/
__init__.py
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/
__init__.py
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"""Convenience functions for opening GUIs."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..utils import _check_mayavi_version, verbose, get_config
from ._backend import _testing_mode
def _initialize_gui(frame, view=None):
"""Initialize GUI depending on testing mode."""
if _testing_mode(): # open without entering mainloop
return frame.edit_traits(view=view), frame
else:
frame.configure_traits(view=view)
return frame
@verbose
def coregistration(tabbed=False, split=True, width=None, inst=None,
subject=None, subjects_dir=None, guess_mri_subject=None,
height=None, head_opacity=None, head_high_res=None,
trans=None, scrollable=True, project_eeg=None,
orient_to_surface=None, scale_by_distance=None,
mark_inside=None, interaction=None, scale=None,
advanced_rendering=None, verbose=None):
"""Coregister an MRI with a subject's head shape.
The recommended way to use the GUI is through bash with:
.. code-block:: bash
$ mne coreg
Parameters
----------
tabbed : bool
Combine the data source panel and the coregistration panel into a
single panel with tabs.
split : bool
Split the main panels with a movable splitter (good for QT4 but
unnecessary for wx backend).
width : int | None
Specify the width for window (in logical pixels).
Default is None, which uses ``MNE_COREG_WINDOW_WIDTH`` config value
(which defaults to 800).
inst : None | str
Path to an instance file containing the digitizer data. Compatible for
Raw, Epochs, and Evoked files.
subject : None | str
Name of the mri subject.
subjects_dir : None | str
Override the SUBJECTS_DIR environment variable
(sys.environ['SUBJECTS_DIR'])
guess_mri_subject : bool
When selecting a new head shape file, guess the subject's name based
on the filename and change the MRI subject accordingly (default True).
height : int | None
Specify a height for window (in logical pixels).
Default is None, which uses ``MNE_COREG_WINDOW_WIDTH`` config value
(which defaults to 400).
head_opacity : float | None
The opacity of the head surface in the range [0., 1.].
Default is None, which uses ``MNE_COREG_HEAD_OPACITY`` config value
(which defaults to 1.).
head_high_res : bool | None
Use a high resolution head surface.
Default is None, which uses ``MNE_COREG_HEAD_HIGH_RES`` config value
(which defaults to True).
trans : str | None
The transform file to use.
scrollable : bool
Make the coregistration panel vertically scrollable (default True).
project_eeg : bool | None
If True (default None), project EEG electrodes to the head surface.
This is only for visualization purposes and does not affect fitting.
.. versionadded:: 0.16
orient_to_surface : bool | None
If True (default None), orient EEG electrode and head shape points
to the head surface.
.. versionadded:: 0.16
scale_by_distance : bool | None
If True (default None), scale the digitization points by their
distance from the scalp surface.
.. versionadded:: 0.16
mark_inside : bool | None
If True (default None), mark points inside the head surface in a
different color.
.. versionadded:: 0.16
interaction : str | None
Can be 'terrain' (default None), use terrain-style interaction (where
"up" is the Z/superior direction), or 'trackball' to use
orientationless interactions.
.. versionadded:: 0.16
scale : float | None
The scaling for the scene.
.. versionadded:: 0.16
advanced_rendering : bool
Use advanced OpenGL rendering techniques (default True).
For some renderers (such as MESA software) this can cause rendering
bugs.
.. versionadded:: 0.18
%(verbose)s
Notes
-----
Many parameters (e.g., ``project_eeg``) take None as a parameter,
which means that the default will be read from the MNE-Python
configuration file (which gets saved when exiting).
Step by step instructions for the coregistrations can be accessed as
slides, `for subjects with structural MRI
<https://www.slideshare.net/mne-python/mnepython-coregistration>`_ and `for
subjects for which no MRI is available
<https://www.slideshare.net/mne-python/mnepython-scale-mri>`_.
"""
config = get_config(home_dir=os.environ.get('_MNE_FAKE_HOME_DIR'))
if guess_mri_subject is None:
guess_mri_subject = config.get(
'MNE_COREG_GUESS_MRI_SUBJECT', 'true') == 'true'
if head_high_res is None:
head_high_res = config.get('MNE_COREG_HEAD_HIGH_RES', 'true') == 'true'
if advanced_rendering is None:
advanced_rendering = \
config.get('MNE_COREG_ADVANCED_RENDERING', 'true') == 'true'
if head_opacity is None:
head_opacity = config.get('MNE_COREG_HEAD_OPACITY', 1.)
if width is None:
width = config.get('MNE_COREG_WINDOW_WIDTH', 800)
if height is None:
height = config.get('MNE_COREG_WINDOW_HEIGHT', 600)
if subjects_dir is None:
if 'SUBJECTS_DIR' in config:
subjects_dir = config['SUBJECTS_DIR']
elif 'MNE_COREG_SUBJECTS_DIR' in config:
subjects_dir = config['MNE_COREG_SUBJECTS_DIR']
if project_eeg is None:
project_eeg = config.get('MNE_COREG_PROJECT_EEG', '') == 'true'
if orient_to_surface is None:
orient_to_surface = (config.get('MNE_COREG_ORIENT_TO_SURFACE', '') ==
'true')
if scale_by_distance is None:
scale_by_distance = (config.get('MNE_COREG_SCALE_BY_DISTANCE', '') ==
'true')
if interaction is None:
interaction = config.get('MNE_COREG_INTERACTION', 'trackball')
if mark_inside is None:
mark_inside = config.get('MNE_COREG_MARK_INSIDE', '') == 'true'
if scale is None:
scale = config.get('MNE_COREG_SCENE_SCALE', 0.16)
head_opacity = float(head_opacity)
width = int(width)
height = int(height)
scale = float(scale)
_check_mayavi_version()
from ._backend import _check_backend
_check_backend()
from ._coreg_gui import CoregFrame, _make_view
view = _make_view(tabbed, split, width, height, scrollable)
frame = CoregFrame(inst, subject, subjects_dir, guess_mri_subject,
head_opacity, head_high_res, trans, config,
project_eeg=project_eeg,
orient_to_surface=orient_to_surface,
scale_by_distance=scale_by_distance,
mark_inside=mark_inside, interaction=interaction,
scale=scale, advanced_rendering=advanced_rendering)
return _initialize_gui(frame, view)
def fiducials(subject=None, fid_file=None, subjects_dir=None):
"""Set the fiducials for an MRI subject.
Parameters
----------
subject : str
Name of the mri subject.
fid_file : None | str
Load a fiducials file different form the subject's default
("{subjects_dir}/{subject}/bem/{subject}-fiducials.fif").
subjects_dir : None | str
Overrule the subjects_dir environment variable.
Notes
-----
All parameters are optional, since they can be set through the GUI.
The functionality in this GUI is also part of :func:`coregistration`.
"""
_check_mayavi_version()
from ._backend import _check_backend
_check_backend()
from ._fiducials_gui import FiducialsFrame
frame = FiducialsFrame(subject, subjects_dir, fid_file=fid_file)
return _initialize_gui(frame)
def kit2fiff():
"""Convert KIT files to the fiff format.
The recommended way to use the GUI is through bash with::
$ mne kit2fiff
"""
_check_mayavi_version()
from ._backend import _check_backend
_check_backend()
from ._kit2fiff_gui import Kit2FiffFrame
frame = Kit2FiffFrame()
return _initialize_gui(frame)