def stimuli(canvas):
cue = reiz.Cue(
canvas=canvas,
audiostim=reiz.audio.library.beep,
visualstim=reiz.visual.library.go,
)
N = reiz.Cue(canvas=canvas, audiostim=None, visualstim=None)
return cue, N
def test_sanitization(rmarker, capsys):
assert rmarker
out, err = capsys.readouterr()
reiz.marker.push("ä ö ü")
out, err = capsys.readouterr()
assert "Sending ae_oe_ue " in out
out, err = capsys.readouterr()
reiz.marker.push("ping")
out, err = capsys.readouterr()
assert 'Sending {"msg": "ping"}' in out
out, err = capsys.readouterr()
reiz.marker.push("poison-pill")
out, err = capsys.readouterr()
assert 'Sending {"msg": "poison-pill"}' in out
c = reiz.Canvas((10, 10))
reiz.audio.library.beep.volume = 0
cue = reiz.Cue(
canvas=c,
audiostim=reiz.audio.library.beep,
visualstim=reiz.visual.library.go,
markerstr="test",
)
out, err = capsys.readouterr()
cue.show()
out, err = capsys.readouterr()
assert "Sending test at" in out
def countdown(canvas, sek):
for i in range(0, sek):
cue = reiz.Cue(canvas,
visualstim=[
bg,
Mural(text=str(sek - i),
color=(0.18, 0.18, 0.18))
])
cue.show(duration=1)
def start(trials=5):
canvas = reiz.Canvas()
canvas.open()
bg = Background(color='red')
def countdown(canvas, sek):
for i in range(0, sek):
cue = reiz.Cue(canvas,
visualstim=[
bg,
Mural(text=str(sek - i),
color=(0.18, 0.18, 0.18))
])
cue.show(duration=1)
pre = reiz.Cue(canvas, visualstim=[bg, reiz.visual.library.pre])
post = reiz.Cue(canvas, visualstim=[bg, reiz.visual.library.post])
f5 = reiz.Cue(canvas,
visualstim=[bg, reiz.visual.Mural('Press F5 to start')])
open_eyes = Message('Open eyes')
close_eyes = Message('Close eyes')
augen_auf = reiz.Cue(canvas,
audiostim=reiz.audio.library.beep,
visualstim=[bg, reiz.visual.library.fixation],
markerstr='augen_auf')
augen_zu = reiz.Cue(canvas,
audiostim=reiz.audio.library.beep,
visualstim=[bg, reiz.visual.library.fixation],
markerstr='augen_zu')
while not canvas.start_run:
f5.show(duration=1)
pre.show(duration=3)
for trl_num in range(trials):
augen_auf.show(duration=30)
augen_zu.show(duration=30)
post.show(duration=3)
canvas.close()
def bmi_main():
import numpy as np
import matplotlib.pyplot as plt
import time, reiz, liesl
from reiz.visual import Mural, Background
canvas = reiz.Canvas()
canvas.open()
def countdown(canvas, sek):
for i in range(0, sek):
cue = reiz.Cue(canvas,
visualstim=[
bg,
Mural(text=str(sek - i),
color=(0.18, 0.18, 0.18))
])
cue.show(duration=1)
def part2(cuetype, image_lib):
if "Nothing" in cuetype:
DispImage = image_lib.Nothing
elif "Imagine" in cuetype:
DispImage = image_lib.Imagine
elif "Open" in cuetype:
DispImage = image_lib.Open
elif "Close" in cuetype:
DispImage = image_lib.Close
return DispImage
bg = Background(color='gray')
states = ("Nothing", "Imagine", "Open", "Close")
image_lib = reiz.visual.read_folder(
r'C:\Users\Messung\Desktop\study-phase-triggered-TMS\phase_triggered_tms\pre_post'
)
nBlocks = 3
tiles = np.tile(states, (4))
block_tiles = np.tile(states, (nBlocks, 4))
for i in range(nBlocks):
block_tiles[i, :] = np.random.permutation(tiles)
canvas.start_run = False
start_protocol = reiz.Cue(canvas,
visualstim=[
bg,
Mural(text='Press F5 to start BMI',
color=(0.18, 0.18, 0.18))
])
while not canvas.start_run:
start_protocol.show(duration=0.1)
countdown(canvas, 3)
reiz.Cue(canvas,
visualstim=[
bg,
reiz.visual.Mural("BMI Task:",
position=[0, 0.5],
fontsize=1.5,
color=(0.18, 0.18, 0.18)),
reiz.visual.Mural("Bitte folgen Sie den Anweisungen",
position=[0, -0.25],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(duration=5)
reiz.Cue(canvas,
visualstim=[
bg,
reiz.visual.Mural("Bilder werden angezeigt.",
position=[0, 0.4],
fontsize=1,
color=(0.18, 0.18, 0.18)),
reiz.visual.Mural("Bitte 3 Sekunden lang durchführen",
position=[0, -0.4],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(5)
reiz.Cue(canvas,
visualstim=[
bg, image_lib.Open,
reiz.visual.Mural("Öffnen Ihre rechte Hand",
position=[0, 0.7],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(5)
reiz.Cue(canvas,
visualstim=[
bg, image_lib.Close,
reiz.visual.Mural("Schließe Ihre rechte Hand",
position=[0, 0.7],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(5)
reiz.Cue(canvas,
visualstim=[
bg, image_lib.Imagine,
reiz.visual.Mural(
"Stellen sich vor Ihre rechte Hand zu öffnen",
position=[0, 0.7],
fontsize=0.7,
color=(0.18, 0.18, 0.18))
]).show(5)
reiz.Cue(canvas,
visualstim=[
bg, image_lib.Nothing,
reiz.visual.Mural("Mach nichts",
position=[0, 0.7],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(10)
reiz.marker.push('bmi_start')
for k in range(nBlocks):
canvas.start_run = False
start_protocol = reiz.Cue(canvas,
visualstim=[
bg,
Mural(text="Press F5 to start block " +
str(k + 1),
color=(0.18, 0.18, 0.18))
])
while not canvas.start_run:
start_protocol.show(duration=0.1)
countdown(canvas, 3)
for cue in range(np.size(block_tiles, 1)):
reiz.marker.push("prepare_" + str(k) + '_' + str(cue))
reiz.Cue(canvas,
visualstim=[
bg,
reiz.visual.Mural("Bereitmachen",
position=[0, 0.4],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(3)
reiz.marker.push(
str(block_tiles[k, cue]) + '_' + str(k) + '_' + str(cue))
reiz.Cue(canvas,
visualstim=[bg, part2(block_tiles[k, cue],
image_lib)]).show(3)
reiz.marker.push("relax_" + str(k) + '_' + str(cue))
reiz.Cue(canvas,
visualstim=[
bg,
reiz.visual.Mural("Entspannen",
position=[0, -0.4],
fontsize=1,
color=(0.18, 0.18, 0.18))
]).show(5)
reiz.marker.push('bmi_end')
canvas.close()
def countdown(canvas, sek):
for i in range(0, sek):
cue = reiz.Cue(canvas, visualstim=Mural(text=str(sek - i)))
cue.show(duration=1)
def start_intervention(cfg, condition, stim_number, verbose: bool = False):
RMT = get_RMT(max_percent_RMT=120)
run_length = int(cfg['main']['run_length'])
condition_idx = condition['index']
"""Save the condition"""
condition_order_directory = cfg['main']['recordings_path'] + "\\" + cfg[
'general']['subject_token'] + '\\condition_%s\\config\\' % condition_idx
condition_order_file_path = condition_order_directory + 'config.json'
try:
with open(condition_order_file_path) as json_file:
stimuli = json.load(json_file)
print('Loaded condition file')
break_idx, timeleft = create_break_idx_timeleft(
stimuli, condition, run_length)
stimuli = stimuli[stim_number:]
except:
stimuli = create_stim_list(condition, cfg)
print('create new condition file')
break_idx, timeleft = create_break_idx_timeleft(
stimuli, condition, run_length)
os.makedirs(condition_order_directory)
with open(condition_order_file_path, 'w') as file:
file.write(json.dumps(stimuli)) #überschreibt immer
print('Created new condition file')
"""Check if all streams are available"""
# streamargs = [{'name':"localite_marker"}, # comments: make a real list
# {'name':"reiz-marker"},
# {'name':"eego"},
# {'name':"LuckyLoop"},
# {'name':"pupil_capture"},
# {'name':"GDX-RB_0K2002A1"}]
streamargs = [{'name': "eego"}]
session = Session(prefix=cfg['general']['subject_token'],
streamargs=streamargs)
"""Define stimulation intensity"""
stimulation_intensity = round(condition['percent_RMT'] * RMT / 100)
print(f"Stimulation intensity {stimulation_intensity}")
""""Calculate the time duration for the intervention"""
# TMS_stimulus = {'stim_type': 'TMS', 'frequency':condition['frequency'], 'phase':condition['phase_in_deg']}
# N = stimuli.count(TMS_stimulus)
# expected_duration = (N * 10) / 60
# print(f'Expected duration is around {expected_duration:.2f} min')
#%%
"""Intit Lucky Client"""
print("Init lucky")
#lucky = LuckyClient('134.2.117.144')
"""Init Coil"""
print("Init coil")
coil = Coil(0)
time.sleep(.8)
coil.amplitude = stimulation_intensity
time.sleep(.8)
"""Init Sandy"""
print("Init sandy")
# sandy_cli = sandy.Arduino(timeout=1.5, version = 'v0.3.1 - StalwartSandy')
# sandy_cli.reset()
# sandy_cli.set_threshold(150)
# sandy_cli.blink(5)
#sandy_cli.set_threshold(0)
print("Sandy in standby")
time.sleep(1)
"""Create the GUI"""
canvas = Canvas()
canvas.open()
labcue = reiz.Cue(canvas, visualstim=reiz.visual.library.logo)
labcue.show(duration=2)
#%%
with session("TMS_intervention"):
print("Started recording")
canvas.window.start_run = False
start_protocol = reiz.Cue(
canvas, visualstim=Mural(text='Start protocol with F5'))
print("Waiting for user to start in GUI")
while not canvas.window.start_run:
start_protocol.show(duration=1)
countdown(canvas, 5)
labcue.show()
t0 = time.time()
break_counter = 0
reaction_times = []
""" set up phase and frequency parameter """
phase = condition['phase_in_deg']
frequency = condition['frequency']
lucky.phase = phase
lucky.frequency = frequency
for single_stimulus in stimuli:
"""get some parameter informations"""
stimulus_idx = single_stimulus['stimulus_idx']
stim_type = single_stimulus['stim_type']
print(f"Stimulation index {single_stimulus['stimulus_idx']}")
time.sleep(0.5)
time_setup_trial = time.time()
# sends current setup as marker
push(json.dumps({
'stimulus_idx': str(stimulus_idx),
'stim_type': stim_type,
'freq': str(frequency),
'phase': str(phase)
}),
sanitize=False)
if verbose:
print("Start " + stim_type + " for frequency " +
str(frequency) + ' and phase ' + str(phase))
# conditional of stimtype, setup TMS and Arduino this trial
if stim_type == 'TMS':
coil.amplitude = stimulation_intensity
time.sleep(.8)
t1 = time.time()
trial_time = t1 - t0
if verbose:
print("\n Trial time: " + str(trial_time))
# TG: wait and trigger phase and frequency dependent, if next stimuli is TMS, then wait 10s, else wait 5s
if stimulus_idx < (stimuli[-1]['stimulus_idx']) and stimuli[
stimulus_idx - stim_number + 1]['stim_type'] == 'TMS':
sleep_time = random_time(min=9.5 - trial_time,
max=10.5 - trial_time)
else:
sleep_time = random_time(min=4.5 - trial_time,
max=5.5 - trial_time)
if stim_type == 'PVT':
coil.amplitude = 0
time.sleep(.8)
# wait and trigger phase and frequency dependent
t1 = time.time()
trial_time = t1 - t0
if verbose:
print("\n Trial time: " + str(trial_time))
sleep_time = random_time(min=4.5 - trial_time,
max=5.5 - trial_time)
try:
sandy_cli.await_blink()
if verbose:
print('Sandy is waiting for blink')
except:
raise ConnectionError('Sandy in unclear state')
print(f"\n Setup: {(time.time()-time_setup_trial):.2f}s")
if sleep_time < 0.75:
sleep_time = 0.75
if True or verbose:
print(f"\n Sleep_time = {sleep_time:.2f}s")
print(f"\n ISI = {sleep_time+trial_time:.2f}s\n")
labcue.show(duration=sleep_time)
t0 = time.time()
# conditional on stimtype, wait for keypress
if stim_type == 'PVT':
event_list = []
sandy_cli.receive()
blink_wait_start = time.time()
while not (event_list) or len(event_list) == 0:
if time.time() - blink_wait_start > 30:
raise ConnectionError(
f"Sandy could not be triggered for 30 seconds. Stimulus idx: {stimulus_idx}"
)
break
print(f"Wait for blink trigger. Stim: {stimulus_idx}")
lucky.trigger()
event_list = sandy_cli.receive()
print(f"Event list: {event_list}")
for event in event_list:
if event['state-change'] == 'blink-started':
time_trigger = int(event['timestamp'])
time_wait_for_press = time.time()
print("Waiting for button pressed")
atleast_one_button_pressed = False
time_reaction = False
while time.time() - time_wait_for_press < 1.25:
response = sandy_cli.receive()
if response:
event_list.extend(response)
if event_list:
for event in event_list:
if event:
print(event)
button_1_pressed = event[
'state-change'] == 'button-1-pressed'
button_2_pressed = event[
'state-change'] == 'button-2-pressed'
both_buttons_pressed = event[
'state-change'] == 'both-buttons-pressed'
atleast_one_button_pressed = button_1_pressed or button_2_pressed or both_buttons_pressed
if atleast_one_button_pressed:
time_reaction = int(event['timestamp'])
break
if atleast_one_button_pressed:
break
if verbose:
print(f"Trigger timestamp= {time_trigger}")
if time_trigger is not None: # led was turned on
if verbose:
print("Reaction timestamp= " + str(time_reaction))
if not (
time_reaction
) or time_reaction - time_trigger < 0 or time_reaction - time_trigger > 1000:
reaction_time = "No reaction"
rt = reiz.Cue(canvas,
visualstim=Mural(text=reaction_time))
else:
reaction_time = time_reaction - time_trigger
reaction_times.append(reaction_time)
rt = reiz.Cue(
canvas,
visualstim=Mural(
text='{0:3.1f} ms'.format(reaction_time)))
if verbose:
print('Reaction time: ' + str(reaction_time))
push(json.dumps({'reaction_time': str(reaction_time)}),
sanitize=False)
rt.show(duration=1)
else:
# when TMS stimulus
lucky.trigger()
try:
if stimuli[stimulus_idx - stim_number]['stim_type'] == "PVT":
coil.amplitude = 0
time.sleep(.8)
except IndexError:
print("Index error")
if stimulus_idx in break_idx: #make a break after cfg.run_length stimuli if experiment is not over
break_counter += 1
if break_counter == 1:
mean_run_reaction_time = np.mean(
reaction_times[:break_idx.index(stimulus_idx)])
else:
mean_run_reaction_time = np.mean(reaction_times[(
break_idx[break_idx.index(stimulus_idx) - 1] -
stim_number +
1):break_idx[break_idx.index(stimulus_idx)]])
mean_overall_reaction_time = np.mean(reaction_times)
#displays run reaction time
v_run_reaction_time = reiz.Cue(
canvas,
visualstim=Mural(
text='Run reaction time = ' +
'{0:3.1f} ms'.format(mean_run_reaction_time)))
v_run_reaction_time.show(duration=2)
#displays overall reaction time
v_overall_reaction_time = reiz.Cue(
canvas,
visualstim=Mural(
text='Overall reaction time = ' +
'{0:3.1f} ms'.format(mean_overall_reaction_time)))
v_overall_reaction_time.show(duration=2)
#calculates and shows the expected duration of the intervention that is left
expected_duration_left = timeleft[break_idx.index(
stimulus_idx)]
print(
f'Expected duration is around {expected_duration_left} min'
)
v_expected_duration_left = reiz.Cue(
canvas,
visualstim=Mural(
text='Expected duration left = ' +
'{0:3.1f} min'.format(expected_duration_left)))
v_expected_duration_left.show(duration=4)
canvas.window.start_run = False
nextrun = reiz.Cue(canvas,
visualstim=Mural(text='Continue with F5'))
while not canvas.window.start_run:
nextrun.show(duration=1)
countdown(canvas, 5)
labcue.show()
v_intervention_finished = reiz.Cue(
canvas,
visualstim=Mural(
text='Intervention is finished. Please stop the recording'))
v_intervention_finished.show(duration=1)
# start the MarkerServer which distributes markerstrings over LSL
reiz.marker.start()
# create a window
canvas = reiz.Canvas()
# initialize a clock for timing control
clock = reiz.Clock()
# initialize Cues
# each Cue reveices information about
# the Window where it will be shown -> canvas
# auditory and visual stimuli, e.g. a tone (Hertz) or text (Mural)
# and a markerstring to be send via LSL when .show() is called
hello = reiz.Cue(canvas,
audiostim=reiz.audio.Hertz(frequency=400,
duration_in_ms=1000),
visualstim=reiz.visual.Mural('Hello World!'),
markerstr='hello')
# there is also a library of typical auditory and visual stimuli and
# we can for example, take the visual "los" and the auditory "beep" stimuli
# for convenience, we use the text of the go stimulus as marker message
los = reiz.Cue(canvas,
audiostim=reiz.audio.library.beep,
visualstim=reiz.visual.library.go,
markerstr=reiz.visual.library.go.text)
# here we show a fixation cross but don't want to play an auditory stimulus.
# we can therefore either set it to None or just leave it out (defaults to None)
fix = reiz.Cue(canvas,
visualstim=reiz.visual.library.fixation,