def get_correlogramsview_data(loader, statscache):
clusters_selected0 = loader.get_clusters_selected()
# Subset of selected clusters if there are too many clusters.
max_nclusters = USERPREF['correlograms_max_nclusters']
if len(clusters_selected0) < max_nclusters:
clusters_selected = clusters_selected0
else:
clusters_selected = clusters_selected0[:max_nclusters]
correlograms = statscache.correlograms.submatrix(
clusters_selected)
# Compute the baselines.
sizes = get_array(select(loader.get_cluster_sizes(), clusters_selected))
colors = select(loader.get_cluster_colors(), clusters_selected)
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
baselines = get_baselines(sizes, duration, corrbin)
data = dict(
correlograms=correlograms,
baselines=baselines,
clusters_selected=clusters_selected,
cluster_colors=colors,
ncorrbins=ncorrbins,
corrbin=corrbin,
)
return data
def get_correlogramsview_data(loader, statscache):
clusters_selected0 = loader.get_clusters_selected()
# Subset of selected clusters if there are too many clusters.
max_nclusters = USERPREF['correlograms_max_nclusters']
if len(clusters_selected0) < max_nclusters:
clusters_selected = clusters_selected0
else:
clusters_selected = clusters_selected0[:max_nclusters]
correlograms = statscache.correlograms.submatrix(clusters_selected)
# Compute the baselines.
sizes = get_array(select(loader.get_cluster_sizes(), clusters_selected))
colors = select(loader.get_cluster_colors(), clusters_selected)
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
baselines = get_baselines(sizes, duration, corrbin)
data = dict(
correlograms=correlograms,
baselines=baselines,
clusters_selected=clusters_selected,
cluster_colors=colors,
ncorrbins=ncorrbins,
corrbin=corrbin,
)
return data
def _compute_correlograms(self, clusters_selected):
# Get the correlograms parameters.
spiketimes = get_array(self.loader.get_spiketimes('all'))
# Make a copy of the array so that it does not change before the
# computation of the correlograms begins.
clusters = np.array(get_array(self.loader.get_clusters('all')))
# corrbin = self.loader.corrbin
# ncorrbins = self.loader.ncorrbins
corrbin = SETTINGS.get('correlograms.corrbin', .001)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', 100)
# Get cluster indices that need to be updated.
clusters_to_update = (
self.statscache.correlograms.not_in_key_indices(clusters_selected))
# If there are pairs that need to be updated, launch the task.
if len(clusters_to_update) > 0:
# Set wait cursor.
self.mainwindow.set_busy(computing_correlograms=True)
# Launch the task.
self.tasks.correlograms_task.compute(
spiketimes,
clusters,
clusters_to_update=clusters_to_update,
clusters_selected=clusters_selected,
ncorrbins=ncorrbins,
corrbin=corrbin)
# Otherwise, update directly the correlograms view without launching
# the task in the external process.
else:
# self.update_correlograms_view()
return '_update_correlograms_view'
def _compute_correlograms(self, clusters_selected):
# Get the correlograms parameters.
spiketimes = get_array(self.loader.get_spiketimes('all'))
# Make a copy of the array so that it does not change before the
# computation of the correlograms begins.
clusters = np.array(get_array(self.loader.get_clusters('all')))
# corrbin = self.loader.corrbin
# ncorrbins = self.loader.ncorrbins
corrbin = SETTINGS.get('correlograms.corrbin', .001)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', 100)
# Get cluster indices that need to be updated.
clusters_to_update = (self.statscache.correlograms.
not_in_key_indices(clusters_selected))
# If there are pairs that need to be updated, launch the task.
if len(clusters_to_update) > 0:
# Set wait cursor.
self.mainwindow.set_busy(computing_correlograms=True)
# Launch the task.
self.tasks.correlograms_task.compute(spiketimes, clusters,
clusters_to_update=clusters_to_update,
clusters_selected=clusters_selected,
ncorrbins=ncorrbins, corrbin=corrbin)
# Otherwise, update directly the correlograms view without launching
# the task in the external process.
else:
# self.update_correlograms_view()
return '_update_correlograms_view'
def _compute_correlograms(self, clusters_selected, wizard=None):
# Get the correlograms parameters.
spiketimes = get_array(self.loader.get_spiketimes("all"))
sample_rate = self.loader.freq
# print spiketimes.dtype
# Make a copy of the array so that it does not change before the
# computation of the correlograms begins.
clusters = np.array(get_array(self.loader.get_clusters("all")))
# Get excerpts
nexcerpts = USERPREF.get("correlograms_nexcerpts", 50)
excerpt_size = USERPREF.get("correlograms_excerpt_size", 10000)
spiketimes_excerpts = get_excerpts(spiketimes, nexcerpts=nexcerpts, excerpt_size=excerpt_size)
clusters_excerpts = get_excerpts(clusters, nexcerpts=nexcerpts, excerpt_size=excerpt_size)
# corrbin = self.loader.corrbin
# ncorrbins = self.loader.ncorrbins
corrbin = SETTINGS.get("correlograms.corrbin", 0.001)
ncorrbins = SETTINGS.get("correlograms.ncorrbins", 101)
# Ensure ncorrbins is odd.
if ncorrbins % 2 == 0:
ncorrbins += 1
# Get cluster indices that need to be updated.
# clusters_to_update = (self.statscache.correlograms.
# not_in_key_indices(clusters_selected))
clusters_to_update = clusters_selected
# If there are pairs that need to be updated, launch the task.
if len(clusters_to_update) > 0:
# Set wait cursor.
self.mainwindow.set_busy(computing_correlograms=True)
# Launch the task.
self.tasks.correlograms_task.compute(
spiketimes_excerpts,
clusters_excerpts,
clusters_to_update=clusters_to_update,
clusters_selected=clusters_selected,
ncorrbins=ncorrbins,
corrbin=corrbin,
sample_rate=sample_rate,
wizard=wizard,
)
# Otherwise, update directly the correlograms view without launching
# the task in the external process.
else:
# self.update_correlograms_view()
return ("_update_correlograms_view", (wizard,), {})
def change_ncorrbins_callback(self, checked=None):
if not self.loader:
return
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
# duration = self.loader.get_correlogram_window()
duration_new, ok = QtGui.QInputDialog.getDouble(self,
"Correlograms time window", "Half width (ms):",
duration / 2 * 1000, 1, 100000, 1)
if ok:
duration_new = duration_new * .001 * 2
ncorrbins_new = 2 * int(np.ceil(.5 * duration_new / corrbin))
# ncorrbins_new = int(duration_new / corrbin * .001)
SETTINGS['correlograms.ncorrbins'] = ncorrbins_new
self.taskgraph.change_correlograms_parameters(ncorrbins=ncorrbins_new)
def change_ncorrbins_callback(self, checked=None):
if not self.loader:
return
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
# duration = self.loader.get_correlogram_window()
duration_new, ok = QtGui.QInputDialog.getDouble(self,
"Correlograms time window", "Half width (ms):",
duration / 2 * 1000, 1, 100000, 1)
if ok:
duration_new = duration_new * .001 * 2
ncorrbins_new = 2 * int(np.ceil(.5 * duration_new / corrbin))
# ncorrbins_new = int(duration_new / corrbin * .001)
SETTINGS['correlograms.ncorrbins'] = ncorrbins_new
self.taskgraph.change_correlograms_parameters(ncorrbins=ncorrbins_new)
def change_corrbin_callback(self, checked=None):
if not self.loader:
return
# ncorrbins = self.loader.ncorrbins
# corrbin = self.loader.corrbin
# duration = self.loader.get_correlogram_window()
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
corrbin_new, ok = QtGui.QInputDialog.getDouble(self,
"Correlograms bin size", "Bin size (ms):",
corrbin * 1000, .01, 1000, 2)
if ok:
corrbin_new = corrbin_new * .001
ncorrbins_new = 2 * int(np.ceil(.5 * duration/ corrbin_new))
SETTINGS['correlograms.corrbin'] = corrbin_new
SETTINGS['correlograms.ncorrbins'] = ncorrbins_new
self.taskgraph.change_correlograms_parameters(corrbin=corrbin_new,
ncorrbins=ncorrbins_new)
def change_corrbin_callback(self, checked=None):
if not self.loader:
return
# ncorrbins = self.loader.ncorrbins
# corrbin = self.loader.corrbin
# duration = self.loader.get_correlogram_window()
corrbin = SETTINGS.get('correlograms.corrbin', CORRBIN_DEFAULT)
ncorrbins = SETTINGS.get('correlograms.ncorrbins', NCORRBINS_DEFAULT)
duration = corrbin * ncorrbins
corrbin_new, ok = QtGui.QInputDialog.getDouble(
self, "Correlograms bin size", "Bin size (ms):", corrbin * 1000,
.01, 1000, 2)
if ok:
corrbin_new = corrbin_new * .001
ncorrbins_new = 2 * int(np.ceil(.5 * duration / corrbin_new))
SETTINGS['correlograms.corrbin'] = corrbin_new
SETTINGS['correlograms.ncorrbins'] = ncorrbins_new
self.taskgraph.change_correlograms_parameters(
corrbin=corrbin_new, ncorrbins=ncorrbins_new)
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(MainWindow, self).closeEvent(e)
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 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(MainWindow, self).closeEvent(e)
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()
def restore_geometry(self):
"""Return a dictionary with the user preferences regarding geometry
in the WaveformView."""
pref = SETTINGS.get('waveform_view.geometry')
self.position_manager.set_geometry_preferences(pref)
def save_geometry(self):
pref = self.position_manager.get_geometry_preferences()
SETTINGS.set('waveform_view.geometry', pref)
def restore_geometry(self):
"""Return a dictionary with the user preferences regarding geometry
in the WaveformView."""
pref = SETTINGS.get('waveform_view.geometry')
self.position_manager.set_geometry_preferences(pref)
def save_geometry(self):
pref = self.position_manager.get_geometry_preferences()
SETTINGS.set('waveform_view.geometry', pref)
