.shape
self._head_geo = dict(rr=rr, tris=tris, nn=nn)
self._check_inside = _CheckInside(head_surf, mode="pyvista")
self._nearest = _DistanceQuery(rr)
def _add_helmet(self):
if self._helmet:
logger.debug("Drawing helmet")
head_mri_t = _get_trans(self.coreg.trans, "head", "mri")[0]
helmet_actor, _, _ = _plot_helmet(
self._renderer, self._info, self._to_cf_t, head_mri_t, self._coord_frame
)
else:
helmet_actor = None
self._update_actor("helmet", helmet_actor)
def _fit_fiducials(self):
with self._lock(scale_mode=True):
self._fits_fiducials()
def _fits_fiducials(self):
with self._lock(params=True, fitting=True):
start = time.time()
self.coreg.fit_fiducials(
lpa_weight=self._lpa_weight,
nasion_weight=self._nasion_weight,
rpa_weight=self._rpa_weight,
verbose=self._verbose,
)
end = time.time()
self._display_message(
f"Fitting fiducials finished in {end - start:.2f} seconds."
)
self._update_plot("sensors")
self._update_parameters()
self._update_distance_estimation()
def _fit_icp(self):
with self._lock(scale_mode=True):
self._fit_icp_real(update_head=False)
def _fits_icp(self):
self._fit_icp_real(update_head=True)
def _fit_icp_real(self, *, update_head):
with self._lock(params=True, fitting=True):
self._current_icp_iterations = 0
updates = ["hsp", "hpi", "sensors", "head_fids", "helmet"]
if update_head:
updates.insert(0, "head")
def callback(iteration, n_iterations):
self._display_message(f"Fitting ICP - iteration {iteration + 1}")
self._update_plot(updates)
self._current_icp_iterations += 1
self._update_distance_estimation()
self._update_parameters()
self._renderer._process_events() # allow a draw or cancel
start = time.time()
self.coreg.fit_icp(
n_iterations=self._icp_n_iterations,
lpa_weight=self._lpa_weight,
nasion_weight=self._nasion_weight,
rpa_weight=self._rpa_weight,
callback=callback,
verbose=self._verbose,
)
end = time.time()
self._display_message()
self._display_message(
f"Fitting ICP finished in {end - start:.2f} seconds and "
f"{self._current_icp_iterations} iterations."
)
del self._current_icp_iterations
def _task_save_subject(self):
from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
if MNE_3D_BACKEND_TESTING:
self._save_subject()
else:
self._job_queue.put(_WorkerData("save_subject", None))
def _task_set_parameter(self, value, mode_name, coord):
from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
if MNE_3D_BACKEND_TESTING:
self._set_parameter(value, mode_name, coord, self._plot_locked)
else:
self._parameter_queue.put(
_WorkerData(
"set_parameter",
dict(
value=value,
mode_name=mode_name,
coord=coord,
plot_locked=self._plot_locked,
),
)
)
def _overwrite_subject_callback(self, button_name):
if button_name == "Yes":
self._save_subject_callback(overwrite=True)
elif button_name == "Cancel":
self._accept_close_event = False
else:
assert button_name == "No" or button_name == "Discard"
def _check_subject_exists(self):
if not self._subject_to:
return False
subject_dirname = os.path.join("{subjects_dir}", "{subject}")
dest = subject_dirname.format(
subject=self._subject_to, subjects_dir=self._subjects_dir
)
return os.path.exists(dest)
def _save_subject(self, exit_mode=False):
dialog = "overwrite_subject_exit" if exit_mode else "overwrite_subject"
if self._check_subject_exists():
self._forward_widget_command(dialog, "show", True)
else:
self._save_subject_callback()
def _save_subject_callback(self, overwrite=False):
self._display_message(f"Saving {self._subject_to}...")
default_cursor = self._renderer._window_get_cursor()
self._renderer._window_set_cursor(
self._renderer._window_new_cursor("WaitCursor")
)
# prepare bem
bem_names = []
if self._scale_mode != "None":
can_prepare_bem = _mri_subject_has_bem(self._subject, self._subjects_dir)
else:
can_prepare_bem = False
if can_prepare_bem:
pattern = bem_fname.format(
subjects_dir=self._subjects_dir, subject=self._subject, name="(.+-bem)"
)
bem_dir, pattern = os.path.split(pattern)
for filename in os.listdir(bem_dir):
match = re.match(pattern, filename)
if match:
bem_names.append(match.group(1))
# save the scaled MRI
try:
self._display_message(f"Scaling {self._subject_to}...")
scale_mri(
subject_from=self._subject,
subject_to=self._subject_to,
scale=self.coreg._scale,
overwrite=overwrite,
subjects_dir=self._subjects_dir,
skip_fiducials=True,
labels=True,
annot=True,
on_defects="ignore",
)
except Exception:
logger.error(f"Error scaling {self._subject_to}")
bem_names = []
else:
self._display_message(f"Scaling {self._subject_to}... Done!")
# Precompute BEM solutions
for bem_name in bem_names:
try:
self._display_message(f"Computing {bem_name} solution...")
bem_file = bem_fname.format(
subjects_dir=self._subjects_dir,
subject=self._subject_to,
name=bem_name,
)
bemsol = make_bem_solution(bem_file)
write_bem_solution(bem_file[:-4] + "-sol.fif", bemsol)
except Exception:
logger.error(f"Error computing {bem_name} solution")
else:
self._display_message(f"Computing {bem_name} solution... Done!")
self._display_message(f"Saving {self._subject_to}... Done!")
self._renderer._window_set_cursor(default_cursor)
self._mri_scale_modified = False
def _save_mri_fiducials(self, fname):
self._display_message(f"Saving {fname}...")
dig_montage = self.coreg.fiducials
write_fiducials(
fname=fname, pts=dig_montage.dig, coord_frame="mri", overwrite=True
)
self._set_fiducials_file(fname)
self._display_message(f"Saving {fname}... Done!")
self._mri_fids_modified = False
def _save_trans(self, fname):
write_trans(fname, self.coreg.trans, overwrite=True)
self._display_message(f"{fname} transform file is saved.")
self._trans_modified = False
def _load_trans(self, trans):
if not isinstance(trans, Transform):
trans = read_trans(trans, return_all=True)
mri_head_t = _ensure_trans(trans, "mri", "head")["trans"]
rot_x, rot_y, rot_z = rotation_angles(mri_head_t)
x, y, z = mri_head_t[:3, 3]
self.coreg._update_params(
rot=np.array([rot_x, rot_y, rot_z]),
tra=np.array([x, y, z]),
)
self._update_parameters()
self._update_distance_estimation()
self._update_plot()
self._display_message(f"{trans} transform file is loaded.")
def _update_fiducials_label(self):
if self._fiducials_file is None:
text = (
"<p><strong>No custom MRI fiducials loaded!</strong></p>"
"<p>MRI fiducials could not be found in the standard "
"location. The displayed initial MRI fiducial locations "
"(diamonds) were derived from fsaverage. Place, lock, and "
"save fiducials to discard this message.</p>"
)
else:
assert self._fiducials_file == fid_fname.format(
subjects_dir=self._subjects_dir, subject=self._subject
)
assert self.coreg._fid_accurate is True
text = (
f"<p><strong>MRI fiducials (diamonds) loaded from "
f"standard location:</strong></p>"
f"<p>{self._fiducials_file}</p>"
)
self._forward_widget_command("mri_fiducials_label", "set_value", text)
def _configure_dock(self):
if self._renderer._kind == "notebook":
collapse = True # collapsible and collapsed
else:
collapse = None # not collapsible
self._renderer._dock_initialize(name="Input", area="left", max_width="375px")
mri_subject_layout = self._renderer._dock_add_group_box(
name="MRI Subject",
collapse=collapse,
)
subjects_dir_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["subjects_dir_field"] = self._renderer._dock_add_text(
name="subjects_dir_field",
value=self._subjects_dir,
placeholder="Subjects Directory",
callback=self._set_subjects_dir,
layout=subjects_dir_layout,
)
self._widgets["subjects_dir"] = self._renderer._dock_add_file_button(
name="subjects_dir",
desc="Load",
func=self._set_subjects_dir,
is_directory=True,
icon=True,
tooltip="Load the path to the directory containing the FreeSurfer subjects",
layout=subjects_dir_layout,
)
self._renderer._layout_add_widget(
layout=mri_subject_layout,
widget=subjects_dir_layout,
)
self._widgets["subject"] = self._renderer._dock_add_combo_box(
name="Subject",
value=self._subject,
rng=_get_subjects(self._subjects_dir),
callback=self._set_subject,
compact=True,
tooltip="Select the FreeSurfer subject name",
layout=mri_subject_layout,
)
mri_fiducials_layout = self._renderer._dock_add_group_box(
name="MRI Fiducials",
collapse=collapse,
)
# Add MRI fiducials I/O widgets
self._widgets["mri_fiducials_label"] = self._renderer._dock_add_label(
value="", # Will be filled via _update_fiducials_label()
layout=mri_fiducials_layout,
selectable=True,
)
# Reload & Save buttons go into their own layout widget
mri_fiducials_button_layout = self._renderer._dock_add_layout(vertical=False)
self._renderer._layout_add_widget(
layout=mri_fiducials_layout, widget=mri_fiducials_button_layout
)
self._widgets["reload_mri_fids"] = self._renderer._dock_add_button(
name="Reload MRI Fid.",
callback=lambda: self._set_fiducials_file(self._fiducials_file),
tooltip="Reload MRI fiducials from the standard location",
layout=mri_fiducials_button_layout,
)
# Disable reload button until we've actually loaded a fiducial file
# (happens in _set_fiducials_file method)
self._forward_widget_command("reload_mri_fids", "set_enabled", False)
self._widgets["save_mri_fids"] = self._renderer._dock_add_button(
name="Save MRI Fid.",
callback=lambda: self._save_mri_fiducials(
fid_fname.format(subjects_dir=self._subjects_dir, subject=self._subject)
),
tooltip="Save MRI fiducials to the standard location. Fiducials "
"must be locked first!",
layout=mri_fiducials_button_layout,
)
self._widgets["lock_fids"] = self._renderer._dock_add_check_box(
name="Lock fiducials",
value=self._lock_fids,
callback=self._set_lock_fids,
tooltip="Lock/Unlock interactive fiducial editing",
layout=mri_fiducials_layout,
)
self._widgets["fids"] = self._renderer._dock_add_radio_buttons(
value=self._defaults["fiducial"],
rng=self._defaults["fiducials"],
callback=self._set_current_fiducial,
vertical=False,
layout=mri_fiducials_layout,
)
fiducial_coords_layout = self._renderer._dock_add_layout()
for coord in ("X", "Y", "Z"):
name = f"fid_{coord}"
self._widgets[name] = self._renderer._dock_add_spin_box(
name=coord,
value=0.0,
rng=[-1e3, 1e3],
callback=partial(
self._set_fiducial,
coord=coord,
),
compact=True,
double=True,
step=1,
tooltip=f"Set the {coord} fiducial coordinate",
layout=fiducial_coords_layout,
)
self._renderer._layout_add_widget(mri_fiducials_layout, fiducial_coords_layout)
dig_source_layout = self._renderer._dock_add_group_box(
name="Info source with digitization",
collapse=collapse,
)
info_file_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["info_file_field"] = self._renderer._dock_add_text(
name="info_file_field",
value=self._info_file,
placeholder="Path to info",
callback=self._set_info_file,
layout=info_file_layout,
)
self._widgets["info_file"] = self._renderer._dock_add_file_button(
name="info_file",
desc="Load",
func=self._set_info_file,
icon=True,
tooltip="Load the FIFF file with digitization data for coregistration",
layout=info_file_layout,
)
self._renderer._layout_add_widget(
layout=dig_source_layout,
widget=info_file_layout,
)
self._widgets["grow_hair"] = self._renderer._dock_add_spin_box(
name="Grow Hair (mm)",
value=self._grow_hair,
rng=[0.0, 10.0],
callback=self._set_grow_hair,
tooltip="Compensate for hair on the digitizer head shape",
layout=dig_source_layout,
)
omit_hsp_layout_1 = self._renderer._dock_add_layout(vertical=False)
omit_hsp_layout_2 = self._renderer._dock_add_layout(vertical=False)
self._widgets["omit_distance"] = self._renderer._dock_add_spin_box(
name="Omit Distance (mm)",
value=self._omit_hsp_distance,
rng=[0.0, 100.0],
callback=self._set_omit_hsp_distance,
tooltip="Set the head shape points exclusion distance",
layout=omit_hsp_layout_1,
)
self._widgets["omit"] = self._renderer._dock_add_button(
name="Omit",
callback=self._omit_hsp,
tooltip="Exclude the head shape points that are far away from the MRI head",
layout=omit_hsp_layout_2,
)
self._widgets["reset_omit"] = self._renderer._dock_add_button(
name="Reset",
callback=self._reset_omit_hsp_filter,
tooltip="Reset all excluded head shape points",
layout=omit_hsp_layout_2,
)
self._renderer._layout_add_widget(dig_source_layout, omit_hsp_layout_1)
self._renderer._layout_add_widget(dig_source_layout, omit_hsp_layout_2)
view_options_layout = self._renderer._dock_add_group_box(
name="View Options",
collapse=collapse,
)
self._widgets["helmet"] = self._renderer._dock_add_check_box(
name="Show MEG helmet",
value=self._helmet,
callback=self._set_helmet,
tooltip="Enable/Disable MEG helmet",
layout=view_options_layout,
)
self._widgets["meg"] = self._renderer._dock_add_check_box(
name="Show MEG sensors",
value=self._meg_channels,
callback=self._set_meg_channels,
tooltip="Enable/Disable MEG sensors",
layout=view_options_layout,
)
self._widgets["high_res_head"] = self._renderer._dock_add_check_box(
name="Show high-resolution head",
value=self._head_resolution,
callback=self._set_head_resolution,
tooltip="Enable/Disable high resolution head surface",
layout=view_options_layout,
)
self._widgets["head_opacity"] = self._renderer._dock_add_slider(
name="Head opacity",
value=self._head_opacity,
rng=[0.25, 1.0],
callback=self._set_head_opacity,
compact=True,
double=True,
layout=view_options_layout,
)
self._renderer._dock_add_stretch()
self._renderer._dock_initialize(
name="Parameters", area="right", max_width="375px"
)
mri_scaling_layout = self._renderer._dock_add_group_box(
name="MRI Scaling",
collapse=collapse,
)
self._widgets["scaling_mode"] = self._renderer._dock_add_combo_box(
name="Scaling Mode",
value=self._defaults["scale_mode"],
rng=self._defaults["scale_modes"],
callback=self._set_scale_mode,
tooltip="Select the scaling mode",
compact=True,
layout=mri_scaling_layout,
)
scale_params_layout = self._renderer._dock_add_group_box(
name="Scaling Parameters",
layout=mri_scaling_layout,
)
coords = ["X", "Y", "Z"]
for coord in coords:
name = f"s{coord}"
attr = getattr(self.coreg, "_scale")
self._widgets[name] = self._renderer._dock_add_spin_box(
name=name,
value=attr[coords.index(coord)] * 1e2,
rng=[1.0, 10000.0], # percent
callback=partial(
self._set_parameter,
mode_name="scale",
coord=coord,
),
compact=True,
double=True,
step=1,
tooltip=f"Set the {coord} scaling parameter (in %)",
layout=scale_params_layout,
)
fit_scale_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["fits_fiducials"] = self._renderer._dock_add_button(
name="Fit fiducials with scaling",
callback=self._fits_fiducials,
tooltip="Find MRI scaling, rotation, and translation to fit all "
"3 fiducials",
layout=fit_scale_layout,
)
self._widgets["fits_icp"] = self._renderer._dock_add_button(
name="Fit ICP with scaling",
callback=self._fits_icp,
tooltip="Find MRI scaling, rotation, and translation to match the "
"head shape points",
layout=fit_scale_layout,
)
self._renderer._layout_add_widget(scale_params_layout, fit_scale_layout)
subject_to_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["subject_to"] = self._renderer._dock_add_text(
name="subject-to",
value=self._subject_to,
placeholder="subject name",
callback=self._set_subject_to,
layout=subject_to_layout,
)
self._widgets["save_subject"] = self._renderer._dock_add_button(
name="Save scaled anatomy",
callback=self._task_save_subject,
tooltip="Save scaled anatomy",
layout=subject_to_layout,
)
self._renderer._layout_add_widget(mri_scaling_layout, subject_to_layout)
param_layout = self._renderer._dock_add_group_box(
name="Translation (t) and Rotation (r)",
collapse=collapse,
)
for coord in coords:
coord_layout = self._renderer._dock_add_layout(vertical=False)
for mode, mode_name in (("t", "Translation"), ("r", "Rotation")):
name = f"{mode}{coord}"
attr = getattr(self.coreg, f"_{mode_name.lower()}")
rng = [-360, 360] if mode_name == "Rotation" else [-100, 100]
unit = "°" if mode_name == "Rotation" else "mm"
self._widgets[name] = self._renderer._dock_add_spin_box(
name=name,
value=attr[coords.index(coord)] * 1e3,
rng=np.array(rng),
callback=partial(
self._task_set_parameter,
mode_name=mode_name.lower(),
coord=coord,
),
compact=True,
double=True,
step=1,
tooltip=f"Set the {coord} {mode_name.lower()}"
f" parameter (in {unit})",
layout=coord_layout,
)
self._renderer._layout_add_widget(param_layout, coord_layout)
fit_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["fit_fiducials"] = self._renderer._dock_add_button(
name="Fit fiducials",
callback=self._fit_fiducials,
tooltip="Find rotation and translation to fit all 3 fiducials",
layout=fit_layout,
)
self._widgets["fit_icp"] = self._renderer._dock_add_button(
name="Fit ICP",
callback=self._fit_icp,
tooltip="Find rotation and translation to match the head shape points",
layout=fit_layout,
)
self._renderer._layout_add_widget(param_layout, fit_layout)
trans_layout = self._renderer._dock_add_group_box(
name="HEAD <> MRI Transform",
collapse=collapse,
)
save_trans_layout = self._renderer._dock_add_layout(vertical=False)
self._widgets["save_trans"] = self._renderer._dock_add_file_button(
name="save_trans",
desc="Save...",
save=True,
func=self._save_trans,
tooltip="Save the transform file to disk",
layout=save_trans_layout,
filter_="Head->MRI transformation (*-trans.fif *_trans.fif)",
initial_directory=self._info_file.parent,
)
self._widgets["load_trans"] = self._renderer._dock_add_file_button(
name="load_trans",
desc="Load...",
func=self._load_trans,
tooltip="Load the transform file from disk",
layout=save_trans_layout,
filter_="Head->MRI transformation (*-trans.fif *_trans.fif)",
initial_directory=self._info_file.parent,
)
self._renderer._layout_add_widget(trans_layout, save_trans_layout)
self._widgets["reset_trans"] = self._renderer._dock_add_button(
name="Reset Parameters",
callback=self._reset,
tooltip="Reset all the parameters affecting the coregistration",
layout=trans_layout,
)
fitting_options_layout = self._renderer._dock_add_group_box(
name="Fitting Options",
collapse=collapse,
)
self._widgets["fit_label"] = self._renderer._dock_add_label(
value="",
layout=fitting_options_layout,
)
self._widgets["icp_n_iterations"] = self._renderer._dock_add_spin_box(
name="Number Of ICP Iterations",
value=self._defaults["icp_n_iterations"],
rng=[1, 100],
callback=self._set_icp_n_iterations,
compact=True,
double=False,
tooltip="Set the number of ICP iterations",
layout=fitting_options_layout,
)
self._widgets["icp_fid_match"] = self._renderer._dock_add_combo_box(
name="Fiducial point matching",
value=self._defaults["icp_fid_match"],
rng=self._defaults["icp_fid_matches"],
callback=self._set_icp_fid_match,
compact=True,
tooltip="Select the fiducial point matching method",
layout=fitting_options_layout,
)
weights_layout = self._renderer._dock_add_group_box(
name="Weights",
layout=fitting_options_layout,
)
for point, fid in zip(("HSP", "EEG", "HPI"), self._defaults["fiducials"]):
weight_layout = self._renderer._dock_add_layout(vertical=False)
point_lower = point.lower()
name = f"{point_lower}_weight"
self._widgets[name] = self._renderer._dock_add_spin_box(
name=point,
value=getattr(self, f"_{point_lower}_weight"),
rng=[0.0, 100.0],
callback=partial(self._set_point_weight, point=point_lower),
compact=True,
double=True,
tooltip=f"Set the {point} weight",
layout=weight_layout,
)
fid_lower = fid.lower()
name = f"{fid_lower}_weight"
self._widgets[name] = self._renderer._dock_add_spin_box(
name=fid,
value=getattr(self, f"_{fid_lower}_weight"),
rng=[0.0, 100.0],
callback=partial(self._set_point_weight, point=fid_lower),
compact=True,
double=True,
tooltip=f"Set the {fid} weight",
layout=weight_layout,
)
self._renderer._layout_add_widget(weights_layout, weight_layout)
self._widgets["reset_fitting_options"] = self._renderer._dock_add_button(
name="Reset Fitting Options",
callback=self._reset_fitting_parameters,
tooltip="Reset all the fitting parameters to default value",
layout=fitting_options_layout,
)
self._renderer._dock_add_stretch()
def _configure_status_bar(self):
self._renderer._status_bar_initialize()
self._widgets["status_message"] = self._renderer._status_bar_add_label(
"", stretch=1
)
self._forward_widget_command(
"status_message", "hide", value=None, input_value=False
)
def _clean(self):
if not self._accept_close_event:
return
self._renderer = None
self._widgets.clear()
self._actors.clear()
self._surfaces.clear()
self._defaults.clear()
self._head_geo = None
self._check_inside = None
self._nearest = None
self._redraw = None
@safe_event
def close(self):
"""Close interface and cleanup data structure."""
if self._renderer is not None:
self._renderer.close()
def _close_dialog_callback(self, button_name):
from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
self._accept_close_event = True
if button_name == "Save":
if self._trans_modified:
self._forward_widget_command("save_trans", "set_value", None)
# cancel means _save_trans is not called
if self._trans_modified:
self._accept_close_event = False
if self._mri_fids_modified:
self._forward_widget_command("save_mri_fids", "set_value", None)
if self._mri_scale_modified:
if self._subject_to:
self._save_subject(exit_mode=True)
else:
dialog = self._renderer._dialog_create(
title="CoregistrationUI",
text="The name of the output subject used to "
"save the scaled anatomy is not set.",
info_text="Please set a subject name",
callback=lambda x: None,
buttons=["Ok"],
modal=not MNE_3D_BACKEND_TESTING,
)
dialog.show()
self._accept_close_event = False
elif button_name == "Cancel":
self._accept_close_event = False
else:
assert button_name == "Discard"
def _close_callback(self):
if self._trans_modified or self._mri_fids_modified or self._mri_scale_modified:
from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
# prepare the dialog's text
text = "The following is/are not saved:"
text += "<ul>"
if self._trans_modified:
text += "<li>Head<>MRI transform</li>"
if self._mri_fids_modified:
text += "<li>MRI fiducials</li>"
if self._mri_scale_modified:
text += "<li>scaled subject MRI</li>"
text += "</ul>"
self._widgets["close_dialog"] = self._renderer._dialog_create(
title="CoregistrationUI",
text=text,
info_text="Do you want to save?",
callback=self._close_dialog_callback,
buttons=["Save", "Discard", "Cancel"],
# modal=True means that the dialog blocks the application
# when show() is called, until one of the buttons is clicked
modal=not MNE_3D_BACKEND_TESTING,
)
self._widgets["close_dialog"].show()
return self._accept_close_event
Datasets
Models
