def parse_args():
arg_parser = misc.default_parser(
description="""
Script to plot mean stimulus response over days.""",
epilog="""
The 'dates' option really only makes sense with a single Mouse.
""", arguments=('mice', 'tags', 'dates', 'overwrite', 'verbose'))
arg_parser.add_argument(
"-T", "--trace_type", choices=('dff', 'deconvolved', 'raw'), default="dff",
help="Trace type to plot.")
arg_parser.add_argument(
"-R", "--t_range_s", nargs=2, type=int, default=(-2, 8),
help="Time range around stimulus to plot.")
arg_parser.add_argument(
"-b", "--baseline", nargs=2, type=int, default=(-1, 0),
help='Baseline used for dFF trace.')
arg_parser.add_argument(
"-e", "--errortrials", choices=(-1, 0, 1, 2), type=int, default=-1,
help="-1 is off, 0 is correct trials, 1 is error trials, 2 is diff of error trials.")
# arg_parser.add_argument(
# "-H", "--hungry_sated", choices=(0, 1, 2), type=int, default=0,
# help="0 is hungry trials, 1 is sated trials, 2 is hungry-sated")
args = arg_parser.parse_args()
return args
def parse_args():
arg_parser = misc.default_parser(
description="""
Script to plot mean stimulus response over days.""",
# epilog="""
# This is the epilog.
# """,
arguments=('mice', 'tags', 'dates', 'overwrite', 'verbose'))
arg_parser.add_argument(
"-T", "--trace_type", choices=('dff', 'deconvolved', 'raw'), default="dff",
help="Trace type to plot.")
arg_parser.add_argument(
"-R", "--t_range_s", nargs=2, type=int, default=(-2, 8),
help="Time range around stimulus to plot.")
arg_parser.add_argument(
"-b", "--baseline", nargs=2, type=int, default=None,
help='Baseline used for dFF trace.')
arg_parser.add_argument(
"-e", "--errortrials", choices=(-1, 0, 1, 2), type=int, default=-1,
help="-1 is off, 0 is correct trials, 1 is error trials, 2 is diff of error trials.")
arg_parser.add_argument(
"-N", "--normalize", action="store_true",
help="If True, normalize each individual trace by z-scoring it.")
arg_parser.add_argument(
"-M", "--maxrois", action="store", type=int, default=10,
help="Pull out the 'maxrois' top ROIs per stim type.")
arg_parser.add_argument(
"-O", '--mode', choices=('traces', 'heatmap'), default='traces',
help="Determines how to plot the data: as traces or heatmaps.")
args = arg_parser.parse_args()
return args
def parse_args():
arg_parser = misc.default_parser(description="""
Script to plot mean response heatmap, sorted by preferred stimulus.""",
arguments=('mouse', 'date'))
arg_parser.add_argument("-T",
"--trace_type",
choices=('dff', 'deconvolved', 'raw'),
default="dff",
help="Trace type to plot.")
arg_parser.add_argument("-R",
"--t_range_s",
nargs=2,
type=int,
default=(-2, 8),
help="Time range around stimulus to plot.")
arg_parser.add_argument("-b",
"--baseline",
nargs=2,
type=int,
default=(-1, 0),
help='Baseline used for dFF trace.')
arg_parser.add_argument(
"-e",
"--errortrials",
choices=(-1, 0, 1, 2),
type=int,
default=-1,
help=
"-1 is off, 0 is correct trials, 1 is error trials, 2 is diff of error trials."
)
arg_parser.add_argument(
"-H",
"--hungry_sated",
choices=(0, 1, 2),
type=int,
default=0,
help="0 is hungry trials, 1 is sated trials, 2 is hungry-sated")
args = arg_parser.parse_args()
return args
def parse_args():
arg_parser = misc.default_parser(description="""
Script to plot mean stimulus response over days.""",
epilog="""
The 'dates' option really only makes sense with a single Mouse.
""",
arguments=('mice', 'tags', 'dates',
'overwrite', 'verbose'))
arg_parser.add_argument(
"-R",
"--t_range_s",
nargs=2,
type=int,
default=(-5, 10),
help=
"Time range around stimulus to plot. If second value <= first or <=0, include all time up to next stim presentation."
)
args = arg_parser.parse_args()
return args
def parse_args():
arg_parser = misc.default_parser(
description="""
Script to plot replays.""", arguments=('mice', 'dates', 'tags'))
arg_parser.add_argument(
"-T", "--trace_type", choices=('dff', 'deconvolved', 'raw'), default="deconvolved",
help="Trace type to plot.")
arg_parser.add_argument(
"-R", "--t_range_m", nargs=2, type=int, default=(-1, 1),
help="Time range to plot.")
arg_parser.add_argument(
"-D", "--display_training", action="store_true",
help="Also plot stimulus responses, otherwise just plots spontaneous time.")
arg_parser.add_argument(
"-M", "--mask_stimuli", action="store_true",
help="Mask out stimulus times from traces and classifier probability.")
arg_parser.add_argument(
"--new_path", action='store_true',
help='Use new save path format: SCRIPT/mouse/cword')
args = arg_parser.parse_args()
return args