def to_cells(self):
"""Convert spikes to cells."""
cells = {
k: self.get_cell(k)
for k in self.ids
}
cells = Cells(cells)
return cells
def spikes2cells(spikes, template_store):
# TODO remove old implementation (was not able to process cells with empty spike trains).
# cells = spikes.to_cells()
# for id_ in cells.ids:
# cells[id_].template = template_store.get(id_)
cells = {}
for id_ in template_store.indices:
cells[id_] = spikes.get_cell(id_)
cells[id_].template = template_store.get(id_)
cells = Cells(cells)
return cells
def __init__(self, params_pipe, number_pipe, templates_pipe, spikes_pipe,
probe_path=None, screen_resolution=None):
QMainWindow.__init__(self)
# Receive parameters.
params = params_pipe[0].recv()
self.probe = load_probe(probe_path)
self._nb_samples = params['nb_samples']
self._sampling_rate = params['sampling_rate']
self._display_list = []
self._params = {
'nb_samples': self._nb_samples,
'sampling_rate': self._sampling_rate,
'time': {
'min': 10.0, # ms
'max': 100.0, # ms
'init': 100.0, # ms
},
'voltage': {
'min': -200, # µV
'max': 20e+1, # µV
'init': 50.0, # µV
},
'templates': self._display_list
}
self._canvas_mea = MEACanvas(probe_path=probe_path, params=self._params)
self._canvas_template = TemplateCanvas(probe_path=probe_path, params=self._params)
self._canvas_rate = RateCanvas(probe_path=probe_path, params=self._params)
self._canvas_isi = ISICanvas(probe_path=probe_path, params=self._params)
self.cells = Cells({})
self._nb_buffer = 0
# TODO ISI
self.isi_bin_width, self.isi_x_max = 2, 25.0
canvas_template_widget = self._canvas_template.native
canvas_mea = self._canvas_mea.native
canvas_rate = self._canvas_rate.native
canvas_isi = self._canvas_isi.native
# Create controls widgets.
label_time = QLabel()
label_time.setText(u"time")
label_time_unit = QLabel()
label_time_unit.setText(u"ms")
self._dsp_time = QDoubleSpinBox()
self._dsp_time.setMinimum(self._params['time']['min'])
self._dsp_time.setMaximum(self._params['time']['max'])
self._dsp_time.setValue(self._params['time']['init'])
self._dsp_time.valueChanged.connect(self._on_time_changed)
label_voltage = QLabel()
label_voltage.setText(u"voltage")
label_voltage_unit = QLabel()
label_voltage_unit.setText(u"µV")
self._dsp_voltage = QDoubleSpinBox()
self._dsp_voltage.setMinimum(self._params['voltage']['min'])
self._dsp_voltage.setMaximum(self._params['voltage']['max'])
self._dsp_voltage.setValue(self._params['voltage']['init'])
self._dsp_voltage.valueChanged.connect(self._on_voltage_changed)
label_binsize = QLabel()
label_binsize.setText(u"Bin size")
label_binsize_unit = QLabel()
label_binsize_unit.setText(u"second")
self._dsp_binsize = QDoubleSpinBox()
self._dsp_binsize.setRange(0.1, 10)
self._dsp_binsize.setSingleStep(0.1)
self.bin_size = 1
self._dsp_binsize.setValue(self.bin_size)
self._dsp_binsize.valueChanged.connect(self._on_binsize_changed)
label_zoomrates = QLabel()
label_zoomrates.setText(u'Zoom rates')
self._zoom_rates = QDoubleSpinBox()
self._zoom_rates.setRange(1, 50)
self._zoom_rates.setSingleStep(0.1)
self._zoom_rates.setValue(1)
self._zoom_rates.valueChanged.connect(self._on_zoomrates_changed)
label_time_window = QLabel()
label_time_window.setText(u'Time window rates')
label_time_window_unit = QLabel()
label_time_window_unit.setText(u'second')
self._dsp_tw_rate = QDoubleSpinBox()
self._dsp_tw_rate.setRange(1, 50)
self._dsp_tw_rate.setSingleStep(self.bin_size)
self._dsp_tw_rate.setValue(50 * self.bin_size)
self._dsp_tw_rate.valueChanged.connect(self._on_time_window_changed)
label_tw_from_start = QLabel()
label_tw_from_start.setText('Time scale from start')
self._tw_from_start = QCheckBox()
self._tw_from_start.setChecked(True)
self._selection_templates = QTableWidget()
self._selection_templates.setSelectionMode(
QAbstractItemView.ExtendedSelection
)
self._selection_templates.setColumnCount(3)
self._selection_templates.setVerticalHeaderLabels(['Nb template', 'Channel', 'Amplitude'])
self._selection_templates.insertRow(0)
self._selection_templates.setItem(0, 0, QTableWidgetItem('Nb template'))
self._selection_templates.setItem(0, 1, QTableWidgetItem('Channel'))
self._selection_templates.setItem(0, 2, QTableWidgetItem('Amplitude'))
# self._selection_channels.setGeometry(QtCore.QRect(10, 10, 211, 291))
# for i in range(self.nb_templates):
# numRows = self.tableWidget.rowCount()
# self.tableWidget.insertRow(numRows)
# item = QTableWidgetItem("Template %i" % i)
# self._selection_templates.addItem(item)
# self._selection_templates.item(i).setSelected(False)
spacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
# Create controls grid.
grid = QGridLayout()
# # Add time row.
grid.addWidget(label_time, 0, 0)
grid.addWidget(self._dsp_time, 0, 1)
grid.addWidget(label_time_unit, 0, 2)
# # Add voltage row.
grid.addWidget(label_voltage, 1, 0)
grid.addWidget(self._dsp_voltage, 1, 1)
grid.addWidget(label_voltage_unit, 1, 2)
# # Add binsize row.
grid.addWidget(label_binsize, 2, 0)
grid.addWidget(self._dsp_binsize, 2, 1)
grid.addWidget(label_binsize_unit, 2, 2)
# # Add zoom rate
grid.addWidget(label_zoomrates, 3, 0)
grid.addWidget(self._zoom_rates, 3, 1)
# Add a double checkbox for time window
grid.addWidget(label_time_window, 4, 0)
grid.addWidget(self._dsp_tw_rate, 4, 1)
grid.addWidget(label_time_window_unit, 4, 2)
## Add checkbox to display the rates from start
grid.addWidget(label_tw_from_start, 5, 0)
grid.addWidget(self._tw_from_start, 5, 1)
# # Add spacer.
grid.addItem(spacer)
# # Create info group.
controls_group = QGroupBox()
controls_group.setLayout(grid)
# Create info grid.
templates_grid = QGridLayout()
# # Add Channel selection
# grid.addWidget(label_selection, 3, 0)
templates_grid.addWidget(self._selection_templates, 0, 1)
def add_template():
items = self._selection_templates.selectedItems()
self._display_list = []
for i in range(len(items)):
self._display_list.append(i)
self._on_templates_changed()
# self._selection_templates.itemClicked.connect(add_template)
# Template selection signals
self._selection_templates.itemSelectionChanged.connect(lambda: self.selected_templates(
self.nb_templates))
# Checkbox to display all the rates
self._tw_from_start.stateChanged.connect(self.time_window_rate_full)
# self._selection_templates.itemPressed(0, 1).connect(self.sort_template())
# # Add spacer.
templates_grid.addItem(spacer)
# Create controls group.
templates_group = QGroupBox()
templates_group.setLayout(templates_grid)
# # Create controls dock.
templates_dock = QDockWidget()
templates_dock.setWidget(templates_group)
templates_dock.setWindowTitle("Channels selection")
# # Create controls dock.
control_dock = QDockWidget()
control_dock.setWidget(controls_group)
control_dock.setWindowTitle("Controls")
# Create info widgets.
label_time = QLabel()
label_time.setText(u"time")
self._label_time_value = QLineEdit()
self._label_time_value.setText(u"0")
self._label_time_value.setReadOnly(True)
self._label_time_value.setAlignment(Qt.AlignRight)
label_time_unit = QLabel()
label_time_unit.setText(u"s")
info_buffer_label = QLabel()
info_buffer_label.setText(u"buffer")
self._info_buffer_value_label = QLineEdit()
self._info_buffer_value_label.setText(u"0")
self._info_buffer_value_label.setReadOnly(True)
self._info_buffer_value_label.setAlignment(Qt.AlignRight)
info_buffer_unit_label = QLabel()
info_buffer_unit_label.setText(u"")
info_probe_label = QLabel()
info_probe_label.setText(u"probe")
info_probe_value_label = QLineEdit()
info_probe_value_label.setText(u"{}".format(probe_path))
info_probe_value_label.setReadOnly(True)
# TODO place the following info in another grid?
info_probe_unit_label = QLabel()
info_probe_unit_label.setText(u"")
info_spacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
# Create info grid.
info_grid = QGridLayout()
# # Time row.
info_grid.addWidget(label_time, 0, 0)
info_grid.addWidget(self._label_time_value, 0, 1)
info_grid.addWidget(label_time_unit, 0, 2)
# # Buffer row.
info_grid.addWidget(info_buffer_label, 1, 0)
info_grid.addWidget(self._info_buffer_value_label, 1, 1)
info_grid.addWidget(info_buffer_unit_label, 1, 2)
# # Probe row.
info_grid.addWidget(info_probe_label, 2, 0)
info_grid.addWidget(info_probe_value_label, 2, 1)
info_grid.addWidget(info_probe_unit_label, 2, 2)
# # Spacer.
info_grid.addItem(info_spacer)
# Create info group.
info_group = QGroupBox()
info_group.setLayout(info_grid)
# Create info dock.
info_dock = QDockWidget()
info_dock.setWidget(info_group)
info_dock.setWindowTitle("Info")
# Create thread.
thread = Thread(number_pipe, templates_pipe, spikes_pipe)
thread.number_signal.connect(self._number_callback)
thread.reception_signal.connect(self._reception_callback)
thread.start()
# Add dockable windows.
self.addDockWidget(Qt.LeftDockWidgetArea, control_dock)
self.addDockWidget(Qt.LeftDockWidgetArea, info_dock)
self.addDockWidget(Qt.LeftDockWidgetArea, templates_dock)
# Add Grid Layout for canvas
canvas_grid = QGridLayout()
group_canv_temp = QDockWidget()
group_canv_temp.setWidget(canvas_template_widget)
group_canv_mea = QDockWidget()
group_canv_mea.setWidget(canvas_mea)
group_canv_rate = QDockWidget()
group_canv_rate.setWidget(canvas_rate)
group_canv_isi = QDockWidget()
group_canv_isi.setWidget(canvas_isi)
canvas_grid.addWidget(group_canv_temp, 0, 0)
canvas_grid.addWidget(group_canv_mea, 0, 1)
canvas_grid.addWidget(group_canv_rate, 1, 1)
canvas_grid.addWidget(group_canv_isi, 1, 0)
canvas_group = QGroupBox()
canvas_group.setLayout(canvas_grid)
# Set central widget.
self.setCentralWidget(canvas_group)
# Set window size.
if screen_resolution is not None:
screen_width = screen_resolution.width()
screen_height = screen_resolution.height()
self.resize(screen_width, screen_height)
# Set window title.
self.setWindowTitle("SpyKING Circus ORT - Read 'n' Qt display")
print(" ") # TODO remove?
from circusort.io.template_store import load_template_store
from circusort.io.cells import load_cells
from circusort.io.spikes import load_spikes, spikes2cells
from circusort.obj.cells import Cells
from circusort.obj.cell import Cell
from circusort.obj.train import Train
from circusort.obj.amplitude import Amplitude
templates = load_template_store('data/templates.h5', 'probe.prb')
fitted_spikes = load_spikes('data/spikes.h5')
# spikes_a = fitted_spikes.get_spike_data(t_min=0, t_max=100, indices=[0])
# train = Train(spikes_a['spike_times'])
# amplitude = Amplitude(spikes_a['amplitudes'], spikes_a['spike_times'])
b = Cells({})
for i in range(len(templates)):
mytemplate = templates[i]
new_cell = Cell(mytemplate, Train([]), Amplitude([], []))
b.append(new_cell)
# b.append(a)
# spikes_b = fitted_spikes.get_spike_data(t_min=100, t_max=120, indices=[0])
# b.add_spikes(spikes_b['spike_times'], spikes_b['amplitudes'], spikes_b['templates'])
spikes_all = fitted_spikes.get_spike_data()
b.add_spikes(spikes_all['spike_times'], spikes_all['amplitudes'],
spikes_all['templates'])
b.set_t_max(150)
def load_cells(path=None, mode='default', **kwargs):
"""Load cells from the specified path.
Parameter:
path: none | string (optional)
The path to the directory from which to load the cells. The default value is None.
mode: string (optional)
The mode to use to load the cells. Either 'default' or 'by cells. The default value is 'default'.
Return:
cells: dictionary
Dictionary of loaded cells.
"""
if mode == 'by elements':
template_directory = os.path.join(path, "templates")
if not os.path.isdir(template_directory):
message = "No such templates directory: {}".format(
template_directory)
raise OSError(message)
template_paths = list_templates(template_directory)
train_directory = os.path.join(path, "trains")
if not os.path.isdir(train_directory):
message = "No such trains directory: {}".format(train_directory)
raise OSError(message)
train_paths = list_trains(train_directory)
position_directory = os.path.join(path, "positions")
if not os.path.isdir(position_directory):
message = "No such positions directory: {}".format(
position_directory)
raise OSError(message)
position_paths = list_positions(position_directory)
string = "Different number of templates and trains between {} and {}"
message = string.format(template_directory, train_directory)
assert len(template_paths) == len(train_paths), message
string = "Different number of templates and positions between {} and {}"
message = string.format(template_directory, position_directory)
assert len(template_paths) == len(position_paths), message
nb_cells = len(template_paths)
cells = {}
for k in range(0, nb_cells):
template = load_template(template_paths[k])
train = load_train(train_paths[k])
position = load_position(position_paths[k])
cell = Cell(template, train, position)
cells[k] = cell
cells = Cells(cells)
elif mode in ['default', 'by cells']:
path = normalize_path(path, **kwargs)
if path[-6:] != "/cells":
path = os.path.join(path, "cells")
if not os.path.isdir(path):
message = "No such cells directory: {}".format(path)
raise OSError(message)
parameters = get_cells_parameters(path)
kwargs.update(parameters['general'])
cell_directories = list_cells(path)
cells = {
k: get_cell(directory=cell_directory, **kwargs)
for k, cell_directory in enumerate(cell_directories)
}
cells = Cells(cells, parameters=parameters)
else:
message = "Unknown mode value: {}".format(mode)
raise ValueError(message)
return cells
def generate_cells(nb_cells=3, **kwargs):
cells = {k: generate_cell(**kwargs) for k in range(0, nb_cells)}
cells = Cells(cells)
return cells