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.device = gen_util.get_device(args.cuda)
args.fontdir = DEFAULT_FONTDIR if DEFAULT_FONTDIR.is_dir() else None
if args.dict_path != "":
plot_dicts.plot_from_dicts(Path(args.dict_path),
source="glm",
plt_bkend=args.plt_bkend,
fontdir=args.fontdir,
parallel=args.parallel,
datetime=not (args.no_datetime),
overwrite=args.overwrite)
else:
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
mouse_df = DEFAULT_MOUSE_DF_PATH
args = reformat_args(args)
# 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)
else:
all_sess_ns = gen_util.list_if_not(args.sess_n)
for sess_n in all_sess_ns:
analys_pars = prep_analyses(sess_n, args, mouse_df)
analyses_parallel = bool(args.parallel * (not args.debug))
run_analyses(*analys_pars,
analyses=args.analyses,
parallel=analyses_parallel)
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.device = "cpu"
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
args.mouse_df = DEFAULT_MOUSE_DF_PATH
args.runtype = "prod"
args.plane = "soma"
args.stimtype = "gabors"
args.omit_sess, args.omit_mice = sess_gen_util.all_omit(
args.stimtype, args.runtype
)
all_sessids = sess_gen_util.get_sess_vals(
args.mouse_df, "sessid", runtype=args.runtype, sess_n=[1, 2, 3],
plane=args.plane, min_rois=1, pass_fail="P", omit_sess=args.omit_sess,
omit_mice=args.omit_mice)
# bsizes =[1, 15, 30] #3
# outchs = [18, 9, 3]
# hiddims = [100, 35, 5]
# numlays = [3, 2, 1]
# lr_exs = [4, 3, 5]
# convs = [True, False]
# args.n_epochs = 0
gen_util.parallel_wrap(
run_sess_lstm, all_sessids, args_list=[args], parallel=args.parallel)
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 = "acr_sess"
if args.modif:
source = "modif"
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:
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
mouse_df = DEFAULT_MOUSE_DF_PATH
args = reformat_args(args)
analys_pars = prep_analyses(args.sess_n, args, mouse_df, args.parallel)
args.parallel = bool(args.parallel * (not args.debug))
run_analyses(*analys_pars,
analyses=args.analyses,
seed=args.seed,
parallel=args.parallel,
datatype=args.datatype)
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)
plot_from_dicts(args.direc,
source=args.source,
plt_bkend=args.plt_bkend,
fontdir=args.fontdir,
plot_tc=not (args.not_plot_tc),
parallel=args.parallel,
datetime=not (args.no_datetime),
pattern=args.pattern,
depth=args.depth)
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 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.device = gen_util.get_device(args.cuda)
args.fontdir = DEFAULT_FONTDIR if DEFAULT_FONTDIR.is_dir() else None
if args.comp == "all":
comps = logreg.get_comps(args.stimtype, args.q1v4, args.exp_v_unexp)
else:
check_args(args.comp, args.stimtype, args.q1v4, args.exp_v_unexp)
comps = gen_util.list_if_not(args.comp)
args.output = format_output(args.output, args.runtype, args.q1v4, args.bal,
args.exp_v_unexp)
args_orig = copy.deepcopy(args)
if args.dict_path is not None:
plot_dicts.plot_from_dicts(Path(args.dict_path),
source="logreg",
plt_bkend=args.plt_bkend,
fontdir=args.fontdir,
parallel=args.parallel)
else:
for comp in comps:
args = copy.deepcopy(args_orig)
args.comp = comp
args.not_ctrl = not (set_ctrl(not (args.not_ctrl), comp=args.comp))
logger.info(
f"Task: {args.task}\nStim: {args.stimtype} "
f"\nComparison: {args.comp}\n",
extra={"spacing": "\n"})
if args.task == "run_regr":
run_regr(args)
# collates regression runs and analyses accuracy
elif args.task == "analyse":
logger.info(f"Folder: {args.output}")
logreg.run_analysis(args.output, args.stimtype, args.comp,
not (args.not_ctrl), args.CI, args.alg,
args.parallel)
elif args.task == "plot":
logreg.run_plot(args.output, args.stimtype, args.comp,
not (args.not_ctrl), args.visflow_dir,
args.fluor, not (args.no_scale), args.CI,
args.alg, args.plt_bkend, args.fontdir,
args.modif)
else:
gen_util.accepted_values_error("args.task", args.task,
["run_regr", "analyse", "plot"])
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)
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
args.mouse_df_path = DEFAULT_MOUSE_DF_PATH
# Directory with additional fonts
args.fontdir = DEFAULT_FONTDIR if DEFAULT_FONTDIR.exists() else None
# warn if parallel is not used
if args.overwrite and not (args.plot_only):
if not args.parallel:
warnings.warn(
"Unless memory demands are too high for the machine being "
"used, it is strongly recommended that paper analyses be run "
"with the '--parallel' argument (enables computations to be "
"distributed across available CPU cores). Otherwise, analyses "
"may be very slow.",
category=UserWarning,
stacklevel=1)
time.sleep(paper_organization.WARNING_SLEEP)
# run through figure(s) and panel(s)
if args.figure == "all":
figures = paper_organization.get_all_figures()
else:
figures = [args.figure]
sessions = None
panel = args.panel
for args.figure in figures:
if panel == "all":
panels = paper_organization.get_all_panels(args.figure)
else:
panels = [panel]
for p, args.panel in enumerate(panels):
new_fig = (p == 0)
try:
with gen_util.TimeIt():
sessions = run_single_panel(args,
sessions=sessions,
new_fig=new_fig)
except Exception as err:
sep = DOUBLE_SEP if new_fig else SEP
if "Cannot plot figure panel" in str(err):
lead = f"{sep}Fig. {args.figure}{args.panel.upper()}"
logger.info(f"{lead}. {err}")
else:
raise err
plot_util.cond_close_figs()