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    
Example #3
0
    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