def create_actions(self):
self.change_color_action = QtGui.QAction("Change &color", self)
self.change_color_action.triggered.connect(self.change_color_callback)
self.add_group_action = QtGui.QAction("&Add group", self)
self.add_group_action.triggered.connect(self.add_group_callback)
self.rename_channel_group_action = QtGui.QAction("Re&name group", self)
self.rename_channel_group_action.setShortcut("F2")
self.rename_channel_group_action.triggered.connect(
self.rename_channel_group_callback)
self.rename_channel_action = QtGui.QAction("Rename c&hannel", self)
self.rename_channel_action.setShortcut("F3")
self.rename_channel_action.triggered.connect(
self.rename_channel_callback)
self.remove_group_action = QtGui.QAction("&Remove group", self)
self.remove_group_action.triggered.connect(self.remove_group_callback)
# Add actions to the widget.
self.addAction(self.change_color_action)
self.addAction(self.add_group_action)
self.addAction(self.rename_channel_group_action)
self.addAction(self.rename_channel_action)
self.addAction(self.remove_group_action)
def create_layout(self):
self.setStyleSheet(DOCKSTYLESHEET)
# Create the title layout.
self.setContentsMargins(0, 0, 0, 0)
box = QtGui.QHBoxLayout()
box.setContentsMargins(0, 2, 0, 2)
box.setSpacing(0)
# Add the title.
self.title_widget = QtGui.QLabel(self.name, self)
box.addSpacing(5)
box.addWidget(self.title_widget)
# Add spacing.
box.addStretch(1000)
# Add the dock-related buttons.
if self.is_floatable():
box.addWidget(self.dockable_button)
box.addWidget(self.maximize_button)
box.addWidget(self.dock_button)
# Add the close button.
if self.is_closable():
box.addWidget(self.close_button)
self.setLayout(box)
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 create_color_dialog(self):
self.color_dialog = QtGui.QColorDialog(self)
self.color_dialog.setOptions(QtGui.QColorDialog.DontUseNativeDialog)
for i in xrange(48):
if i < len(COLORMAP):
rgb = COLORMAP[i] * 255
else:
rgb = (255, 255, 255)
# rgb = (1., 1., 1.)
k = 6 * (np.mod(i, 8)) + i // 8
self.color_dialog.setStandardColor(k, QtGui.qRgb(*rgb))
def __init__(self, parent=None, getfocus=None):
super(LogView, self).__init__(parent)
# Create the text edit widget.
self.textedit = QtGui.QTextEdit()
self.textedit.setReadOnly(True)
# Add the text edit widget to the layout.
box = QtGui.QVBoxLayout()
box.addWidget(self.textedit)
box.setContentsMargins(0, 0, 0, 0)
box.setSpacing(0)
self.setLayout(box)
def create_layout(self):
self.projection_view = ProjectionView(self, getfocus=False)
self.feature_view = FeatureView(self, getfocus=False)
self.set_data()
# Connect the FeatureView signal to the top-level widget signals.
self.feature_view.spikesHighlighted.connect(self.spikesHighlighted)
self.feature_view.spikesSelected.connect(self.spikesSelected)
# Connect the bottom-level projectionChanged signals to the top-level
# widget signals.
self.feature_view.projectionChanged.connect(self.projectionChanged)
self.projection_view.projectionChanged.connect(self.projectionChanged)
# Interconnect the projectionChanged between the two bottom-level widgets.
self.projection_view.projectionChanged.connect(
self.projection_changed_projection_callback)
self.feature_view.projectionChanged.connect(
self.projection_changed_feature_callback)
box = QtGui.QVBoxLayout()
# HACK: pyside does not have this function
if hasattr(box, 'setMargin'):
box.setMargin(0)
box.addWidget(self.projection_view)
box.addWidget(self.feature_view)
self.setLayout(box)
def __init__(self, parent=None, getfocus=None):
super(IPythonView, self).__init__(parent)
# Create an in-process kernel
self.kernel_manager = QtInProcessKernelManager()
self.kernel_manager.start_kernel()
self.kernel = self.kernel_manager.kernel
self.kernel.gui = 'qt4'
self.shell = self.kernel.shell
self.kernel_client = self.kernel_manager.client()
self.kernel_client.start_channels()
self.control = RichIPythonWidget()
self.control.set_default_style(colors='linux')
self.control.kernel_manager = self.kernel_manager
self.control.kernel_client = self.kernel_client
self.control.exit_requested.connect(self.stop)
# Enable Pylab mode.
self.shell.enable_pylab()
self.shell.automagic = True
# Add some variables in the namespace.
self.push(galry=galry)
box = QtGui.QVBoxLayout()
box.addWidget(self.control)
box.setContentsMargins(0, 0, 0, 0)
box.setSpacing(0)
self.setLayout(box)
def shortcuts_callback(self, checked=None):
e = QtGui.QKeyEvent(
QtCore.QEvent.KeyPress,
QtCore.Qt.Key_H,
QtCore.Qt.NoModifier,
)
self.keyPressEvent(e)
def set_data(self,
fetdim=None,
nchannels=None,
nextrafet=None,
channels=None):
if fetdim is None:
fetdim = 3
if nchannels is None:
nchannels = 1
if nextrafet is None:
nextrafet = 0
if channels is None:
channels = range(nchannels)
# No need to update the widget if the data has not changed.
if not self._has_changed(fetdim, nchannels, nextrafet):
return
self.fetdim = fetdim
self.nchannels = nchannels
self.channels = channels
self.nextrafet = nextrafet
# Remove the existing layout.
if self.layout():
QtGui.QWidget().setLayout(self.layout())
self.box = self.create_widget()
self.setLayout(self.box)
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)
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 get_icon(name):
"""Get an icon from the icons folder in the current package,
or directly from galry."""
path = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(path, "../icons/%s.png" % name)
if not os.path.exists(path):
return galry.get_icon(name)
else:
return QtGui.QIcon(path)
def add_button(self, name, text, callback=None, shortcut=None,
checkable=False, icon=None):
# Creation action.
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)
# Create button
button = QtGui.QToolButton(self)
button.setContentsMargins(*((5,)*4))
button.setDefaultAction(action)
return button
def create_context_menu(self):
self.create_color_dialog()
self.context_menu = QtGui.QMenu(self)
self.context_menu.addAction(self.change_color_action)
self.context_menu.addSeparator()
self.context_menu.addAction(self.add_group_action)
self.context_menu.addAction(self.rename_channel_group_action)
self.context_menu.addAction(self.rename_channel_action)
self.context_menu.addAction(self.remove_group_action)
def create_feature_widget(self, coord=0):
# coord => (channel, feature)
self.projection = [(0, 0), (0, 1)]
hbox = QtGui.QHBoxLayout()
hbox.setSpacing(0)
# HACK: pyside does not have this function
if hasattr(hbox, 'setMargin'):
hbox.setMargin(0)
# channel selection
comboBox = QtGui.QComboBox(self)
comboBox.setEditable(True)
comboBox.setMaximumWidth(100)
comboBox.setInsertPolicy(QtGui.QComboBox.NoInsert)
comboBox.addItems(["%d" % i for i in self.channels])
comboBox.addItems(["Extra %d" % i for i in xrange(self.nextrafet)])
comboBox.editTextChanged.connect(partial(self.select_channel, coord))
# comboBox.setFocusPolicy(QtCore.Qt.ClickFocus)
self.channel_box[coord] = comboBox
hbox.addWidget(comboBox)
# create 3 buttons for selecting the feature
widths = [30] * self.fetdim
labels = ['PC%d' % i for i in xrange(1, self.fetdim + 1)]
hbox.addSpacing(10)
# ensure exclusivity of the group of buttons
pushButtonGroup = QtGui.QButtonGroup(self)
for i in xrange(len(labels)):
# selecting feature i
pushButton = QtGui.QPushButton(labels[i], self)
pushButton.setCheckable(True)
if coord == i:
pushButton.setChecked(True)
pushButton.setMaximumSize(QtCore.QSize(widths[i], 20))
pushButton.clicked.connect(partial(self.select_feature, coord, i))
pushButtonGroup.addButton(pushButton, i)
self.feature_buttons[coord][i] = pushButton
hbox.addWidget(pushButton)
return hbox
def create_widget(self):
box = QtGui.QHBoxLayout()
if hasattr(box, 'setMargin'):
box.setContentsMargins(QtCore.QMargins(10, 2, 10, 2))
# box.addSpacing(10)
# coord => channel combo box
self.channel_box = [None, None]
# coord => (butA, butB, butC)
self.feature_buttons = [[None] * self.fetdim, [None] * self.fetdim]
# add feature widget
self.feature_widget1 = self.create_feature_widget(0)
box.addLayout(self.feature_widget1)
box.addSpacing(10)
# Switch button.
# button = QtGui.QPushButton('Flip', self)
button = QtGui.QPushButton(self)
button.setIcon(get_icon('flip'))
button.setMaximumWidth(40)
button.clicked.connect(self.flip_projections_callback)
box.addWidget(button)
box.addSpacing(10)
# add feature widget
self.feature_widget2 = self.create_feature_widget(1)
box.addLayout(self.feature_widget2)
# box.addSpacing(10)
self.setTabOrder(self.channel_box[0], self.channel_box[1])
# self.setMaximumWidth(300)
# self.setMaximumHeight(80)
return box
def create_color_dialog(self):
self.color_dialog = QtGui.QColorDialog(self)
self.color_dialog.setOptions(QtGui.QColorDialog.DontUseNativeDialog)
for i in xrange(48):
if i < len(COLORMAP):
rgb = COLORMAP[i] * 255
else:
rgb = (255, 255, 255)
# rgb = (1., 1., 1.)
k = 6 * (np.mod(i, 8)) + i // 8
self.color_dialog.setStandardColor(k, QtGui.qRgb(*rgb))
def create_context_menu(self):
self.create_color_dialog()
self.context_menu = QtGui.QMenu(self)
self.context_menu.addAction(self.change_color_action)
self.context_menu.addSeparator()
self.context_menu.addAction(self.move_to_noise_action)
self.context_menu.addAction(self.move_to_mua_action)
self.context_menu.addAction(self.move_to_good_action)
self.context_menu.addSeparator()
self.context_menu.addAction(self.add_group_action)
self.context_menu.addAction(self.rename_group_action)
self.context_menu.addAction(self.remove_group_action)
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 data(self, index, role):
item = index.internalPointer()
col = index.column()
# group item
if type(item) == GroupItem:
if col == 0:
if role == QtCore.Qt.DisplayRole:
return str(item.name())
# color
elif col == self.columnCount() - 1:
if role == QtCore.Qt.BackgroundRole:
if item.color() >= 0:
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(*color)
elif role == QtCore.Qt.DisplayRole:
return ""
# channel item
if type(item) == ChannelItem:
# name
if col == 0:
if role == QtCore.Qt.DisplayRole:
return str(item.name())
elif role == QtCore.Qt.BackgroundRole:
if item.bgcolor is None:
return
elif item.bgcolor == 'candidate':
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 90)
elif item.bgcolor == 'target':
# return QtGui.QColor(177, 177, 177, 255)
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 255)
elif role == QtCore.Qt.ForegroundRole:
if item.bgcolor is None:
return QtGui.QColor(177, 177, 177, 255)
elif item.bgcolor == 'target':
return QtGui.QColor(0, 0, 0, 255)
# color
elif col == self.columnCount() - 1:
if role == QtCore.Qt.BackgroundRole:
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(*color)
# default
if role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
return item.data(col)
if role == QtCore.Qt.ForegroundRole:
return QtGui.QColor(177, 177, 177, 255)
def select(self, channels, groups=None, wizard=False):
"""Select multiple channels from their indices."""
self.wizard = wizard
if channels is None:
channels = []
if groups is None:
groups = []
if isinstance(channels, (int, long, np.integer)):
channels = [channels]
if isinstance(groups, (int, long, np.integer)):
groups = [groups]
if len(channels) == len(groups) == 0:
return
# Convert to lists.
channels = list(channels)
groups = list(groups)
selection_model = self.selectionModel()
selection = QtGui.QItemSelection()
# Select groups.
for groupidx in groups:
group = self.model.get_group(groupidx)
if group is not None:
selection.select(group.index, group.index)
# Select channels.
for channelidx in channels:
channel = self.model.get_channel(channelidx)
if channel is not None:
selection.select(channel.index, channel.index)
# Process selection.
selection_model.select(selection,
selection_model.Clear |
selection_model.Current |
selection_model.Select |
selection_model.Rows
)
if len(channels) > 0:
channel = self.model.get_channel(channels[-1])
if channel is not None:
# Set current index in the selection.
selection_model.setCurrentIndex(
channel.index,
QtGui.QItemSelectionModel.NoUpdate)
# Scroll to that channel.
self.scrollTo(channel.index)
def change_color_callback(self, checked=None):
item = self.current_item
initial_color = item.color()
if initial_color >= 0:
initial_color = 255 * COLORMAP[initial_color]
initial_color = QtGui.QColor(*initial_color)
color = QtGui.QColorDialog.getColor(initial_color)
else:
color = QtGui.QColorDialog.getColor()
# return if the user canceled
if not color.isValid():
return
# get the RGB values of the chosen color
rgb = np.array(color.getRgbF()[:3]).reshape((1, -1))
# take the closest color in the palette
color = np.argmin(np.abs(COLORMAP[1:, :] - rgb).sum(axis=1)) + 1
# Change the color and emit the signal.
if isinstance(item, ChannelItem):
self.change_channel_color(item.channelidx(), color)
elif isinstance(item, GroupItem):
self.change_group_color(item.groupidx(), color)
def create_actions(self):
self.change_color_action = QtGui.QAction("Change &color", self)
self.change_color_action.triggered.connect(self.change_color_callback)
self.add_group_action = QtGui.QAction("&Add group", self)
self.add_group_action.triggered.connect(self.add_group_callback)
self.rename_group_action = QtGui.QAction("Re&name group", self)
self.rename_group_action.setShortcut("F2")
self.rename_group_action.triggered.connect(self.rename_group_callback)
self.remove_group_action = QtGui.QAction("&Remove group", self)
self.remove_group_action.triggered.connect(self.remove_group_callback)
self.move_to_mua_action = QtGui.QAction("Move to &MUA", self)
self.move_to_mua_action.setShortcut("Delete")
self.move_to_mua_action.setIcon(get_icon('multiunit'))
self.move_to_mua_action.triggered.connect(self.move_to_mua_callback)
self.move_to_noise_action = QtGui.QAction("Move to &noise", self)
self.move_to_noise_action.setShortcut('Shift+Delete')
self.move_to_noise_action.setIcon(get_icon('noise'))
self.move_to_noise_action.triggered.connect(
self.move_to_noise_callback)
self.move_to_good_action = QtGui.QAction("Move to &good", self)
# self.move_to_good_action.setIcon(get_icon('noise'))
self.move_to_good_action.triggered.connect(self.move_to_good_callback)
# Add actions to the widget.
self.addAction(self.change_color_action)
self.addAction(self.add_group_action)
self.addAction(self.rename_group_action)
self.addAction(self.remove_group_action)
self.addAction(self.move_to_noise_action)
self.addAction(self.move_to_mua_action)
self.addAction(self.move_to_good_action)
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 = HDF5Loader()
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 data(self, index, role):
item = index.internalPointer()
col = index.column()
# group item
if type(item) == GroupItem:
if col == 0:
if role == QtCore.Qt.DisplayRole:
return str(item.name())
# quality
elif col == 1:
if role == QtCore.Qt.TextAlignmentRole:
return QtCore.Qt.AlignRight
if role == QtCore.Qt.DisplayRole:
return #"%." % item.quality()
# spkcount
elif col == 2:
if role == QtCore.Qt.TextAlignmentRole:
return QtCore.Qt.AlignRight
if role == QtCore.Qt.DisplayRole:
return str(item.spkcount())
# color
elif col == self.columnCount() - 1:
if role == QtCore.Qt.BackgroundRole:
if item.color() >= 0:
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(*color)
elif role == QtCore.Qt.DisplayRole:
return ""
# cluster item
if type(item) == ClusterItem:
# clusteridx
if col == 0:
if role == QtCore.Qt.DisplayRole:
return str(item.clusteridx())
elif role == QtCore.Qt.BackgroundRole:
if item.bgcolor is None:
return
elif item.bgcolor == 'candidate':
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 90)
elif item.bgcolor == 'target':
# return QtGui.QColor(177, 177, 177, 255)
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 255)
elif role == QtCore.Qt.ForegroundRole:
if item.bgcolor is None:
return QtGui.QColor(177, 177, 177, 255)
elif item.bgcolor == 'target':
return QtGui.QColor(0, 0, 0, 255)
# quality
elif col == 1:
if role == QtCore.Qt.TextAlignmentRole:
return QtCore.Qt.AlignRight
elif role == QtCore.Qt.DisplayRole:
return "%.3f" % item.quality()
elif role == QtCore.Qt.BackgroundRole:
if item.bgcolor is None:
return
elif item.bgcolor == 'candidate':
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 90)
elif item.bgcolor == 'target':
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 255)
# return QtGui.QColor(177, 177, 177, 255)
elif role == QtCore.Qt.ForegroundRole:
if item.bgcolor is None:
return QtGui.QColor(177, 177, 177, 255)
elif item.bgcolor == 'target':
return QtGui.QColor(0, 0, 0, 255)
# spkcount
elif col == 2:
if role == QtCore.Qt.TextAlignmentRole:
return QtCore.Qt.AlignRight
if role == QtCore.Qt.DisplayRole:
return "%d" % item.spkcount()
elif role == QtCore.Qt.BackgroundRole:
if item.bgcolor is None:
return
elif item.bgcolor == 'candidate':
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 90)
elif item.bgcolor == 'target':
# return QtGui.QColor(177, 177, 177, 255)
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(color[0], color[1], color[2], 255)
elif role == QtCore.Qt.ForegroundRole:
if item.bgcolor is None:
return QtGui.QColor(177, 177, 177, 255)
elif item.bgcolor == 'target':
return QtGui.QColor(0, 0, 0, 255)
# color
elif col == self.columnCount() - 1:
if role == QtCore.Qt.BackgroundRole:
color = np.array(COLORMAP[item.color()]) * 255
return QtGui.QColor(*color)
# default
if role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
return item.data(col)
if role == QtCore.Qt.ForegroundRole:
return QtGui.QColor(177, 177, 177, 255)