def setup_context(self):
context_path = Path(os.path.join(self.working_directory, '.kilosort', self.raw_data.name))
self.context = Context(context_path=context_path)
self.context.probe = self.probe_layout
self.context.params = self.params
self.context.raw_data = self.raw_data
self.context.load()
self.update_context_with_good_channels()
def setup_context(self):
context_path = Path(
os.path.join(self.working_directory, ".kilosort",
self.raw_data.name))
self.context = Context(context_path=context_path)
probe_layout = self.probe_layout
probe_layout.Nchan = self.num_channels
self.context.probe = extend_probe(probe_layout)
self.context.raw_probe = extend_probe(copy_bunch(probe_layout))
self.context.params = self.params
self.context.raw_data = self.raw_data
self.context.load()
def test_context_1(tmp_path):
arr = np.random.randn(10, 20)
c = Context(tmp_path)
c.intermediate.test1 = arr
ae(c.read('test1'), arr)
c.write(test1=arr)
ae(c.read('test1'), arr)
c.write(test2=12.34)
assert c.read('test2') == 12.34
def test_context_2(tmp_path):
arr = np.random.randn(10, 20)
c = Context(tmp_path)
c.intermediate.test1 = arr
c.intermediate.test2 = 12.34
c.save()
c.load()
ae(c.intermediate.test1, arr)
assert c.intermediate.test2 == 12.34
c = Context(tmp_path)
assert 'test1' not in c.intermediate
c.load()
ae(c.intermediate.test1, arr)
assert c.intermediate.test2 == 12.34
class KiloSortGUI(QtWidgets.QMainWindow):
def __init__(self, application, *args, **kwargs):
super(KiloSortGUI, self).__init__(*args, **kwargs)
self.app = application
self.data_path = None
self.probe_layout = None
self.params = None
self.working_directory = None
self.results_directory = None
self.probe_files_path = Path(probes.__file__).parent
assert self.probe_files_path.exists()
self.local_config_path = Path.home() / ".pykilosort"
self.local_config_path.mkdir(exist_ok=True)
self.new_probe_files_path = self.local_config_path / "probes"
self.new_probe_files_path.mkdir(exist_ok=True)
self.time_range = None
self.num_channels = None
self.context = None
self.raw_data = None
self.content = QtWidgets.QWidget(self)
self.content_layout = QtWidgets.QVBoxLayout()
self.header_box = HeaderBox(self)
self.boxes = QtWidgets.QWidget()
self.boxes_layout = QtWidgets.QHBoxLayout(self.boxes)
self.first_boxes_layout = QtWidgets.QVBoxLayout()
self.second_boxes_layout = QtWidgets.QHBoxLayout()
self.third_boxes_layout = QtWidgets.QVBoxLayout()
self.settings_box = SettingsBox(self)
self.probe_view_box = ProbeViewBox(self)
self.data_view_box = DataViewBox(self)
self.run_box = RunBox(self)
self.message_log_box = MessageLogBox(self)
self.setup()
def keyPressEvent(self, event):
QtWidgets.QMainWindow.keyPressEvent(self, event)
if type(event) == QtGui.QKeyEvent:
modifiers = event.modifiers()
if event.key() == QtCore.Qt.Key_Up:
if modifiers:
if modifiers == QtCore.Qt.ControlModifier:
# logger.debug("Ctrl+Up")
self.change_channel_display(1)
elif modifiers == QtCore.Qt.AltModifier:
# logger.debug("Alt+Up")
self.scale_data(1)
elif modifiers == QtCore.Qt.ShiftModifier:
# logger.debug("Shift+Up")
self.zoom_data_view_in_time(1)
else:
# logger.debug("Only Up")
self.change_displayed_channel_count(shift=1)
elif event.key() == QtCore.Qt.Key_Down:
if modifiers:
if modifiers == QtCore.Qt.ControlModifier:
# logger.debug("Ctrl+Down")
self.change_channel_display(-1)
elif modifiers == QtCore.Qt.AltModifier:
# logger.debug("Alt+Down")
self.scale_data(-1)
elif modifiers == QtCore.Qt.ShiftModifier:
# logger.debug("Shift+Down")
self.zoom_data_view_in_time(-1)
else:
# logger.debug("Only Down")
self.change_displayed_channel_count(shift=-1)
elif event.key() == QtCore.Qt.Key_Left:
self.shift_data(time_shift=-1)
elif event.key() == QtCore.Qt.Key_Right:
self.shift_data(time_shift=1)
elif event.key() == QtCore.Qt.Key_C:
self.toggle_view()
elif event.key() == QtCore.Qt.Key_1:
self.toggle_mode("raw")
elif event.key() == QtCore.Qt.Key_2:
self.toggle_mode("whitened")
elif event.key() == QtCore.Qt.Key_3:
self.toggle_mode("prediction")
elif event.key() == QtCore.Qt.Key_4:
self.toggle_mode("residual")
else:
pass
event.accept()
else:
event.ignore()
def setup(self):
self.setWindowTitle(f"Kilosort{__version__}")
self.content_layout.addWidget(self.header_box, 3)
self.third_boxes_layout.addWidget(self.settings_box, 85)
self.third_boxes_layout.addWidget(self.run_box, 15)
self.second_boxes_layout.addLayout(self.third_boxes_layout, 60)
self.second_boxes_layout.addWidget(self.probe_view_box, 40)
self.first_boxes_layout.addLayout(self.second_boxes_layout, 79)
self.first_boxes_layout.addWidget(self.message_log_box, 21)
self.boxes_layout.addLayout(self.first_boxes_layout, 30)
self.boxes_layout.addWidget(self.data_view_box, 70)
self.boxes.setLayout(self.boxes_layout)
self.content_layout.addWidget(self.boxes, 90)
self.content_layout.setContentsMargins(10, 10, 10, 10)
self.content.setLayout(self.content_layout)
self.setCentralWidget(self.content)
self.header_box.reset_gui_button.clicked.connect(self.reset_gui)
self.settings_box.settingsUpdated.connect(self.set_parameters)
self.settings_box.previewProbe.connect(
self.probe_view_box.preview_probe)
self.data_view_box.channelChanged.connect(
self.probe_view_box.update_probe_view)
self.data_view_box.modeChanged.connect(
self.probe_view_box.synchronize_data_view_mode)
self.probe_view_box.channelSelected.connect(
self.data_view_box.change_primary_channel)
self.run_box.updateContext.connect(self.update_context)
self.run_box.disableInput.connect(self.disable_all_input)
self.run_box.sortingStepStatusUpdate.connect(
self.update_sorting_status)
def change_channel_display(self, direction):
if self.context is not None:
self.data_view_box.shift_primary_channel(direction)
def shift_data(self, time_shift):
if self.context is not None:
self.data_view_box.shift_current_time(time_shift)
def change_displayed_channel_count(self, shift):
if self.context is not None:
self.data_view_box.change_displayed_channel_count(shift)
def zoom_data_view_in_time(self, direction):
if self.context is not None:
self.data_view_box.change_plot_range(direction)
def scale_data(self, direction):
if self.context is not None:
self.data_view_box.change_plot_scaling(direction)
def toggle_view(self):
self.data_view_box.toggle_mode()
def toggle_mode(self, mode):
if mode == "raw":
self.data_view_box.raw_button.click()
elif mode == "whitened":
self.data_view_box.whitened_button.click()
elif mode == "prediction":
self.data_view_box.prediction_button.click()
elif mode == "residual":
self.data_view_box.residual_button.click()
else:
raise ValueError("Invalid mode requested!")
@QtCore.pyqtSlot(bool)
def disable_all_input(self, value):
self.settings_box.disable_all_input(value)
self.run_box.disable_all_input(value)
def set_parameters(self):
settings = self.settings_box.settings
advanced_options = self.settings_box.advanced_options
self.data_path = settings.pop("data_file_path")
self.working_directory = settings.pop("working_directory")
self.results_directory = settings.pop("results_directory")
self.probe_layout = settings.pop("probe_layout")
self.time_range = settings.pop("time_range")
self.num_channels = settings.pop("num_channels")
params = KilosortParams()
params = params.parse_obj(advanced_options)
params = params.parse_obj(settings)
assert params
self.params = params
self.disable_all_input(True)
QtWidgets.QApplication.setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.prepare_for_new_context()
self.load_raw_data()
self.setup_context()
self.update_probe_view()
self.setup_data_view()
self.update_run_box()
self.disable_all_input(False)
QtWidgets.QApplication.restoreOverrideCursor()
def load_raw_data(self):
# TODO: account for these temporary hardcoded params
n_channels = self.num_channels
dtype = np.int16
sample_rate = self.params.fs
raw_data = get_ephys_reader(self.data_path,
sample_rate=sample_rate,
dtype=dtype,
n_channels=n_channels)
self.raw_data = raw_data
def setup_data_view(self):
self.data_view_box.calculate_approx_whitening_matrix(self.context)
self.data_view_box.setup_seek(self.context)
self.data_view_box.create_plot_items()
self.data_view_box.update_plot(self.context)
def setup_context(self):
context_path = Path(
os.path.join(self.working_directory, ".kilosort",
self.raw_data.name))
self.context = Context(context_path=context_path)
probe_layout = self.probe_layout
probe_layout.Nchan = self.num_channels
self.context.probe = extend_probe(probe_layout)
self.context.raw_probe = extend_probe(copy_bunch(probe_layout))
self.context.params = self.params
self.context.raw_data = self.raw_data
self.context.load()
@QtCore.pyqtSlot(object)
def update_context(self, context):
self.context = context
self.update_probe_view()
self.update_data_view()
@QtCore.pyqtSlot()
def update_probe_view(self):
self.probe_view_box.set_layout(self.context)
def update_data_view(self):
self.data_view_box.set_whitening_matrix(self.context.intermediate.Wrot)
self.data_view_box.clear_cached_traces()
self.data_view_box.update_plot(self.context)
def update_run_box(self):
self.run_box.set_data_path(self.data_path)
self.run_box.set_working_directory(self.working_directory)
self.run_box.set_results_directory(self.results_directory)
@QtCore.pyqtSlot(dict)
def update_sorting_status(self, status_dict):
self.run_box.change_sorting_status(status_dict)
self.data_view_box.change_sorting_status(status_dict)
self.probe_view_box.change_sorting_status(status_dict)
def get_context(self):
return self.context
def get_probe(self):
return self.probe_layout
def get_params(self):
return self.params
def prepare_for_new_context(self):
self.data_view_box.prepare_for_new_context()
self.probe_view_box.prepare_for_new_context()
self.message_log_box.prepare_for_new_context()
self.context = None
def reset_gui(self):
self.time_range = None
self.num_channels = None
self.context = None
self.raw_data = None
self.probe_view_box.reset()
self.data_view_box.reset()
self.settings_box.reset()
self.message_log_box.reset()
def closeEvent(self, event: QtGui.QCloseEvent):
self.message_log_box.save_log_file()
event.accept()