def __init__(self, parent=None, dolog=True, filename=None):
self.views = {}
super(MainWindow, self).__init__(parent)
self.views = {}
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.klustaviewa'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
self.initialize_view_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KlustaViewa')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader(userpref=USERPREF)
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.taskgraph = TaskGraph(self)
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_correlograms_actions()
self.create_control_actions()
self.create_wizard_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename)
self.show()
class KwikSkope(QtGui.QMainWindow):
def __init__(self, parent=None, dolog=True, filename=None):
super(KwikSkope, self).__init__(parent)
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.kwikskope'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KwikSkope')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
# self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader()
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename)
self.show()
def set_styles(self):
# set stylesheet
path = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(path, "styles.css")
with open(path, 'r') as f:
stylesheet = f.read()
stylesheet = stylesheet.replace('%ACCENT%', '#cdcdcd')
stylesheet = stylesheet.replace('%ACCENT2%', '#a0a0a0')
stylesheet = stylesheet.replace('%ACCENT3%', '#909090')
stylesheet = stylesheet.replace('%ACCENT4%', '#cdcdcd')
self.setStyleSheet(stylesheet)
# Actions.
# --------
def add_action(self, name, text, callback=None, shortcut=None,
checkable=False, checked=False, icon=None):
action = QtGui.QAction(text, self)
if callback is None:
callback = getattr(self, name + '_callback', None)
if callback:
action.triggered.connect(callback)
if shortcut:
action.setShortcut(shortcut)
if icon:
action.setIcon(get_icon(icon))
action.setCheckable(checkable)
action.setChecked(checked)
setattr(self, name + '_action', action)
def create_file_actions(self):
# Open actions.
self.add_action('open', '&Open', shortcut='Ctrl+O', icon='open')
# Open last file action
path = SETTINGS['main_window.last_data_file']
if path:
lastfile = os.path.basename(path)
if len(lastfile) > 30:
lastfile = '...' + lastfile[-30:]
self.add_action('open_last', 'Open &last ({0:s})'.format(
lastfile), shortcut='Ctrl+Alt+O')
else:
self.add_action('open_last', 'Open &last', shortcut='Ctrl+Alt+O')
self.open_last_action.setEnabled(False)
self.add_action('save', '&Save', shortcut='Ctrl+S', icon='save')
self.add_action('close', '&Close file')
# Quit action.
self.add_action('quit', '&Quit', shortcut='Ctrl+Q')
def create_edit_actions(self):
self.add_action('undo', '&Undo', shortcut='Ctrl+Z', icon='undo')
self.add_action('redo', '&Redo', shortcut='Ctrl+Y', icon='redo')
def create_view_actions(self):
self.add_action('add_ipython_view', 'Add &IPythonView')
self.add_action('reset_views', '&Reset views')
self.add_action('toggle_fullscreen', 'Toggle fullscreen', shortcut='F')
self.add_action('override_color', 'Override channel &color',
icon='override_color')#, shortcut='C')
def create_help_actions(self):
self.add_action('about', '&About')
self.add_action('manual', 'Show &manual')
self.add_action('shortcuts', 'Show &shortcuts')
self.add_action('open_preferences', '&Open preferences')
self.add_action('refresh_preferences', '&Refresh preferences',
shortcut='CTRL+R')
def create_menu(self):
# File menu.
file_menu = self.menuBar().addMenu("&File")
file_menu.addAction(self.open_action)
file_menu.addAction(self.open_last_action)
file_menu.addSeparator()
# file_menu.addSeparator()
file_menu.addAction(self.save_action)
file_menu.addSeparator()
file_menu.addAction(self.quit_action)
# Edit menu.
# edit_menu = self.menuBar().addMenu("&Edit")
# edit_menu.addAction(self.undo_action)
# edit_menu.addAction(self.redo_action)
# View menu.
views_menu = self.menuBar().addMenu("&View")
if vw.IPYTHON:
views_menu.addAction(self.add_ipython_view_action)
views_menu.addSeparator()
# views_menu.addAction(self.override_color_action)
# views_menu.addSeparator()
views_menu.addAction(self.reset_views_action)
views_menu.addAction(self.toggle_fullscreen_action)
# Help menu.
help_menu = self.menuBar().addMenu("&Help")
help_menu.addAction(self.open_preferences_action)
help_menu.addAction(self.refresh_preferences_action)
help_menu.addSeparator()
help_menu.addAction(self.shortcuts_action)
help_menu.addAction(self.manual_action)
help_menu.addAction(self.about_action)
def create_toolbar(self):
self.toolbar = self.addToolBar("KlustaViewaToolbar")
self.toolbar.setObjectName("KlustaViewaToolbar")
self.toolbar.addAction(self.open_action)
self.toolbar.addAction(self.save_action)
self.toolbar.addAction(self.undo_action)
self.toolbar.addAction(self.redo_action)
# self.toolbar.addSeparator()
# self.toolbar.addAction(self.override_color_action)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)
def create_open_progress_dialog(self):
self.open_progress = QtGui.QProgressDialog("Converting to Kwik...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.open_progress.setWindowModality(QtCore.Qt.WindowModal)
self.open_progress.setValue(0)
self.open_progress.setWindowTitle('Loading')
self.open_progress.setCancelButton(None)
self.open_progress.setMinimumDuration(0)
def create_save_progress_dialog(self):
self.save_progress = QtGui.QProgressDialog("Saving...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.save_progress.setWindowModality(QtCore.Qt.WindowModal)
self.save_progress.setValue(0)
self.save_progress.setWindowTitle('Saving')
self.save_progress.setCancelButton(None)
self.save_progress.setMinimumDuration(0)
# Action enabled.
# ---------------
def update_action_enabled(self):
self.undo_action.setEnabled(self.can_undo())
self.redo_action.setEnabled(self.can_redo())
def can_undo(self):
if self.controller is None:
return False
return self.controller.can_undo()
def can_redo(self):
if self.controller is None:
return False
return self.controller.can_redo()
# View methods.
# -------------
def create_view(self, view_class, position=None,
closable=True, floatable=True, index=0, floating=None, title=None,
**kwargs):
"""Add a widget to the main window."""
view = view_class(self, getfocus=False)
view.set_data(**kwargs)
# Create the dock widget.
name = view_class.__name__ + '_' + str(index)
dockwidget = ViewDockWidget(view_class.__name__)
# dockwidget = ViewDockWidget(name)
dockwidget.setObjectName(name)
dockwidget.setWidget(view)
dockwidget.closed.connect(self.dock_widget_closed)
# Set dock widget options.
options = QtGui.QDockWidget.DockWidgetMovable
if closable:
options = options | QtGui.QDockWidget.DockWidgetClosable
if floatable:
options = options | QtGui.QDockWidget.DockWidgetFloatable
dockwidget.setFeatures(options)
dockwidget.setAllowedAreas(
QtCore.Qt.LeftDockWidgetArea |
QtCore.Qt.RightDockWidgetArea |
QtCore.Qt.TopDockWidgetArea |
QtCore.Qt.BottomDockWidgetArea)
dockwidget.visibilityChanged.connect(partial(
self.dock_visibility_changed_callback, view))
if position is not None:
# Add the dock widget to the main window.
self.addDockWidget(position, dockwidget)
if floating is not None:
dockwidget.setFloating(floating)
if title is None:
title = view_class.__name__
dockwidget.setTitleBarWidget(DockTitleBar(dockwidget, title))
# Return the view widget.
return view
def add_channel_view(self, do_update=None, floating=False):
view = self.create_view(vw.ChannelView,
position=QtCore.Qt.LeftDockWidgetArea,
index=len(self.views['ChannelView']),
closable=False,
# floatable=False
)
# Connect callback functions.
# view.channelsSelected.connect(self.channels_selected_callback)
# view.channelColorChanged.connect(self.channel_color_changed_callback)
# view.groupColorChanged.connect(self.group_color_changed_callback)
# view.groupRenamed.connect(self.group_renamed_callback)
# view.channelsMoved.connect(self.channels_moved_callback)
# view.groupAdded.connect(self.group_added_callback)
# view.groupRemoved.connect(self.group_removed_callback)
self.views['ChannelView'].append(view)
if do_update:
self.update_channel_view()
def dock_visibility_changed_callback(self, view, visibility):
# Register dock widget visibility.
view.visibility = visibility
def restore_last_view(self, name):
"""Return True if the last view was successfully restored,
False if the view needs to be restored manually by creating a new
view."""
# No existing view: need to create a new view.
if not self.views[name]:
return False
view = self.views[name][-1]
# A view exists and it is hidden: restore it.
if getattr(view, 'visibility', None) is False:
view.parent().toggleViewAction().activate(QtGui.QAction.Trigger)
return True
# A view exists but it is not hidden: just add a new view.
else:
return False
def add_ipython_view(self, floating=None):
view = self.create_view(vw.IPythonView,
index=len(self.views['IPythonView']),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
# Create namespace for the interactive session.
namespace = dict(
window=self,
select=self.get_view('ChannelView').select,
loader=self.loader,
# stats=self.statscache,
wizard=self.wizard,
)
view.set_data(**namespace)
# Load all .py files in the code directory.
paths = USERPREF['ipython_import_paths'] or []
if isinstance(paths, basestring):
paths = [paths]
for path in paths:
path = os.path.realpath(os.path.expanduser(path))
if os.path.exists(path):
files = [file for file in os.listdir(path) if file.endswith('.py')]
for file in files:
log.debug("Running {0:s}".format(file))
view.run_file(os.path.join(path, file))
self.views['IPythonView'].append(view)
def add_trace_view(self, do_update=None, floating=False):
if len(self.views['TraceView']) >= 1:
return
view = self.create_view(vw.TraceView,
index=len(self.views['TraceView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
self.views['TraceView'].append(view)
if do_update and self.is_file_open:
self.update_trace_view()
def update_trace_view(self):
data = vd.get_traceview_data(self.loader)
[view.set_data(**data) for view in self.get_views('TraceView')]
def update_channel_view(self, channels=None):
"""Update the channel view using the data stored in the loader
object."""
data = vd.get_channelview_data(self.loader, channels=channels)
self.get_view('ChannelView').set_data(**data)
if channels is not None:
return
def get_view(self, name, index=0):
views = self.views[name]
if not views:
return None
else:
return views[index]
def get_views(self, name):
return self.views[name]
def create_views(self):
"""Create all views at initialization."""
# Create the default layout.
self.views = dict(
ChannelView=[],
IPythonView=[],
TraceView=[],
)
# count = SETTINGS['main_window.views']
count = None
if count is None:
self.create_default_views()
else:
self.create_custom_views(count)
def create_default_views(self, do_update=None, floating=False):
self.add_channel_view(do_update=do_update)
self.add_trace_view(do_update=do_update)
def create_custom_views(self, count):
[self.add_channel_view() for _ in xrange(count['ChannelView'])]
[self.add_ipython_view() for _ in xrange(count['IPythonView'])]
[self.add_trace_view() for _ in xrange(count['TraceView'])]
def dock_widget_closed(self, dock):
for key in self.views.keys():
self.views[key] = [view for view in self.views[key] if view.parent() != dock]
# Threads.
# --------
def create_threads(self):
# Create the external threads.
self.open_task = inthread(OpenTask)()
self.open_task.dataOpened.connect(self.open_done)
self.open_task.dataSaved.connect(self.save_done)
self.open_task.dataOpenFailed.connect(self.open_failed)
def join_threads(self):
self.open_task.join()
# File menu callbacks.
# --------------------
def open_callback(self, checked=None):
# HACK: Force release of Ctrl key.
self.force_key_release()
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(self,
"Open a file (.clu or other)", folder)[0]
# If a file has been selected, open it.
if path:
# Launch the loading task in the background asynchronously.
self.open_task.open(self.loader, path)
# Save the folder.
folder = os.path.dirname(path)
SETTINGS['main_window.last_data_dir'] = folder
SETTINGS['main_window.last_data_file'] = path
def save_callback(self, checked=None):
self.open_task.save(self.loader)
def open_last_callback(self, checked=None):
path = SETTINGS['main_window.last_data_file']
if path:
self.open_task.open(self.loader, path)
def close_callback(self, checked=None):
self.is_file_open = False
channels = self.get_view('ChannelView').selected_channels()
if channels:
self.get_view('ChannelView').unselect()
time.sleep(.25)
# Update the views.
self.update_channel_view()
self.update_trace_view()
# Clear the ChannelView.
self.get_view('ChannelView').clear()
def quit_callback(self, checked=None):
self.close()
# Open callbacks.
# --------------
def open_done(self):
self.is_file_open = True
# HACK: force release of Control key.
self.force_key_release()
channels = self.get_view('ChannelView').selected_channels()
if channels:
self.get_view('ChannelView').unselect()
# Create the Controller.
self.controller = Controller(self.loader)
# Create the cache for the channel statistics that need to be
# computed in the background.
# self.statscache = StatsCache(self.loader.ncorrbins)
# Update stats cache in IPython view.
ipython = self.get_view('IPythonView')
# if ipython:
# ipython.set_data(stats=self.statscache)
# Initialize the wizard.
self.wizard = Wizard()
# Update the views.
self.update_channel_view()
self.update_trace_view()
def open_failed(self, message):
self.open_progress.setValue(0)
QtGui.QMessageBox.warning(self, "Error while opening the file",
"An error occurred: {0:s}".format(message),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def open_progress_reported(self, progress, progress_max):
self.open_progress.setMaximum(progress_max)
self.open_progress.setValue(progress)
def save_progress_reported(self, progress, progress_max):
self.save_progress.setMaximum(progress_max)
self.save_progress.setValue(progress)
def save_done(self):
self.need_save = False
# Selection methods.
# ------------------
# def buffer_accepted_callback(self, (channels, wizard)):
# self._wizard = wizard
# # The wizard boolean specifies whether the autozoom is activated or not.
# self.taskgraph.select(channels, wizard and
# self.automatic_projection_action.isChecked())
def channels_selected_callback(self, channels, wizard=False):
self.buffer.request((channels, wizard))
def channel_pair_selected_callback(self, channels):
"""Callback when the user clicks on a pair in the
SimilarityMatrixView."""
self.get_view('ChannelView').select(channels)
# Views menu callbacks.
# ---------------------
def add_trace_view_callback(self, checked=None):
self.add_trace_view(do_update=True, floating=True)
def add_ipython_view_callback(self, checked=None):
self.add_ipython_view()
def reset_views_callback(self, checked=None):
# Delete all views.
for key, views in self.views.iteritems():
for view in views:
self.removeDockWidget(view.parent())
self.views[key] = []
# Re-create the default views.
self.create_default_views(do_update=self.is_file_open, floating=False)
def toggle_fullscreen_callback(self):
if self.isFullScreen():
self.showNormal()
else:
self.showFullScreen()
# Override color callback.
# ------------------------
# def override_color_callback(self, checked=None):
# self.override_color = not self.override_color
# self.taskgraph.override_color(self.override_color)
# Actions callbacks.
# ------------------
#
# def undo_callback(self, checked=None):
# if self.is_busy:
# return
# self.taskgraph.undo(self._wizard)
# self.update_action_enabled()
#
# def redo_callback(self, checked=None):
# if self.is_busy:
# return
# self.taskgraph.redo(self._wizard)
# self.update_action_enabled()
#
# def channel_color_changed_callback(self, channel, color):
# self.taskgraph.channel_color_changed(channel, color, self._wizard)
# self.update_action_enabled()
#
# def group_color_changed_callback(self, group, color):
# self.taskgraph.group_color_changed(group, color)
# self.update_action_enabled()
#
# def group_renamed_callback(self, group, name):
# self.taskgraph.group_renamed(group, name)
# self.update_action_enabled()
#
# def channels_moved_callback(self, channels, group):
# self.taskgraph.channels_moved(channels, group)
# self.update_action_enabled()
#
# def group_removed_callback(self, group):
# self.taskgraph.group_removed(group)
# self.update_action_enabled()
#
# def group_added_callback(self, group, name, color):
# self.taskgraph.group_added(group, name, color)
# self.update_action_enabled()
#
# Help callbacks.
# ---------------
def manual_callback(self, checked=None):
url = "https://github.com/klusta-team/klustaviewa/tree/master/docs/manual.md"
webbrowser.open(url)
def about_callback(self, checked=None):
QtGui.QMessageBox.about(self, "KlustaViewa", ABOUT)
def shortcuts_callback(self, checked=None):
e = QtGui.QKeyEvent(QtCore.QEvent.KeyPress,
QtCore.Qt.Key_H,
QtCore.Qt.NoModifier,)
self.keyPressEvent(e)
def open_preferences_callback(self, checked=None):
url = USERPREF.filepath
log.debug("Opening preferences file at '{0:s}'".format(url))
QtGui.QDesktopServices.openUrl(QtCore.QUrl('file:///' + url))
def refresh_preferences_callback(self, checked=None):
log.debug("Refreshing user preferences.")
USERPREF.refresh()
# Geometry.
# ---------
def save_geometry(self):
"""Save the arrangement of the whole window."""
# SETTINGS['main_window.views'] = {name: len(self.get_views(name))
# for name in self.views.keys()}
SETTINGS['main_window.geometry'] = encode_bytearray(
self.saveGeometry())
SETTINGS['main_window.state'] = encode_bytearray(self.saveState())
def restore_geometry(self):
"""Restore the arrangement of the whole window."""
g = SETTINGS['main_window.geometry']
s = SETTINGS['main_window.state']
if s:
self.restoreState(decode_bytearray(s))
if g:
self.restoreGeometry(decode_bytearray(g))
# Event handlers.
# ---------------
def force_key_release(self):
"""HACK: force release of Ctrl, Shift and Alt when focus out."""
self.keyReleaseEvent(QtGui.QKeyEvent(QtCore.QEvent.KeyRelease,
QtCore.Qt.Key_Control, QtCore.Qt.NoModifier))
self.keyReleaseEvent(QtGui.QKeyEvent(QtCore.QEvent.KeyRelease,
QtCore.Qt.Key_Shift, QtCore.Qt.NoModifier))
self.keyReleaseEvent(QtGui.QKeyEvent(QtCore.QEvent.KeyRelease,
QtCore.Qt.Key_Alt, QtCore.Qt.NoModifier))
def event(self, e):
if e.type() == QtCore.QEvent.WindowActivate:
pass
elif e.type() == QtCore.QEvent.WindowDeactivate:
self.force_key_release()
return super(KwikSkope, self).event(e)
def contextMenuEvent(self, e):
"""Disable the context menu in the main window."""
return
def keyPressEvent(self, e):
super(KwikSkope, self).keyPressEvent(e)
for views in self.views.values():
[view.keyPressEvent(e) for view in views]
def keyReleaseEvent(self, e):
super(KwikSkope, self).keyReleaseEvent(e)
for views in self.views.values():
[view.keyReleaseEvent(e) for view in views]
def closeEvent(self, e):
prompt_save_on_exit = USERPREF['prompt_save_on_exit']
if prompt_save_on_exit is None:
prompt_save_on_exit = True
if self.need_save and prompt_save_on_exit:
reply = QtGui.QMessageBox.question(self, 'Save',
"Do you want to save?",
(
QtGui.QMessageBox.Save |
QtGui.QMessageBox.Close |
QtGui.QMessageBox.Cancel
),
QtGui.QMessageBox.Save)
if reply == QtGui.QMessageBox.Save:
folder = SETTINGS.get('main_window.last_data_file')
self.loader.save()
elif reply == QtGui.QMessageBox.Cancel:
e.ignore()
return
elif reply == QtGui.QMessageBox.Close:
pass
# Save the window geometry when closing the software.
self.save_geometry()
# End the threads.
self.join_threads()
# Close the loader.
self.loader.close()
# Close all views.
for views in self.views.values():
for view in views:
if hasattr(view, 'closeEvent'):
view.closeEvent(e)
# Close the logger file.
if self.dolog:
close_file_logger()
# Close the main window.
return super(KwikSkope, self).closeEvent(e)
def sizeHint(self):
return QtCore.QSize(1200, 800)
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None, dolog=True, filename=None):
self.views = {}
super(MainWindow, self).__init__(parent)
self.views = {}
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.klustaviewa'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
self.initialize_view_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KlustaViewa')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader(userpref=USERPREF)
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.taskgraph = TaskGraph(self)
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_correlograms_actions()
self.create_control_actions()
self.create_wizard_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename)
self.show()
def set_styles(self):
# set stylesheet
path = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(path, "styles.css")
with open(path, 'r') as f:
stylesheet = f.read()
stylesheet = stylesheet.replace('%ACCENT%', '#cdcdcd')
stylesheet = stylesheet.replace('%ACCENT2%', '#a0a0a0')
stylesheet = stylesheet.replace('%ACCENT3%', '#909090')
stylesheet = stylesheet.replace('%ACCENT4%', '#cdcdcd')
self.setStyleSheet(stylesheet)
def set_busy_cursor(self):
cursor = QtGui.QApplication.overrideCursor()
if cursor is None or cursor.shape() != QtCore.Qt.BusyCursor:
QtGui.QApplication.setOverrideCursor(self.busy_cursor)
def set_normal_cursor(self):
# QtGui.QApplication.setOverrideCursor(self.normal_cursor)
QtGui.QApplication.restoreOverrideCursor()
def set_busy(self, computing_correlograms=None, computing_matrix=None):
if computing_correlograms is not None:
self.computing_correlograms = computing_correlograms
if computing_matrix is not None:
self.computing_matrix = computing_matrix
busy = self.computing_correlograms or self.computing_matrix
if busy:
self.set_busy_cursor()
self.is_busy = True
else:
self.set_normal_cursor()
self.is_busy = False
def initialize_view_logger(self):
# Initialize the view logger.
viewlogger = vw.ViewLogger(name='viewlogger', fmt='%(message)s',
level=USERPREF['loglevel'], print_caller=False)
register(viewlogger)
viewlogger.outlog.writeRequested.connect(self.log_view_write_callback)
self.view_logger_text = StringIO()
# Actions.
# --------
def add_action(self, name, text, callback=None, shortcut=None,
checkable=False, checked=False, icon=None):
action = QtGui.QAction(text, self)
if callback is None:
callback = getattr(self, name + '_callback', None)
if callback:
action.triggered.connect(callback)
if shortcut:
action.setShortcut(shortcut)
if icon:
action.setIcon(get_icon(icon))
action.setCheckable(checkable)
action.setChecked(checked)
setattr(self, name + '_action', action)
def create_file_actions(self):
# Open actions.
self.add_action('open', '&Open', shortcut='Ctrl+O', icon='open')
# Open last file action
path = SETTINGS['main_window.last_data_file']
if path:
lastfile = os.path.basename(path)
if len(lastfile) > 30:
lastfile = '...' + lastfile[-30:]
self.add_action('open_last', 'Open &last ({0:s})'.format(
lastfile), shortcut='Ctrl+Alt+O')
else:
self.add_action('open_last', 'Open &last', shortcut='Ctrl+Alt+O')
self.open_last_action.setEnabled(False)
self.add_action('switch', 'S&witch shank')
self.add_action('import', '&Import clustering')
self.add_action('reset', '&Reset clustering')
self.add_action('save', '&Save', shortcut='Ctrl+S', icon='save')
# self.add_action('renumber', 'Save &renumbered')
self.add_action('close', '&Close file')
def create_edit_actions(self):
# Undo/redo actions.
self.add_action('undo', '&Undo', shortcut='Ctrl+Z', icon='undo')
self.add_action('redo', '&Redo', shortcut='Ctrl+Y', icon='redo')
# self.add_action('reset', 'Re&set')
# Quit action.
self.add_action('quit', '&Quit', shortcut='Ctrl+Q')
def create_view_actions(self):
self.add_action('add_feature_view', 'Add &FeatureView')
self.add_action('add_waveform_view', 'Add &WaveformView')
self.add_action('add_similarity_matrix_view',
'Add &SimilarityMatrixView')
self.add_action('add_correlograms_view', 'Add &CorrelogramsView')
self.add_action('add_ipython_view', 'Add &IPythonView')
self.add_action('add_log_view', 'Add &LogView')
self.add_action('add_trace_view', 'Add &TraceView')
self.add_action('reset_views', '&Reset views')
self.add_action('toggle_fullscreen', 'Toggle fullscreen', shortcut='F')
self.add_action('override_color', 'Override cluster &color',
icon='override_color')#, shortcut='C')
def create_control_actions(self):
self.add_action('merge', '&Merge', shortcut='G', icon='merge')
self.add_action('split', '&Split', shortcut='K', icon='split')
self.add_action('recluster', '&Recluster', shortcut='CTRL+R')
def create_correlograms_actions(self):
self.add_action('change_ncorrbins', 'Change time &window')
self.add_action('change_corrbin', 'Change &bin size')
self.add_action('change_corr_normalization', 'Change &normalization')
def create_wizard_actions(self):
self.add_action('reset_navigation', '&Reinitialize wizard',
shortcut='CTRL+ALT+Space')
self.add_action('automatic_projection', '&Automatic projection',
checkable=True, checked=True)
self.add_action('change_candidate_color',
'Change &color of the closest match',
shortcut='C')
self.add_action('previous_candidate', '&Previous closest match',
shortcut='SHIFT+Space')
self.add_action('next_candidate', '&Skip closest match',
shortcut='Space')
self.add_action('skip_target', '&Skip best unsorted',
# shortcut='Space'
)
self.add_action('delete_candidate', 'Move closest match to &MUA',
shortcut='CTRL+M')
self.add_action('delete_candidate_noise', 'Move closest match to &noise',
shortcut='CTRL+N')
self.add_action('next_target', 'Move best unsorted to &good',
shortcut='ALT+G')
self.add_action('delete_target', 'Move best unsorted to &MUA',
shortcut='ALT+M')
self.add_action('delete_target_noise', 'Move best unsorted to &noise',
shortcut='ALT+N')
self.add_action('delete_both', 'Move &both to MUA',
shortcut='CTRL+ALT+M')
self.add_action('delete_both_noise', 'Move both to noise',
shortcut='CTRL+ALT+N')
def create_help_actions(self):
self.add_action('about', '&About')
self.add_action('manual', 'Show &manual')
self.add_action('shortcuts', 'Show &shortcuts')
self.add_action('open_preferences', '&Open preferences')
self.add_action('refresh_preferences', '&Refresh preferences')
def create_menu(self):
# File menu.
file_menu = self.menuBar().addMenu("&File")
file_menu.addAction(self.open_action)
file_menu.addAction(self.open_last_action)
file_menu.addSeparator()
file_menu.addAction(self.reset_action)
# file_menu.addAction(self.import_action)
file_menu.addSeparator()
file_menu.addAction(self.save_action)
# file_menu.addAction(self.renumber_action)
file_menu.addSeparator()
file_menu.addAction(self.switch_action)
file_menu.addSeparator()
file_menu.addAction(self.close_action)
file_menu.addAction(self.quit_action)
# Edit menu.
edit_menu = self.menuBar().addMenu("&Edit")
edit_menu.addAction(self.undo_action)
edit_menu.addAction(self.redo_action)
# View menu.
views_menu = self.menuBar().addMenu("&View")
views_menu.addAction(self.add_feature_view_action)
views_menu.addAction(self.add_waveform_view_action)
views_menu.addAction(self.add_correlograms_view_action)
views_menu.addAction(self.add_similarity_matrix_view_action)
views_menu.addAction(self.add_trace_view_action)
views_menu.addSeparator()
views_menu.addAction(self.add_log_view_action)
if vw.IPYTHON:
views_menu.addAction(self.add_ipython_view_action)
views_menu.addSeparator()
views_menu.addAction(self.override_color_action)
views_menu.addSeparator()
views_menu.addAction(self.reset_views_action)
views_menu.addAction(self.toggle_fullscreen_action)
# Correlograms menu.
correlograms_menu = self.menuBar().addMenu("&Correlograms")
correlograms_menu.addAction(self.change_ncorrbins_action)
correlograms_menu.addAction(self.change_corrbin_action)
correlograms_menu.addSeparator()
correlograms_menu.addAction(self.change_corr_normalization_action)
# Actions menu.
actions_menu = self.menuBar().addMenu("&Actions")
actions_menu.addSeparator()
actions_menu.addAction(self.get_view('ClusterView').move_to_mua_action)
actions_menu.addAction(self.get_view('ClusterView').move_to_noise_action)
actions_menu.addSeparator()
actions_menu.addAction(self.merge_action)
actions_menu.addAction(self.split_action)
actions_menu.addSeparator()
actions_menu.addAction(self.recluster_action)
# Wizard menu.
wizard_menu = self.menuBar().addMenu("&Wizard")
# Previous/skip candidate.
wizard_menu.addAction(self.next_candidate_action)
wizard_menu.addAction(self.previous_candidate_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.skip_target_action)
wizard_menu.addSeparator()
# Good group.
# wizard_menu.addSeparator()
# Delete.
wizard_menu.addAction(self.delete_candidate_action)
wizard_menu.addAction(self.delete_candidate_noise_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.next_target_action)
wizard_menu.addAction(self.delete_target_action)
wizard_menu.addAction(self.delete_target_noise_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.delete_both_action)
wizard_menu.addAction(self.delete_both_noise_action)
wizard_menu.addSeparator()
# Misc.
wizard_menu.addAction(self.change_candidate_color_action)
wizard_menu.addAction(self.automatic_projection_action)
wizard_menu.addAction(self.reset_navigation_action)
# Help menu.
help_menu = self.menuBar().addMenu("&Help")
help_menu.addAction(self.open_preferences_action)
help_menu.addAction(self.refresh_preferences_action)
help_menu.addSeparator()
help_menu.addAction(self.shortcuts_action)
help_menu.addAction(self.manual_action)
help_menu.addAction(self.about_action)
def create_toolbar(self):
self.toolbar = self.addToolBar("KlustaViewaToolbar")
self.toolbar.setObjectName("KlustaViewaToolbar")
self.toolbar.addAction(self.open_action)
self.toolbar.addAction(self.save_action)
# self.toolbar.addAction(self.saveas_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.merge_action)
self.toolbar.addAction(self.split_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.get_view('ClusterView').move_to_mua_action)
self.toolbar.addAction(self.get_view('ClusterView').move_to_noise_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.undo_action)
self.toolbar.addAction(self.redo_action)
# self.toolbar.addSeparator()
# self.toolbar.addAction(self.override_color_action)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)
def create_open_progress_dialog(self):
self.open_progress = QtGui.QProgressDialog("Converting to Kwik...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.open_progress.setWindowModality(QtCore.Qt.WindowModal)
self.open_progress.setValue(0)
self.open_progress.setWindowTitle('Loading')
self.open_progress.setCancelButton(None)
self.open_progress.setMinimumDuration(0)
def create_save_progress_dialog(self):
self.save_progress = QtGui.QProgressDialog("Saving...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.save_progress.setWindowModality(QtCore.Qt.WindowModal)
self.save_progress.setValue(0)
self.save_progress.setWindowTitle('Saving')
self.save_progress.setCancelButton(None)
self.save_progress.setMinimumDuration(0)
# Action enabled.
# ---------------
def update_action_enabled(self):
self.undo_action.setEnabled(self.can_undo())
self.redo_action.setEnabled(self.can_redo())
self.merge_action.setEnabled(self.can_merge())
self.split_action.setEnabled(self.can_split())
def can_undo(self):
if self.controller is None:
return False
return self.controller.can_undo()
def can_redo(self):
if self.controller is None:
return False
return self.controller.can_redo()
def can_merge(self):
cluster_view = self.get_view('ClusterView')
clusters = cluster_view.selected_clusters()
return len(clusters) >= 2
def can_split(self):
cluster_view = self.get_view('ClusterView')
clusters = cluster_view.selected_clusters()
spikes_selected = self.spikes_selected
return len(spikes_selected) >= 1
# View methods.
# -------------
def create_view(self, view_class, position=None,
closable=True, floatable=True, index=0, floating=None, title=None,
**kwargs):
"""Add a widget to the main window."""
view = view_class(self, getfocus=False)
view.set_data(**kwargs)
# Create the dock widget.
name = view_class.__name__ + '_' + str(index)
dockwidget = ViewDockWidget(view_class.__name__)
# dockwidget = ViewDockWidget(name)
dockwidget.setObjectName(name)
dockwidget.setWidget(view)
dockwidget.closed.connect(self.dock_widget_closed)
# Set dock widget options.
options = QtGui.QDockWidget.DockWidgetMovable
if closable:
options = options | QtGui.QDockWidget.DockWidgetClosable
if floatable:
options = options | QtGui.QDockWidget.DockWidgetFloatable
dockwidget.setFeatures(options)
dockwidget.setAllowedAreas(
QtCore.Qt.LeftDockWidgetArea |
QtCore.Qt.RightDockWidgetArea |
QtCore.Qt.TopDockWidgetArea |
QtCore.Qt.BottomDockWidgetArea)
dockwidget.visibilityChanged.connect(partial(
self.dock_visibility_changed_callback, view))
if position is not None:
# Add the dock widget to the main window.
self.addDockWidget(position, dockwidget)
if floating is not None:
dockwidget.setFloating(floating)
if title is None:
title = view_class.__name__
dockwidget.setTitleBarWidget(DockTitleBar(dockwidget, title))
# Return the view widget.
return view
def add_cluster_view(self, do_update=None, floating=False):
view = self.create_view(vw.ClusterView,
position=QtCore.Qt.LeftDockWidgetArea,
index=len(self.views['ClusterView']),
closable=False,
# floatable=False
)
# Connect callback functions.
view.clustersSelected.connect(self.clusters_selected_callback)
view.clusterColorChanged.connect(self.cluster_color_changed_callback)
view.groupColorChanged.connect(self.group_color_changed_callback)
view.groupRenamed.connect(self.group_renamed_callback)
view.clustersMoved.connect(self.clusters_moved_callback)
view.groupAdded.connect(self.group_added_callback)
view.groupRemoved.connect(self.group_removed_callback)
self.views['ClusterView'].append(view)
if do_update:
self.taskgraph.update_cluster_view()
def dock_visibility_changed_callback(self, view, visibility):
# Register dock widget visibility.
view.visibility = visibility
def restore_last_view(self, name):
"""Return True if the last view was successfully restored,
False if the view needs to be restored manually by creating a new
view."""
# No existing view: need to create a new view.
if not self.views[name]:
return False
view = self.views[name][-1]
# A view exists and it is hidden: restore it.
if getattr(view, 'visibility', None) is False:
view.parent().toggleViewAction().activate(QtGui.QAction.Trigger)
return True
# A view exists but it is not hidden: just add a new view.
else:
return False
def add_similarity_matrix_view(self, do_update=None, floating=False):
# Try restoring the last view if it exists and it is hidden, and if
# successfully restored, do nothing more. Otherwise, need to create
# a new view.
if self.restore_last_view('SimilarityMatrixView'):
return
view = self.create_view(vw.SimilarityMatrixView,
index=len(self.views['SimilarityMatrixView']),
position=QtCore.Qt.LeftDockWidgetArea,
floating=floating)
view.clustersSelected.connect(self.cluster_pair_selected_callback)
self.views['SimilarityMatrixView'].append(view)
if do_update and self.is_file_open:
self.taskgraph.update_similarity_matrix_view()
def add_waveform_view(self, do_update=None, floating=False):
view = self.create_view(vw.WaveformView,
index=len(self.views['WaveformView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
view.spikesHighlighted.connect(
self.waveform_spikes_highlighted_callback)
view.boxClicked.connect(self.waveform_box_clicked_callback)
self.views['WaveformView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_waveform_view()
def add_feature_view(self, do_update=None, floating=False):
view = self.create_view(vw.FeatureProjectionView,
index=len(self.views['FeatureView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating,
title='FeatureView')
view.spikesHighlighted.connect(
self.features_spikes_highlighted_callback)
view.spikesSelected.connect(
self.features_spikes_selected_callback)
self.views['FeatureView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_feature_view()
def add_ipython_view(self, floating=None):
view = self.create_view(vw.IPythonView,
index=len(self.views['IPythonView']),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
# Create namespace for the interactive session.
namespace = dict(
window=self,
select=self.get_view('ClusterView').select,
loader=self.loader,
stats=self.statscache,
wizard=self.wizard,
)
view.set_data(**namespace)
# Load all .py files in the code directory.
paths = USERPREF['ipython_import_paths'] or []
if isinstance(paths, basestring):
paths = [paths]
for path in paths:
path = os.path.realpath(os.path.expanduser(path))
if os.path.exists(path):
files = [file for file in os.listdir(path) if file.endswith('.py')]
for file in files:
log.debug("Running {0:s}".format(file))
view.run_file(os.path.join(path, file))
self.views['IPythonView'].append(view)
def add_log_view(self, floating=None):
if len(self.views['LogView']) >= 1:
return
view = self.create_view(vw.LogView,
text=self.view_logger_text.getvalue(),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
self.views['LogView'].append(view)
def log_view_write_callback(self, message):
view = self.get_view('LogView')
if view:
view.append(message)
self.view_logger_text.write(message)
def add_correlograms_view(self, do_update=None, floating=False):
view = self.create_view(vw.CorrelogramsView,
index=len(self.views['CorrelogramsView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
self.views['CorrelogramsView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_correlograms_view()
def add_trace_view(self, do_update=None, floating=None):
# if len(self.views['TraceView']) >= 1:
# return
view = self.create_view(vw.TraceView,
index=len(self.views['TraceView']),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
self.views['TraceView'].append(view)
if do_update and self.is_file_open:
self.taskgraph.update_trace_view()
def get_view(self, name, index=0):
views = self.views.get(name, [])
if not views:
return None
else:
return views[index]
def get_views(self, name):
return self.views[name]
def create_views(self):
"""Create all views at initialization."""
# Create the default layout.
self.views = dict(
ClusterView=[],
SimilarityMatrixView=[],
WaveformView=[],
FeatureView=[],
CorrelogramsView=[],
IPythonView=[],
TraceView=[],
LogView=[],
)
count = SETTINGS['main_window.views']
if count is None:
self.create_default_views()
else:
self.create_custom_views(count)
def create_default_views(self, do_update=None, floating=False):
self.add_cluster_view(do_update=do_update, floating=floating)
self.add_similarity_matrix_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('ClusterView').parentWidget(),
self.get_view('SimilarityMatrixView').parentWidget(),
QtCore.Qt.Vertical
)
self.add_waveform_view(do_update=do_update, floating=floating)
self.add_feature_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('WaveformView').parentWidget(),
self.get_view('FeatureView').parentWidget(),
QtCore.Qt.Horizontal
)
self.add_correlograms_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('FeatureView').parentWidget(),
self.get_view('CorrelogramsView').parentWidget(),
QtCore.Qt.Vertical
)
def create_custom_views(self, count):
[self.add_cluster_view() for _ in xrange(count.get('ClusterView', 0))]
[self.add_similarity_matrix_view() for _ in xrange(count.get('SimilarityMatrixView', 0))]
[self.add_waveform_view() for _ in xrange(count.get('WaveformView', 0))]
[self.add_feature_view() for _ in xrange(count.get('FeatureView', 0))]
[self.add_log_view() for _ in xrange(count.get('LogView', 0))]
[self.add_ipython_view() for _ in xrange(count.get('IPythonView', 0))]
[self.add_correlograms_view() for _ in xrange(count.get('CorrelogramsView', 0))]
#[self.add_trace_view() for _ in xrange(count.get('TraceView', 0))]
def dock_widget_closed(self, dock):
for key in self.views.keys():
self.views[key] = [view for view in self.views[key] if view.parent() != dock]
# Threads.
# --------
def create_threads(self):
# Create the external threads.
self.open_task = inthread(OpenTask)()
self.open_task.dataOpened.connect(self.open_done)
self.open_task.dataSaved.connect(self.save_done)
self.open_task.dataOpenFailed.connect(self.open_failed)
def join_threads(self):
self.open_task.join()
self.taskgraph.join()
# File menu callbacks.
# --------------------
def open_callback(self, checked=None):
# HACK: Force release of Ctrl key.
self.force_key_release()
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(self,
"Open a file (.clu or other)", folder, "XML or KWIK (*.xml *.kwik)")[0]
# If a file has been selected, open it.
if path:
# Launch the loading task in the background asynchronously.
self._path = path
self.open_task.open(self.loader, path)
# Save the folder.
folder = os.path.dirname(path)
SETTINGS['main_window.last_data_dir'] = folder
SETTINGS['main_window.last_data_file'] = path
def import_callback(self, checked=None):
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(self,
"Open a .clu file", folder, "CLU file (*.clu.* *.clu_original.*)")[0]
# If a file has been selected, open it.
if path and self.loader is not None:
clu = read_clusters(path)
# TODO
self.open_done()
def save_callback(self, checked=None):
self.open_task.save(self.loader)
def reset_callback(self, checked=None):
# reply = QtGui.QMessageBox.question(self, 'Reset clustering',
# "Do you *really* want to erase permanently your manual clustering and reset it to the original (automatic) clustering? You won't be able to undo this operation!",
# (
# QtGui.QMessageBox.Yes |
# QtGui.QMessageBox.Cancel
# ),
# QtGui.QMessageBox.Cancel)
# if reply == QtGui.QMessageBox.Yes:
clustering_name, ok = QtGui.QInputDialog.getText(self, "Clustering name", "Copy from (you'll lose the current clustering):",
QtGui.QLineEdit.Normal, 'original')
if ok:
self.loader.copy_clustering(clustering_from=clustering_name,
clustering_to='main')
# Reload the file.
self.loader.close()
self.open_task.open(self.loader, self._path)
# elif reply == QtGui.QMessageBox.Cancel:
# return
# def renumber_callback(self, checked=None):
# # folder = SETTINGS.get('main_window.last_data_file')
# self.loader.save(renumber=True)
# # self.need_save = False
# self.open_last_callback()
def open_last_callback(self, checked=None):
path = SETTINGS['main_window.last_data_file']
if path:
self._path = path
self.open_task.open(self.loader, path)
def close_callback(self, checked=None):
# clusters = self.get_view('ClusterView').selected_clusters()
# if clusters:
# self.get_view('ClusterView').unselect()
# time.sleep(.25)
# Clear the views.
self.clear_view('ClusterView')
self.clear_view('SimilarityMatrixView')
self.clear_view('FeatureView')
self.clear_view('WaveformView')
self.clear_view('CorrelogramsView')
self.clear_view('TraceView')
self.loader.close()
self.is_file_open = False
def switch_callback(self, checked=None):
shank, ok = QtGui.QInputDialog.getInt(self,
"Shank number", "Shank number:",
self.loader.shank,
min(self.loader.shanks),
max(self.loader.shanks),
1)
if ok:
if shank in self.loader.shanks:
self.loader.set_shank(shank)
self.open_done()
else:
QtGui.QMessageBox.warning(self, "Wrong shank number",
("The selected shank '{0:d}' is not in "
"the list of shanks: {1:s}.").format(shank,
str(self.loader.shanks)),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def clear_view(self, view_name):
for v in self.get_views(view_name):
v.set_data()
if hasattr(v, 'clear'):
v.clear()
def quit_callback(self, checked=None):
self.close()
# Open callbacks.
# --------------
def open_done(self):
self.is_file_open = True
self.setWindowTitle('KlustaViewa: {0:s}'.format(
os.path.basename(self.loader.filename)
))
register(FileLogger(self.loader.log_filename, name='kwik',
level=logging.INFO))
# Start the selection buffer.
self.buffer = Buffer(self,
# delay_timer=.1, delay_buffer=.2
delay_timer=USERPREF['delay_timer'],
delay_buffer=USERPREF['delay_buffer']
)
self.buffer.start()
self.buffer.accepted.connect(self.buffer_accepted_callback)
# HACK: force release of Control key.
self.force_key_release()
clusters = self.get_view('ClusterView').selected_clusters()
if clusters:
self.get_view('ClusterView').unselect()
# Create the Controller.
self.controller = Controller(self.loader)
# Create the cache for the cluster statistics that need to be
# computed in the background.
self.statscache = StatsCache(SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT))
# Update stats cache in IPython view.
ipython = self.get_view('IPythonView')
if ipython:
ipython.set_data(stats=self.statscache)
# Initialize the wizard.
self.wizard = Wizard()
# Update the task graph.
self.taskgraph.set(self)
# self.taskgraph.update_projection_view()
self.taskgraph.update_cluster_view()
self.taskgraph.compute_similarity_matrix()
self.taskgraph.update_trace_view()
def open_failed(self, message):
self.open_progress.setValue(0)
QtGui.QMessageBox.warning(self, "Error while opening the file",
"An error occurred: {0:s}".format(message),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def open_progress_reported(self, progress, progress_max):
self.open_progress.setMaximum(progress_max)
self.open_progress.setValue(progress)
def save_progress_reported(self, progress, progress_max):
self.save_progress.setMaximum(progress_max)
self.save_progress.setValue(progress)
def save_done(self):
self.need_save = False
# Selection methods.
# ------------------
def buffer_accepted_callback(self, (clusters, wizard)):
self._wizard = wizard
# The wizard boolean specifies whether the autozoom is activated or not.
self.taskgraph.select(clusters, wizard and
self.automatic_projection_action.isChecked(), )
class KwikSkope(QtGui.QMainWindow):
def __init__(self, parent=None, dolog=True, filename=None):
super(KwikSkope, self).__init__(parent)
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.kwikskope'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(
myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KwikSkope')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
# self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader()
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename)
self.show()
def set_styles(self):
# set stylesheet
path = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(path, "styles.css")
with open(path, 'r') as f:
stylesheet = f.read()
stylesheet = stylesheet.replace('%ACCENT%', '#cdcdcd')
stylesheet = stylesheet.replace('%ACCENT2%', '#a0a0a0')
stylesheet = stylesheet.replace('%ACCENT3%', '#909090')
stylesheet = stylesheet.replace('%ACCENT4%', '#cdcdcd')
self.setStyleSheet(stylesheet)
# Actions.
# --------
def add_action(self,
name,
text,
callback=None,
shortcut=None,
checkable=False,
checked=False,
icon=None):
action = QtGui.QAction(text, self)
if callback is None:
callback = getattr(self, name + '_callback', None)
if callback:
action.triggered.connect(callback)
if shortcut:
action.setShortcut(shortcut)
if icon:
action.setIcon(get_icon(icon))
action.setCheckable(checkable)
action.setChecked(checked)
setattr(self, name + '_action', action)
def create_file_actions(self):
# Open actions.
self.add_action('open', '&Open', shortcut='Ctrl+O', icon='open')
# Open last file action
path = SETTINGS['main_window.last_data_file']
if path:
lastfile = os.path.basename(path)
if len(lastfile) > 30:
lastfile = '...' + lastfile[-30:]
self.add_action('open_last',
'Open &last ({0:s})'.format(lastfile),
shortcut='Ctrl+Alt+O')
else:
self.add_action('open_last', 'Open &last', shortcut='Ctrl+Alt+O')
self.open_last_action.setEnabled(False)
self.add_action('save', '&Save', shortcut='Ctrl+S', icon='save')
self.add_action('close', '&Close file')
# Quit action.
self.add_action('quit', '&Quit', shortcut='Ctrl+Q')
def create_edit_actions(self):
self.add_action('undo', '&Undo', shortcut='Ctrl+Z', icon='undo')
self.add_action('redo', '&Redo', shortcut='Ctrl+Y', icon='redo')
def create_view_actions(self):
self.add_action('add_ipython_view', 'Add &IPythonView')
self.add_action('reset_views', '&Reset views')
self.add_action('toggle_fullscreen', 'Toggle fullscreen', shortcut='F')
self.add_action('override_color',
'Override channel &color',
icon='override_color') #, shortcut='C')
def create_help_actions(self):
self.add_action('about', '&About')
self.add_action('manual', 'Show &manual')
self.add_action('shortcuts', 'Show &shortcuts')
self.add_action('open_preferences', '&Open preferences')
self.add_action('refresh_preferences',
'&Refresh preferences',
shortcut='CTRL+R')
def create_menu(self):
# File menu.
file_menu = self.menuBar().addMenu("&File")
file_menu.addAction(self.open_action)
file_menu.addAction(self.open_last_action)
file_menu.addSeparator()
# file_menu.addSeparator()
file_menu.addAction(self.save_action)
file_menu.addSeparator()
file_menu.addAction(self.quit_action)
# Edit menu.
# edit_menu = self.menuBar().addMenu("&Edit")
# edit_menu.addAction(self.undo_action)
# edit_menu.addAction(self.redo_action)
# View menu.
views_menu = self.menuBar().addMenu("&View")
if vw.IPYTHON:
views_menu.addAction(self.add_ipython_view_action)
views_menu.addSeparator()
# views_menu.addAction(self.override_color_action)
# views_menu.addSeparator()
views_menu.addAction(self.reset_views_action)
views_menu.addAction(self.toggle_fullscreen_action)
# Help menu.
help_menu = self.menuBar().addMenu("&Help")
help_menu.addAction(self.open_preferences_action)
help_menu.addAction(self.refresh_preferences_action)
help_menu.addSeparator()
help_menu.addAction(self.shortcuts_action)
help_menu.addAction(self.manual_action)
help_menu.addAction(self.about_action)
def create_toolbar(self):
self.toolbar = self.addToolBar("KlustaViewaToolbar")
self.toolbar.setObjectName("KlustaViewaToolbar")
self.toolbar.addAction(self.open_action)
self.toolbar.addAction(self.save_action)
self.toolbar.addAction(self.undo_action)
self.toolbar.addAction(self.redo_action)
# self.toolbar.addSeparator()
# self.toolbar.addAction(self.override_color_action)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)
def create_open_progress_dialog(self):
self.open_progress = QtGui.QProgressDialog("Converting to Kwik...",
"Cancel", 0, 0, self,
QtCore.Qt.Tool)
self.open_progress.setWindowModality(QtCore.Qt.WindowModal)
self.open_progress.setValue(0)
self.open_progress.setWindowTitle('Loading')
self.open_progress.setCancelButton(None)
self.open_progress.setMinimumDuration(0)
def create_save_progress_dialog(self):
self.save_progress = QtGui.QProgressDialog("Saving...", "Cancel", 0, 0,
self, QtCore.Qt.Tool)
self.save_progress.setWindowModality(QtCore.Qt.WindowModal)
self.save_progress.setValue(0)
self.save_progress.setWindowTitle('Saving')
self.save_progress.setCancelButton(None)
self.save_progress.setMinimumDuration(0)
# Action enabled.
# ---------------
def update_action_enabled(self):
self.undo_action.setEnabled(self.can_undo())
self.redo_action.setEnabled(self.can_redo())
def can_undo(self):
if self.controller is None:
return False
return self.controller.can_undo()
def can_redo(self):
if self.controller is None:
return False
return self.controller.can_redo()
# View methods.
# -------------
def create_view(self,
view_class,
position=None,
closable=True,
floatable=True,
index=0,
floating=None,
title=None,
**kwargs):
"""Add a widget to the main window."""
view = view_class(self, getfocus=False)
view.set_data(**kwargs)
# Create the dock widget.
name = view_class.__name__ + '_' + str(index)
dockwidget = ViewDockWidget(view_class.__name__)
# dockwidget = ViewDockWidget(name)
dockwidget.setObjectName(name)
dockwidget.setWidget(view)
dockwidget.closed.connect(self.dock_widget_closed)
# Set dock widget options.
options = QtGui.QDockWidget.DockWidgetMovable
if closable:
options = options | QtGui.QDockWidget.DockWidgetClosable
if floatable:
options = options | QtGui.QDockWidget.DockWidgetFloatable
dockwidget.setFeatures(options)
dockwidget.setAllowedAreas(QtCore.Qt.LeftDockWidgetArea
| QtCore.Qt.RightDockWidgetArea
| QtCore.Qt.TopDockWidgetArea
| QtCore.Qt.BottomDockWidgetArea)
dockwidget.visibilityChanged.connect(
partial(self.dock_visibility_changed_callback, view))
if position is not None:
# Add the dock widget to the main window.
self.addDockWidget(position, dockwidget)
if floating is not None:
dockwidget.setFloating(floating)
if title is None:
title = view_class.__name__
dockwidget.setTitleBarWidget(DockTitleBar(dockwidget, title))
# Return the view widget.
return view
def add_channel_view(self, do_update=None, floating=False):
view = self.create_view(
vw.ChannelView,
position=QtCore.Qt.LeftDockWidgetArea,
index=len(self.views['ChannelView']),
closable=False,
# floatable=False
)
# Connect callback functions.
# view.channelsSelected.connect(self.channels_selected_callback)
# view.channelColorChanged.connect(self.channel_color_changed_callback)
# view.groupColorChanged.connect(self.group_color_changed_callback)
# view.groupRenamed.connect(self.group_renamed_callback)
# view.channelsMoved.connect(self.channels_moved_callback)
# view.groupAdded.connect(self.group_added_callback)
# view.groupRemoved.connect(self.group_removed_callback)
self.views['ChannelView'].append(view)
if do_update:
self.update_channel_view()
def dock_visibility_changed_callback(self, view, visibility):
# Register dock widget visibility.
view.visibility = visibility
def restore_last_view(self, name):
"""Return True if the last view was successfully restored,
False if the view needs to be restored manually by creating a new
view."""
# No existing view: need to create a new view.
if not self.views[name]:
return False
view = self.views[name][-1]
# A view exists and it is hidden: restore it.
if getattr(view, 'visibility', None) is False:
view.parent().toggleViewAction().activate(QtGui.QAction.Trigger)
return True
# A view exists but it is not hidden: just add a new view.
else:
return False
def add_ipython_view(self, floating=None):
view = self.create_view(vw.IPythonView,
index=len(self.views['IPythonView']),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
# Create namespace for the interactive session.
namespace = dict(
window=self,
select=self.get_view('ChannelView').select,
loader=self.loader,
# stats=self.statscache,
wizard=self.wizard,
)
view.set_data(**namespace)
# Load all .py files in the code directory.
paths = USERPREF['ipython_import_paths'] or []
if isinstance(paths, basestring):
paths = [paths]
for path in paths:
path = os.path.realpath(os.path.expanduser(path))
if os.path.exists(path):
files = [
file for file in os.listdir(path) if file.endswith('.py')
]
for file in files:
log.debug("Running {0:s}".format(file))
view.run_file(os.path.join(path, file))
self.views['IPythonView'].append(view)
def add_trace_view(self, do_update=None, floating=False):
if len(self.views['TraceView']) >= 1:
return
view = self.create_view(vw.TraceView,
index=len(self.views['TraceView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
self.views['TraceView'].append(view)
if do_update and self.is_file_open:
self.update_trace_view()
def update_trace_view(self):
data = vd.get_traceview_data(self.loader)
[view.set_data(**data) for view in self.get_views('TraceView')]
def update_channel_view(self, channels=None):
"""Update the channel view using the data stored in the loader
object."""
data = vd.get_channelview_data(self.loader, channels=channels)
self.get_view('ChannelView').set_data(**data)
if channels is not None:
return
def get_view(self, name, index=0):
views = self.views[name]
if not views:
return None
else:
return views[index]
def get_views(self, name):
return self.views[name]
def create_views(self):
"""Create all views at initialization."""
# Create the default layout.
self.views = dict(
ChannelView=[],
IPythonView=[],
TraceView=[],
)
# count = SETTINGS['main_window.views']
count = None
if count is None:
self.create_default_views()
else:
self.create_custom_views(count)
def create_default_views(self, do_update=None, floating=False):
self.add_channel_view(do_update=do_update)
self.add_trace_view(do_update=do_update)
def create_custom_views(self, count):
[self.add_channel_view() for _ in xrange(count['ChannelView'])]
[self.add_ipython_view() for _ in xrange(count['IPythonView'])]
[self.add_trace_view() for _ in xrange(count['TraceView'])]
def dock_widget_closed(self, dock):
for key in self.views.keys():
self.views[key] = [
view for view in self.views[key] if view.parent() != dock
]
# Threads.
# --------
def create_threads(self):
# Create the external threads.
self.open_task = inthread(OpenTask)()
self.open_task.dataOpened.connect(self.open_done)
self.open_task.dataSaved.connect(self.save_done)
self.open_task.dataOpenFailed.connect(self.open_failed)
def join_threads(self):
self.open_task.join()
# File menu callbacks.
# --------------------
def open_callback(self, checked=None):
# HACK: Force release of Ctrl key.
self.force_key_release()
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(
self, "Open a file (.clu or other)", folder)[0]
# If a file has been selected, open it.
if path:
# Launch the loading task in the background asynchronously.
self.open_task.open(self.loader, path)
# Save the folder.
folder = os.path.dirname(path)
SETTINGS['main_window.last_data_dir'] = folder
SETTINGS['main_window.last_data_file'] = path
def save_callback(self, checked=None):
self.open_task.save(self.loader)
def open_last_callback(self, checked=None):
path = SETTINGS['main_window.last_data_file']
if path:
self.open_task.open(self.loader, path)
def close_callback(self, checked=None):
self.is_file_open = False
channels = self.get_view('ChannelView').selected_channels()
if channels:
self.get_view('ChannelView').unselect()
time.sleep(.25)
# Update the views.
self.update_channel_view()
self.update_trace_view()
# Clear the ChannelView.
self.get_view('ChannelView').clear()
def quit_callback(self, checked=None):
self.close()
# Open callbacks.
# --------------
def open_done(self):
self.is_file_open = True
# HACK: force release of Control key.
self.force_key_release()
channels = self.get_view('ChannelView').selected_channels()
if channels:
self.get_view('ChannelView').unselect()
# Create the Controller.
self.controller = Controller(self.loader)
# Create the cache for the channel statistics that need to be
# computed in the background.
# self.statscache = StatsCache(self.loader.ncorrbins)
# Update stats cache in IPython view.
ipython = self.get_view('IPythonView')
# if ipython:
# ipython.set_data(stats=self.statscache)
# Initialize the wizard.
self.wizard = Wizard()
# Update the views.
self.update_channel_view()
self.update_trace_view()
def open_failed(self, message):
self.open_progress.setValue(0)
QtGui.QMessageBox.warning(self, "Error while opening the file",
"An error occurred: {0:s}".format(message),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def open_progress_reported(self, progress, progress_max):
self.open_progress.setMaximum(progress_max)
self.open_progress.setValue(progress)
def save_progress_reported(self, progress, progress_max):
self.save_progress.setMaximum(progress_max)
self.save_progress.setValue(progress)
def save_done(self):
self.need_save = False
# Selection methods.
# ------------------
# def buffer_accepted_callback(self, (channels, wizard)):
# self._wizard = wizard
# # The wizard boolean specifies whether the autozoom is activated or not.
# self.taskgraph.select(channels, wizard and
# self.automatic_projection_action.isChecked())
def channels_selected_callback(self, channels, wizard=False):
self.buffer.request((channels, wizard))
def channel_pair_selected_callback(self, channels):
"""Callback when the user clicks on a pair in the
SimilarityMatrixView."""
self.get_view('ChannelView').select(channels)
# Views menu callbacks.
# ---------------------
def add_trace_view_callback(self, checked=None):
self.add_trace_view(do_update=True, floating=True)
def add_ipython_view_callback(self, checked=None):
self.add_ipython_view()
def reset_views_callback(self, checked=None):
# Delete all views.
for key, views in self.views.iteritems():
for view in views:
self.removeDockWidget(view.parent())
self.views[key] = []
# Re-create the default views.
self.create_default_views(do_update=self.is_file_open, floating=False)
def toggle_fullscreen_callback(self):
if self.isFullScreen():
self.showNormal()
else:
self.showFullScreen()
# Override color callback.
# ------------------------
# def override_color_callback(self, checked=None):
# self.override_color = not self.override_color
# self.taskgraph.override_color(self.override_color)
# Actions callbacks.
# ------------------
#
# def undo_callback(self, checked=None):
# if self.is_busy:
# return
# self.taskgraph.undo(self._wizard)
# self.update_action_enabled()
#
# def redo_callback(self, checked=None):
# if self.is_busy:
# return
# self.taskgraph.redo(self._wizard)
# self.update_action_enabled()
#
# def channel_color_changed_callback(self, channel, color):
# self.taskgraph.channel_color_changed(channel, color, self._wizard)
# self.update_action_enabled()
#
# def group_color_changed_callback(self, group, color):
# self.taskgraph.group_color_changed(group, color)
# self.update_action_enabled()
#
# def group_renamed_callback(self, group, name):
# self.taskgraph.group_renamed(group, name)
# self.update_action_enabled()
#
# def channels_moved_callback(self, channels, group):
# self.taskgraph.channels_moved(channels, group)
# self.update_action_enabled()
#
# def group_removed_callback(self, group):
# self.taskgraph.group_removed(group)
# self.update_action_enabled()
#
# def group_added_callback(self, group, name, color):
# self.taskgraph.group_added(group, name, color)
# self.update_action_enabled()
#
# Help callbacks.
# ---------------
def manual_callback(self, checked=None):
url = "https://github.com/klusta-team/klustaviewa/tree/master/docs/manual.md"
webbrowser.open(url)
def about_callback(self, checked=None):
QtGui.QMessageBox.about(self, "KlustaViewa", ABOUT)
def shortcuts_callback(self, checked=None):
e = QtGui.QKeyEvent(
QtCore.QEvent.KeyPress,
QtCore.Qt.Key_H,
QtCore.Qt.NoModifier,
)
self.keyPressEvent(e)
def open_preferences_callback(self, checked=None):
url = USERPREF.filepath
log.debug("Opening preferences file at '{0:s}'".format(url))
QtGui.QDesktopServices.openUrl(QtCore.QUrl('file:///' + url))
def refresh_preferences_callback(self, checked=None):
log.debug("Refreshing user preferences.")
USERPREF.refresh()
# Geometry.
# ---------
def save_geometry(self):
"""Save the arrangement of the whole window."""
# SETTINGS['main_window.views'] = {name: len(self.get_views(name))
# for name in self.views.keys()}
SETTINGS['main_window.geometry'] = encode_bytearray(
self.saveGeometry())
SETTINGS['main_window.state'] = encode_bytearray(self.saveState())
def restore_geometry(self):
"""Restore the arrangement of the whole window."""
g = SETTINGS['main_window.geometry']
s = SETTINGS['main_window.state']
if s:
self.restoreState(decode_bytearray(s))
if g:
self.restoreGeometry(decode_bytearray(g))
# Event handlers.
# ---------------
def force_key_release(self):
"""HACK: force release of Ctrl, Shift and Alt when focus out."""
self.keyReleaseEvent(
QtGui.QKeyEvent(QtCore.QEvent.KeyRelease, QtCore.Qt.Key_Control,
QtCore.Qt.NoModifier))
self.keyReleaseEvent(
QtGui.QKeyEvent(QtCore.QEvent.KeyRelease, QtCore.Qt.Key_Shift,
QtCore.Qt.NoModifier))
self.keyReleaseEvent(
QtGui.QKeyEvent(QtCore.QEvent.KeyRelease, QtCore.Qt.Key_Alt,
QtCore.Qt.NoModifier))
def event(self, e):
if e.type() == QtCore.QEvent.WindowActivate:
pass
elif e.type() == QtCore.QEvent.WindowDeactivate:
self.force_key_release()
return super(KwikSkope, self).event(e)
def contextMenuEvent(self, e):
"""Disable the context menu in the main window."""
return
def keyPressEvent(self, e):
super(KwikSkope, self).keyPressEvent(e)
for views in self.views.values():
[view.keyPressEvent(e) for view in views]
def keyReleaseEvent(self, e):
super(KwikSkope, self).keyReleaseEvent(e)
for views in self.views.values():
[view.keyReleaseEvent(e) for view in views]
def closeEvent(self, e):
prompt_save_on_exit = USERPREF['prompt_save_on_exit']
if prompt_save_on_exit is None:
prompt_save_on_exit = True
if self.need_save and prompt_save_on_exit:
reply = QtGui.QMessageBox.question(
self, 'Save', "Do you want to save?",
(QtGui.QMessageBox.Save | QtGui.QMessageBox.Close
| QtGui.QMessageBox.Cancel), QtGui.QMessageBox.Save)
if reply == QtGui.QMessageBox.Save:
folder = SETTINGS.get('main_window.last_data_file')
self.loader.save()
elif reply == QtGui.QMessageBox.Cancel:
e.ignore()
return
elif reply == QtGui.QMessageBox.Close:
pass
# Save the window geometry when closing the software.
self.save_geometry()
# End the threads.
self.join_threads()
# Close the loader.
self.loader.close()
# Close all views.
for views in self.views.values():
for view in views:
if hasattr(view, 'closeEvent'):
view.closeEvent(e)
# Close the logger file.
if self.dolog:
close_file_logger()
# Close the main window.
return super(KwikSkope, self).closeEvent(e)
def sizeHint(self):
return QtCore.QSize(1200, 800)
def __init__(self, parent=None, dolog=True, filename=None):
super(KwikSkope, self).__init__(parent)
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.kwikskope'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(
myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KwikSkope')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
# self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader()
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename)
self.show()
def test_kwik_loader_1():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
# features_some = l.get_some_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
# probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check the shape of the data sets.
# ---------------------------------
assert check_shape(features, (nspikes, nchannels * fetdim + 1))
# assert features_some.shape[1] == nchannels * fetdim + 1
assert check_shape(masks, (nspikes, nchannels * fetdim + 1))
assert check_shape(waveforms, (nspikes, nsamples, nchannels))
assert check_shape(clusters, (nspikes, ))
assert check_shape(spiketimes, (nspikes, ))
# assert check_shape(probe, (nchannels, 2))
assert check_shape(cluster_colors, (nclusters, ))
assert check_shape(cluster_groups, (nclusters, ))
assert check_shape(group_colors, (4, ))
assert check_shape(group_names, (4, ))
assert check_shape(cluster_sizes, (nclusters, ))
# Check the data type of the data sets.
# -------------------------------------
assert check_dtype(features, np.float32)
assert check_dtype(masks, np.float32)
# HACK: Panel has no dtype(s) attribute
# assert check_dtype(waveforms, np.float32)
assert check_dtype(clusters, np.int32)
assert check_dtype(spiketimes, np.float64)
# assert check_dtype(probe, np.float32)
assert check_dtype(cluster_colors, np.int32)
assert check_dtype(cluster_groups, np.int32)
assert check_dtype(group_colors, np.int32)
assert check_dtype(group_names, object)
assert check_dtype(cluster_sizes, np.int32)
l.close()
def test_kwik_loader_control():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
# Take all spikes in cluster 3.
spikes = get_indices(l.get_clusters(clusters=3))
# Put them in cluster 4.
l.set_cluster(spikes, 4)
spikes_new = get_indices(l.get_clusters(clusters=4))
# Ensure all spikes in old cluster 3 are now in cluster 4.
assert np.all(np.in1d(spikes, spikes_new))
# Change cluster groups.
clusters = [2, 3, 4]
group = 0
l.set_cluster_groups(clusters, group)
groups = l.get_cluster_groups(clusters)
assert np.all(groups == group)
# Change cluster colors.
clusters = [2, 3, 4]
color = 12
l.set_cluster_colors(clusters, color)
colors = l.get_cluster_colors(clusters)
assert np.all(colors == color)
# Change group name.
group = 0
name = l.get_group_names(group)
name_new = 'Noise new'
assert name == 'Noise'
l.set_group_names(group, name_new)
assert l.get_group_names(group) == name_new
# Change group color.
groups = [1, 2]
colors = l.get_group_colors(groups)
color_new = 10
l.set_group_colors(groups, color_new)
assert np.all(l.get_group_colors(groups) == color_new)
# Add cluster and group.
spikes = get_indices(l.get_clusters(clusters=3))[:10]
# Create new group 100.
l.add_group(100, 'New group', 10)
# Create new cluster 10000 and put it in group 100.
l.add_cluster(10000, 100, 10)
# Put some spikes in the new cluster.
l.set_cluster(spikes, 10000)
clusters = l.get_clusters(spikes=spikes)
assert np.all(clusters == 10000)
groups = l.get_cluster_groups(10000)
assert groups == 100
l.set_cluster(spikes, 2)
# Remove the new cluster and group.
l.remove_cluster(10000)
l.remove_group(100)
assert np.all(~np.in1d(10000, l.get_clusters()))
assert np.all(~np.in1d(100, l.get_cluster_groups()))
l.close()
def test_kwik_save():
"""WARNING: this test should occur at the end of the module since it
changes the mock data sets."""
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
clusters = l.get_clusters()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
# Set clusters.
indices = get_indices(clusters)
l.set_cluster(indices[::2], 2)
l.set_cluster(indices[1::2], 3)
# Set cluster info.
cluster_indices = l.get_clusters_unique()
l.set_cluster_colors(cluster_indices[::2], 10)
l.set_cluster_colors(cluster_indices[1::2], 20)
l.set_cluster_groups(cluster_indices[::2], 1)
l.set_cluster_groups(cluster_indices[1::2], 0)
# Save.
l.remove_empty_clusters()
l.save()
clusters = l.get_clusters()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
assert np.all(clusters[::2] == 2)
assert np.all(clusters[1::2] == 3)
assert np.all(cluster_colors[::2] == 10)
assert np.all(cluster_colors[1::2] == 20)
print cluster_groups
assert np.all(cluster_groups[::2] == 1)
assert np.all(cluster_groups[1::2] == 0)
l.close()
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None, dolog=True, filename=None, shank=None):
self.views = {}
super(MainWindow, self).__init__(parent)
self.views = {}
# HACK: display the icon in Windows' taskbar.
if os.name == 'nt':
try:
import ctypes
myappid = 'klustateam.klustaviewa'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
except:
pass
self.dolog = dolog
if self.dolog:
create_file_logger()
self.initialize_view_logger()
log.debug("Using {0:s}.".format(QT_BINDING))
# Main window options.
self.move(50, 50)
self.setWindowTitle('KlustaViewa')
# Focus options.
self.setFocusPolicy(QtCore.Qt.WheelFocus)
self.setMouseTracking(True)
# Dock widgets options.
self.setDockNestingEnabled(True)
self.setAnimated(False)
self.setWindowIcon(get_icon('logo'))
# Initialize some variables.
self.statscache = None
# self.loader = KlustersLoader()
self.loader = KwikLoader(userpref=USERPREF)
self.loader.progressReported.connect(self.open_progress_reported)
self.loader.saveProgressReported.connect(self.save_progress_reported)
self.wizard = Wizard()
self.controller = None
self.spikes_highlighted = []
self.spikes_selected = []
self._wizard = False
self.is_file_open = False
self.need_save = False
self.taskgraph = TaskGraph(self)
self.busy_cursor = QtGui.QCursor(QtCore.Qt.BusyCursor)
self.normal_cursor = QtGui.QCursor(QtCore.Qt.ArrowCursor)
self.is_busy = False
self.override_color = False
self.computing_correlograms = False
self.computing_matrix = False
# Create the main window.
self.create_views()
self.create_file_actions()
self.create_edit_actions()
self.create_view_actions()
self.create_correlograms_actions()
self.create_control_actions()
self.create_wizard_actions()
self.create_help_actions()
self.create_menu()
self.create_toolbar()
self.create_open_progress_dialog()
self.create_save_progress_dialog()
self.create_threads()
# Update action enabled/disabled property.
self.update_action_enabled()
# Show the main window.
self.set_styles()
self.restore_geometry()
# Automatically load a file upon startup if requested.
if filename:
filename = os.path.realpath(filename)
self.open_task.open(self.loader, filename, shank)
self.show()
def set_styles(self):
# set stylesheet
path = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(path, "styles.css")
with open(path, 'r') as f:
stylesheet = f.read()
stylesheet = stylesheet.replace('%ACCENT%', '#cdcdcd')
stylesheet = stylesheet.replace('%ACCENT2%', '#a0a0a0')
stylesheet = stylesheet.replace('%ACCENT3%', '#909090')
stylesheet = stylesheet.replace('%ACCENT4%', '#cdcdcd')
self.setStyleSheet(stylesheet)
def set_busy_cursor(self):
cursor = QtGui.QApplication.overrideCursor()
if cursor is None or cursor.shape() != QtCore.Qt.BusyCursor:
QtGui.QApplication.setOverrideCursor(self.busy_cursor)
def set_normal_cursor(self):
# QtGui.QApplication.setOverrideCursor(self.normal_cursor)
QtGui.QApplication.restoreOverrideCursor()
def set_busy(self, computing_correlograms=None, computing_matrix=None):
if computing_correlograms is not None:
self.computing_correlograms = computing_correlograms
if computing_matrix is not None:
self.computing_matrix = computing_matrix
busy = self.computing_correlograms or self.computing_matrix
if busy:
self.set_busy_cursor()
self.is_busy = True
else:
self.set_normal_cursor()
self.is_busy = False
def initialize_view_logger(self):
# Initialize the view logger.
viewlogger = vw.ViewLogger(name='viewlogger', fmt='%(message)s',
level=USERPREF['loglevel'], print_caller=False)
register(viewlogger)
viewlogger.outlog.writeRequested.connect(self.log_view_write_callback)
self.view_logger_text = StringIO()
# Actions.
# --------
def add_action(self, name, text, callback=None, shortcut=None,
checkable=False, checked=False, icon=None):
action = QtGui.QAction(text, self)
if callback is None:
callback = getattr(self, name + '_callback', None)
if callback:
action.triggered.connect(callback)
if shortcut:
action.setShortcut(shortcut)
if icon:
action.setIcon(get_icon(icon))
action.setCheckable(checkable)
action.setChecked(checked)
setattr(self, name + '_action', action)
def create_file_actions(self):
# Open actions.
self.add_action('open', '&Open', shortcut='Ctrl+O', icon='open')
# Open last file action
path = SETTINGS['main_window.last_data_file']
if path:
lastfile = os.path.basename(path)
if len(lastfile) > 30:
lastfile = '...' + lastfile[-30:]
self.add_action('open_last', 'Open &last ({0:s})'.format(
lastfile), shortcut='Ctrl+Alt+O')
else:
self.add_action('open_last', 'Open &last', shortcut='Ctrl+Alt+O')
self.open_last_action.setEnabled(False)
self.add_action('switch', 'S&witch shank')
self.add_action('import', '&Import clustering')
self.add_action('reset', '&Reset clustering')
self.add_action('save', '&Save', shortcut='Ctrl+S', icon='save')
# self.add_action('renumber', 'Save &renumbered')
self.add_action('close', '&Close file')
def create_edit_actions(self):
# Undo/redo actions.
self.add_action('undo', '&Undo', shortcut='Ctrl+Z', icon='undo')
self.add_action('redo', '&Redo', shortcut='Ctrl+Y', icon='redo')
# self.add_action('reset', 'Re&set')
# Quit action.
self.add_action('quit', '&Quit', shortcut='Ctrl+Q')
def create_view_actions(self):
self.add_action('add_feature_view', 'Add &FeatureView')
self.add_action('add_waveform_view', 'Add &WaveformView')
self.add_action('add_similarity_matrix_view',
'Add &SimilarityMatrixView')
self.add_action('add_correlograms_view', 'Add &CorrelogramsView')
self.add_action('add_ipython_view', 'Add &IPythonView')
self.add_action('add_log_view', 'Add &LogView')
# self.add_action('add_trace_view', 'Add &TraceView')
self.add_action('reset_views', '&Reset views')
self.add_action('toggle_fullscreen', 'Toggle fullscreen', shortcut='F')
self.add_action('override_color', 'Override cluster &color',
icon='override_color')#, shortcut='C')
def create_control_actions(self):
self.add_action('merge', '&Merge', shortcut='G', icon='merge')
self.add_action('split', '&Split', shortcut='K', icon='split')
self.add_action('recluster', '&Recluster', shortcut='CTRL+R')
def create_correlograms_actions(self):
self.add_action('change_ncorrbins', 'Change time &window')
self.add_action('change_corrbin', 'Change &bin size')
self.add_action('change_corr_normalization', 'Change &normalization')
def create_wizard_actions(self):
self.add_action('reset_navigation', '&Reinitialize wizard',
shortcut='CTRL+ALT+Space')
self.add_action('automatic_projection', '&Automatic projection',
checkable=True, checked=True)
self.add_action('change_candidate_color',
'Change &color of the closest match',
shortcut='C')
self.add_action('previous_candidate', '&Previous closest match',
shortcut='SHIFT+Space')
self.add_action('next_candidate', '&Skip closest match',
shortcut='Space')
self.add_action('skip_target', '&Skip best unsorted',
# shortcut='Space'
)
self.add_action('delete_candidate', 'Move closest match to &MUA',
shortcut='CTRL+M')
self.add_action('delete_candidate_noise', 'Move closest match to &noise',
shortcut='CTRL+N')
self.add_action('next_target', 'Move best unsorted to &good',
shortcut='ALT+G')
self.add_action('delete_target', 'Move best unsorted to &MUA',
shortcut='ALT+M')
self.add_action('delete_target_noise', 'Move best unsorted to &noise',
shortcut='ALT+N')
self.add_action('delete_both', 'Move &both to MUA',
shortcut='CTRL+ALT+M')
self.add_action('delete_both_noise', 'Move both to noise',
shortcut='CTRL+ALT+N')
def create_help_actions(self):
self.add_action('about', '&About')
self.add_action('manual', 'Show &manual')
self.add_action('shortcuts', 'Show &shortcuts')
self.add_action('open_preferences', '&Open preferences')
self.add_action('refresh_preferences', '&Refresh preferences')
def create_menu(self):
# File menu.
file_menu = self.menuBar().addMenu("&File")
file_menu.addAction(self.open_action)
file_menu.addAction(self.open_last_action)
file_menu.addSeparator()
file_menu.addAction(self.reset_action)
# file_menu.addAction(self.import_action)
file_menu.addSeparator()
file_menu.addAction(self.save_action)
# file_menu.addAction(self.renumber_action)
file_menu.addSeparator()
file_menu.addAction(self.switch_action)
file_menu.addSeparator()
file_menu.addAction(self.close_action)
file_menu.addAction(self.quit_action)
# Edit menu.
edit_menu = self.menuBar().addMenu("&Edit")
edit_menu.addAction(self.undo_action)
edit_menu.addAction(self.redo_action)
# View menu.
views_menu = self.menuBar().addMenu("&View")
views_menu.addAction(self.add_feature_view_action)
views_menu.addAction(self.add_waveform_view_action)
views_menu.addAction(self.add_correlograms_view_action)
views_menu.addAction(self.add_similarity_matrix_view_action)
# views_menu.addAction(self.add_trace_view_action)
views_menu.addSeparator()
views_menu.addAction(self.add_log_view_action)
if vw.IPYTHON:
views_menu.addAction(self.add_ipython_view_action)
views_menu.addSeparator()
views_menu.addAction(self.override_color_action)
views_menu.addSeparator()
views_menu.addAction(self.reset_views_action)
views_menu.addAction(self.toggle_fullscreen_action)
# Correlograms menu.
correlograms_menu = self.menuBar().addMenu("&Correlograms")
correlograms_menu.addAction(self.change_ncorrbins_action)
correlograms_menu.addAction(self.change_corrbin_action)
correlograms_menu.addSeparator()
correlograms_menu.addAction(self.change_corr_normalization_action)
# Actions menu.
actions_menu = self.menuBar().addMenu("&Actions")
actions_menu.addSeparator()
actions_menu.addAction(self.get_view('ClusterView').move_to_mua_action)
actions_menu.addAction(self.get_view('ClusterView').move_to_noise_action)
actions_menu.addSeparator()
actions_menu.addAction(self.merge_action)
actions_menu.addAction(self.split_action)
# actions_menu.addSeparator()
# actions_menu.addAction(self.recluster_action)
# Wizard menu.
wizard_menu = self.menuBar().addMenu("&Wizard")
# Previous/skip candidate.
wizard_menu.addAction(self.next_candidate_action)
wizard_menu.addAction(self.previous_candidate_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.skip_target_action)
wizard_menu.addSeparator()
# Good group.
# wizard_menu.addSeparator()
# Delete.
wizard_menu.addAction(self.delete_candidate_action)
wizard_menu.addAction(self.delete_candidate_noise_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.next_target_action)
wizard_menu.addAction(self.delete_target_action)
wizard_menu.addAction(self.delete_target_noise_action)
wizard_menu.addSeparator()
wizard_menu.addAction(self.delete_both_action)
wizard_menu.addAction(self.delete_both_noise_action)
wizard_menu.addSeparator()
# Misc.
wizard_menu.addAction(self.change_candidate_color_action)
wizard_menu.addAction(self.automatic_projection_action)
wizard_menu.addAction(self.reset_navigation_action)
# Help menu.
help_menu = self.menuBar().addMenu("&Help")
help_menu.addAction(self.open_preferences_action)
help_menu.addAction(self.refresh_preferences_action)
help_menu.addSeparator()
help_menu.addAction(self.shortcuts_action)
help_menu.addAction(self.manual_action)
help_menu.addAction(self.about_action)
def create_toolbar(self):
self.toolbar = self.addToolBar("KlustaViewaToolbar")
self.toolbar.setObjectName("KlustaViewaToolbar")
self.toolbar.addAction(self.open_action)
self.toolbar.addAction(self.save_action)
# self.toolbar.addAction(self.saveas_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.merge_action)
self.toolbar.addAction(self.split_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.get_view('ClusterView').move_to_mua_action)
self.toolbar.addAction(self.get_view('ClusterView').move_to_noise_action)
self.toolbar.addSeparator()
self.toolbar.addAction(self.undo_action)
self.toolbar.addAction(self.redo_action)
# self.toolbar.addSeparator()
# self.toolbar.addAction(self.override_color_action)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)
def create_open_progress_dialog(self):
self.open_progress = QtGui.QProgressDialog("Converting to Kwik...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.open_progress.setWindowModality(QtCore.Qt.WindowModal)
self.open_progress.setValue(0)
self.open_progress.setWindowTitle('Loading')
self.open_progress.setCancelButton(None)
self.open_progress.setMinimumDuration(0)
def create_save_progress_dialog(self):
self.save_progress = QtGui.QProgressDialog("Saving...",
"Cancel", 0, 0, self, QtCore.Qt.Tool)
self.save_progress.setWindowModality(QtCore.Qt.WindowModal)
self.save_progress.setValue(0)
self.save_progress.setWindowTitle('Saving')
self.save_progress.setCancelButton(None)
self.save_progress.setMinimumDuration(0)
# Action enabled.
# ---------------
def update_action_enabled(self):
self.undo_action.setEnabled(self.can_undo())
self.redo_action.setEnabled(self.can_redo())
self.merge_action.setEnabled(self.can_merge())
self.split_action.setEnabled(self.can_split())
def can_undo(self):
if self.controller is None:
return False
return self.controller.can_undo()
def can_redo(self):
if self.controller is None:
return False
return self.controller.can_redo()
def can_merge(self):
cluster_view = self.get_view('ClusterView')
clusters = cluster_view.selected_clusters()
return len(clusters) >= 2
def can_split(self):
cluster_view = self.get_view('ClusterView')
clusters = cluster_view.selected_clusters()
spikes_selected = self.spikes_selected
return len(spikes_selected) >= 1
# View methods.
# -------------
def create_view(self, view_class, position=None,
closable=True, floatable=True, index=0, floating=None, title=None,
**kwargs):
"""Add a widget to the main window."""
view = view_class(self, getfocus=False)
view.set_data(**kwargs)
# Create the dock widget.
name = view_class.__name__ + '_' + str(index)
dockwidget = ViewDockWidget(view_class.__name__)
# dockwidget = ViewDockWidget(name)
dockwidget.setObjectName(name)
dockwidget.setWidget(view)
dockwidget.closed.connect(self.dock_widget_closed)
# Set dock widget options.
options = QtGui.QDockWidget.DockWidgetMovable
if closable:
options = options | QtGui.QDockWidget.DockWidgetClosable
if floatable:
options = options | QtGui.QDockWidget.DockWidgetFloatable
dockwidget.setFeatures(options)
dockwidget.setAllowedAreas(
QtCore.Qt.LeftDockWidgetArea |
QtCore.Qt.RightDockWidgetArea |
QtCore.Qt.TopDockWidgetArea |
QtCore.Qt.BottomDockWidgetArea)
dockwidget.visibilityChanged.connect(partial(
self.dock_visibility_changed_callback, view))
if position is not None:
# Add the dock widget to the main window.
self.addDockWidget(position, dockwidget)
if floating is not None:
dockwidget.setFloating(floating)
if title is None:
title = view_class.__name__
dockwidget.setTitleBarWidget(DockTitleBar(dockwidget, title))
# Return the view widget.
return view
def add_cluster_view(self, do_update=None, floating=False):
view = self.create_view(vw.ClusterView,
position=QtCore.Qt.LeftDockWidgetArea,
index=len(self.views['ClusterView']),
closable=False,
# floatable=False
)
# Connect callback functions.
view.clustersSelected.connect(self.clusters_selected_callback)
view.clusterColorChanged.connect(self.cluster_color_changed_callback)
view.groupColorChanged.connect(self.group_color_changed_callback)
view.groupRenamed.connect(self.group_renamed_callback)
view.clustersMoved.connect(self.clusters_moved_callback)
view.groupAdded.connect(self.group_added_callback)
view.groupRemoved.connect(self.group_removed_callback)
self.views['ClusterView'].append(view)
if do_update:
self.taskgraph.update_cluster_view()
def dock_visibility_changed_callback(self, view, visibility):
# Register dock widget visibility.
view.visibility = visibility
def restore_last_view(self, name):
"""Return True if the last view was successfully restored,
False if the view needs to be restored manually by creating a new
view."""
# No existing view: need to create a new view.
if not self.views[name]:
return False
view = self.views[name][-1]
# A view exists and it is hidden: restore it.
if getattr(view, 'visibility', None) is False:
view.parent().toggleViewAction().activate(QtGui.QAction.Trigger)
return True
# A view exists but it is not hidden: just add a new view.
else:
return False
def add_similarity_matrix_view(self, do_update=None, floating=False):
# Try restoring the last view if it exists and it is hidden, and if
# successfully restored, do nothing more. Otherwise, need to create
# a new view.
if self.restore_last_view('SimilarityMatrixView'):
return
view = self.create_view(vw.SimilarityMatrixView,
index=len(self.views['SimilarityMatrixView']),
position=QtCore.Qt.LeftDockWidgetArea,
floating=floating)
view.clustersSelected.connect(self.cluster_pair_selected_callback)
self.views['SimilarityMatrixView'].append(view)
if do_update and self.is_file_open:
self.taskgraph.update_similarity_matrix_view()
def add_waveform_view(self, do_update=None, floating=False):
view = self.create_view(vw.WaveformView,
index=len(self.views['WaveformView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
view.spikesHighlighted.connect(
self.waveform_spikes_highlighted_callback)
view.boxClicked.connect(self.waveform_box_clicked_callback)
self.views['WaveformView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_waveform_view()
def add_feature_view(self, do_update=None, floating=False):
view = self.create_view(vw.FeatureProjectionView,
index=len(self.views['FeatureView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating,
title='FeatureView')
view.spikesHighlighted.connect(
self.features_spikes_highlighted_callback)
view.spikesSelected.connect(
self.features_spikes_selected_callback)
self.views['FeatureView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_feature_view()
def add_ipython_view(self, floating=None):
view = self.create_view(vw.IPythonView,
index=len(self.views['IPythonView']),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
# Create namespace for the interactive session.
namespace = dict(
window=self,
select=self.get_view('ClusterView').select,
loader=self.loader,
stats=self.statscache,
wizard=self.wizard,
)
view.set_data(**namespace)
# Load all .py files in the code directory.
paths = USERPREF['ipython_import_paths'] or []
if isinstance(paths, basestring):
paths = [paths]
for path in paths:
path = os.path.realpath(os.path.expanduser(path))
if os.path.exists(path):
files = [file for file in os.listdir(path) if file.endswith('.py')]
for file in files:
log.debug("Running {0:s}".format(file))
view.run_file(os.path.join(path, file))
self.views['IPythonView'].append(view)
def add_log_view(self, floating=None):
if len(self.views['LogView']) >= 1:
return
view = self.create_view(vw.LogView,
text=self.view_logger_text.getvalue(),
position=QtCore.Qt.BottomDockWidgetArea,
floating=True)
self.views['LogView'].append(view)
def log_view_write_callback(self, message):
view = self.get_view('LogView')
if view:
view.append(message)
self.view_logger_text.write(message)
def add_correlograms_view(self, do_update=None, floating=False):
view = self.create_view(vw.CorrelogramsView,
index=len(self.views['CorrelogramsView']),
position=QtCore.Qt.RightDockWidgetArea,
floating=floating)
self.views['CorrelogramsView'].append(view)
if do_update and self.is_file_open and self.loader.has_selection():
self.taskgraph.update_correlograms_view()
# def add_trace_view(self, do_update=None, floating=None):
# # if len(self.views['TraceView']) >= 1:
# # return
# view = self.create_view(vw.TraceView,
# index=len(self.views['TraceView']),
# position=QtCore.Qt.BottomDockWidgetArea,
# floating=True)
# self.views['TraceView'].append(view)
# if do_update and self.is_file_open:
# self.taskgraph.update_trace_view()
def get_view(self, name, index=0):
views = self.views.get(name, [])
if not views:
return None
else:
return views[index]
def get_views(self, name):
return self.views[name]
def create_views(self):
"""Create all views at initialization."""
# Create the default layout.
self.views = dict(
ClusterView=[],
SimilarityMatrixView=[],
WaveformView=[],
FeatureView=[],
CorrelogramsView=[],
IPythonView=[],
TraceView=[],
LogView=[],
)
count = SETTINGS['main_window.views']
if count is None:
self.create_default_views()
else:
self.create_custom_views(count)
def create_default_views(self, do_update=None, floating=False):
self.add_cluster_view(do_update=do_update, floating=floating)
self.add_similarity_matrix_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('ClusterView').parentWidget(),
self.get_view('SimilarityMatrixView').parentWidget(),
QtCore.Qt.Vertical
)
self.add_waveform_view(do_update=do_update, floating=floating)
self.add_feature_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('WaveformView').parentWidget(),
self.get_view('FeatureView').parentWidget(),
QtCore.Qt.Horizontal
)
self.add_correlograms_view(do_update=do_update, floating=floating)
self.splitDockWidget(
self.get_view('FeatureView').parentWidget(),
self.get_view('CorrelogramsView').parentWidget(),
QtCore.Qt.Vertical
)
def create_custom_views(self, count):
[self.add_cluster_view() for _ in xrange(count.get('ClusterView', 0))]
[self.add_similarity_matrix_view() for _ in xrange(count.get('SimilarityMatrixView', 0))]
[self.add_waveform_view() for _ in xrange(count.get('WaveformView', 0))]
[self.add_feature_view() for _ in xrange(count.get('FeatureView', 0))]
[self.add_log_view() for _ in xrange(count.get('LogView', 0))]
[self.add_ipython_view() for _ in xrange(count.get('IPythonView', 0))]
[self.add_correlograms_view() for _ in xrange(count.get('CorrelogramsView', 0))]
#[self.add_trace_view() for _ in xrange(count.get('TraceView', 0))]
def dock_widget_closed(self, dock):
for key in self.views.keys():
self.views[key] = [view for view in self.views[key] if view.parent() != dock]
# Threads.
# --------
def create_threads(self):
# Create the external threads.
self.open_task = inthread(OpenTask)()
self.open_task.dataOpened.connect(self.open_done)
self.open_task.dataSaved.connect(self.save_done)
self.open_task.dataOpenFailed.connect(self.open_failed)
def join_threads(self):
self.open_task.join()
self.taskgraph.join()
# File menu callbacks.
# --------------------
def open_callback(self, checked=None):
# HACK: Force release of Ctrl key.
self.force_key_release()
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(self,
"Open a .kwik file", folder, ".kwik file")[0]
# If a file has been selected, open it.
if path:
# Launch the loading task in the background asynchronously.
self._path = path
self.open_task.open(self.loader, path)
# Save the folder.
folder = os.path.dirname(path)
SETTINGS['main_window.last_data_dir'] = folder
SETTINGS['main_window.last_data_file'] = path
def import_callback(self, checked=None):
folder = SETTINGS['main_window.last_data_dir']
path = QtGui.QFileDialog.getOpenFileName(self,
"Open a .kwik file", folder, ".kwik file")[0]
# If a file has been selected, open it.
if path and self.loader is not None:
clu = read_clusters(path)
# TODO
self.open_done()
def save_callback(self, checked=None):
self.open_task.save(self.loader)
def reset_callback(self, checked=None):
# reply = QtGui.QMessageBox.question(self, 'Reset clustering',
# "Do you *really* want to erase permanently your manual clustering and reset it to the original (automatic) clustering? You won't be able to undo this operation!",
# (
# QtGui.QMessageBox.Yes |
# QtGui.QMessageBox.Cancel
# ),
# QtGui.QMessageBox.Cancel)
# if reply == QtGui.QMessageBox.Yes:
clustering_name, ok = QtGui.QInputDialog.getText(self, "Clustering name", "Copy from (you'll lose the current clustering):",
QtGui.QLineEdit.Normal, 'original')
if ok:
self.loader.copy_clustering(clustering_from=clustering_name,
clustering_to='main')
# Reload the file.
self.loader.close()
self.open_task.open(self.loader, self._path)
# elif reply == QtGui.QMessageBox.Cancel:
# return
# def renumber_callback(self, checked=None):
# # folder = SETTINGS.get('main_window.last_data_file')
# self.loader.save(renumber=True)
# # self.need_save = False
# self.open_last_callback()
def open_last_callback(self, checked=None):
path = SETTINGS['main_window.last_data_file']
if path:
self._path = path
self.open_task.open(self.loader, path)
def close_callback(self, checked=None):
# clusters = self.get_view('ClusterView').selected_clusters()
# if clusters:
# self.get_view('ClusterView').unselect()
# time.sleep(.25)
# Clear the views.
self.clear_view('ClusterView')
self.clear_view('SimilarityMatrixView')
self.clear_view('FeatureView')
self.clear_view('WaveformView')
self.clear_view('CorrelogramsView')
self.clear_view('TraceView')
self.loader.close()
self.is_file_open = False
def switch_callback(self, checked=None):
shank, ok = QtGui.QInputDialog.getInt(self,
"Shank number", "Shank number:",
self.loader.shank,
min(self.loader.shanks),
max(self.loader.shanks),
1)
if ok:
if shank in self.loader.shanks:
self.loader.set_shank(shank)
self.open_done()
else:
QtGui.QMessageBox.warning(self, "Wrong shank number",
("The selected shank '{0:d}' is not in "
"the list of shanks: {1:s}.").format(shank,
str(self.loader.shanks)),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def clear_view(self, view_name):
for v in self.get_views(view_name):
v.set_data()
if hasattr(v, 'clear'):
v.clear()
def quit_callback(self, checked=None):
self.close()
# Open callbacks.
# --------------
def open_done(self):
self.is_file_open = True
self.setWindowTitle('KlustaViewa: {0:s}'.format(
os.path.basename(self.loader.filename)
))
register(FileLogger(self.loader.log_filename, name='kwik',
level=logging.INFO))
# Start the selection buffer.
self.buffer = Buffer(self,
# delay_timer=.1, delay_buffer=.2
delay_timer=USERPREF['delay_timer'],
delay_buffer=USERPREF['delay_buffer']
)
self.buffer.start()
self.buffer.accepted.connect(self.buffer_accepted_callback)
# HACK: force release of Control key.
self.force_key_release()
clusters = self.get_view('ClusterView').selected_clusters()
if clusters:
self.get_view('ClusterView').unselect()
# Create the Controller.
self.controller = Controller(self.loader)
# Create the cache for the cluster statistics that need to be
# computed in the background.
self.statscache = StatsCache(SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT))
# Update stats cache in IPython view.
ipython = self.get_view('IPythonView')
if ipython:
ipython.set_data(stats=self.statscache)
# Initialize the wizard.
self.wizard = Wizard()
# Update the task graph.
self.taskgraph.set(self)
# self.taskgraph.update_projection_view()
self.taskgraph.update_cluster_view()
self.taskgraph.compute_similarity_matrix()
# self.taskgraph.update_trace_view()
def open_failed(self, message):
self.open_progress.setValue(0)
QtGui.QMessageBox.warning(self, "Error while opening the file",
"An error occurred: {0:s}".format(message),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
def open_progress_reported(self, progress, progress_max):
self.open_progress.setMaximum(progress_max)
self.open_progress.setValue(progress)
def save_progress_reported(self, progress, progress_max):
self.save_progress.setMaximum(progress_max)
self.save_progress.setValue(progress)
def save_done(self):
self.need_save = False
# Selection methods.
# ------------------
def buffer_accepted_callback(self, (clusters, wizard)):
self._wizard = wizard
# The wizard boolean specifies whether the autozoom is activated or not.
self.taskgraph.select(clusters, wizard and
self.automatic_projection_action.isChecked(), )
def test_kwik_loader_control():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
# Take all spikes in cluster 3.
spikes = get_indices(l.get_clusters(clusters=3))
# Put them in cluster 4.
l.set_cluster(spikes, 4)
spikes_new = get_indices(l.get_clusters(clusters=4))
# Ensure all spikes in old cluster 3 are now in cluster 4.
assert np.all(np.in1d(spikes, spikes_new))
# Change cluster groups.
clusters = [2, 3, 4]
group = 0
l.set_cluster_groups(clusters, group)
groups = l.get_cluster_groups(clusters)
assert np.all(groups == group)
# Change cluster colors.
clusters = [2, 3, 4]
color = 12
l.set_cluster_colors(clusters, color)
colors = l.get_cluster_colors(clusters)
assert np.all(colors == color)
# Change group name.
group = 0
name = l.get_group_names(group)
name_new = 'Noise new'
assert name == 'Noise'
l.set_group_names(group, name_new)
assert l.get_group_names(group) == name_new
# Change group color.
groups = [1, 2]
colors = l.get_group_colors(groups)
color_new = 10
l.set_group_colors(groups, color_new)
assert np.all(l.get_group_colors(groups) == color_new)
# Add cluster and group.
spikes = get_indices(l.get_clusters(clusters=3))[:10]
# Create new group 100.
l.add_group(100, 'New group', 10)
# Create new cluster 10000 and put it in group 100.
l.add_cluster(10000, 100, 10)
# Put some spikes in the new cluster.
l.set_cluster(spikes, 10000)
clusters = l.get_clusters(spikes=spikes)
assert np.all(clusters == 10000)
groups = l.get_cluster_groups(10000)
assert groups == 100
l.set_cluster(spikes, 2)
# Remove the new cluster and group.
l.remove_cluster(10000)
l.remove_group(100)
assert np.all(~np.in1d(10000, l.get_clusters()))
assert np.all(~np.in1d(100, l.get_cluster_groups()))
l.close()
def test_kwik_loader_1():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
# features_some = l.get_some_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
# probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check the shape of the data sets.
# ---------------------------------
assert check_shape(features, (nspikes, nchannels * fetdim + 1))
# assert features_some.shape[1] == nchannels * fetdim + 1
assert check_shape(masks, (nspikes, nchannels * fetdim + 1))
assert check_shape(waveforms, (nspikes, nsamples, nchannels))
assert check_shape(clusters, (nspikes,))
assert check_shape(spiketimes, (nspikes,))
# assert check_shape(probe, (nchannels, 2))
assert check_shape(cluster_colors, (nclusters,))
assert check_shape(cluster_groups, (nclusters,))
assert check_shape(group_colors, (4,))
assert check_shape(group_names, (4,))
assert check_shape(cluster_sizes, (nclusters,))
# Check the data type of the data sets.
# -------------------------------------
assert check_dtype(features, np.float32)
assert check_dtype(masks, np.float32)
# HACK: Panel has no dtype(s) attribute
# assert check_dtype(waveforms, np.float32)
assert check_dtype(clusters, np.int32)
assert check_dtype(spiketimes, np.float64)
# assert check_dtype(probe, np.float32)
assert check_dtype(cluster_colors, np.int32)
assert check_dtype(cluster_groups, np.int32)
assert check_dtype(group_colors, np.int32)
assert check_dtype(group_names, object)
assert check_dtype(cluster_sizes, np.int32)
l.close()
def test_kwik_save():
"""WARNING: this test should occur at the end of the module since it
changes the mock data sets."""
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KwikLoader(filename=xmlfile)
clusters = l.get_clusters()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
# Set clusters.
indices = get_indices(clusters)
l.set_cluster(indices[::2], 2)
l.set_cluster(indices[1::2], 3)
# Set cluster info.
cluster_indices = l.get_clusters_unique()
l.set_cluster_colors(cluster_indices[::2], 10)
l.set_cluster_colors(cluster_indices[1::2], 20)
l.set_cluster_groups(cluster_indices[::2], 1)
l.set_cluster_groups(cluster_indices[1::2], 0)
# Save.
l.remove_empty_clusters()
l.save()
clusters = l.get_clusters()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
assert np.all(clusters[::2] == 2)
assert np.all(clusters[1::2] == 3)
assert np.all(cluster_colors[::2] == 10)
assert np.all(cluster_colors[1::2] == 20)
print cluster_groups
assert np.all(cluster_groups[::2] == 1)
assert np.all(cluster_groups[1::2] == 0)
l.close()
