def reformat_args(args):
"""
reformat_args(args)
Returns reformatted args for analyses, specifically
- Sets stimulus parameters to "none" if they are irrelevant to the
stimtype
- Changes stimulus parameters from "both" to actual values
- Sets seed, though doesn't seed
- Modifies analyses (if "all" or "all_" in parameter)
Adds the following args:
- dend (str) : type of dendrites to use ("allen", "extr")
- omit_sess (str): sess to omit
- omit_mice (str): mice to omit
Required args:
- args (Argument parser): parser with the following attributes:
runtype (str) : runtype ("pilot" or "prod")
stimtype (str) : stimulus to analyse (visflow or gabors)
Returns:
- args (Argument parser): input parser, with the following attributes
added:
visflow_dir, visflow_size, gabfr, gabk,
gab_oriomit_sess, omit_mice, dend,
analyses, seed
"""
args = copy.deepcopy(args)
[args.visflow_dir, args.visflow_size, args.gabfr, args.gabk,
args.gab_ori] = sess_gen_util.get_params(args.stimtype, "both", 128,
"any", 16, "any")
if args.plane == "soma":
args.dend = "allen"
args.omit_sess, args.omit_mice = sess_gen_util.all_omit(
args.stimtype, args.runtype, args.visflow_dir, args.visflow_size,
args.gabk)
# choose a seed if none is provided (i.e., args.seed=-1), but seed later
args.seed = rand_util.seed_all(args.seed,
"cpu",
log_seed=False,
seed_now=False)
# collect analysis letters
all_analyses = "".join(get_analysis_fcts().keys())
if "all" in args.analyses:
if "_" in args.analyses:
excl = args.analyses.split("_")[1]
args.analyses, _ = gen_util.remove_lett(all_analyses, excl)
else:
args.analyses = all_analyses
elif "_" in args.analyses:
raise ValueError("Use '_' in args.analyses only with 'all'.")
return args
def reformat_args(args):
"""
reformat_args(args)
Returns reformatted args for analyses, specifically
- Sets stimulus parameters to "none" if they are irrelevant to the
stimtype
- Changes stimulus parameters from "both" to actual values
- Sets seed, though doesn't seed
- Modifies analyses (if "all" or "all_" in parameter)
Adds the following args:
- omit_sess (str): sess to omit
- omit_mice (str): mice to omit
Required args:
- args (Argument parser): parser with the following attributes:
visflow_dir (str) : visual flow direction values to include
(e.g., "right", "left" or "both")
visflow_size (int or str): visual flow size values to include
(e.g., 128, 256, "both")
gabfr (int) : gabor frame value to start sequences at
(e.g., 0, 1, 2, 3)
gabk (int or str) : gabor kappa values to include
(e.g., 4, 16 or "both")
gab_ori (int or str) : gabor orientation values to include
(e.g., 0, 45, 90, 135, 180, 225 or "all")
runtype (str) : runtype ("pilot" or "prod")
stimtype (str) : stimulus to analyse (visflow or gabors)
Returns:
- args (Argument parser): input parser, with the following attributes
modified:
visflow_dir, visflow_size, gabfr, gabk,
gab_ori, grps, analyses, seed
and the following attributes added:
omit_sess, omit_mice
"""
args = copy.deepcopy(args)
[args.visflow_dir, args.visflow_size, args.gabfr, args.gabk,
args.gab_ori] = sess_gen_util.get_params(args.stimtype, args.visflow_dir,
args.visflow_size, args.gabfr,
args.gabk, args.gab_ori)
args.omit_sess, args.omit_mice = sess_gen_util.all_omit(
args.stimtype, args.runtype, args.visflow_dir, args.visflow_size,
args.gabk)
# choose a seed if none is provided (i.e., args.seed=-1), but seed later
args.seed = rand_util.seed_all(args.seed,
"cpu",
log_seed=False,
seed_now=False)
# collect analysis letters
all_analyses = "".join(get_analysis_fcts().keys())
if "all" in args.analyses:
if "_" in args.analyses:
excl = args.analyses.split("_")[1]
args.analyses, _ = gen_util.remove_lett(all_analyses, excl)
else:
args.analyses = all_analyses
elif "_" in args.analyses:
raise ValueError("Use '_' in args.analyses only with 'all'.")
return args
def main(args):
"""
main(args)
Runs analyses with parser arguments.
Required args:
- args (dict): parser argument dictionary
"""
# set logger to the specified level
logger_util.set_level(level=args.log_level)
args.fontdir = DEFAULT_FONTDIR if DEFAULT_FONTDIR.is_dir() else None
if args.dict_path is not None:
source = "modif" if args.modif else "run"
plot_dicts.plot_from_dicts(Path(args.dict_path),
source=source,
plt_bkend=args.plt_bkend,
fontdir=args.fontdir,
parallel=args.parallel,
datetime=not (args.no_datetime),
overwrite=args.overwrite)
else:
args = reformat_args(args)
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
mouse_df = DEFAULT_MOUSE_DF_PATH
# get numbers of sessions to analyse
if args.sess_n == "all":
all_sess_ns = sess_gen_util.get_sess_vals(mouse_df,
"sess_n",
runtype=args.runtype,
plane=args.plane,
line=args.line,
min_rois=args.min_rois,
pass_fail=args.pass_fail,
incl=args.incl,
omit_sess=args.omit_sess,
omit_mice=args.omit_mice,
sort=True)
else:
all_sess_ns = gen_util.list_if_not(args.sess_n)
# get analysis parameters for each session number
all_analys_pars = gen_util.parallel_wrap(prep_analyses,
all_sess_ns,
args_list=[args, mouse_df],
parallel=args.parallel)
# split parallel from sequential analyses
bool(args.parallel * (not args.debug))
if args.parallel:
run_seq = "" # should be run parallel within analysis
all_analyses = gen_util.remove_lett(args.analyses, run_seq)
sess_parallels = [True, False]
analyses_parallels = [False, True]
else:
all_analyses = [args.analyses]
sess_parallels, analyses_parallels = [False], [False]
for analyses, sess_parallel, analyses_parallel in zip(
all_analyses, sess_parallels, analyses_parallels):
if len(analyses) == 0:
continue
args_dict = {
"analyses": analyses,
"seed": args.seed,
"parallel": analyses_parallel,
}
# run analyses for each parameter set
gen_util.parallel_wrap(run_analyses,
all_analys_pars,
args_dict=args_dict,
parallel=sess_parallel,
mult_loop=True)
def reformat_args(args):
"""
reformat_args(args)
Returns reformatted args for analyses, specifically
- Sets stimulus parameters to "none" if they are irrelevant to the
stimtype
- Changes stimulus parameters from "both" to actual values
- Modifies the session number parameter
- Sets seed, though doesn't seed
- Modifies analyses (if "all" or "all_" in parameter)
- Sets latency parameters based on lat_method
Adds the following args:
- dend (str) : type of dendrites to use ("allen" or "extr")
- omit_sess (str): sess to omit
- omit_mice (str): mice to omit
Required args:
- args (Argument parser): parser with the following attributes:
visflow_dir (str) : visual flow direction values to include
(e.g., "right", "left" or "both")
visflow_size (int or str): visual flow size values to include
(e.g., 128, 256, "both")
gabfr (int) : gabor frame value to start sequences at
(e.g., 0, 1, 2, 3)
gabk (int or str) : gabor kappa values to include
(e.g., 4, 16 or "both")
gab_ori (int or str) : gabor orientation values to include
(e.g., 0, 45, 90, 135, 180, 225 or "all")
mouse_ns (str) : mouse numbers or range
(e.g., 1, "1,3", "1-3", "all")
runtype (str) : runtype ("pilot" or "prod")
sess_n (str) : session number range (e.g., "1-1", "all")
stimtype (str) : stimulus to analyse (visflow or gabors)
Returns:
- args (Argument parser): input parser, with the following attributes
modified:
visflow_dir, visflow_size, gabfr, gabk,
gab_ori, sess_n, mouse_ns, analyses, seed,
lat_p_val_thr, lat_rel_std
and the following attributes added:
omit_sess, omit_mice, dend
"""
args = copy.deepcopy(args)
if args.plane == "soma":
args.dend = "allen"
[args.visflow_dir, args.visflow_size, args.gabfr, args.gabk,
args.gab_ori] = sess_gen_util.get_params(args.stimtype, args.visflow_dir,
args.visflow_size, args.gabfr,
args.gabk, args.gab_ori)
if args.datatype == "run":
args.fluor = "n/a"
if args.plane == "soma":
args.dend = "allen"
args.omit_sess, args.omit_mice = sess_gen_util.all_omit(
args.stimtype, args.runtype, args.visflow_dir, args.visflow_size,
args.gabk)
if "-" in str(args.sess_n):
vals = str(args.sess_n).split("-")
if len(vals) != 2:
raise ValueError(
"If args.sess_n is a range, must have format 1-3.")
st = int(vals[0])
end = int(vals[1]) + 1
args.sess_n = list(range(st, end))
if args.lat_method == "ratio":
args.lat_p_val_thr = None
elif args.lat_method == "ttest":
args.lat_rel_std = None
# choose a seed if none is provided (i.e., args.seed=-1), but seed later
args.seed = rand_util.seed_all(args.seed,
"cpu",
log_seed=False,
seed_now=False)
# collect mouse numbers from args.mouse_ns
if "," in args.mouse_ns:
args.mouse_ns = [int(n) for n in args.mouse_ns.split(",")]
elif "-" in args.mouse_ns:
vals = str(args.mouse_ns).split("-")
if len(vals) != 2:
raise ValueError(
"If args.mouse_ns is a range, must have format 1-3.")
st = int(vals[0])
end = int(vals[1]) + 1
args.mouse_ns = list(range(st, end))
elif args.mouse_ns not in ["all", "any"]:
args.mouse_ns = int(args.mouse_ns)
# collect analysis letters
all_analyses = "".join(get_analysis_fcts().keys())
if "all" in args.analyses:
if "_" in args.analyses:
excl = args.analyses.split("_")[1]
args.analyses, _ = gen_util.remove_lett(all_analyses, excl)
else:
args.analyses = all_analyses
elif "_" in args.analyses:
raise ValueError("Use '_' in args.analyses only with 'all'.")
return args