def test2():
seg = neo.Spike2IO(filename='Rat9_11_08_21_10-00-00.SMR').read_segment()
#~ seg = neo.Spike2IO(filename = 'R28-C4-B.SMR').read_segment()
#~ seg = neo.MicromedIO(filename = 'EEG_1503.TRC').read_segment()
app = QApplication([])
w1 = SegmentViewer(segment=seg, xsize=15)
w1.show()
app.exec_()
def read_laser_file(filepath, neo_version_check):
filename = os.path.basename(filepath)
file_extension = filename.split('.') [-1]
## Depending on the file extension, the laser information is stored differently
if file_extension == 'smrx':
if not neo_version_check:
enforce_neo_version_satisfaction()
neo_version_check = True
neo_obj = neo.CedIO(filepath)
analogsignals = read_neo_file_return_analogsignals(filename, neo_obj)
# keep the signal as a 16 bit float
laser_series = np.float16(analogsignals[1]) # the laser information is stored as the second analog signal
else:
neo_obj = neo.Spike2IO(filepath)
analogsignals = read_neo_file_return_analogsignals(filename, neo_obj)
# keep the signal as a 16 bit float
laser_series = np.float16(analogsignals[1][:,1]) # the laser information is stored as the second column in the
# the second analog signal
return laser_series
CLI = argparse.ArgumentParser()
CLI.add_argument("--output", nargs='?', type=str)
CLI.add_argument("--data", nargs='?', type=str)
CLI.add_argument("--electrode_location", type=str, nargs='+')
CLI.add_argument("--electrode_color", type=str, nargs='+')
CLI.add_argument("--annotation_name", type=str)
CLI.add_argument("--coordiantes", type=str, nargs='+')
CLI.add_argument("--grid_size", type=int, nargs='+')
args = CLI.parse_args()
electrode_location = str2dict(args.electrode_location)
electrode_color = str2dict(args.electrode_color)
electrode_coords = str2dict(args.coordiantes)
io = neo.Spike2IO(args.data)
segment = io.read_segment()
segment = enrich(segment,
grid_size=args.grid_size,
electrode_location=electrode_location,
electrode_color=electrode_color,
electrode_coordinates=electrode_coords,
annotation_name=args.annotation_name,
file_origin=args.data)
data_dir = os.path.dirname(args.output)
if not os.path.exists(data_dir):
os.makedirs(data_dir)
def __init__(self, file):
reader = neo.Spike2IO(filename=file).read()[0] # 1 block, 1 segment
segment = reader.segments[0]
self.signals = segment.analogsignals
self.event_times = segment.events[0].times