def parse_plot_channels(channels, input_file):
channels = channels if isinstance(channels, list) else [channels]
channels = [none_or_int(channel) for channel in channels]
# ToDo:
# * check is channel exists, even when there is no None
# * use annotation channel ids instead of array indices
if None in channels:
dim_t, channel_num = load_neo(input_file,
object='analogsignal',
lazy=True).shape
for i, channel in enumerate(channels):
if channel is None or channel >= channel_num:
channels[i] = random.randint(0, channel_num)
return channels
import neo
import numpy as np
import argparse
from utils.io import load_neo
if __name__ == '__main__':
CLI = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
CLI.add_argument("--data",
nargs='?',
type=str,
required=True,
help="path to input data in neo format")
CLI.add_argument("--output",
nargs='?',
type=str,
required=True,
help="path of output thresholds (numpy array)")
CLI.add_argument("--threshold", nargs='?', type=float, required=True)
args, unknown = CLI.parse_known_args()
asig = load_neo(args.data, 'analogsignal')
dim_t, channel_num = asig.shape
np.save(args.output, np.ones(channel_num) * args.threshold)
CLI = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
CLI.add_argument("--data",
nargs='?',
type=str,
required=True,
help="path to input data in neo format")
CLI.add_argument("--output",
nargs='?',
type=str,
required=True,
help="path of output file")
args = CLI.parse_args()
block = load_neo(args.data)
block = analogsignals_to_imagesequences(block)
imgseq = block.filter(name='optical_flow', objects="ImageSequence")
if imgseq:
imgseq = imgseq[0]
else:
raise ValueError("Input does not contain a signal with name " \
+ "'optical_flow'!")
crit_point_evt = detect_critical_points(
imgseq, block.segments[0].analogsignals[0].times)
block.segments[0].events.append(crit_point_evt)
type=str,
required=True,
help="path to input data in neo format")
CLI.add_argument("--properties",
nargs='?',
type=lambda v: v.split(','),
default=[''],
help="paths to input data in neo format")
CLI.add_argument("--output",
nargs='?',
type=str,
required=True,
help="path of output file")
args = CLI.parse_args()
waves_block = load_neo(args.waves)
asig_names = [asig.name for asig in waves_block.segments[0].analogsignals]
event_names = [event.name for event in waves_block.segments[0].events]
if not args.properties or not args.properties[0]:
args.properties = []
for property in args.properties:
block = load_neo(property)
for asig in block.segments[0].analogsignals:
if asig.name not in asig_names:
waves_block.segments[0].analogsignals.append(asig)
for event in block.segments[0].events:
return ax
if __name__ == '__main__':
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=str)
CLI.add_argument("--frame_folder",nargs='?', type=str)
CLI.add_argument("--frame_name", nargs='?', type=str)
CLI.add_argument("--frame_format",nargs='?', type=str)
CLI.add_argument("--frame_rate", nargs='?', type=none_or_float)
CLI.add_argument("--colormap", nargs='?', type=str)
CLI.add_argument("--event", nargs='?', type=none_or_str, default=None)
CLI.add_argument("--markercolor", nargs='?', type=str, default='k')
args = CLI.parse_args()
blk = load_neo(args.data)
blk = analogsignals_to_imagesequences(blk)
# get data
imgseq = blk.segments[0].imagesequences[0]
times = blk.segments[0].analogsignals[0].times # to be replaced
t_start = blk.segments[0].analogsignals[0].t_start # to be replaced
t_stop = blk.segments[0].analogsignals[0].t_stop # to be replaced
dim_t, dim_x, dim_y = imgseq.shape
optical_flow = get_opticalflow(blk.segments[0].imagesequences)
if args.event is not None:
up_coords = get_events(blk.segments[0].events,
frame_times=times,
event_name=args.event)
help="path of output figure")
CLI.add_argument("--t_start",
nargs='?',
type=float,
default=0,
help="start time in seconds")
CLI.add_argument("--t_stop",
nargs='?',
type=float,
default=10,
help="stop time in seconds")
CLI.add_argument("--channels",
nargs='+',
type=none_or_int,
default=0,
help="list of channels to plot")
args = CLI.parse_args()
asig = load_neo(args.data, 'analogsignal', lazy=True)
channels = parse_plot_channels(args.channels, args.data)
asig = time_slice(asig,
t_start=args.t_start,
t_stop=args.t_stop,
lazy=True,
channel_indexes=channels)
ax = plot_traces(asig, channels)
save_plot(args.output)
CLI.add_argument("--original_data", nargs='?', type=str, required=True,
help="path to input data in neo format")
CLI.add_argument("--processed_data", nargs='?', type=str, required=True,
help="path to input data in neo format")
CLI.add_argument("--img_dir", nargs='?', type=str, required=True,
help="path of output figure directory")
CLI.add_argument("--img_name", nargs='?', type=str,
default='processed_trace_channel0.png',
help='example filename for channel 0')
CLI.add_argument("--t_start", nargs='?', type=float, default=0,
help="start time in seconds")
CLI.add_argument("--t_stop", nargs='?', type=float, default=10,
help="stop time in seconds")
CLI.add_argument("--channels", nargs='+', type=int, default=0,
help="channel to plot")
args = CLI.parse_args()
orig_asig = load_neo(args.original_data, 'analogsignal', lazy=False)
orig_asig = time_slice(orig_asig, t_start=args.t_start, t_stop=args.t_stop,
lazy=False, channel_indexes=args.channels)
proc_asig = load_neo(args.processed_data, 'analogsignal', lazy=False)
proc_asig = time_slice(proc_asig, t_start=args.t_start, t_stop=args.t_stop,
lazy=False, channel_indexes=args.channels)
for channel in args.channels:
plot_traces(orig_asig, proc_asig, channel)
output_path = os.path.join(args.img_dir,
args.img_name.replace('_channel0', f'_channel{channel}'))
save_plot(output_path)
