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()
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)
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 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 !')