"""Convenience functions for opening GUIs.""" # Authors: Christian Brodbeck # # 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, 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 | path 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 verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). 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 `_ and `for subjects for which no MRI is available `_. """ 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 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) 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)