def setup_ui(self):
super(AtlasUI, self).setup_ui()
image_clear_btn = QPushButton(text="清空")
image_clear_btn.clicked.connect(self.on_image_clear_btn_clicked)
image_listview = QListView()
image_listview.setAcceptDrops(True)
image_list_model = QStandardItemModel(image_listview)
image_list_model.itemChanged.connect(self.on_image_changed)
image_listview.setModel(image_list_model)
self.main_layout.addWidget(image_clear_btn, 0, 0, 1, 1, QtCore.Qt.AlignLeft)
self.main_layout.addWidget(image_listview, 1, 0, 1, 1)
self.image_clear_btn = image_clear_btn
self.image_listview = image_listview
self.image_list_model = image_list_model
self.refresh_images()
def addOutputFolder(self, name: str):
listview = QListView(self)
listview.setObjectName("tab_" + name.lower())
listview.setSelectionMode(QListView.ExtendedSelection)
listview.setAcceptDrops(True)
listview.setMouseTracking(True)
listview.setModel(
TargetListModel(listview, self._network, self._shared_states))
listview.pressed.connect(self.updateSelectedOutput)
listview.entered.connect(self.updateHighlightOutput)
listview.enterEvent = self.listOutputViewEnter
listview.leaveEvent = self.listOutputViewLeave
listview.setContextMenuPolicy(Qt.CustomContextMenu)
listview.customContextMenuRequested.connect(
lambda pos: self.outputContextMenu(listview, pos))
self._meta.folders[name] = FolderMeta()
self.tab_folders.addTab(listview, name.upper())
self.updateFolderNames()
class MainWindow(QMainWindow):
"""MNELAB main window."""
def __init__(self, model):
"""Initialize MNELAB main window.
Parameters
----------
model : mnelab.model.Model instance
The main window needs to connect to a model containing all data sets. This
decouples the GUI from the data (model/view).
"""
super().__init__()
self.model = model # data model
self.setWindowTitle("MNELAB")
# restore settings
settings = read_settings()
self.recent = settings["recent"] # list of recent files
self.resize(settings["size"])
self.move(settings["pos"])
# remove None entries from self.recent
self.recent = [recent for recent in self.recent if recent is not None]
# trigger theme setting
QIcon.setThemeSearchPaths([str(Path(__file__).parent / "icons")])
self.event(QEvent(QEvent.PaletteChange))
self.actions = {} # contains all actions
# initialize menus
file_menu = self.menuBar().addMenu("&File")
icon = QIcon.fromTheme("open-file")
self.actions["open_file"] = file_menu.addAction(
icon, "&Open...", self.open_data, QKeySequence.Open)
self.recent_menu = file_menu.addMenu("Open recent")
self.recent_menu.aboutToShow.connect(self._update_recent_menu)
self.recent_menu.triggered.connect(self._load_recent)
if not self.recent:
self.recent_menu.setEnabled(False)
self.actions["close_file"] = file_menu.addAction(
"&Close", self.model.remove_data, QKeySequence.Close)
self.actions["close_all"] = file_menu.addAction(
"Close all", self.close_all)
file_menu.addSeparator()
icon = QIcon.fromTheme("meta-info")
self.actions["meta_info"] = file_menu.addAction(
icon, "Show information...", self.meta_info)
file_menu.addSeparator()
self.actions["import_bads"] = file_menu.addAction(
"Import bad channels...", lambda: self.import_file(
model.import_bads, "Import bad channels", "*.csv"))
self.actions["import_events"] = file_menu.addAction(
"Import events...", lambda: self.import_file(
model.import_events, "Import events", "*.csv"))
self.actions["import_annotations"] = file_menu.addAction(
"Import annotations...", lambda: self.import_file(
model.import_annotations, "Import annotations", "*.csv"))
self.actions["import_ica"] = file_menu.addAction(
"Import &ICA...", lambda: self.open_file(
model.import_ica, "Import ICA", "*.fif *.fif.gz"))
file_menu.addSeparator()
self.export_menu = file_menu.addMenu("Export data")
for ext, description in writers.items():
action = "export_data" + ext.replace(".", "_")
self.actions[action] = self.export_menu.addAction(
f"{ext[1:].upper()} ({description[1]})...",
partial(self.export_file, model.export_data, "Export data",
"*" + ext))
self.actions["export_bads"] = file_menu.addAction(
"Export &bad channels...", lambda: self.export_file(
model.export_bads, "Export bad channels", "*.csv"))
self.actions["export_events"] = file_menu.addAction(
"Export &events...", lambda: self.export_file(
model.export_events, "Export events", "*.csv"))
self.actions["export_annotations"] = file_menu.addAction(
"Export &annotations...", lambda: self.export_file(
model.export_annotations, "Export annotations", "*.csv"))
self.actions["export_ica"] = file_menu.addAction(
"Export ICA...", lambda: self.export_file(
model.export_ica, "Export ICA", "*.fif *.fif.gz"))
file_menu.addSeparator()
self.actions["xdf_chunks"] = file_menu.addAction(
"Show XDF chunks...", self.xdf_chunks)
file_menu.addSeparator()
self.actions["quit"] = file_menu.addAction("&Quit", self.close,
QKeySequence.Quit)
edit_menu = self.menuBar().addMenu("&Edit")
self.actions["pick_chans"] = edit_menu.addAction(
"P&ick channels...", self.pick_channels)
icon = QIcon.fromTheme("chan-props")
self.actions["chan_props"] = edit_menu.addAction(
icon, "Channel &properties...", self.channel_properties)
self.actions["set_montage"] = edit_menu.addAction(
"Set &montage...", self.set_montage)
edit_menu.addSeparator()
self.actions["set_ref"] = edit_menu.addAction("Set &reference...",
self.set_reference)
edit_menu.addSeparator()
self.actions["annotations"] = edit_menu.addAction(
"&Annotations...", self.edit_annotations)
self.actions["events"] = edit_menu.addAction("&Events...",
self.edit_events)
edit_menu.addSeparator()
self.actions["crop"] = edit_menu.addAction("&Crop data...", self.crop)
self.actions["append_data"] = edit_menu.addAction(
"Appen&d data...", self.append_data)
plot_menu = self.menuBar().addMenu("&Plot")
icon = QIcon.fromTheme("plot-data")
self.actions["plot_data"] = plot_menu.addAction(
icon, "&Data", self.plot_data)
icon = QIcon.fromTheme("plot-psd")
self.actions["plot_psd"] = plot_menu.addAction(
icon, "&Power spectral density", self.plot_psd)
icon = QIcon.fromTheme("plot-locations")
self.actions["plot_locations"] = plot_menu.addAction(
icon, "&Channel locations", self.plot_locations)
self.actions["plot_erds"] = plot_menu.addAction(
"&ERDS maps...", self.plot_erds)
plot_menu.addSeparator()
self.actions["plot_ica_components"] = plot_menu.addAction(
"ICA &components...", self.plot_ica_components)
self.actions["plot_ica_sources"] = plot_menu.addAction(
"ICA &sources...", self.plot_ica_sources)
tools_menu = self.menuBar().addMenu("&Tools")
icon = QIcon.fromTheme("filter-data")
self.actions["filter"] = tools_menu.addAction(icon, "&Filter data...",
self.filter_data)
icon = QIcon.fromTheme("find-events")
self.actions["find_events"] = tools_menu.addAction(
icon, "Find &events...", self.find_events)
self.actions["events_from_annotations"] = tools_menu.addAction(
"Create events from annotations", self.events_from_annotations)
self.actions["annotations_from_events"] = tools_menu.addAction(
"Create annotations from events", self.annotations_from_events)
tools_menu.addSeparator()
nirs_menu = tools_menu.addMenu("NIRS")
self.actions["convert_od"] = nirs_menu.addAction(
"Convert to &optical density", self.convert_od)
self.actions["convert_bl"] = nirs_menu.addAction(
"Convert to &haemoglobin", self.convert_bl)
tools_menu.addSeparator()
icon = QIcon.fromTheme("run-ica")
self.actions["run_ica"] = tools_menu.addAction(icon, "Run &ICA...",
self.run_ica)
self.actions["apply_ica"] = tools_menu.addAction(
"Apply &ICA", self.apply_ica)
tools_menu.addSeparator()
self.actions["interpolate_bads"] = tools_menu.addAction(
"Interpolate bad channels...", self.interpolate_bads)
tools_menu.addSeparator()
icon = QIcon.fromTheme("epoch-data")
self.actions["epoch_data"] = tools_menu.addAction(
icon, "Create epochs...", self.epoch_data)
view_menu = self.menuBar().addMenu("&View")
self.actions["history"] = view_menu.addAction("&History...",
self.show_history)
self.actions["toolbar"] = view_menu.addAction("&Toolbar",
self._toggle_toolbar)
self.actions["toolbar"].setCheckable(True)
self.actions["statusbar"] = view_menu.addAction(
"&Statusbar", self._toggle_statusbar)
self.actions["statusbar"].setCheckable(True)
help_menu = self.menuBar().addMenu("&Help")
self.actions["about"] = help_menu.addAction("&About", self.show_about)
self.actions["about_qt"] = help_menu.addAction("About &Qt",
self.show_about_qt)
# actions that are always enabled
self.always_enabled = [
"open_file", "about", "about_qt", "quit", "xdf_chunks", "toolbar",
"statusbar"
]
# set up toolbar
self.toolbar = self.addToolBar("toolbar")
self.toolbar.setObjectName("toolbar")
self.toolbar.addAction(self.actions["open_file"])
self.toolbar.addAction(self.actions["meta_info"])
self.toolbar.addSeparator()
self.toolbar.addAction(self.actions["chan_props"])
self.toolbar.addSeparator()
self.toolbar.addAction(self.actions["plot_data"])
self.toolbar.addAction(self.actions["plot_psd"])
self.toolbar.addAction(self.actions["plot_locations"])
self.toolbar.addSeparator()
self.toolbar.addAction(self.actions["filter"])
self.toolbar.addAction(self.actions["find_events"])
self.toolbar.addAction(self.actions["epoch_data"])
self.toolbar.addAction(self.actions["run_ica"])
self.toolbar.setMovable(False)
self.setUnifiedTitleAndToolBarOnMac(True)
if settings["toolbar"]:
self.toolbar.show()
self.actions["toolbar"].setChecked(True)
else:
self.toolbar.hide()
self.actions["toolbar"].setChecked(False)
# set up data model for sidebar (list of open files)
self.names = QStringListModel()
self.names.dataChanged.connect(self._update_names)
splitter = QSplitter()
self.sidebar = QListView()
self.sidebar.setFrameStyle(QFrame.NoFrame)
self.sidebar.setFocusPolicy(Qt.NoFocus)
self.sidebar.setModel(self.names)
self.sidebar.clicked.connect(self._update_data)
splitter.addWidget(self.sidebar)
self.infowidget = InfoWidget()
splitter.addWidget(self.infowidget)
width = splitter.size().width()
splitter.setSizes((int(width * 0.3), int(width * 0.7)))
self.setCentralWidget(splitter)
self.status_label = QLabel()
self.statusBar().addPermanentWidget(self.status_label)
if settings["statusbar"]:
self.statusBar().show()
self.actions["statusbar"].setChecked(True)
else:
self.statusBar().hide()
self.actions["statusbar"].setChecked(False)
self.setAcceptDrops(True)
self.data_changed()
def data_changed(self):
# update sidebar
self.names.setStringList(self.model.names)
self.sidebar.setCurrentIndex(self.names.index(self.model.index))
# update info widget
if self.model.data:
self.infowidget.set_values(self.model.get_info())
else:
self.infowidget.clear()
# update status bar
if self.model.data:
mb = self.model.nbytes / 1024**2
self.status_label.setText(f"Total Memory: {mb:.2f} MB")
else:
self.status_label.clear()
# toggle actions
if len(self.model) == 0: # disable if no data sets are currently open
enabled = False
else:
enabled = True
for name, action in self.actions.items(): # toggle
if name not in self.always_enabled:
action.setEnabled(enabled)
if self.model.data: # toggle if specific conditions are met
bads = bool(self.model.current["data"].info["bads"])
self.actions["export_bads"].setEnabled(enabled and bads)
events = self.model.current["events"] is not None
self.actions["export_events"].setEnabled(enabled and events)
if self.model.current["dtype"] == "raw":
annot = bool(self.model.current["data"].annotations)
else:
annot = False
self.actions["export_annotations"].setEnabled(enabled and annot)
self.actions["annotations"].setEnabled(enabled and annot)
locations = has_locations(self.model.current["data"].info)
self.actions["plot_locations"].setEnabled(enabled and locations)
ica = bool(self.model.current["ica"])
self.actions["apply_ica"].setEnabled(enabled and ica)
self.actions["export_ica"].setEnabled(enabled and ica)
self.actions["plot_erds"].setEnabled(
enabled and self.model.current["dtype"] == "epochs")
self.actions["plot_ica_components"].setEnabled(enabled and ica
and locations)
self.actions["plot_ica_sources"].setEnabled(enabled and ica)
self.actions["interpolate_bads"].setEnabled(enabled and locations
and bads)
self.actions["events"].setEnabled(enabled and events)
self.actions["events_from_annotations"].setEnabled(enabled
and annot)
self.actions["annotations_from_events"].setEnabled(enabled
and events)
self.actions["find_events"].setEnabled(
enabled and self.model.current["dtype"] == "raw")
self.actions["epoch_data"].setEnabled(
enabled and events and self.model.current["dtype"] == "raw")
self.actions["crop"].setEnabled(
enabled and self.model.current["dtype"] == "raw")
append = bool(self.model.get_compatibles())
self.actions["append_data"].setEnabled(
enabled and append
and (self.model.current["dtype"] in ("raw", "epochs")))
self.actions["meta_info"].setEnabled(
enabled
and self.model.current["ftype"] in ["XDF", "XDFZ", "XDF.GZ"])
self.actions["convert_od"].setEnabled(
len(
mne.pick_types(self.model.current["data"].info,
fnirs="fnirs_cw_amplitude")))
self.actions["convert_bl"].setEnabled(
len(
mne.pick_types(self.model.current["data"].info,
fnirs="fnirs_od")))
# disable unsupported exporters for epochs (all must support raw)
if self.model.current["dtype"] == "epochs":
for ext, description in writers.items():
action = "export_data" + ext.replace(".", "_")
if "epoch" in description[2]:
self.actions[action].setEnabled(True)
else:
self.actions[action].setEnabled(False)
# add to recent files
if len(self.model) > 0:
self._add_recent(self.model.current["fname"])
def open_data(self, fname=None):
"""Open raw file."""
if fname is None:
fname = QFileDialog.getOpenFileName(self, "Open raw")[0]
if fname:
if not (Path(fname).is_file() or Path(fname).is_dir()):
self._remove_recent(fname)
QMessageBox.critical(self, "File does not exist",
f"File {fname} does not exist anymore.")
return
ext = "".join(Path(fname).suffixes)
if any([ext.endswith(e) for e in (".xdf", ".xdfz", ".xdf.gz")]):
rows, disabled = [], []
for idx, s in enumerate(resolve_streams(fname)):
rows.append([
s["stream_id"], s["name"], s["type"],
s["channel_count"], s["channel_format"],
s["nominal_srate"]
])
is_marker = (s["nominal_srate"] == 0
or s["channel_format"] == "string")
if is_marker: # disable marker streams
disabled.append(idx)
enabled = list(set(range(len(rows))) - set(disabled))
if enabled:
selected = enabled[0]
else:
selected = None
dialog = XDFStreamsDialog(self,
rows,
selected=selected,
disabled=disabled)
if dialog.exec():
row = dialog.view.selectionModel().selectedRows()[0].row()
stream_id = dialog.model.data(dialog.model.index(row, 0))
srate = "effective" if dialog.effective_srate else "nominal"
prefix_markers = dialog.prefix_markers
kwargs = {}
if srate == "nominal":
kwargs["srate"] = srate
if prefix_markers:
kwargs["prefix_markers"] = prefix_markers
self.model.load(fname, stream_id=stream_id, **kwargs)
else: # all other file formats
try:
self.model.load(fname)
except FileNotFoundError as e:
QMessageBox.critical(self, "File not found", str(e))
except ValueError as e:
QMessageBox.critical(self, "Unknown file type", str(e))
def open_file(self, f, text, ffilter="*"):
"""Open file."""
fname = QFileDialog.getOpenFileName(self, text, filter=ffilter)[0]
if fname:
f(fname)
def xdf_chunks(self):
"""Show XDF chunks."""
fname = QFileDialog.getOpenFileName(self,
"Select XDF file",
filter="*.xdf *.xdfz *.xdf.gz")[0]
if fname:
chunks = list_chunks(fname)
dialog = XDFChunksDialog(self, chunks, fname)
dialog.exec_()
def export_file(self, f, text, ffilter="*"):
"""Export to file."""
fname = QFileDialog.getSaveFileName(self, text, filter=ffilter)[0]
if fname:
if ffilter != "*":
exts = [ext.replace("*", "") for ext in ffilter.split()]
maxsuffixes = max([ext.count(".") for ext in exts])
suffixes = Path(fname).suffixes
for i in range(-maxsuffixes, 0):
ext = "".join(suffixes[i:])
if ext in exts:
return f(fname)
fname = fname + exts[0]
return f(fname)
def import_file(self, f, text, ffilter="*"):
"""Import file."""
fname = QFileDialog.getOpenFileName(self, text, filter=ffilter)[0]
if fname:
try:
f(fname)
except LabelsNotFoundError as e:
QMessageBox.critical(self, "Channel labels not found", str(e))
except InvalidAnnotationsError as e:
QMessageBox.critical(self, "Invalid annotations", str(e))
def close_all(self):
"""Close all currently open data sets."""
msg = QMessageBox.question(self, "Close all data sets",
"Close all data sets?")
if msg == QMessageBox.Yes:
while len(self.model) > 0:
self.model.remove_data()
def meta_info(self):
"""Show XDF meta info."""
xml = get_xml(self.model.current["fname"])
dialog = MetaInfoDialog(self, xml)
dialog.exec()
def pick_channels(self):
"""Pick channels in current data set."""
channels = self.model.current["data"].info["ch_names"]
dialog = PickChannelsDialog(self, channels, selected=channels)
if dialog.exec():
picks = [item.data(0) for item in dialog.channels.selectedItems()]
drops = list(set(channels) - set(picks))
if drops:
self.auto_duplicate()
self.model.drop_channels(drops)
self.model.history.append(f"data.drop_channels({drops})")
def channel_properties(self):
"""Show channel properties dialog."""
info = self.model.current["data"].info
dialog = ChannelPropertiesDialog(self, info)
if dialog.exec():
dialog.model.sort(0)
bads = []
renamed = {}
types = {}
for i in range(dialog.model.rowCount()):
new_label = dialog.model.item(i, 1).data(Qt.DisplayRole)
old_label = info["ch_names"][i]
if new_label != old_label:
renamed[old_label] = new_label
new_type = dialog.model.item(i, 2).data(Qt.DisplayRole).lower()
old_type = channel_type(info, i).lower()
if new_type != old_type:
types[new_label] = new_type
if dialog.model.item(i, 3).checkState() == Qt.Checked:
bads.append(info["ch_names"][i])
self.model.set_channel_properties(bads, renamed, types)
def set_montage(self):
"""Set montage."""
montages = mne.channels.get_builtin_montages()
# TODO: currently it is not possible to remove an existing montage
dialog = MontageDialog(self, montages)
if dialog.exec():
name = dialog.montages.selectedItems()[0].data(0)
montage = mne.channels.make_standard_montage(name)
ch_names = self.model.current["data"].info["ch_names"]
# check if at least one channel name matches a name in the montage
if set(ch_names) & set(montage.ch_names):
self.model.set_montage(name)
else:
QMessageBox.critical(
self, "No matching channel names",
"Channel names defined in the "
"montage do not match any channel name in the data.")
def edit_annotations(self):
fs = self.model.current["data"].info["sfreq"]
pos = self.model.current["data"].annotations.onset
pos = (pos * fs).astype(int).tolist()
dur = self.model.current["data"].annotations.duration
dur = (dur * fs).astype(int).tolist()
desc = self.model.current["data"].annotations.description.tolist()
dialog = AnnotationsDialog(self, pos, dur, desc)
if dialog.exec():
rows = dialog.table.rowCount()
onset, duration, description = [], [], []
for i in range(rows):
data = dialog.table.item(i, 0).data(Qt.DisplayRole)
onset.append(float(data) / fs)
data = dialog.table.item(i, 1).data(Qt.DisplayRole)
duration.append(float(data) / fs)
data = dialog.table.item(i, 2).data(Qt.DisplayRole)
description.append(data)
self.model.set_annotations(onset, duration, description)
def edit_events(self):
pos = self.model.current["events"][:, 0].tolist()
desc = self.model.current["events"][:, 2].tolist()
dialog = EventsDialog(self, pos, desc)
if dialog.exec():
rows = dialog.table.rowCount()
events = np.zeros((rows, 3), dtype=int)
for i in range(rows):
pos = int(dialog.table.item(i, 0).data(Qt.DisplayRole))
desc = int(dialog.table.item(i, 1).data(Qt.DisplayRole))
events[i] = pos, 0, desc
self.model.set_events(events)
def crop(self):
"""Crop data."""
fs = self.model.current["data"].info["sfreq"]
length = self.model.current["data"].n_times / fs
dialog = CropDialog(self, 0, length)
if dialog.exec():
self.auto_duplicate()
self.model.crop(dialog.start or 0, dialog.stop)
def append_data(self):
"""Concatenate raw data objects to current one."""
compatibles = self.model.get_compatibles()
dialog = AppendDialog(self, compatibles)
if dialog.exec():
self.auto_duplicate()
self.model.append_data(dialog.names)
def plot_data(self):
"""Plot data."""
# self.bad is needed to update history if bad channels are selected in
# the interactive plot window (see also self.eventFilter)
self.bads = self.model.current["data"].info["bads"]
events = self.model.current["events"]
nchan = self.model.current["data"].info["nchan"]
fig = self.model.current["data"].plot(events=events,
n_channels=nchan,
title=self.model.current["name"],
scalings="auto",
show=False)
if events is not None:
hist = f"data.plot(events=events, n_channels={nchan})"
else:
hist = f"data.plot(n_channels={nchan})"
self.model.history.append(hist)
win = fig.canvas.manager.window
win.setWindowTitle(self.model.current["name"])
win.statusBar().hide() # not necessary since matplotlib 3.3
win.installEventFilter(self) # detect if the figure is closed
# prevent closing the window with the escape key
try:
fig._mne_params["close_key"] = None
except AttributeError: # does not exist in older MNE versions
pass
fig.show()
def plot_psd(self):
"""Plot power spectral density (PSD)."""
kwds = {}
if self.model.current["dtype"] == "raw":
kwds.update({"average": False, "spatial_colors": False})
fig = self.model.current["data"].plot_psd(show=False, **kwds)
if kwds:
tmp = ", ".join(f"{key}={value}" for key, value in kwds.items())
hist = f"data.plot_psd({tmp})"
else:
hist = "data.plot_psd()"
self.model.history.append(hist)
win = fig.canvas.manager.window
win.setWindowTitle("Power spectral density")
fig.show()
def plot_locations(self):
"""Plot current montage."""
fig = self.model.current["data"].plot_sensors(show_names=True,
show=False)
win = fig.canvas.manager.window
win.setWindowTitle("Montage")
win.statusBar().hide() # not necessary since matplotlib 3.3
fig.show()
def plot_ica_components(self):
self.model.current["ica"].plot_components(
inst=self.model.current["data"])
def plot_ica_sources(self):
self.model.current["ica"].plot_sources(inst=self.model.current["data"])
def plot_erds(self):
"""Plot ERDS maps."""
data = self.model.current["data"]
t_range = [data.tmin, data.tmax]
f_range = [1, data.info["sfreq"] / 2]
dialog = ERDSDialog(self, t_range, f_range)
if dialog.exec():
freqs = np.arange(dialog.f1, dialog.f2, dialog.step)
baseline = [dialog.b1, dialog.b2]
times = [dialog.t1, dialog.t2]
figs = plot_erds(data, freqs, freqs, baseline, times)
for fig in figs:
fig.show()
def run_ica(self):
"""Run ICA calculation."""
methods = ["Infomax"]
if have["picard"]:
methods.insert(0, "Picard")
if have["sklearn"]:
methods.append("FastICA")
dialog = RunICADialog(self, self.model.current["data"].info["nchan"],
methods)
if dialog.exec():
calc = CalcDialog(self, "Calculating ICA", "Calculating ICA.")
method = dialog.method.currentText().lower()
exclude_bad_segments = dialog.exclude_bad_segments.isChecked()
fit_params = {}
if dialog.extended.isEnabled():
fit_params["extended"] = dialog.extended.isChecked()
if dialog.ortho.isEnabled():
fit_params["ortho"] = dialog.ortho.isChecked()
ica = mne.preprocessing.ICA(method=method, fit_params=fit_params)
history = f"ica = mne.preprocessing.ICA(method='{method}'"
if fit_params:
history += f", fit_params={fit_params})"
else:
history += ")"
self.model.history.append(history)
pool = mp.Pool(processes=1)
def callback(x):
QMetaObject.invokeMethod(calc, "accept", Qt.QueuedConnection)
res = pool.apply_async(
func=ica.fit,
args=(self.model.current["data"], ),
kwds={"reject_by_annotation": exclude_bad_segments},
callback=callback)
pool.close()
if not calc.exec():
pool.terminate()
print("ICA calculation aborted...")
else:
self.model.current["ica"] = res.get(timeout=1)
self.model.history.append(
f"ica.fit(inst=raw, reject_by_annotation="
f"{exclude_bad_segments})")
self.data_changed()
def apply_ica(self):
"""Apply current fitted ICA."""
self.auto_duplicate()
self.model.apply_ica()
def interpolate_bads(self):
"""Interpolate bad channels"""
dialog = InterpolateBadsDialog(self)
if dialog.exec():
duplicated = self.auto_duplicate()
try:
self.model.interpolate_bads(dialog.reset_bads, dialog.mode,
dialog.origin)
except ValueError as e:
if duplicated: # undo
self.model.remove_data()
self.model.index -= 1
self.data_changed()
msgbox = ErrorMessageBox(self,
"Could not interpolate bad channels",
str(e), traceback.format_exc())
msgbox.show()
def filter_data(self):
"""Filter data."""
dialog = FilterDialog(self)
if dialog.exec():
self.auto_duplicate()
self.model.filter(dialog.low, dialog.high)
def find_events(self):
info = self.model.current["data"].info
# use first stim channel as default in dialog
default_stim = 0
for i in range(info["nchan"]):
if mne.io.pick.channel_type(info, i) == "stim":
default_stim = i
break
dialog = FindEventsDialog(self, info["ch_names"], default_stim)
if dialog.exec():
stim_channel = dialog.stimchan.currentText()
consecutive = dialog.consecutive.isChecked()
initial_event = dialog.initial_event.isChecked()
uint_cast = dialog.uint_cast.isChecked()
min_dur = dialog.minduredit.value()
shortest_event = dialog.shortesteventedit.value()
self.model.find_events(stim_channel=stim_channel,
consecutive=consecutive,
initial_event=initial_event,
uint_cast=uint_cast,
min_duration=min_dur,
shortest_event=shortest_event)
def events_from_annotations(self):
self.model.events_from_annotations()
def annotations_from_events(self):
self.model.annotations_from_events()
def epoch_data(self):
"""Epoch raw data."""
dialog = EpochDialog(self, self.model.current["events"])
if dialog.exec():
events = [
int(item.text()) for item in dialog.events.selectedItems()
]
tmin = dialog.tmin.value()
tmax = dialog.tmax.value()
if dialog.baseline.isChecked():
baseline = dialog.a.value(), dialog.b.value()
else:
baseline = None
duplicated = self.auto_duplicate()
try:
self.model.epoch_data(events, tmin, tmax, baseline)
except ValueError as e:
if duplicated: # undo
self.model.remove_data()
self.model.index -= 1
self.data_changed()
msgbox = ErrorMessageBox(self, "Could not create epochs",
str(e), traceback.format_exc())
msgbox.show()
def convert_od(self):
"""Convert to optical density."""
self.auto_duplicate()
self.model.convert_od()
def convert_bl(self):
"""Convert to haemoglobin."""
self.auto_duplicate()
self.model.convert_beer_lambert()
def set_reference(self):
"""Set reference."""
dialog = ReferenceDialog(self)
if dialog.exec():
self.auto_duplicate()
if dialog.average.isChecked():
self.model.set_reference("average")
else:
ref = [c.strip() for c in dialog.channellist.text().split(",")]
self.model.set_reference(ref)
def show_history(self):
"""Show history."""
dialog = HistoryDialog(self, "\n".join(self.model.history))
dialog.exec()
def show_about(self):
"""Show About dialog."""
from . import __version__
msg_box = QMessageBox(self)
text = (
f"<img src='{image_path('mnelab_logo.png')}'><p>MNELAB {__version__}</p>"
)
msg_box.setText(text)
mnelab_url = "github.com/cbrnr/mnelab"
mne_url = "github.com/mne-tools/mne-python"
pkgs = []
for key, value in have.items():
if value:
pkgs.append(f"{key} ({value})")
else:
pkgs.append(f"{key} (not installed)")
version = ".".join(str(k) for k in version_info[:3])
text = (
f"<nobr><p>This program uses Python {version} and the following packages:"
f"</p></nobr><p>{', '.join(pkgs)}</p>"
f"<nobr><p>MNELAB repository: <a href=https://{mnelab_url}>{mnelab_url}</a>"
f"</p></nobr><nobr><p>MNE repository: "
f"<a href=https://{mne_url}>{mne_url}</a></p></nobr>"
f"<p>Licensed under the BSD 3-clause license.</p>"
f"<p>Copyright 2017–2021 by Clemens Brunner.</p>")
msg_box.setInformativeText(text)
msg_box.exec()
def show_about_qt(self):
"""Show About Qt dialog."""
QMessageBox.aboutQt(self, "About Qt")
def auto_duplicate(self):
"""Automatically duplicate current data set.
If the current data set is stored in a file (i.e. was loaded directly from a file),
a new data set is automatically created. If the current data set is not stored in a
file (i.e. was created by operations in MNELAB), a dialog box asks the user if the
current data set should be overwritten or duplicated.
Returns
-------
duplicated : bool
True if the current data set was automatically duplicated, False if the current
data set was overwritten.
"""
# if current data is stored in a file create a new data set
if self.model.current["fname"]:
self.model.duplicate_data()
return True
# otherwise ask the user
else:
msg = QMessageBox.question(self, "Overwrite existing data set",
"Overwrite existing data set?")
if msg == QMessageBox.No: # create new data set
self.model.duplicate_data()
return True
return False
def _add_recent(self, fname):
"""Add a file to recent file list.
Parameters
----------
fname : str
File name.
"""
if fname in self.recent: # avoid duplicates
self.recent.remove(fname)
self.recent.insert(0, fname)
while len(self.recent) > MAX_RECENT: # prune list
self.recent.pop()
write_settings(recent=self.recent)
if not self.recent_menu.isEnabled():
self.recent_menu.setEnabled(True)
def _remove_recent(self, fname):
"""Remove file from recent file list.
Parameters
----------
fname : str
File name.
"""
if fname in self.recent:
self.recent.remove(fname)
write_settings(recent=self.recent)
if not self.recent:
self.recent_menu.setEnabled(False)
@Slot(QModelIndex)
def _update_data(self, selected):
"""Update index and information based on the state of the sidebar.
Parameters
----------
selected : QModelIndex
Index of the selected row.
"""
if selected.row() != self.model.index:
self.model.index = selected.row()
self.data_changed()
self.model.history.append(f"data = datasets[{self.model.index}]")
@Slot(QModelIndex, QModelIndex)
def _update_names(self, start, stop):
"""Update names in DataSets after changes in sidebar."""
for index in range(start.row(), stop.row() + 1):
self.model.data[index]["name"] = self.names.stringList()[index]
@Slot()
def _update_recent_menu(self):
self.recent_menu.clear()
for recent in self.recent:
self.recent_menu.addAction(recent)
@Slot(QAction)
def _load_recent(self, action):
self.open_data(fname=action.text())
@Slot()
def _toggle_toolbar(self):
if self.toolbar.isHidden():
self.toolbar.show()
else:
self.toolbar.hide()
write_settings(toolbar=not self.toolbar.isHidden())
@Slot()
def _toggle_statusbar(self):
if self.statusBar().isHidden():
self.statusBar().show()
else:
self.statusBar().hide()
write_settings(statusbar=not self.statusBar().isHidden())
@Slot(QDropEvent)
def dragEnterEvent(self, event):
if event.mimeData().hasUrls():
event.acceptProposedAction()
@Slot(QDropEvent)
def dropEvent(self, event):
mime = event.mimeData()
if mime.hasUrls():
urls = mime.urls()
for url in urls:
try:
self.open_data(url.toLocalFile())
except FileNotFoundError as e:
QMessageBox.critical(self, "File not found", str(e))
@Slot(QEvent)
def closeEvent(self, event):
"""Close application.
Parameters
----------
event : QEvent
Close event.
"""
write_settings(size=self.size(), pos=self.pos())
if self.model.history:
print("\n# Command History\n")
print("\n".join(self.model.history))
QApplication.quit()
def eventFilter(self, source, event):
# currently the only source is the raw plot window
if event.type() == QEvent.Close:
self.data_changed()
bads = self.model.current["data"].info["bads"]
if self.bads != bads:
self.model.history.append(f'data.info["bads"] = {bads}')
return QObject.eventFilter(self, source, event)
def event(self, ev):
"""Catch system events."""
if ev.type() == QEvent.PaletteChange: # detect theme switches
style = interface_style() # light or dark
if style is not None:
QIcon.setThemeName(style)
else:
QIcon.setThemeName("light") # fallback
return super().event(ev)
class Window(QDialog):
def __init__(self, parent=None):
super(Window, self).__init__(parent)
self.createTrayIcon()
self.createProgramsList()
self.createCodeEditPage()
self.logsPage = QTextBrowser()
self.documentation = QTextBrowser()
self.tabWidget = QTabWidget()
self.tabWidget.setIconSize(QSize(64, 64))
self.tabWidget.addTab(self.programsListPage, QIcon(":/images/Adventure-Map-icon.png"), "Programs")
self.tabWidget.addTab(self.codeEditPage, QIcon(":/images/Sword-icon.png"), "Edit Program")
self.tabWidget.addTab(self.logsPage, QIcon(":/images/Spell-Scroll-icon.png"), "Logs")
self.tabWidget.addTab(self.documentation, QIcon(":/images/Spell-Book-icon.png"), "Documentation")
self.mainLayout = QVBoxLayout()
self.mainLayout.addWidget(self.tabWidget)
self.setLayout(self.mainLayout)
self.setWindowTitle(APP_NAME)
self.setWindowFlags(Qt.WindowStaysOnTopHint | Qt.Dialog)
self.resize(800, 600)
self.systrayHintMsgShowed = False
self.firstShow = True
self.fromQuit = False
def createProgramsList(self):
self.programsListModel = QStandardItemModel(0, 1, self)
self.programsList = QListView()
self.programsList.setModel(self.programsListModel)
self.programsListPage = QWidget()
self.programsListLayout = QVBoxLayout()
self.programsListButtons = QHBoxLayout()
self.programsListButtonNew = QPushButton("New")
self.programsListButtonDelete = QPushButton("Delete")
self.programsListButtonEdit = QPushButton("Edit")
self.programsListButtonSet = QPushButton("Set")
self.programsListButtons.addWidget(self.programsListButtonNew)
self.programsListButtons.addWidget(self.programsListButtonSet)
self.programsListButtons.addWidget(self.programsListButtonEdit)
self.programsListButtons.addWidget(self.programsListButtonDelete)
self.programsListLayout.addLayout(self.programsListButtons)
self.programsListLayout.addWidget(self.programsList)
self.programsListPage.setLayout(self.programsListLayout)
self.programsListButtonNew.clicked.connect(self.newProgram)
self.programsListButtonEdit.clicked.connect(self.editProgram)
self.programsListButtonDelete.clicked.connect(self.deleteProgram)
self.programsListButtonSet.clicked.connect(self.setProgram)
def createCodeEditPage(self):
self.codeEditPage = QWidget()
self.codeEditLayout = QVBoxLayout()
self.codeEditNameBox = QHBoxLayout()
self.codeEditNameBoxNameLabel = QLabel("Name:")
self.codeEditNameBoxNameInput = QLineEdit()
self.codeEditNameBoxSaveButton = QPushButton("Save")
self.codeEditNameBoxCancelButton = QPushButton("Cancel")
self.codeEditNameBox.addWidget(self.codeEditNameBoxNameLabel)
self.codeEditNameBox.addWidget(self.codeEditNameBoxNameInput)
self.codeEditNameBox.addWidget(self.codeEditNameBoxSaveButton)
self.codeEditNameBox.addWidget(self.codeEditNameBoxCancelButton)
self.codeEdit = QTextEdit()
self.codeEditLayout.addLayout(self.codeEditNameBox)
self.codeEditLayout.addWidget(self.codeEdit)
self.codeEditPage.setLayout(self.codeEditLayout)
self.codeEditLastCode = ''
self.codeEditNameBoxSaveButton.clicked.connect(self.saveEditProgram)
self.codeEditNameBoxCancelButton.clicked.connect(self.cancelEditProgram)
def showEvent(self, event):
super().showEvent(event)
if self.firstShow:
self.firstShow = False
self.createWaitDialog()
self.findKeyboard()
def closeWaitDialog(self):
time.sleep(1)
self.waitDialog.close()
@Slot()
def newProgram(self):
self.showNormal()
self.tabWidget.setCurrentWidget(self.codeEditPage)
self.codeEdit.setPlainText("")
self.codeEditLastCode = ''
self.codeEditNameBoxNameInput.setText("")
@Slot()
def editProgram(self):
selected = self.programsList.selectedIndexes()
if not selected:
return
selected = selected[0].data()
loadProgram = LoadProgram(self.cmdSocket, selected)
loadProgram.loaded.connect(self.programLoaded)
loadProgram.start()
self.showWaitDialog("Loading program ...")
@Slot()
def saveEditProgram(self):
name = self.codeEditNameBoxNameInput.text()
program = self.codeEdit.toPlainText()
if not name:
return
editProgramWorker = EditProgram(self.cmdSocket, name, program)
editProgramWorker.edited.connect(self.programSaved)
editProgramWorker.start()
self.showWaitDialog("Saving program ...")
@Slot()
def cancelEditProgram(self):
self.codeEdit.setPlainText(self.codeEditLastCode)
@Slot()
def deleteProgram(self):
selected = self.programsList.selectedIndexes()
if not selected:
return
selected = selected[0].data()
deleteWorker = DeleteProgram(self.cmdSocket, selected)
deleteWorker.deleted.connect(self.programDeleted)
deleteWorker.start()
self.showWaitDialog("Deleting program ...")
@Slot()
def setProgram(self):
selected = self.programsList.selectedIndexes()
if not selected:
return
selected = selected[0].data()
setWorker = SetProgram(self.cmdSocket, selected)
setWorker.setDone.connect(self.programSet)
setWorker.start()
self.showWaitDialog("Setting program ...")
@Slot(str, str)
def programLoaded(self, name, program):
self.closeWaitDialog()
self.tabWidget.setCurrentWidget(self.codeEditPage)
self.codeEdit.setPlainText(program)
self.codeEditLastCode = program
self.codeEditNameBoxNameInput.setText(name)
@Slot(str)
def programDeleted(self, name):
self.updateProgramsList()
@Slot(str)
def programSet(self, name):
self.updateProgramsList()
@Slot(str)
def programSaved(self, name):
self.updateProgramsList()
self.tabWidget.setCurrentWidget(self.programsListPage)
def createWaitDialog(self):
self.waitDialog = QDialog(self)
self.waitDialogLayout = QHBoxLayout()
self.waitDialogLabel = QLabel()
self.waitDialogLayout.addWidget(self.waitDialogLabel)
self.waitDialog.setLayout(self.waitDialogLayout)
self.waitDialog.setWindowFlags(Qt.Dialog | Qt.FramelessWindowHint)
def showWaitDialog(self, text='Please wait...'):
self.waitDialogLabel.setText(text)
self.waitDialog.exec_()
def findKeyboard(self):
find = ConnectKeyboard()
find.connected.connect(self.keyboardConnected)
find.start()
self.showWaitDialog('Finding and connecting Fruit2Pi Keyboard ...')
@Slot(BluetoothSocket)
def keyboardConnected(self, socket):
self.cmdSocket = socket
self.updateProgramsList()
def updateProgramsList(self):
self.listProgram = ListProgram(self.cmdSocket)
self.listProgram.listed.connect(self.programListUpdated)
self.listProgram.start()
@Slot(list, str)
def programListUpdated(self, programs, current_program):
print(programs)
print(current_program)
self.closeWaitDialog()
self.programsListModel.clear()
for p in programs:
item = QStandardItem(p)
if p == current_program:
item.setForeground(QBrush(QColor(0, 0, 255, 127)))
self.programsListModel.appendRow(item)
def setVisible(self, visible):
super().setVisible(visible)
def closeEvent(self, event):
if self.fromQuit:
return
if not event.spontaneous() or not self.isVisible():
return
if not self.systrayHintMsgShowed:
self.systrayHintMsgShowed = True
icon = QIcon(":/images/yammi-banana-icon.png")
self.trayIcon.showMessage(APP_NAME,
"Running on background"
"To quit, choose <b>Quit</b> in the icon menu",
icon,
5000
)
self.hide()
event.ignore()
@Slot(str)
def iconActivated(self, reason):
print(reason)
if reason == QSystemTrayIcon.Trigger:
self.showNormal()
if reason == QSystemTrayIcon.DoubleClick:
self.showNormal()
@Slot()
def showProgramsPage(self):
self.showNormal()
self.tabWidget.setCurrentWidget(self.programsListPage)
@Slot()
def showLogsPage(self):
self.showNormal()
self.tabWidget.setCurrentWidget(self.logsPage)
@Slot()
def showDocumentation(self):
self.showNormal()
self.tabWidget.setCurrentWidget(self.documentation)
@Slot()
def quit(self):
self.fromQuit = True
qApp.quit()
def createTrayIcon(self):
self.showProgramsAction = QAction("Programs", self)
self.showProgramsAction.triggered.connect(self.showProgramsPage)
self.showNewProgramAction = QAction("New Program", self)
self.showNewProgramAction.triggered.connect(self.newProgram)
self.showSetProgramAction = QAction("Logs", self)
self.showSetProgramAction.triggered.connect(self.showLogsPage)
self.showDocumentationAction = QAction("Documentation", self)
self.showDocumentationAction.triggered.connect(self.showDocumentation)
self.quitAction = QAction("Quit", self)
self.quitAction.triggered.connect(self.quit)
self.trayIconMenu = QMenu(self)
self.trayIconMenu.addAction(self.showProgramsAction)
self.trayIconMenu.addAction(self.showSetProgramAction)
self.trayIconMenu.addAction(self.showNewProgramAction)
self.trayIconMenu.addAction(self.showDocumentationAction)
self.trayIconMenu.addSeparator()
self.trayIconMenu.addAction(self.quitAction)
self.trayIcon = QSystemTrayIcon(self)
self.trayIcon.setContextMenu(self.trayIconMenu)
self.trayIcon.activated.connect(self.iconActivated)
self.trayIcon.setIcon(QIcon(":/images/yammi-banana-icon.png"))
self.trayIcon.show()