def send_CaImaging_Stop_signal(self):
self.statusBar.showMessage('sending stop signal for 2-Photon acq.')
acq = Acquisition(
dt=1e-3, # 1kHz
Nchannel_analog_in=1,
Nchannel_digital_in=0,
max_time=1.1,
buffer_time=0.1,
output_steps=[self.config['STEP_FOR_CA_IMAGING_TRIGGER']],
filename=None)
acq.launch()
time.sleep(1.1)
acq.close()
def initialize(self):
self.bufferButton.setEnabled(
False) # should be already blocked, but for security
self.runButton.setEnabled(False) # acq blocked during init
self.metadata = self.check_gui_to_init_metadata()
self.set_filename_and_folder()
max_time = 2 * 60 * 60 # 2 hours by default, so should be stopped manually
if self.metadata['VisualStim']:
self.statusBar.showMessage(
'[...] initializing acquisition & stimulation')
self.init_visual_stim()
np.save(
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'),
self.stim.experiment)
print('[ok] Visual-stimulation data saved as "%s"' %
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'))
if ('time_stop'
in self.stim.experiment) and self.stim.buffer is not None:
# if buffered, it won't be much longer than the scheduled time
max_time = 1.5 * np.max(self.stim.experiment['time_stop'])
else:
self.statusBar.showMessage('[...] initializing acquisition')
self.stim = None
print('max_time of NIdaq recording: %.2dh:%.2dm:%.2ds' %
(max_time / 3600, (max_time % 3600) / 60, (max_time % 60)))
output_steps = []
if self.metadata['CaImaging']:
output_steps.append(self.config['STEP_FOR_CA_IMAGING_TRIGGER'])
self.NIdaq_metadata_init()
if not self.demoW.isChecked():
try:
self.acq = Acquisition(
dt=1. / self.metadata['NIdaq-acquisition-frequency'],
Nchannel_analog_in=self.
metadata['NIdaq-analog-input-channels'],
Nchannel_digital_in=self.
metadata['NIdaq-digital-input-channels'],
max_time=max_time,
output_steps=output_steps,
filename=self.filename.replace('metadata', 'NIdaq'))
except BaseException as e:
print(e)
print(' /!\ PB WITH NI-DAQ /!\ ')
self.acq = None
self.init = True
if self.stim is not None:
self.bufferButton.setEnabled(True)
self.runButton.setEnabled(True)
self.save_experiment(
self.metadata) # saving all metadata after full initialization
if self.metadata['VisualStim']:
self.statusBar.showMessage('Acquisition & Stimulation ready !')
else:
self.statusBar.showMessage('Acquisition ready !')
class MainWindow(QtWidgets.QMainWindow):
MODALITIES = [
'Locomotion', 'FaceCamera', 'EphysLFP', 'EphysVm', 'CaImaging'
]
def __init__(self, app, args=None, demo=False, width=550):
"""
"""
super(MainWindow, self).__init__()
self.app = app
self.setWindowTitle('Experimental module')
Y = 5 # coordinates of the current buttons
##########################################################
######## Multiprocessing quantities
##########################################################
self.run_event = multiprocessing.Event(
) # to turn on and off recordings execute through multiprocessing.Process
self.run_event.clear()
self.closeFaceCamera_event = multiprocessing.Event()
self.closeFaceCamera_event.clear()
self.quit_event = multiprocessing.Event()
self.quit_event.clear()
self.manager = multiprocessing.Manager(
) # Useful to share a string across processes :
self.datafolder = self.manager.Value(
c_char_p,
str(os.path.join(os.path.expanduser('~'), 'DATA', 'trash')))
##########################################################
######## class values
##########################################################
self.stim, self.acq, self.init, self.screen, self.stop_flag = None, None, False, None, False
self.FaceCamera_process = None
self.RigView_process = None
self.params_window = None
##########################################################
####### GUI settings
##########################################################
rml = QtWidgets.QLabel(
' ' + '-' * 40 + " Recording modalities " + '-' * 40, self)
rml.move(35, Y)
rml.setMinimumWidth(500)
Y += 35
for i, k in enumerate(self.MODALITIES):
setattr(self, k + 'Button', QtWidgets.QPushButton(k, self))
getattr(self, k + 'Button').move(
30 + i * 0.9 * width / len(self.MODALITIES), Y)
getattr(self, k + 'Button').setFixedWidth(0.8 * width /
len(self.MODALITIES))
getattr(self, k + 'Button').setCheckable(True)
self.FaceCameraButton.clicked.connect(self.toggle_FaceCamera_process)
Y += 50
# screen choice
QtWidgets.QLabel(" Screen :", self).move(250, Y)
self.cbsc = QtWidgets.QComboBox(self)
self.cbsc.setMinimumWidth(200)
self.cbsc.move(320, Y)
self.cbsc.activated.connect(self.update_screen)
self.cbsc.addItems(SCREENS.keys())
self.demoW = QtWidgets.QCheckBox('demo', self)
self.demoW.move(40, Y)
if demo:
self.demoW.setChecked(True)
Y += 35
# config choice
QtWidgets.QLabel(" => Config :", self).move(160, Y)
self.cbc = QtWidgets.QComboBox(self)
self.cbc.setMinimumWidth(270)
self.cbc.move(250, Y)
self.cbc.activated.connect(self.update_config)
Y += 35
# subject choice
QtWidgets.QLabel("-> Subject :", self).move(100, Y)
self.cbs = QtWidgets.QComboBox(self)
self.cbs.setMinimumWidth(340)
self.cbs.move(180, Y)
self.cbs.activated.connect(self.update_subject)
Y += 35
# protocol choice
QtWidgets.QLabel(" Visual Protocol :", self).move(20, Y)
self.cbp = QtWidgets.QComboBox(self)
self.cbp.setMinimumWidth(390)
self.cbp.move(130, Y)
self.cbp.activated.connect(self.update_protocol)
Y += 35
# protocol choice
QtWidgets.QLabel(" Intervention :", self).move(20, Y)
self.cbi = QtWidgets.QComboBox(self)
self.cbi.addItems(['', 'CNO injection', 'Compound-21 injection'])
self.cbi.setMinimumWidth(390)
self.cbi.move(130, Y)
# self.cbi.activated.connect(self.update_protocol)
Y += 45
# buttons and functions
LABELS = ["i) Initialize", "b) Buffer", "r) Run", "s) Stop", "q) Quit"]
FUNCTIONS = [
self.initialize, self.buffer, self.run, self.stop, self.quit
]
mainMenu = self.menuBar()
self.fileMenu = mainMenu.addMenu('')
self.statusBar = QtWidgets.QStatusBar()
self.setStatusBar(self.statusBar)
self.statusBar.showMessage('ready to select a protocol/config')
for func, label, name, shift in zip(FUNCTIONS, LABELS, [
'initButton', 'bufferButton', 'runButton', 'stopButton',
'quitButton'
], 90 * np.arange(5)):
setattr(self, name, QtWidgets.QPushButton(label, self))
getattr(self, name).clicked.connect(func)
getattr(self, name).setFixedWidth(85)
getattr(self, name).move(50 + shift, Y)
action = QtWidgets.QAction(label, self)
action.setShortcut(label.split(')')[0])
action.triggered.connect(func)
self.fileMenu.addAction(action)
self.bufferButton.setEnabled(False)
self.runButton.setEnabled(False)
Y += 45
QtWidgets.QLabel("Notes: ", self).move(25, Y + 10)
self.qmNotes = QtWidgets.QTextEdit('', self)
self.qmNotes.move(90, Y)
self.qmNotes.setMinimumWidth(250)
self.qmNotes.setMinimumHeight(60)
btn = QtWidgets.QPushButton('Save\nSettings', self)
btn.clicked.connect(self.save_settings)
btn.setMinimumWidth(70)
btn.setMinimumHeight(50)
btn.move(380, Y + 5)
self.setGeometry(400, 50, width, Y + 95)
##########################################################
##########################################################
##########################################################
self.config, self.protocol, self.subject = None, {}, None
self.get_config_list()
self.load_settings()
# self.toggle_FaceCamera_process() # initialize if pre-set
self.experiment = {} # storing the specifics of an experiment
self.show()
### GUI FUNCTIONS ###
def toggle_FaceCamera_process(self):
if self.FaceCameraButton.isChecked() and (self.FaceCamera_process is
None):
# need to launch it
self.statusBar.showMessage(' starting FaceCamera stream [...] ')
self.show()
self.closeFaceCamera_event.clear()
self.FaceCamera_process = multiprocessing.Process(
target=launch_FaceCamera,
args=(self.run_event, self.closeFaceCamera_event,
self.datafolder, {
'frame_rate': self.config['FaceCamera-frame-rate']
}))
self.FaceCamera_process.start()
self.statusBar.showMessage(
'[ok] FaceCamera initialized (in 5-6s) ! ')
elif (not self.FaceCameraButton.isChecked()) and (
self.FaceCamera_process is not None):
# need to shut it down
self.closeFaceCamera_event.set()
self.statusBar.showMessage(' FaceCamera stream interupted !')
self.FaceCamera_process = None
def save_settings(self):
settings = {
'config': self.cbc.currentText(),
'protocol': self.cbp.currentText(),
'subject': self.cbs.currentText()
}
for i, k in enumerate(self.MODALITIES):
settings[k] = getattr(self, k + 'Button').isChecked()
np.save(settings_filename, settings)
self.statusBar.showMessage('settings succesfully saved !')
def load_settings(self):
if os.path.isfile(settings_filename):
settings = np.load(settings_filename, allow_pickle=True).item()
if settings['config'] in self.config_list:
self.cbc.setCurrentText(settings['config'])
self.update_config()
if settings['protocol'] in self.protocol_list:
self.cbp.setCurrentText(settings['protocol'])
self.update_protocol()
if settings['subject'] in self.subjects:
self.cbs.setCurrentText(settings['subject'])
self.update_subject()
for i, k in enumerate(self.MODALITIES):
getattr(self, k + 'Button').setChecked(settings[k])
if (self.config is None) or (self.protocol
== {}) or (self.subject is None):
self.statusBar.showMessage(
' /!\ Problem in loading settings /!\ ')
def get_config_list(self):
files = os.listdir(os.path.join(base_path, 'configs'))
self.config_list = [
f.replace('.json', '') for f in files[::-1] if f.endswith('.json')
]
self.cbc.addItems(self.config_list)
self.update_config()
def update_config(self):
fn = os.path.join(base_path, 'configs',
self.cbc.currentText() + '.json')
with open(fn) as f:
self.config = json.load(f)
self.get_protocol_list()
self.get_subject_list()
self.root_datafolder = os.path.join(os.path.expanduser('~'),
self.config['root_datafolder'])
self.Screen = self.config['Screen']
def get_protocol_list(self):
if self.config['protocols'] == 'all':
files = os.listdir(os.path.join(base_path, 'protocols'))
self.protocol_list = [
f.replace('.json', '') for f in files if f.endswith('.json')
]
else:
self.protocol_list = self.config['protocols']
self.cbp.clear()
self.cbp.addItems(['None'] + self.protocol_list)
def update_protocol(self):
if self.cbp.currentText() == 'None':
self.protocol = {}
else:
fn = os.path.join(base_path, 'protocols',
self.cbp.currentText() + '.json')
with open(fn) as f:
self.protocol = json.load(f)
self.protocol['Screen'] = self.config['Screen'] # override params
self.protocol['data-folder'] = self.root_datafolder
def update_screen(self):
print(self.cbsc.currentText())
def get_subject_list(self):
with open(
os.path.join(base_path, 'subjects',
self.config['subjects_file'])) as f:
self.subjects = json.load(f)
self.cbs.clear()
self.cbs.addItems(self.subjects.keys())
def update_subject(self):
self.subject = self.subjects[self.cbs.currentText()]
def rigview(self):
if self.RigView_process is not None:
self.RigView_process.terminate()
self.statusBar.showMessage('Initializing RigView stream [...]')
self.RigView_process = multiprocessing.Process(target=launch_RigView,
args=(self.run_event,
self.quit_event,
self.datafolder))
self.RigView_process.start()
time.sleep(5)
self.statusBar.showMessage('Screen ready')
def NIdaq_metadata_init(self):
# --------------- #
### NI daq init ### ## we override parameters based on the chosen modalities if needed
# --------------- #
if self.metadata['VisualStim'] and (
self.metadata['NIdaq-analog-input-channels'] < 1):
self.metadata[
'NIdaq-analog-input-channels'] = 1 # at least one (AI0), -> the photodiode
if self.metadata['Locomotion'] and (
self.metadata['NIdaq-digital-input-channels'] < 2):
self.metadata['NIdaq-digital-input-channels'] = 2
if self.metadata['EphysLFP'] and self.metadata['EphysVm']:
self.metadata[
'NIdaq-analog-input-channels'] = 3 # both channels, -> channel AI1 for Vm, AI2 for LFP
elif self.metadata['EphysLFP']:
self.metadata['NIdaq-analog-input-channels'] = 2 # AI1 for LFP
elif self.metadata['EphysVm']:
self.metadata['NIdaq-analog-input-channels'] = 2 # AI1 for Vm
def check_gui_to_init_metadata(self):
### set up all metadata based on GUI infos
metadata = {
'config': self.cbc.currentText(),
'protocol': self.cbp.currentText(),
'VisualStim': self.cbp.currentText() != 'None',
'notes': self.qmNotes.toPlainText(),
'subject_ID': self.cbs.currentText(),
'subject_props': self.subjects[self.cbs.currentText()]
}
for d in [self.config, self.protocol]:
if d is not None:
for key in d:
metadata[key] = d[key]
for k in self.MODALITIES:
metadata[k] = bool(getattr(self, k + 'Button').isChecked())
return metadata
def set_filename_and_folder(self):
self.filename = generate_filename_path(
self.root_datafolder,
filename='metadata',
extension='.npy',
with_FaceCamera_frames_folder=self.metadata['FaceCamera'])
self.datafolder.set(os.path.dirname(self.filename))
def init_visual_stim(self):
with open(
os.path.join(base_path, 'protocols',
self.metadata['protocol'] + '.json'), 'r') as fp:
self.protocol = json.load(fp)
self.protocol['screen'] = self.metadata['Screen']
if self.demoW.isChecked():
self.protocol['demo'] = True
else:
self.protocol['demo'] = False
self.stim = build_stim(self.protocol)
def initialize(self):
self.bufferButton.setEnabled(
False) # should be already blocked, but for security
self.runButton.setEnabled(False) # acq blocked during init
self.metadata = self.check_gui_to_init_metadata()
self.set_filename_and_folder()
max_time = 2 * 60 * 60 # 2 hours by default, so should be stopped manually
if self.metadata['VisualStim']:
self.statusBar.showMessage(
'[...] initializing acquisition & stimulation')
self.init_visual_stim()
np.save(
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'),
self.stim.experiment)
print('[ok] Visual-stimulation data saved as "%s"' %
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'))
if ('time_stop'
in self.stim.experiment) and self.stim.buffer is not None:
# if buffered, it won't be much longer than the scheduled time
max_time = 1.5 * np.max(self.stim.experiment['time_stop'])
else:
self.statusBar.showMessage('[...] initializing acquisition')
self.stim = None
print('max_time of NIdaq recording: %.2dh:%.2dm:%.2ds' %
(max_time / 3600, (max_time % 3600) / 60, (max_time % 60)))
output_steps = []
if self.metadata['CaImaging']:
output_steps.append(self.config['STEP_FOR_CA_IMAGING_TRIGGER'])
self.NIdaq_metadata_init()
if not self.demoW.isChecked():
try:
self.acq = Acquisition(
dt=1. / self.metadata['NIdaq-acquisition-frequency'],
Nchannel_analog_in=self.
metadata['NIdaq-analog-input-channels'],
Nchannel_digital_in=self.
metadata['NIdaq-digital-input-channels'],
max_time=max_time,
output_steps=output_steps,
filename=self.filename.replace('metadata', 'NIdaq'))
except BaseException as e:
print(e)
print(' /!\ PB WITH NI-DAQ /!\ ')
self.acq = None
self.init = True
if self.stim is not None:
self.bufferButton.setEnabled(True)
self.runButton.setEnabled(True)
self.save_experiment(
self.metadata) # saving all metadata after full initialization
if self.metadata['VisualStim']:
self.statusBar.showMessage('Acquisition & Stimulation ready !')
else:
self.statusBar.showMessage('Acquisition ready !')
def buffer(self):
self.bufferButton.setEnabled(False)
self.initButton.setEnabled(False)
self.stopButton.setEnabled(False)
self.runButton.setEnabled(False)
# ----------------------------------
# buffers the visual stimulus
self.stim.buffer_stim(self, gui_refresh_func=self.app.processEvents)
self.update()
# ----------------------------------
self.initButton.setEnabled(True)
self.stopButton.setEnabled(True)
self.runButton.setEnabled(True)
self.show()
def check_metadata(self):
new_metadata = self.check_gui_to_init_metadata()
same, same_protocol = True, new_metadata['protocol'] == self.metadata[
'protocol']
for k in new_metadata:
if self.metadata[k] != new_metadata[k]:
same = False
if not same:
print(
' /!\ metadata were changed since the initialization ! /!\ ')
print(" ---> updating the metadata file !")
self.save_experiment(new_metadata)
return same_protocol
def run(self):
if self.check_metadata(): # invalid if not the same protocol !
self.initButton.setEnabled(False)
self.bufferButton.setEnabled(False)
self.stop_flag = False
self.run_event.set() # start the run flag for the facecamera
if ((self.acq is None) and (self.stim is None)) or not self.init:
self.statusBar.showMessage(
'Need to initialize the stimulation !')
elif (self.stim is None) and (self.acq is not None):
self.acq.launch()
self.statusBar.showMessage('Acquisition running [...]')
else:
self.statusBar.showMessage(
'Stimulation & Acquisition running [...]')
# Ni-Daq
if self.acq is not None:
self.acq.launch()
# run visual stim
if self.metadata['VisualStim']:
self.stim.run(self)
# ========================
# ---- HERE IT RUNS [...]
# ========================
# stop and clean up things
if self.metadata['FaceCamera']:
self.run_event.clear(
) # this will close the camera process
# close visual stim
if self.metadata['VisualStim']:
self.stim.close() # close the visual stim
if self.acq is not None:
self.acq.close()
if self.metadata[
'CaImaging'] and not self.stop_flag: # outside the pure acquisition case
self.send_CaImaging_Stop_signal()
self.init = False
self.initButton.setEnabled(True)
self.runButton.setEnabled(False)
print(100 * '-', '\n', 50 * '=')
else:
print(
'\n /!\ the visual stimulation was changed, need to REDO the initialization !! /!\ '
)
self.statusBar.showMessage(' /!\ Need to re-initialize /!\ ')
def stop(self):
self.run_event.clear() # this will close the camera process
self.stop_flag = True
if self.acq is not None:
self.acq.close()
if self.stim is not None:
self.stim.close()
self.init = False
if self.metadata['CaImaging']:
self.send_CaImaging_Stop_signal()
self.statusBar.showMessage('stimulation stopped !')
self.runButton.setEnabled(False)
print(100 * '-', '\n', 50 * '=')
def send_CaImaging_Stop_signal(self):
self.statusBar.showMessage('sending stop signal for 2-Photon acq.')
acq = Acquisition(
dt=1e-3, # 1kHz
Nchannel_analog_in=1,
Nchannel_digital_in=0,
max_time=1.1,
buffer_time=0.1,
output_steps=[self.config['STEP_FOR_CA_IMAGING_TRIGGER']],
filename=None)
acq.launch()
time.sleep(1.1)
acq.close()
def quit(self):
self.quit_event.set()
if self.FaceCamera_process is not None:
self.closeFaceCamera_event.set()
if self.acq is not None:
self.acq.close()
if self.stim is not None:
self.stim.quit()
QtWidgets.QApplication.quit()
def save_experiment(self, metadata):
# SAVING THE METADATA FILES
metadata['filename'] = str(self.datafolder.get())
for key in self.protocol:
metadata[key] = self.protocol[key]
np.save(os.path.join(str(self.datafolder.get()), 'metadata.npy'),
metadata)
print('[ok] Metadata data saved as: %s ' %
os.path.join(str(self.datafolder.get()), 'metadata.npy'))
self.statusBar.showMessage(
'Metadata saved as: "%s" ' %
os.path.join(str(self.datafolder.get()), 'metadata.npy'))
original_freq=metadata['NIdaq-acquisition-frequency'],
new_freq=50.,
post_smoothing=2. / 50.,
verbose=True)
print('mean speed: %.1f cm/s' % np.mean(speed))
plt.plot(t_array, speed)
plt.ylabel('speed (cm/s)')
plt.xlabel('time (s)')
plt.show()
else:
import time
from hardware_control.NIdaq.main import Acquisition
acq = Acquisition(dt=args.acq_time_step,
Nchannel_analog_in=0,
Nchannel_digital_in=2,
max_time=args.recording_time)
print('You have %i s to do 5 rotations of the disk [...]' %
args.recording_time)
acq.launch()
time.sleep(args.recording_time)
_, digital_inputs, dt = acq.close(return_data=True)
t_array = np.arange(len(digital_inputs[0])) * dt
A, B = process_binary_signal(digital_inputs[0, :])
plt.plot(t_array, A)
class MainWindow(QtWidgets.QMainWindow):
def __init__(self, app, args=None):
"""
"""
super(MainWindow, self).__init__()
self.setWindowTitle('Experimental module')
self.setGeometry(400, 50, 550, 400)
##########################################################
######## Multiprocessing quantities
##########################################################
self.run_event = multiprocessing.Event(
) # to turn on and off recordings execute through multiprocessing.Process
self.run_event.clear()
self.closeFaceCamera_event = multiprocessing.Event()
self.closeFaceCamera_event.clear()
self.quit_event = multiprocessing.Event()
self.quit_event.clear()
self.manager = multiprocessing.Manager(
) # Useful to share a string across processes :
self.datafolder = self.manager.Value(
c_char_p,
str(os.path.join(os.path.expanduser('~'), 'DATA', 'trash')))
##########################################################
######## class values
##########################################################
self.stim, self.acq, self.init, self.screen, self.stop_flag = None, None, False, None, False
self.FaceCamera_process = None
self.RigView_process = None
self.params_window = None
##########################################################
####### GUI settings
##########################################################
rml = QtWidgets.QLabel(
' ' + '-' * 40 + " Recording modalities " + '-' * 40, self)
rml.move(30, 5)
rml.setMinimumWidth(500)
self.VisualStimButton = QtWidgets.QPushButton("Visual-Stim", self)
self.VisualStimButton.move(30, 40)
self.LocomotionButton = QtWidgets.QPushButton("Locomotion", self)
self.LocomotionButton.move(130, 40)
self.ElectrophyButton = QtWidgets.QPushButton("Electrophy", self)
self.ElectrophyButton.move(230, 40)
self.FaceCameraButton = QtWidgets.QPushButton("FaceCamera", self)
self.FaceCameraButton.clicked.connect(self.toggle_FaceCamera_process)
self.FaceCameraButton.move(330, 40)
self.CaImagingButton = QtWidgets.QPushButton("CaImaging", self)
self.CaImagingButton.move(430, 40)
for button in [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton, self.FaceCameraButton,
self.CaImagingButton
]:
button.setCheckable(True)
for button in [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton
]:
button.setChecked(True)
# screen choice
QtWidgets.QLabel(" Screen :", self).move(250, 90)
self.cbsc = QtWidgets.QComboBox(self)
self.cbsc.setMinimumWidth(200)
self.cbsc.move(320, 90)
self.cbsc.activated.connect(self.update_screen)
self.cbsc.addItems(SCREENS.keys())
# config choice
QtWidgets.QLabel(" => Config :", self).move(160, 125)
self.cbc = QtWidgets.QComboBox(self)
self.cbc.setMinimumWidth(270)
self.cbc.move(250, 125)
self.cbc.activated.connect(self.update_config)
# subject choice
QtWidgets.QLabel("-> Subject :", self).move(100, 160)
self.cbs = QtWidgets.QComboBox(self)
self.cbs.setMinimumWidth(340)
self.cbs.move(180, 160)
self.cbs.activated.connect(self.update_subject)
# protocol choice
QtWidgets.QLabel(" Visual Protocol :", self).move(20, 195)
self.cbp = QtWidgets.QComboBox(self)
self.cbp.setMinimumWidth(390)
self.cbp.move(130, 195)
self.cbp.activated.connect(self.update_protocol)
# buttons and functions
LABELS = ["i) Initialize", "r) Run", "s) Stop", "q) Quit"]
FUNCTIONS = [self.initialize, self.run, self.stop, self.quit]
mainMenu = self.menuBar()
self.fileMenu = mainMenu.addMenu('')
self.statusBar = QtWidgets.QStatusBar()
self.setStatusBar(self.statusBar)
self.statusBar.showMessage('ready to select a protocol/config')
for func, label, shift in zip(FUNCTIONS, LABELS,\
110*np.arange(len(LABELS))):
btn = QtWidgets.QPushButton(label, self)
btn.clicked.connect(func)
btn.setMinimumWidth(110)
btn.move(50 + shift, 250)
action = QtWidgets.QAction(label, self)
action.setShortcut(label.split(')')[0])
action.triggered.connect(func)
self.fileMenu.addAction(action)
QtWidgets.QLabel("Notes: ", self).move(40, 300)
self.qmNotes = QtWidgets.QTextEdit('', self)
self.qmNotes.move(90, 300)
self.qmNotes.setMinimumWidth(250)
self.qmNotes.setMinimumHeight(60)
btn = QtWidgets.QPushButton('Save\nSettings', self)
btn.clicked.connect(self.save_settings)
btn.setMinimumWidth(70)
btn.setMinimumHeight(50)
btn.move(380, 310)
##########################################################
##########################################################
##########################################################
self.config, self.protocol, self.subject = None, None, None
self.get_config_list()
self.load_settings()
# self.toggle_FaceCamera_process() # initialize if pre-set
self.experiment = {} # storing the specifics of an experiment
self.show()
### GUI FUNCTIONS ###
def toggle_FaceCamera_process(self):
if self.FaceCameraButton.isChecked() and (self.FaceCamera_process is
None):
# need to launch it
self.statusBar.showMessage(' starting FaceCamera stream [...] ')
self.show()
self.closeFaceCamera_event.clear()
self.FaceCamera_process = multiprocessing.Process(
target=launch_FaceCamera,
args=(self.run_event, self.closeFaceCamera_event,
self.datafolder, {
'frame_rate': self.config['FaceCamera-frame-rate']
}))
self.FaceCamera_process.start()
time.sleep(6)
self.statusBar.showMessage('[ok] FaceCamera ready ! ')
elif (not self.FaceCameraButton.isChecked()) and (
self.FaceCamera_process is not None):
# need to shut it down
self.closeFaceCamera_event.set()
self.statusBar.showMessage(' FaceCamera stream interupted !')
self.FaceCamera_process = None
def save_settings(self):
settings = {
'config': self.cbc.currentText(),
'protocol': self.cbp.currentText(),
'subject': self.cbs.currentText()
}
for label, button in zip([
'VisualStimButton', 'LocomotionButton', 'ElectrophyButton',
'FaceCameraButton', 'CaImagingButton'
], [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton, self.FaceCameraButton,
self.CaImagingButton
]):
settings[label] = button.isChecked()
np.save(settings_filename, settings)
self.statusBar.showMessage('settings succesfully saved !')
def load_settings(self):
if os.path.isfile(settings_filename):
settings = np.load(settings_filename, allow_pickle=True).item()
if settings['config'] in self.config_list:
self.cbc.setCurrentText(settings['config'])
self.update_config()
if settings['protocol'] in self.protocol_list:
self.cbp.setCurrentText(settings['protocol'])
self.update_protocol()
if settings['subject'] in self.subjects:
self.cbs.setCurrentText(settings['subject'])
self.update_subject()
for label, button in zip([
'VisualStimButton', 'LocomotionButton', 'ElectrophyButton',
'FaceCameraButton', 'CaImagingButton'
], [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton, self.FaceCameraButton,
self.CaImagingButton
]):
button.setChecked(settings[label])
if (self.config is None) or (self.protocol is None) or (self.subject is
None):
self.statusBar.showMessage(
' /!\ Problem in loading settings /!\ ')
def get_config_list(self):
files = os.listdir(os.path.join(base_path, 'configs'))
self.config_list = [
f.replace('.json', '') for f in files if f.endswith('.json')
]
self.cbc.addItems(self.config_list)
self.update_config()
def update_config(self):
fn = os.path.join(base_path, 'configs',
self.cbc.currentText() + '.json')
with open(fn) as f:
self.config = json.load(f)
self.get_protocol_list()
self.get_subject_list()
self.root_datafolder = os.path.join(os.path.expanduser('~'),
self.config['root_datafolder'])
self.Screen = self.config['Screen']
def get_protocol_list(self):
if self.config['protocols'] == 'all':
files = os.listdir(os.path.join(base_path, 'protocols'))
self.protocol_list = [
f.replace('.json', '') for f in files if f.endswith('.json')
]
else:
self.protocol_list = self.config['protocols']
self.cbp.clear()
self.cbp.addItems(['None'] + self.protocol_list)
def update_protocol(self):
if self.cbp.currentText() == 'None':
self.protocol = {}
else:
fn = os.path.join(base_path, 'protocols',
self.cbp.currentText() + '.json')
with open(fn) as f:
self.protocol = json.load(f)
self.protocol['Screen'] = self.config['Screen'] # override params
self.protocol['data-folder'] = self.root_datafolder
def update_screen(self):
print(self.cbsc.currentText())
def get_subject_list(self):
with open(
os.path.join(base_path, 'subjects',
self.config['subjects_file'])) as f:
self.subjects = json.load(f)
self.cbs.clear()
self.cbs.addItems(self.subjects.keys())
def update_subject(self):
self.subject = self.subjects[self.cbs.currentText()]
def rigview(self):
if self.RigView_process is not None:
self.RigView_process.terminate()
self.statusBar.showMessage('Initializing RigView stream [...]')
self.RigView_process = multiprocessing.Process(target=launch_RigView,
args=(self.run_event,
self.quit_event,
self.datafolder))
self.RigView_process.start()
time.sleep(5)
self.statusBar.showMessage('Screen ready')
def initialize(self):
### set up all metadata
self.metadata = {
'config': self.cbc.currentText(),
'protocol': self.cbp.currentText(),
'notes': self.qmNotes.toPlainText(),
'subject_ID': self.cbs.currentText(),
'subject_props': self.subjects[self.cbs.currentText()]
}
for d in [self.config, self.protocol]:
if d is not None:
for key in d:
self.metadata[key] = d[key]
# Setup configuration
for modality, button in zip([
'VisualStim', 'Locomotion', 'Electrophy', 'FaceCamera',
'CaImaging'
], [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton, self.FaceCameraButton,
self.CaImagingButton
]):
self.metadata[modality] = bool(button.isChecked())
if self.cbp.currentText() == 'None':
self.statusBar.showMessage('[...] initializing acquisition')
else:
self.statusBar.showMessage(
'[...] initializing acquisition & stimulation')
self.filename = generate_filename_path(
self.root_datafolder,
filename='metadata',
extension='.npy',
with_FaceCamera_frames_folder=self.metadata['FaceCamera'],
with_screen_frames_folder=self.metadata['VisualStim'])
self.datafolder.set(os.path.dirname(self.filename))
if self.metadata['protocol'] != 'None':
with open(
os.path.join(base_path, 'protocols',
self.metadata['protocol'] + '.json'),
'r') as fp:
self.protocol = json.load(fp)
else:
self.protocol = {}
# init visual stimulation
if self.metadata['VisualStim'] and len(self.protocol.keys()) > 0:
self.protocol['screen'] = self.metadata['Screen']
self.stim = build_stim(self.protocol)
np.save(
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'),
self.stim.experiment)
print('[ok] Visual-stimulation data saved as "%s"' %
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'))
if 'time_stop' in self.stim.experiment:
max_time = int(
1.5 *
self.stim.experiment['time_stop'][-1]) # for security
else:
max_time = 1 * 60 * 60 # 1 hour, should be stopped manually
else:
max_time = 1 * 60 * 60 # 1 hour, should be stopped manually
self.stim = None
output_steps = []
if self.metadata['CaImaging']:
output_steps.append(self.config['STEP_FOR_CA_IMAGING_TRIGGER'])
# --------------- #
### NI daq init ### ## we override parameters based on the chosen modalities if needed
# --------------- #
if self.metadata['VisualStim'] and (
self.metadata['NIdaq-analog-input-channels'] < 1):
self.metadata['NIdaq-analog-input-channels'] = 1 # at least one
if self.metadata['Electrophy'] and (
self.metadata['NIdaq-analog-input-channels'] < 2):
self.metadata['NIdaq-analog-input-channels'] = 2
if self.metadata['Locomotion'] and (
self.metadata['NIdaq-digital-input-channels'] < 2):
self.metadata['NIdaq-digital-input-channels'] = 2
try:
print(max_time)
self.acq = Acquisition(
dt=1. / self.metadata['NIdaq-acquisition-frequency'],
Nchannel_analog_in=self.
metadata['NIdaq-analog-input-channels'],
Nchannel_digital_in=self.
metadata['NIdaq-digital-input-channels'],
max_time=max_time,
output_steps=output_steps,
filename=self.filename.replace('metadata', 'NIdaq'))
except BaseException as e:
print(e)
print(' /!\ PB WITH NI-DAQ /!\ ')
self.acq = None
self.init = True
self.save_experiment() # saving all metadata after full initialization
if self.cbp.currentText() == 'None':
self.statusBar.showMessage('Acquisition ready !')
else:
self.statusBar.showMessage('Acquisition & Stimulation ready !')
def run(self):
self.stop_flag = False
self.run_event.set() # start the run flag for the facecamera
if ((self.acq is None) and (self.stim is None)) or not self.init:
self.statusBar.showMessage('Need to initialize the stimulation !')
elif self.stim is None and self.acq is not None:
self.acq.launch()
self.statusBar.showMessage('Acquisition running [...]')
else:
self.statusBar.showMessage(
'Stimulation & Acquisition running [...]')
# Ni-Daq
if self.acq is not None:
self.acq.launch()
# run visual stim
if self.metadata['VisualStim']:
self.stim.run(self)
# ========================
# ---- HERE IT RUNS [...]
# ========================
# stop and clean up things
if self.metadata['FaceCamera']:
self.run_event.clear() # this will close the camera process
# close visual stim
if self.metadata['VisualStim']:
self.stim.close() # close the visual stim
if self.acq is not None:
self.acq.close()
if self.metadata[
'CaImaging'] and not self.stop_flag: # outside the pure acquisition case
self.send_CaImaging_Stop_signal()
self.init = False
print(100 * '-', '\n', 50 * '=')
def stop(self):
self.run_event.clear() # this will close the camera process
self.stop_flag = True
if self.acq is not None:
self.acq.close()
if self.stim is not None:
self.stim.close()
self.init = False
if self.metadata['CaImaging']:
self.send_CaImaging_Stop_signal()
self.statusBar.showMessage('stimulation stopped !')
print(100 * '-', '\n', 50 * '=')
def send_CaImaging_Stop_signal(self):
self.statusBar.showMessage('sending stop signal for 2-Photon acq.')
acq = Acquisition(
dt=1e-3, # 1kHz
Nchannel_analog_in=1,
Nchannel_digital_in=0,
max_time=1.1,
buffer_time=0.1,
output_steps=[self.config['STEP_FOR_CA_IMAGING_TRIGGER']],
filename=None)
acq.launch()
time.sleep(1.1)
acq.close()
def quit(self):
self.quit_event.set()
if self.FaceCamera_process is not None:
self.closeFaceCamera_event.set()
if self.acq is not None:
self.acq.close()
if self.stim is not None:
self.stim.quit()
QtWidgets.QApplication.quit()
def save_experiment(self):
# SAVING THE METADATA FILES
self.metadata['filename'] = str(self.datafolder.get())
for key in self.protocol:
self.metadata[key] = self.protocol[key]
np.save(os.path.join(str(self.datafolder.get()), 'metadata.npy'),
self.metadata)
print('[ok] Metadata data saved as: %s ' %
os.path.join(str(self.datafolder.get()), 'metadata.npy'))
self.statusBar.showMessage(
'Metadata saved as: "%s" ' %
os.path.join(str(self.datafolder.get()), 'metadata.npy'))
def initialize(self):
### set up all metadata
self.metadata = {
'config': self.cbc.currentText(),
'protocol': self.cbp.currentText(),
'notes': self.qmNotes.toPlainText(),
'subject_ID': self.cbs.currentText(),
'subject_props': self.subjects[self.cbs.currentText()]
}
for d in [self.config, self.protocol]:
if d is not None:
for key in d:
self.metadata[key] = d[key]
# Setup configuration
for modality, button in zip([
'VisualStim', 'Locomotion', 'Electrophy', 'FaceCamera',
'CaImaging'
], [
self.VisualStimButton, self.LocomotionButton,
self.ElectrophyButton, self.FaceCameraButton,
self.CaImagingButton
]):
self.metadata[modality] = bool(button.isChecked())
if self.cbp.currentText() == 'None':
self.statusBar.showMessage('[...] initializing acquisition')
else:
self.statusBar.showMessage(
'[...] initializing acquisition & stimulation')
self.filename = generate_filename_path(
self.root_datafolder,
filename='metadata',
extension='.npy',
with_FaceCamera_frames_folder=self.metadata['FaceCamera'],
with_screen_frames_folder=self.metadata['VisualStim'])
self.datafolder.set(os.path.dirname(self.filename))
if self.metadata['protocol'] != 'None':
with open(
os.path.join(base_path, 'protocols',
self.metadata['protocol'] + '.json'),
'r') as fp:
self.protocol = json.load(fp)
else:
self.protocol = {}
# init visual stimulation
if self.metadata['VisualStim'] and len(self.protocol.keys()) > 0:
self.protocol['screen'] = self.metadata['Screen']
self.stim = build_stim(self.protocol)
np.save(
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'),
self.stim.experiment)
print('[ok] Visual-stimulation data saved as "%s"' %
os.path.join(str(self.datafolder.get()), 'visual-stim.npy'))
if 'time_stop' in self.stim.experiment:
max_time = int(
1.5 *
self.stim.experiment['time_stop'][-1]) # for security
else:
max_time = 1 * 60 * 60 # 1 hour, should be stopped manually
else:
max_time = 1 * 60 * 60 # 1 hour, should be stopped manually
self.stim = None
output_steps = []
if self.metadata['CaImaging']:
output_steps.append(self.config['STEP_FOR_CA_IMAGING_TRIGGER'])
# --------------- #
### NI daq init ### ## we override parameters based on the chosen modalities if needed
# --------------- #
if self.metadata['VisualStim'] and (
self.metadata['NIdaq-analog-input-channels'] < 1):
self.metadata['NIdaq-analog-input-channels'] = 1 # at least one
if self.metadata['Electrophy'] and (
self.metadata['NIdaq-analog-input-channels'] < 2):
self.metadata['NIdaq-analog-input-channels'] = 2
if self.metadata['Locomotion'] and (
self.metadata['NIdaq-digital-input-channels'] < 2):
self.metadata['NIdaq-digital-input-channels'] = 2
try:
print(max_time)
self.acq = Acquisition(
dt=1. / self.metadata['NIdaq-acquisition-frequency'],
Nchannel_analog_in=self.
metadata['NIdaq-analog-input-channels'],
Nchannel_digital_in=self.
metadata['NIdaq-digital-input-channels'],
max_time=max_time,
output_steps=output_steps,
filename=self.filename.replace('metadata', 'NIdaq'))
except BaseException as e:
print(e)
print(' /!\ PB WITH NI-DAQ /!\ ')
self.acq = None
self.init = True
self.save_experiment() # saving all metadata after full initialization
if self.cbp.currentText() == 'None':
self.statusBar.showMessage('Acquisition ready !')
else:
self.statusBar.showMessage('Acquisition & Stimulation ready !')