def run_gui(recordState, protocolState, record_dir, recordLogger=logger, amp_name=None, amp_serial=None, eeg_only=False, queue=None): redirect_stdout_to_queue(recordLogger, queue, 'INFO') # configure LSL server name and device serial if available if not amp_name: amp_name, amp_serial = pu.search_lsl(recordState, recordLogger, ignore_markers=True) recordLogger.info('\nOutput directory: %s' % (record_dir)) # spawn the recorder as a child process recordLogger.info('\n>> Recording started.') #proc = mp.Process(target=record, args=[recordState, amp_name, amp_serial, record_dir, eeg_only, recordLogger, queue]) proc = mp.Process(target=record, args=[recordState, amp_name, amp_serial, record_dir, eeg_only]) proc.start() # Launching the protocol (shared variable) with protocolState.get_lock(): protocolState.value = 1 # Continue recording until the shared variable changes to 0. while recordState.value: time.sleep(1) recordLogger.info('(main) Waiting for recorder process to finish.') proc.join(10) if proc.is_alive(): recordLogger.error('Recorder process not finishing. Are you running from Spyder?') recordLogger.error('Dropping into a shell') qc.shell() sys.stdout.flush() recordLogger.info('Recording finished.')
def run(cfg, state=mp.Value('i', 1), queue=None): """ Training protocol for Alpha/Theta neurofeedback. """ redirect_stdout_to_queue(logger, queue, 'INFO') # add tdef object cfg.tdef = trigger_def(cfg.TRIGGER_FILE) # Extract features if not state.value: sys.exit(-1) raw = mne.io.read_raw_brainvision(cfg.DATA_PATH, preload=True) outfile = cfg.OUT_MICROSTATES_FILE ch_names = [ 'P3', 'C3', 'F3', 'Fz', 'F4', 'C4', 'P4', 'Cz', 'Pz', 'Fp1', 'Fp2', 'T3', 'T5', 'O1', 'O2', 'F7', 'F8', 'T6', 'T4' ] raw.pick_channels(ch_names) raw.set_montage('standard_1005') raw.set_eeg_reference('average') raw.filter(1, 30) maps, segmentation = microstates.segment(raw.get_data(), n_states=4, max_n_peaks=10000000, max_iter=5000, normalize=True) np.savetxt(outfile, maps, delimiter=" ")
def run(cfg, state=mp.Value('i', 1), queue=None): redirect_stdout_to_queue(logger, queue, 'INFO') # Wait the recording to start (GUI) while state.value == 2: # 0: stop, 1:start, 2:wait pass
def run(cfg, state=mp.Value('i', 1), queue=None, interactive=False, cv_file=None, feat_file=None, logger=logger): redirect_stdout_to_queue(logger, queue, 'INFO') # add tdef object cfg.tdef = trigger_def(cfg.TRIGGER_FILE) # Extract features if not state.value: sys.exit(-1) featdata = features.compute_features(cfg) # Find optimal threshold for TPR balancing #balance_tpr(cfg, featdata) # Perform cross validation if not state.value: sys.exit(-1) if cfg.CV_PERFORM[cfg.CV_PERFORM['selected']] is not None: cross_validate(cfg, featdata, cv_file=cv_file) # Train a decoder if not state.value: sys.exit(-1) if cfg.EXPORT_CLS is True: train_decoder(cfg, featdata, feat_file=feat_file) with state.get_lock(): state.value = 0
def record(recordState, amp_name, amp_serial, record_dir, eeg_only, recordLogger=logger, queue=None): redirect_stdout_to_queue(recordLogger, queue, 'INFO') # set data file name timestamp = time.strftime('%Y%m%d-%H%M%S', time.localtime()) pcl_file = "%s/%s-raw.pcl" % (record_dir, timestamp) eve_file = '%s/%s-eve.txt' % (record_dir, timestamp) recordLogger.info('>> Output file: %s' % (pcl_file)) # test writability try: qc.make_dirs(record_dir) open(pcl_file, 'w').write('The data will written when the recording is finished.') except: raise RuntimeError('Problem writing to %s. Check permission.' % pcl_file) # start a server for sending out data pcl_file when software trigger is used outlet = start_server('StreamRecorderInfo', channel_format='string',\ source_id=eve_file, stype='Markers') # connect to EEG stream server sr = StreamReceiver(buffer_size=0, amp_name=amp_name, amp_serial=amp_serial, eeg_only=eeg_only) # start recording recordLogger.info('\n>> Recording started (PID %d).' % os.getpid()) qc.print_c('\n>> Press Enter to stop recording', 'G') tm = qc.Timer(autoreset=True) next_sec = 1 while recordState.value == 1: sr.acquire() if sr.get_buflen() > next_sec: duration = str(datetime.timedelta(seconds=int(sr.get_buflen()))) recordLogger.info('RECORDING %s' % duration) next_sec += 1 tm.sleep_atleast(0.001) # record stop recordLogger.info('>> Stop requested. Copying buffer') buffers, times = sr.get_buffer() signals = buffers events = None # channels = total channels from amp, including trigger channel data = {'signals':signals, 'timestamps':times, 'events':events, 'sample_rate':sr.get_sample_rate(), 'channels':sr.get_num_channels(), 'ch_names':sr.get_channel_names(), 'lsl_time_offset':sr.lsl_time_offset} recordLogger.info('Saving raw data ...') qc.save_obj(pcl_file, data) recordLogger.info('Saved to %s\n' % pcl_file) # automatically convert to fif and use event file if it exists (software trigger) if os.path.exists(eve_file): recordLogger.info('Found matching event file, adding events.') else: eve_file = None recordLogger.info('Converting raw file into fif.') pcl2fif(pcl_file, external_event=eve_file)
def __init__(self, amp_name, amp_serial, state=mp.Value('i', 1), queue=None): super(Scope, self).__init__() self.ui = Ui_MainWindow() self.ui.setupUi(self) redirect_stdout_to_queue(logger, queue, 'INFO') logger.info('Viewer launched') self.amp_name = amp_name self.amp_serial = amp_serial self.state = state self.init_scope()
def run(cfg, queue=None, interactive=False, cv_file=None, feat_file=None): redirect_stdout_to_queue(queue) cfg.tdef = trigger_def(cfg.TRIGGER_FILE) # Extract features featdata = features.compute_features(cfg) # Find optimal threshold for TPR balancing #balance_tpr(cfg, featdata) # Perform cross validation if cfg.CV_PERFORM[cfg.CV_PERFORM['selected']] is not None: cross_validate(cfg, featdata, cv_file=cv_file) # Train a decoder if cfg.EXPORT_CLS is True: train_decoder(cfg, featdata, feat_file=feat_file)
def run(cfg, queue=None): qc.print_c('WITH_STIMO = %s' % cfg.WITH_STIMO, 'G') redirect_stdout_to_queue(queue) if cfg.FAKE_CLS is None: # chooose amp if cfg.AMP_NAME is None and cfg.AMP_SERIAL is None: amp_name, amp_serial = pu.search_lsl(ignore_markers=True) else: amp_name = cfg.AMP_NAME amp_serial = cfg.AMP_SERIAL fake_dirs = None else: amp_name = None amp_serial = None fake_dirs = [v for (k, v) in cfg.DIRECTIONS] # events and triggers tdef = trigger_def(cfg.TRIGGER_FILE) #if cfg.TRIGGER_DEVICE is None: # input('\n** Warning: No trigger device set. Press Ctrl+C to stop or Enter to continue.') trigger = pyLptControl.Trigger(cfg.TRIGGER_DEVICE) if trigger.init(50) == False: logger.error( 'Cannot connect to USB2LPT device. Use a mock trigger instead?') input('Press Ctrl+C to stop or Enter to continue.') trigger = pyLptControl.MockTrigger() trigger.init(50) # init classification decoder = BCIDecoderDaemon( cfg.DECODER_FILE, buffer_size=1.0, fake=(cfg.FAKE_CLS is not None), amp_name=amp_name, amp_serial=amp_serial, fake_dirs=fake_dirs, parallel=cfg.PARALLEL_DECODING[cfg.PARALLEL_DECODING['selected']], alpha_new=cfg.PROB_ALPHA_NEW) # OLD: requires trigger values to be always defined #labels = [tdef.by_value[x] for x in decoder.get_labels()] # NEW: events can be mapped into integers: labels = [] dirdata = set([d[1] for d in cfg.DIRECTIONS]) for x in decoder.get_labels(): if x not in dirdata: labels.append(tdef.by_value[x]) else: labels.append(x) # map class labels to bar directions bar_def = {label: str(dir) for dir, label in cfg.DIRECTIONS} bar_dirs = [bar_def[l] for l in labels] dir_seq = [] for x in range(cfg.TRIALS_EACH): dir_seq.extend(bar_dirs) if cfg.TRIALS_RANDOMIZE: random.shuffle(dir_seq) else: dir_seq = [d[0] for d in cfg.DIRECTIONS] * cfg.TRIALS_EACH num_trials = len(dir_seq) logger.info('Initializing decoder.') while decoder.is_running() is 0: time.sleep(0.01) # bar visual object if cfg.FEEDBACK_TYPE == 'BAR': from pycnbi.protocols.viz_bars import BarVisual visual = BarVisual(cfg.GLASS_USE, screen_pos=cfg.SCREEN_POS, screen_size=cfg.SCREEN_SIZE) elif cfg.FEEDBACK_TYPE == 'BODY': assert hasattr(cfg, 'FEEDBACK_IMAGE_PATH' ), 'FEEDBACK_IMAGE_PATH is undefined in your config.' from pycnbi.protocols.viz_human import BodyVisual visual = BodyVisual(cfg.FEEDBACK_IMAGE_PATH, use_glass=cfg.GLASS_USE, screen_pos=cfg.SCREEN_POS, screen_size=cfg.SCREEN_SIZE) visual.put_text('Waiting to start') if cfg.LOG_PROBS: logdir = qc.parse_path_list(cfg.DECODER_FILE)[0] probs_logfile = time.strftime(logdir + "probs-%Y%m%d-%H%M%S.txt", time.localtime()) else: probs_logfile = None feedback = Feedback(cfg, visual, tdef, trigger, probs_logfile) # start trial = 1 dir_detected = [] prob_history = {c: [] for c in bar_dirs} while trial <= num_trials: if cfg.SHOW_TRIALS: title_text = 'Trial %d / %d' % (trial, num_trials) else: title_text = 'Ready' true_label = dir_seq[trial - 1] # profiling feedback #import cProfile #pr = cProfile.Profile() #pr.enable() result = feedback.classify(decoder, true_label, title_text, bar_dirs, prob_history=prob_history) #pr.disable() #pr.print_stats(sort='time') if result is None: break else: pred_label = result dir_detected.append(pred_label) if cfg.WITH_REX is True and pred_label == true_label: # if cfg.WITH_REX is True: if pred_label == 'U': rex_dir = 'N' elif pred_label == 'L': rex_dir = 'W' elif pred_label == 'R': rex_dir = 'E' elif pred_label == 'D': rex_dir = 'S' else: logger.warning('Rex cannot execute undefined action %s' % pred_label) rex_dir = None if rex_dir is not None: visual.move(pred_label, 100, overlay=False, barcolor='B') visual.update() logger.info('Executing Rex action %s' % rex_dir) os.system('%s/Rex/RexControlSimple.exe %s %s' % (pycnbi.ROOT, cfg.REX_COMPORT, rex_dir)) time.sleep(8) if true_label == pred_label: msg = 'Correct' else: msg = 'Wrong' if cfg.TRIALS_RETRY is False or true_label == pred_label: logger.info('Trial %d: %s (%s -> %s)' % (trial, msg, true_label, pred_label)) trial += 1 if len(dir_detected) > 0: # write performance and log results fdir, _, _ = qc.parse_path_list(cfg.DECODER_FILE) logfile = time.strftime(fdir + "/online-%Y%m%d-%H%M%S.txt", time.localtime()) with open(logfile, 'w') as fout: fout.write('Ground-truth,Prediction\n') for gt, dt in zip(dir_seq, dir_detected): fout.write('%s,%s\n' % (gt, dt)) cfmat, acc = qc.confusion_matrix(dir_seq, dir_detected) fout.write('\nAccuracy %.3f\nConfusion matrix\n' % acc) fout.write(cfmat) logger.info('Log exported to %s' % logfile) print('\nAccuracy %.3f\nConfusion matrix\n' % acc) print(cfmat) visual.finish() if decoder: decoder.stop() ''' # automatic thresholding if prob_history and len(bar_dirs) == 2: total = sum(len(prob_history[c]) for c in prob_history) fout = open(probs_logfile, 'a') msg = 'Automatic threshold optimization.\n' max_acc = 0 max_bias = 0 for bias in np.arange(-0.99, 1.00, 0.01): corrects = 0 for p in prob_history[bar_dirs[0]]: p_biased = (p + bias) / (bias + 1) # new sum = (p+bias) + (1-p) = bias+1 if p_biased >= 0.5: corrects += 1 for p in prob_history[bar_dirs[1]]: p_biased = (p + bias) / (bias + 1) # new sum = (p+bias) + (1-p) = bias+1 if p_biased < 0.5: corrects += 1 acc = corrects / total msg += '%s%.2f: %.3f\n' % (bar_dirs[0], bias, acc) if acc > max_acc: max_acc = acc max_bias = bias msg += 'Max acc = %.3f at bias %.2f\n' % (max_acc, max_bias) fout.write(msg) fout.close() print(msg) ''' logger.info('Finished.')
def run(cfg, state=mp.Value('i', 1), queue=None): redirect_stdout_to_queue(logger, queue, 'INFO') # Wait the recording to start (GUI) while state.value == 2: # 0: stop, 1:start, 2:wait pass # Protocol start if equals to 1 if not state.value: sys.exit() refresh_delay = 1.0 / cfg.REFRESH_RATE cfg.tdef = trigger_def(cfg.TRIGGER_FILE) # visualizer keys = { 'left': 81, 'right': 83, 'up': 82, 'down': 84, 'pgup': 85, 'pgdn': 86, 'home': 80, 'end': 87, 'space': 32, 'esc': 27, ',': 44, '.': 46, 's': 115, 'c': 99, '[': 91, ']': 93, '1': 49, '!': 33, '2': 50, '@': 64, '3': 51, '#': 35 } color = dict(G=(20, 140, 0), B=(210, 0, 0), R=(0, 50, 200), Y=(0, 215, 235), K=(0, 0, 0), w=(200, 200, 200)) dir_sequence = [] for x in range(cfg.TRIALS_EACH): dir_sequence.extend(cfg.DIRECTIONS) random.shuffle(dir_sequence) num_trials = len(cfg.DIRECTIONS) * cfg.TRIALS_EACH event = 'start' trial = 1 # Hardware trigger if cfg.TRIGGER_DEVICE is None: logger.warning( 'No trigger device set. Press Ctrl+C to stop or Enter to continue.' ) #input() trigger = pyLptControl.Trigger(state, cfg.TRIGGER_DEVICE) if trigger.init(50) == False: logger.error( '\n** Error connecting to USB2LPT device. Use a mock trigger instead?' ) input('Press Ctrl+C to stop or Enter to continue.') trigger = pyLptControl.MockTrigger() trigger.init(50) # timers timer_trigger = qc.Timer() timer_dir = qc.Timer() timer_refresh = qc.Timer() t_dir = cfg.TIMINGS['DIR'] + random.uniform(-cfg.TIMINGS['DIR_RANDOMIZE'], cfg.TIMINGS['DIR_RANDOMIZE']) t_dir_ready = cfg.TIMINGS['READY'] + random.uniform( -cfg.TIMINGS['READY_RANDOMIZE'], cfg.TIMINGS['READY_RANDOMIZE']) bar = BarVisual(cfg.GLASS_USE, screen_pos=cfg.SCREEN_POS, screen_size=cfg.SCREEN_SIZE) bar.fill() bar.glass_draw_cue() # start while trial <= num_trials: timer_refresh.sleep_atleast(refresh_delay) timer_refresh.reset() # segment= { 'cue':(s,e), 'dir':(s,e), 'label':0-4 } (zero-based) if event == 'start' and timer_trigger.sec() > cfg.TIMINGS['INIT']: event = 'gap_s' bar.fill() timer_trigger.reset() trigger.signal(cfg.tdef.INIT) elif event == 'gap_s': if cfg.TRIAL_PAUSE: bar.put_text('Press any key') bar.update() key = cv2.waitKey() if key == keys['esc'] or not state.value: break bar.fill() bar.put_text('Trial %d / %d' % (trial, num_trials)) event = 'gap' timer_trigger.reset() elif event == 'gap' and timer_trigger.sec() > cfg.TIMINGS['GAP']: event = 'cue' bar.fill() bar.draw_cue() trigger.signal(cfg.tdef.CUE) timer_trigger.reset() elif event == 'cue' and timer_trigger.sec() > cfg.TIMINGS['CUE']: event = 'dir_r' dir = dir_sequence[trial - 1] if dir == 'L': # left bar.move('L', 100, overlay=True) trigger.signal(cfg.tdef.LEFT_READY) elif dir == 'R': # right bar.move('R', 100, overlay=True) trigger.signal(cfg.tdef.RIGHT_READY) elif dir == 'U': # up bar.move('U', 100, overlay=True) trigger.signal(cfg.tdef.UP_READY) elif dir == 'D': # down bar.move('D', 100, overlay=True) trigger.signal(cfg.tdef.DOWN_READY) elif dir == 'B': # both hands bar.move('L', 100, overlay=True) bar.move('R', 100, overlay=True) trigger.signal(cfg.tdef.BOTH_READY) else: raise RuntimeError('Unknown direction %d' % dir) timer_trigger.reset() elif event == 'dir_r' and timer_trigger.sec() > t_dir_ready: bar.fill() bar.draw_cue() event = 'dir' timer_trigger.reset() timer_dir.reset() if dir == 'L': # left trigger.signal(cfg.tdef.LEFT_GO) elif dir == 'R': # right trigger.signal(cfg.tdef.RIGHT_GO) elif dir == 'U': # up trigger.signal(cfg.tdef.UP_GO) elif dir == 'D': # down trigger.signal(cfg.tdef.DOWN_GO) elif dir == 'B': # both trigger.signal(cfg.tdef.BOTH_GO) else: raise RuntimeError('Unknown direction %d' % dir) elif event == 'dir' and timer_trigger.sec() > t_dir: event = 'gap_s' bar.fill() trial += 1 logger.info('trial ' + str(trial - 1) + ' done') trigger.signal(cfg.tdef.BLANK) timer_trigger.reset() t_dir = cfg.TIMINGS['DIR'] + random.uniform( -cfg.TIMINGS['DIR_RANDOMIZE'], cfg.TIMINGS['DIR_RANDOMIZE']) t_dir_ready = cfg.TIMINGS['READY'] + random.uniform( -cfg.TIMINGS['READY_RANDOMIZE'], cfg.TIMINGS['READY_RANDOMIZE']) # protocol if event == 'dir': dx = min(100, int(100.0 * timer_dir.sec() / t_dir) + 1) if dir == 'L': # L bar.move('L', dx, overlay=True) elif dir == 'R': # R bar.move('R', dx, overlay=True) elif dir == 'U': # U bar.move('U', dx, overlay=True) elif dir == 'D': # D bar.move('D', dx, overlay=True) elif dir == 'B': # Both bar.move('L', dx, overlay=True) bar.move('R', dx, overlay=True) # wait for start if event == 'start': bar.put_text('Waiting to start') bar.update() key = 0xFF & cv2.waitKey(1) if key == keys['esc'] or not state.value: break bar.finish() with state.get_lock(): state.value = 0