def run_full_traces(sessions,
analysis,
analyspar,
sesspar,
figpar,
datatype="roi"):
"""
run_full_traces(sessions, analysis, analyspar, sesspar, figpar)
Plots full traces across an entire session. If ROI traces are plotted,
each ROI is scaled and plotted separately and an average is plotted.
Saves results and parameters relevant to analysis in a dictionary.
Required args:
- sessions (list) : list of Session objects
- analysis (str) : analysis type (e.g., "f")
- analyspar (AnalysPar): named tuple containing analysis parameters
- sesspar (SessPar) : named tuple containing session parameters
- figpar (dict) : dictionary containing figure parameters
Optional args:
- datatype (str): type of data (e.g., "roi", "run")
"""
dendstr_pr = sess_str_util.dend_par_str(analyspar.dend, sesspar.plane,
datatype, "print")
sessstr_pr = (f"session: {sesspar.sess_n}, "
f"plane: {sesspar.plane}{dendstr_pr}")
datastr = sess_str_util.datatype_par_str(datatype)
logger.info(
f"Plotting {datastr} traces across an entire "
f"session\n({sessstr_pr}).",
extra={"spacing": "\n"})
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
all_tr, roi_tr, all_edges, all_pars = [], [], [], []
for sess in sessions:
# get the block edges and parameters
edge_fr, par_descrs = [], []
for stim in sess.stims:
stim_str = stim.stimtype
if stim.stimtype == "visflow":
stim_str = "vis. flow"
if datatype == "roi":
fr_type = "twop"
elif datatype == "run":
fr_type = "stim"
else:
gen_util.accepted_values_error("datatype", datatype,
["roi", "run"])
for b in stim.block_params.index:
row = stim.block_params.loc[b]
edge_fr.append([
int(row[f"start_frame_{fr_type}"]),
int(row[f"stop_frame_{fr_type}"])
])
par_vals = [row[param] for param in stim.stim_params]
pars_str = "\n".join([str(par) for par in par_vals][0:2])
par_descrs.append(
sess_str_util.pars_to_descr(
f"{stim_str.capitalize()}\n{pars_str}"))
if datatype == "roi":
if sess.only_tracked_rois != analyspar.tracked:
raise RuntimeError(
"sess.only_tracked_rois should match analyspar.tracked.")
nanpol = None
if not analyspar.rem_bad:
nanpol = "omit"
all_rois = gen_util.reshape_df_data(sess.get_roi_traces(
None, analyspar.fluor, analyspar.rem_bad,
analyspar.scale)["roi_traces"],
squeeze_cols=True)
full_tr = math_util.get_stats(all_rois,
analyspar.stats,
analyspar.error,
axes=0,
nanpol=nanpol).tolist()
roi_tr.append(all_rois.tolist())
elif datatype == "run":
full_tr = sess.get_run_velocity(
rem_bad=analyspar.rem_bad,
scale=analyspar.scale).to_numpy().squeeze().tolist()
roi_tr = None
all_tr.append(full_tr)
all_edges.append(edge_fr)
all_pars.append(par_descrs)
extrapar = {
"analysis": analysis,
"datatype": datatype,
}
trace_info = {
"all_tr": all_tr,
"all_edges": all_edges,
"all_pars": all_pars
}
sess_info = sess_gen_util.get_sess_info(sessions,
analyspar.fluor,
incl_roi=(datatype == "roi"),
rem_bad=analyspar.rem_bad)
info = {
"analyspar": analyspar._asdict(),
"sesspar": sesspar._asdict(),
"extrapar": extrapar,
"sess_info": sess_info,
"trace_info": trace_info
}
fulldir, savename = gen_plots.plot_full_traces(roi_tr=roi_tr,
figpar=figpar,
**info)
file_util.saveinfo(info, savename, fulldir, "json")
def run_trace_corr_acr_sess(sessions,
analysis,
analyspar,
sesspar,
stimpar,
figpar,
datatype="roi"):
"""
run_trace_corr_acr_sess(sessions, analysis, analyspar, sesspar,
stimpar, quantpar, figpar)
Retrieves trace statistics by session x unexp val and calculates
correlations across sessions per unexp val.
Currently only logs results to the console. Does NOT save results and
parameters relevant to analysis in a dictionary.
Required args:
- sessions (list) : list of Session objects
- analysis (str) : analysis type (e.g., "r")
- analyspar (AnalysPar): named tuple containing analysis parameters
- sesspar (SessPar) : named tuple containing session parameters
- stimpar (StimPar) : named tuple containing stimulus parameters
- figpar (dict) : dictionary containing figure parameters
Optional args:
- datatype (str): type of data (e.g., "roi", "run")
"""
sessstr_pr = sess_str_util.sess_par_str(sesspar.sess_n, stimpar.stimtype,
sesspar.plane, stimpar.visflow_dir,
stimpar.visflow_size, stimpar.gabk,
"print")
# dendstr_pr = sess_str_util.dend_par_str(
# analyspar.dend, sesspar.plane, datatype, "print")
datastr = sess_str_util.datatype_par_str(datatype)
if sesspar.plane in ["any", "all"] and sesspar.runtype == "pilot":
logger.warning("Planes may not match between sessions for a mouse!")
logger.info(
"Analysing and plotting correlations between unexpected vs "
f"expected {datastr} traces between sessions ({sessstr_pr}).",
extra={"spacing": "\n"})
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
prev_level = logger.level
if prev_level > logging.INFO:
logger.setLevel(logging.INFO)
logger.warning("Temporarily lowered log level for correlation "
"analysis results.")
unexps = ["exp", "unexp"]
# correlate average traces between sessions for each mouse and each
# unexpected value
all_counts = []
all_me_tr = []
all_corrs = []
logger.info("Intramouse correlations", extra={"spacing": "\n"})
for sess_grp in sessions:
logger.info(f"Mouse {sess_grp[0].mouse_n}, sess {sess_grp[0].sess_n} "
f"vs {sess_grp[1].sess_n} corr:")
trace_info = quant_analys.trace_stats_by_qu_sess(sess_grp,
analyspar,
stimpar,
1, [0],
byroi=False,
by_exp=True,
datatype=datatype)
# remove quant dim
grp_stats = np.asarray(trace_info[1]).squeeze(2)
all_counts.append([[qu_c[0] for qu_c in c] for c in trace_info[2]])
# get mean/median per grp (sess x unexp_val x frame)
grp_me = grp_stats[:, :, 0]
grp_corrs = []
# collect correlations
corrs = [
st.pearsonr(grp_me[0, s], grp_me[1, s]) for s in range(len(unexps))
]
corr_max = np.argmax([corr[0] for corr in corrs])
for s, (unexp, corr) in enumerate(zip(unexps, corrs)):
sig_str = "*" if corr[1] < 0.05 else ""
high_str = " +" if corr_max == s else ""
logger.info(
f"{unexp}: {corr[0]:.4f} "
f"(p={corr[1]:.2f}{sig_str}){high_str}",
extra={"spacing": TAB})
corr = corr[0]
grp_corrs.append(corr)
all_corrs.append(grp_corrs)
all_me_tr.append(grp_me)
# mice x sess x unexp x frame
all_me_tr = np.asarray(all_me_tr)
logger.info("Intermouse correlations", extra={"spacing": "\n"})
all_mouse_corrs = []
for n, m1_sess_mes in enumerate(all_me_tr):
if n + 1 < len(all_me_tr):
mouse_corrs = []
for n_add, m2_sess_mes in enumerate(all_me_tr[n + 1:]):
sess_corrs = []
logger.info(f"Mouse {sessions[n][0].mouse_n} vs "
f"{sessions[n + 1 + n_add][0].mouse_n} corr:")
for se, m1_s1_me in enumerate(m1_sess_mes):
unexp_corrs = []
logger.info(f"sess {sessions[n][se].sess_n}:",
extra={"spacing": TAB})
# collect correlations
corrs = [
st.pearsonr(m1_s1_me[s], m2_sess_mes[se][s])
for s in range(len(unexps))
]
corr_max = np.argmax([corr[0] for corr in corrs])
for s, (unexp, corr) in enumerate(zip(unexps, corrs)):
sig_str = "*" if corr[1] < 0.05 else ""
high_str = " +" if corr_max == s else ""
logger.info(
f"{unexp}: {corr[0]:.4f} "
f"(p={corr[1]:.2f}{sig_str}){high_str}",
extra={"spacing": f"{TAB}{TAB}"})
corr = corr[0]
unexp_corrs.append(corr)
sess_corrs.append(unexp_corrs)
mouse_corrs.append(sess_corrs)
all_mouse_corrs.append(mouse_corrs)
# reset logger level
logger.setLevel(prev_level)
def run_traces_by_qu_unexp_sess(sessions,
analysis,
analyspar,
sesspar,
stimpar,
quantpar,
figpar,
datatype="roi"):
"""
run_traces_by_qu_unexp_sess(sessions, analysis, analyspar, sesspar,
stimpar, quantpar, figpar)
Retrieves trace statistics by session x unexp val x quantile and
plots traces across ROIs by quantile/unexpected with each session in a
separate subplot.
Also runs analysis for one quantile (full data).
Saves results and parameters relevant to analysis in a dictionary.
Required args:
- sessions (list) : list of Session objects
- analysis (str) : analysis type (e.g., "t")
- analyspar (AnalysPar): named tuple containing analysis parameters
- sesspar (SessPar) : named tuple containing session parameters
- stimpar (StimPar) : named tuple containing stimulus parameters
- quantpar (QuantPar) : named tuple containing quantile analysis
parameters
- figpar (dict) : dictionary containing figure parameters
Optional args:
- datatype (str): type of data (e.g., "roi", "run")
"""
sessstr_pr = sess_str_util.sess_par_str(sesspar.sess_n, stimpar.stimtype,
sesspar.plane, stimpar.visflow_dir,
stimpar.visflow_size, stimpar.gabk,
"print")
dendstr_pr = sess_str_util.dend_par_str(analyspar.dend, sesspar.plane,
datatype, "print")
datastr = sess_str_util.datatype_par_str(datatype)
logger.info(
f"Analysing and plotting unexpected vs expected {datastr} "
f"traces by quantile ({quantpar.n_quants}) \n({sessstr_pr}"
f"{dendstr_pr}).",
extra={"spacing": "\n"})
# modify quantpar to retain all quantiles
quantpar_one = sess_ntuple_util.init_quantpar(1, 0)
n_quants = quantpar.n_quants
quantpar_mult = sess_ntuple_util.init_quantpar(n_quants, "all")
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
for quantpar in [quantpar_one, quantpar_mult]:
logger.info(f"{quantpar.n_quants} quant", extra={"spacing": "\n"})
# get the stats (all) separating by session, unexpected and quantiles
trace_info = quant_analys.trace_stats_by_qu_sess(sessions,
analyspar,
stimpar,
quantpar.n_quants,
quantpar.qu_idx,
byroi=False,
by_exp=True,
datatype=datatype)
extrapar = {
"analysis": analysis,
"datatype": datatype,
}
xrans = [xran.tolist() for xran in trace_info[0]]
all_stats = [sessst.tolist() for sessst in trace_info[1]]
trace_stats = {
"xrans": xrans,
"all_stats": all_stats,
"all_counts": trace_info[2]
}
sess_info = sess_gen_util.get_sess_info(sessions,
analyspar.fluor,
incl_roi=(datatype == "roi"),
rem_bad=analyspar.rem_bad)
info = {
"analyspar": analyspar._asdict(),
"sesspar": sesspar._asdict(),
"stimpar": stimpar._asdict(),
"quantpar": quantpar._asdict(),
"extrapar": extrapar,
"sess_info": sess_info,
"trace_stats": trace_stats
}
fulldir, savename = gen_plots.plot_traces_by_qu_unexp_sess(
figpar=figpar, **info)
file_util.saveinfo(info, savename, fulldir, "json")
def run_traces_by_qu_lock_sess(sessions,
analysis,
seed,
analyspar,
sesspar,
stimpar,
quantpar,
figpar,
datatype="roi"):
"""
run_traces_by_qu_lock_sess(sessions, analysis, analyspar, sesspar,
stimpar, quantpar, figpar)
Retrieves trace statistics by session x quantile at the transition of
expected to unexpected sequences (or v.v.) and plots traces across ROIs by
quantile with each session in a separate subplot.
Also runs analysis for one quantile (full data) with different unexpected
lengths grouped separated
Saves results and parameters relevant to analysis in a dictionary.
Required args:
- sessions (list) : list of Session objects
- analysis (str) : analysis type (e.g., "l")
- seed (int) : seed value to use. (-1 treated as None)
- analyspar (AnalysPar): named tuple containing analysis parameters
- sesspar (SessPar) : named tuple containing session parameters
- stimpar (StimPar) : named tuple containing stimulus parameters
- quantpar (QuantPar) : named tuple containing quantile analysis
parameters
- figpar (dict) : dictionary containing figure parameters
Optional args:
- datatype (str): type of data (e.g., "roi", "run")
"""
sessstr_pr = sess_str_util.sess_par_str(sesspar.sess_n, stimpar.stimtype,
sesspar.plane, stimpar.visflow_dir,
stimpar.visflow_size, stimpar.gabk,
"print")
dendstr_pr = sess_str_util.dend_par_str(analyspar.dend, sesspar.plane,
datatype, "print")
datastr = sess_str_util.datatype_par_str(datatype)
logger.info(
f"Analysing and plotting unexpected vs expected {datastr} "
f"traces locked to unexpected onset by quantile ({quantpar.n_quants}) "
f"\n({sessstr_pr}{dendstr_pr}).",
extra={"spacing": "\n"})
seed = rand_util.seed_all(seed, "cpu", log_seed=False)
# modify quantpar to retain all quantiles
quantpar_one = sess_ntuple_util.init_quantpar(1, 0)
n_quants = quantpar.n_quants
quantpar_mult = sess_ntuple_util.init_quantpar(n_quants, "all")
if stimpar.stimtype == "visflow":
pre_post = [2.0, 6.0]
elif stimpar.stimtype == "gabors":
pre_post = [2.0, 8.0]
else:
gen_util.accepted_values_error("stimpar.stimtype", stimpar.stimtype,
["visflow", "gabors"])
logger.warning("Setting pre to {}s and post to {}s.".format(*pre_post))
stimpar = sess_ntuple_util.get_modif_ntuple(stimpar, ["pre", "post"],
pre_post)
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
for baseline in [None, stimpar.pre]:
basestr_pr = sess_str_util.base_par_str(baseline, "print")
for quantpar in [quantpar_one, quantpar_mult]:
locks = ["unexp", "exp"]
if quantpar.n_quants == 1:
locks.append("unexp_split")
# get the stats (all) separating by session and quantiles
for lock in locks:
logger.info(
f"{quantpar.n_quants} quant, {lock} lock{basestr_pr}",
extra={"spacing": "\n"})
if lock == "unexp_split":
trace_info = quant_analys.trace_stats_by_exp_len_sess(
sessions,
analyspar,
stimpar,
quantpar.n_quants,
quantpar.qu_idx,
byroi=False,
nan_empty=True,
baseline=baseline,
datatype=datatype)
else:
trace_info = quant_analys.trace_stats_by_qu_sess(
sessions,
analyspar,
stimpar,
quantpar.n_quants,
quantpar.qu_idx,
byroi=False,
lock=lock,
nan_empty=True,
baseline=baseline,
datatype=datatype)
# for comparison, locking to middle of expected sample (1 quant)
exp_samp = quant_analys.trace_stats_by_qu_sess(
sessions,
analyspar,
stimpar,
quantpar_one.n_quants,
quantpar_one.qu_idx,
byroi=False,
lock="exp_samp",
nan_empty=True,
baseline=baseline,
datatype=datatype)
extrapar = {
"analysis": analysis,
"datatype": datatype,
"seed": seed,
}
xrans = [xran.tolist() for xran in trace_info[0]]
all_stats = [sessst.tolist() for sessst in trace_info[1]]
exp_stats = [expst.tolist() for expst in exp_samp[1]]
trace_stats = {
"xrans": xrans,
"all_stats": all_stats,
"all_counts": trace_info[2],
"lock": lock,
"baseline": baseline,
"exp_stats": exp_stats,
"exp_counts": exp_samp[2]
}
if lock == "unexp_split":
trace_stats["unexp_lens"] = trace_info[3]
sess_info = sess_gen_util.get_sess_info(
sessions,
analyspar.fluor,
incl_roi=(datatype == "roi"),
rem_bad=analyspar.rem_bad)
info = {
"analyspar": analyspar._asdict(),
"sesspar": sesspar._asdict(),
"stimpar": stimpar._asdict(),
"quantpar": quantpar._asdict(),
"extrapar": extrapar,
"sess_info": sess_info,
"trace_stats": trace_stats
}
fulldir, savename = gen_plots.plot_traces_by_qu_lock_sess(
figpar=figpar, **info)
file_util.saveinfo(info, savename, fulldir, "json")
def plot_glm_expl_var(analyspar, sesspar, stimpar, extrapar, glmpar,
sess_info, all_expl_var, figpar=None, savedir=None):
"""
plot_glm_expl_var(analyspar, sesspar, stimpar, extrapar,
sess_info, all_expl_var)
From dictionaries, plots explained variance for different variables for
each ROI.
Required args:
- analyspar (dict) : dictionary with keys of AnalysPar namedtuple
- sesspar (dict) : dictionary with keys of SessPar namedtuple
- stimpar (dict) : dictionary with keys of StimPar namedtuple
- glmpar (dict) : dictionary with keys of GLMPar namedtuple
- extrapar (dict) : dictionary containing additional analysis
parameters
["analysis"] (str): analysis type (e.g., "v")
- sess_info (dict) : dictionary containing information from each
session
["mouse_ns"] (list) : mouse numbers
["sess_ns"] (list) : session numbers
["lines"] (list) : mouse lines
["planes"] (list) : imaging planes
["nrois"] (list) : number of ROIs in session
- all_expl_var (list) : list of dictionaries with explained variance
for each session set, with each glm
coefficient as a key:
["full"] (list) : list of full explained variance stats for
every ROI, structured as ROI x stats
["coef_all"] (dict): max explained variance for each ROI with each
coefficient as a key, structured as ROI x stats
["coef_uni"] (dict): unique explained variance for each ROI with
each coefficient as a key,
structured as ROI x stats
["rois"] (list) : ROI numbers (-1 for GLMs fit to
mean/median ROI activity)
Optional args:
- figpar (dict): dictionary containing the following figure parameter
dictionaries
default: None
["init"] (dict): dictionary with figure initialization parameters
["save"] (dict): dictionary with figure saving parameters
["dirs"] (dict): dictionary with additional figure parameters
- savedir (str): path of directory in which to save plots.
default: None
Returns:
- fulldir (str) : final path of the directory in which the figure is
saved (may differ from input savedir, if datetime
subfolder is added.)
- savename (str): name under which the figure is saved
"""
stimstr_pr = sess_str_util.stim_par_str(
stimpar["stimtype"], stimpar["visflow_dir"], stimpar["visflow_size"],
stimpar["gabk"], "print")
dendstr_pr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], "roi", "print")
sessstr = sess_str_util.sess_par_str(
sesspar["sess_n"], stimpar["stimtype"], sesspar["plane"],
stimpar["visflow_dir"], stimpar["visflow_size"], stimpar["gabk"])
dendstr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], "roi")
# extract some info from sess_info
keys = ["mouse_ns", "sess_ns", "lines", "planes"]
[mouse_ns, sess_ns, lines, planes] = [sess_info[key] for key in keys]
n_sess = len(mouse_ns)
nroi_strs = sess_str_util.get_nroi_strs(sess_info, style="par")
plot_bools = [ev["rois"] not in [[-1], "all"] for ev in all_expl_var]
n_sess = sum(plot_bools)
if stimpar["stimtype"] == "gabors":
xyzc_dims = ["unexpected", "gabor_frame", "run_data", "pup_diam_data"]
log_dims = xyzc_dims + ["gabor_mean_orientation"]
elif stimpar["stimtype"] == "visflow":
xyzc_dims = [
"unexpected", "main_flow_direction", "run_data", "pup_diam_data"
]
log_dims = xyzc_dims
# start plotting
logger.info("Plotting GLM full and unique explained variance for "
f"{', '.join(xyzc_dims)}.", extra={"spacing": "\n"})
if n_sess > 0:
if figpar is None:
figpar = sess_plot_util.init_figpar()
figpar = copy.deepcopy(figpar)
cmap = plot_util.linclab_colormap(nbins=100, no_white=True)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
figpar["init"]["ncols"] = n_sess
figpar["init"]["sharex"] = False
figpar["init"]["sharey"] = False
figpar["init"]["gs"] = {"wspace": 0.2, "hspace": 0.35}
figpar["save"]["fig_ext"] = "png"
fig, ax = plot_util.init_fig(2 * n_sess, **figpar["init"], proj="3d")
fig.suptitle("Explained variance per ROI", y=1)
# get colormap range
c_range = [np.inf, -np.inf]
c_key = xyzc_dims[3]
for expl_var in all_expl_var:
for var_type in ["coef_all", "coef_uni"]:
rs = np.where(np.asarray(expl_var["rois"]) != -1)[0]
if c_key in expl_var[var_type].keys():
c_data = np.asarray(expl_var[var_type][c_key])[rs, 0]
# adjust colormap range
c_range[0] = np.min([c_range[0], min(c_data)])
c_range[1] = np.max([c_range[1], max(c_data)])
if not np.isfinite(sum(c_range)):
c_range = [-0.5, 0.5] # dummy range
else:
c_range = plot_util.rounded_lims(c_range, out=True)
else:
logger.info("No plots, as only results across ROIs are included")
fig = None
i = 0
for expl_var in all_expl_var:
# collect info for plotting and logging results across ROIs
rs = np.where(np.asarray(expl_var["rois"]) != -1)[0]
all_rs = np.where(np.asarray(expl_var["rois"]) == -1)[0]
if len(all_rs) != 1:
raise RuntimeError("Expected only one result for all ROIs.")
else:
all_rs = all_rs[0]
full_ev = expl_var["full"][all_rs]
title = (f"Mouse {mouse_ns[i]} - {stimstr_pr}\n(sess {sess_ns[i]}, "
f"{lines[i]} {planes[i]}{dendstr_pr},{nroi_strs[i]})")
logger.info(title, extra={"spacing": "\n"})
math_util.log_stats(full_ev, stat_str="\nFull explained variance")
dim_length = max([len(dim) for dim in log_dims])
for v, var_type in enumerate(["coef_all", "coef_uni"]):
if var_type == "coef_all":
sub_title = "Explained variance per coefficient"
elif var_type == "coef_uni":
sub_title = "Unique explained variance\nper coefficient"
logger.info(sub_title, extra={"spacing": "\n"})
dims_all = []
for key in log_dims:
if key in xyzc_dims:
# get mean/med
if key not in expl_var[var_type].keys():
dims_all.append("dummy")
continue
dims_all.append(np.asarray(expl_var[var_type][key])[rs, 0])
math_util.log_stats(
expl_var[var_type][key][all_rs],
stat_str=key.ljust(dim_length), log_spacing=TAB
)
if not plot_bools[-1]:
continue
if v == 0:
y = 1.12
subpl_title = f"{title}\n{sub_title}"
else:
y = 1.02
subpl_title = sub_title
# retrieve values and names for each dimension, including dummy
# dimensions
use_xyzc_dims = []
n_vals = None
dummies = []
pads = [16, 16, 20]
for d, dim in enumerate(dims_all):
dim_name = xyzc_dims[d].replace("_", " ")
if " direction" in dim_name:
dim_name = dim_name.replace(" direction", "\ndirection")
pads[d] = 24
if isinstance(dim, str) and dim == "dummy":
dummies.append(d)
use_xyzc_dims.append(f"{dim_name} (dummy)")
else:
n_vals = len(dim)
use_xyzc_dims.append(dim_name)
for d in dummies:
dims_all[d] = np.zeros(n_vals)
[x_data, y_data, z_data, c_data] = dims_all
sub_ax = ax[v, i]
im = sub_ax.scatter(
x_data, y_data, z_data, c=c_data, cmap=cmap,
vmin=c_range[0], vmax=c_range[1]
)
sub_ax.set_title(subpl_title, y=y)
# sub_ax.set_zlim3d(0, 1.0)
# adjust padding for z axis
sub_ax.tick_params(axis='z', which='major', pad=10)
# add labels
sub_ax.set_xlabel(use_xyzc_dims[0], labelpad=pads[0])
sub_ax.set_ylabel(use_xyzc_dims[1], labelpad=pads[1])
sub_ax.set_zlabel(use_xyzc_dims[2], labelpad=pads[2])
if v == 0:
full_ev_lab = math_util.log_stats(
full_ev, stat_str="Full EV", ret_str_only=True
)
sub_ax.plot([], [], c="k", label=full_ev_lab)
sub_ax.legend()
i += 1
if fig is not None:
plot_util.add_colorbar(
fig, im, n_sess, label=use_xyzc_dims[3],
space_fact=np.max([2, n_sess])
)
# plot 0 planes, and lines
for sub_ax in ax.reshape(-1):
sub_ax.autoscale(False)
all_lims = [sub_ax.get_xlim(), sub_ax.get_ylim(), sub_ax.get_zlim()]
xs, ys, zs = [
[vs[0] - (vs[1] - vs[0]) * 0.02, vs[1] + (vs[1] - vs[0]) * 0.02]
for vs in all_lims
]
for plane in ["x", "y", "z"]:
if plane == "x":
xx, yy = np.meshgrid(xs, ys)
zz = xx * 0
x_flat = xs
y_flat, z_flat = [0, 0], [0, 0]
elif plane == "y":
yy, zz = np.meshgrid(ys, zs)
xx = yy * 0
y_flat = ys
z_flat, x_flat = [0, 0], [0, 0]
elif plane == "z":
zz, xx = np.meshgrid(zs, xs)
yy = zz * 0
z_flat = zs
x_flat, y_flat = [0, 0], [0, 0]
sub_ax.plot_surface(xx, yy, zz, alpha=0.05, color="k")
sub_ax.plot(
x_flat, y_flat, z_flat, alpha=0.4, color="k", ls=(0, (2, 2))
)
if savedir is None:
savedir = Path(
figpar["dirs"]["roi"],
figpar["dirs"]["glm"])
savename = (f"roi_glm_ev_{sessstr}{dendstr}")
fulldir = plot_util.savefig(fig, savename, savedir, **figpar["save"])
return fulldir, savename
def plot_mag_change(analyspar, sesspar, stimpar, extrapar, permpar, quantpar,
sess_info, mags, figpar=None, savedir=None):
"""
plot_mag_change(analyspar, sesspar, stimpar, extrapar, permpar, quantpar,
sess_info, mags)
From dictionaries, plots magnitude of change in unexpected and expected
responses across quantiles.
Returns figure name and save directory path.
Required args:
- analyspar (dict): dictionary with keys of AnalysPar namedtuple
- sesspar (dict) : dictionary with keys of SessPar namedtuple
- stimpar (dict) : dictionary with keys of StimPar namedtuple
- extrapar (dict) : dictionary containing additional analysis
parameters
["analysis"] (str): analysis type (e.g., "m")
["datatype"] (str): datatype (e.g., "run", "roi")
["seed"] (int): seed value used
- permpar (dict) : dictionary with keys of PermPar namedtuple
- quantpar (dict) : dictionary with keys of QuantPar namedtuple
- roigrppar (dict): dictionary with keys of RoiGrpPar namedtuple
- sess_info (dict): dictionary containing information from each
session
["mouse_ns"] (list) : mouse numbers
["sess_ns"] (list) : session numbers
["lines"] (list) : mouse lines
["planes"] (list) : imaging planes
["nrois"] (list) : number of ROIs in session
- mags (dict) : dictionary containing magnitude data to plot
["L2"] (array-like) : nested list containing L2 norms,
structured as:
sess x scaling x unexp
["L2_sig"] (list) : L2 significance results for each session
("hi", "lo" or "no")
["mag_sig"] (list) : magnitude significance results for each
session
("hi", "lo" or "no")
["mag_st"] (array-like): array or nested list containing magnitude
stats across ROIs, structured as:
sess x scaling x unexp x stats
Optional args:
- figpar (dict): dictionary containing the following figure parameter
dictionaries
default: None
["init"] (dict): dictionary with figure initialization parameters
["save"] (dict): dictionary with figure saving parameters
["dirs"] (dict): dictionary with additional figure parameters
- savedir (str): path of directory in which to save plots.
default: None
Returns:
- fulldir (str) : final path of the directory in which the figure is
saved (may differ from input savedir, if datetime
subfolder is added.)
- savename (str): name under which the figure is saved
"""
sessstr_pr = sess_str_util.sess_par_str(
sesspar["sess_n"], stimpar["stimtype"], sesspar["plane"],
stimpar["visflow_dir"], stimpar["visflow_size"], stimpar["gabk"],
"print")
statstr_pr = sess_str_util.stat_par_str(
analyspar["stats"], analyspar["error"], "print")
dendstr_pr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"], "print")
sessstr = sess_str_util.sess_par_str(
sesspar["sess_n"], stimpar["stimtype"], sesspar["plane"],
stimpar["visflow_dir"],stimpar["visflow_size"], stimpar["gabk"])
dendstr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"])
datatype = extrapar["datatype"]
dimstr = sess_str_util.datatype_dim_str(datatype)
# extract some info from sess_info
keys = ["mouse_ns", "sess_ns", "lines", "planes"]
[mouse_ns, sess_ns, lines, planes] = [sess_info[key] for key in keys]
nroi_strs = sess_str_util.get_nroi_strs(
sess_info, empty=(datatype!="roi"), style="par"
)
n_sess = len(mouse_ns)
qu_ns = [gen_util.pos_idx(q, quantpar["n_quants"]) + 1
for q in quantpar["qu_idx"]]
if len(qu_ns) != 2:
raise ValueError(f"Expected 2 quantiles, not {len(qu_ns)}.")
mag_st = np.asarray(mags["mag_st"])
if figpar is None:
figpar = sess_plot_util.init_figpar()
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
figpar["init"]["subplot_wid"] *= n_sess/2.0
scales = [False, True]
# get plot elements
barw = 0.75
# scaling strings for printing and filenames
leg = ["exp", "unexp"]
cent, bar_pos, xlims = plot_util.get_barplot_xpos(n_sess, len(leg), barw)
title = (u"Magnitude ({}) of difference in activity".format(statstr_pr) +
f"\nbetween Q{qu_ns[0]} and {qu_ns[1]} across {dimstr} "
f"\n({sessstr_pr})")
labels = [f"Mouse {mouse_ns[i]} sess {sess_ns[i]},\n {lines[i]} {planes[i]}"
f"{dendstr_pr}{nroi_strs[i]}" for i in range(n_sess)]
figs, axs = [], []
for sc, scale in enumerate(scales):
scalestr_pr = sess_str_util.scale_par_str(scale, "print")
fig, ax = plot_util.init_fig(1, **figpar["init"])
figs.append(fig)
axs.append(ax)
sub_ax = ax[0, 0]
# always set ticks (even again) before setting labels
sub_ax.set_xticks(cent)
sub_ax.set_xticklabels(labels)
title_scale = u"{}{}".format(title, scalestr_pr)
sess_plot_util.add_axislabels(
sub_ax, fluor=analyspar["fluor"], area=True, scale=scale, x_ax="",
datatype=datatype)
for s, lab in enumerate(leg):
xpos = list(zip(*bar_pos))[s]
plot_util.plot_bars(
sub_ax, xpos, mag_st[:, sc, s, 0], err=mag_st[:, sc, s, 1:],
width=barw, xlims=xlims, xticks="None", label=lab, capsize=4,
title=title_scale, hline=0)
# add significance markers
for i in range(n_sess):
signif = mags["mag_sig"][i]
if signif in ["hi", "lo"]:
xpos = bar_pos[i]
for sc, (ax, scale) in enumerate(zip(axs, scales)):
yval = mag_st[i, sc, :, 0]
yerr = mag_st[i, sc, :, 1:]
plot_util.plot_barplot_signif(ax[0, 0], xpos, yval, yerr)
plot_util.turn_off_extra(ax, n_sess)
# figure directory
if savedir is None:
savedir = Path(
figpar["dirs"][datatype],
figpar["dirs"]["unexp_qu"],
figpar["dirs"]["mags"])
log_dir = False
for i, (fig, scale) in enumerate(zip(figs, scales)):
if i == len(figs) - 1:
log_dir = True
scalestr = sess_str_util.scale_par_str(scale)
savename = f"{datatype}_mag_diff_{sessstr}{dendstr}"
savename_full = f"{savename}{scalestr}"
fulldir = plot_util.savefig(
fig, savename_full, savedir, log_dir=log_dir, ** figpar["save"])
return fulldir, savename
def run_regr(args):
"""
run_regr(args)
Does runs of a logistic regressions on the specified comparison and range
of sessions.
Required args:
- args (Argument parser): parser with analysis parameters as attributes:
alg (str) : algorithm to use ("sklearn" or "pytorch")
bal (bool) : if True, classes are balanced
batchsize (int) : nbr of samples dataloader will load per
batch (for "pytorch" alg)
visflow_dir (str) : visual flow direction to analyse
visflow_per (float) : number of seconds to include before visual
flow segments
visflow_size (int or list): visual flow square sizes to include
comp (str) : type of comparison
datadir (str) : data directory
dend (str) : type of dendrites to use ("allen" or "dend")
device (str) : device name (i.e., "cuda" or "cpu")
ep_freq (int) : frequency at which to log loss to
console
error (str) : error to take, i.e., "std" (for std
or quantiles) or "sem" (for SEM or MAD)
fluor (str) : fluorescence trace type
fontdir (str) : directory in which additional fonts are
located
gabfr (int) : gabor frame of reference if comparison
is "unexp"
gabk (int or list) : gabor kappas to include
gab_ori (list or str) : gabor orientations to include
incl (str or list) : sessions to include ("yes", "no", "all")
lr (num) : model learning rate (for "pytorch" alg)
mouse_n (int) : mouse number
n_epochs (int) : number of epochs
n_reg (int) : number of regular runs
n_shuff (int) : number of shuffled runs
scale (bool) : if True, each ROI is scaled
output (str) : general directory in which to save
output
parallel (bool) : if True, runs are done in parallel
plt_bkend (str) : pyplot backend to use
q1v4 (bool) : if True, analysis is trained on first and
tested on last quartiles
exp_v_unexp (bool) : if True, analysis is trained on
expected and tested on unexpected sequences
runtype (str) : type of run ("prod" or "pilot")
seed (int) : seed to seed random processes with
sess_n (int) : session number
stats (str) : stats to take, i.e., "mean" or "median"
stimtype (str) : stim to analyse ("gabors" or "visflow")
train_p (list) : proportion of dataset to allocate to
training
uniqueid (str or int) : unique ID for analysis
wd (float) : weight decay value (for "pytorch" arg)
"""
args = copy.deepcopy(args)
if args.datadir is None:
args.datadir = DEFAULT_DATADIR
else:
args.datadir = Path(args.datadir)
if args.uniqueid == "datetime":
args.uniqueid = gen_util.create_time_str()
elif args.uniqueid in ["None", "none"]:
args.uniqueid = None
reseed = False
if args.seed in [None, "None"]:
reseed = True
# deal with parameters
extrapar = {"uniqueid": args.uniqueid, "seed": args.seed}
techpar = {
"reseed": reseed,
"device": args.device,
"alg": args.alg,
"parallel": args.parallel,
"plt_bkend": args.plt_bkend,
"fontdir": args.fontdir,
"output": args.output,
"ep_freq": args.ep_freq,
"n_reg": args.n_reg,
"n_shuff": args.n_shuff,
}
mouse_df = DEFAULT_MOUSE_DF_PATH
stimpar = logreg.get_stimpar(args.comp,
args.stimtype,
args.visflow_dir,
args.visflow_size,
args.gabfr,
args.gabk,
gab_ori=args.gab_ori,
visflow_pre=args.visflow_pre)
analyspar = sess_ntuple_util.init_analyspar(args.fluor,
stats=args.stats,
error=args.error,
scale=not (args.no_scale),
dend=args.dend)
if args.q1v4:
quantpar = sess_ntuple_util.init_quantpar(4, [0, -1])
else:
quantpar = sess_ntuple_util.init_quantpar(1, 0)
logregpar = sess_ntuple_util.init_logregpar(args.comp, not (args.not_ctrl),
args.q1v4, args.exp_v_unexp,
args.n_epochs, args.batchsize,
args.lr, args.train_p, args.wd,
args.bal, args.alg)
omit_sess, omit_mice = sess_gen_util.all_omit(stimpar.stimtype,
args.runtype,
stimpar.visflow_dir,
stimpar.visflow_size,
stimpar.gabk)
sessids = sorted(
sess_gen_util.get_sess_vals(mouse_df,
"sessid",
args.mouse_n,
args.sess_n,
args.runtype,
incl=args.incl,
omit_sess=omit_sess,
omit_mice=omit_mice))
if len(sessids) == 0:
logger.warning(
f"No sessions found (mouse: {args.mouse_n}, sess: {args.sess_n}, "
f"runtype: {args.runtype})")
for sessid in sessids:
sess = sess_gen_util.init_sessions(sessid,
args.datadir,
mouse_df,
args.runtype,
full_table=False,
fluor=analyspar.fluor,
dend=analyspar.dend,
temp_log="warning")[0]
logreg.run_regr(sess, analyspar, stimpar, logregpar, quantpar,
extrapar, techpar)
plot_util.cond_close_figs()
def plot_pup_diff_corr(analyspar, sesspar, stimpar, extrapar,
sess_info, corr_data, figpar=None, savedir=None):
"""
plot_pup_diff_corr(analyspar, sesspar, stimpar, extrapar,
sess_info, corr_data)
From dictionaries, plots correlation between unexpected-locked changes in
pupil diameter and running or ROI data for each session.
Required args:
- analyspar (dict) : dictionary with keys of AnalysPar namedtuple
- sesspar (dict) : dictionary with keys of SessPar namedtuple
- stimpar (dict) : dictionary with keys of StimPar namedtuple
- extrapar (dict) : dictionary containing additional analysis
parameters
["analysis"] (str): analysis type (e.g., "c")
["datatype"] (str): datatype (e.g., "run", "roi")
- sess_info (dict) : dictionary containing information from each
session
["mouse_ns"] (list) : mouse numbers
["sess_ns"] (list) : session numbers
["lines"] (list) : mouse lines
["planes"] (list) : imaging planes
["nrois"] (list) : number of ROIs in session
- corr_data (dict) : dictionary containing data to plot:
["corrs"] (list): list of correlation values between pupil and
running or ROI differences for each session
["diffs"] (list): list of differences for each session, structured
as [pupil, ROI/run] x trials x frames
Optional args:
- figpar (dict) : dictionary containing the following figure parameter
dictionaries
default: None
["init"] (dict): dictionary with figure initialization parameters
["save"] (dict): dictionary with figure saving parameters
["dirs"] (dict): dictionary with additional figure parameters
- savedir (Path): path of directory in which to save plots.
default: None
Returns:
- fulldir (Path): final path of the directory in which the figure is
saved (may differ from input savedir, if datetime
subfolder is added.)
- savename (str): name under which the figure is saved
"""
statstr_pr = sess_str_util.stat_par_str(
analyspar["stats"], analyspar["error"], "print")
stimstr_pr = sess_str_util.stim_par_str(
stimpar["stimtype"], stimpar["visflow_dir"], stimpar["visflow_size"],
stimpar["gabk"], "print")
dendstr_pr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"], "print")
sessstr = sess_str_util.sess_par_str(
sesspar["sess_n"], stimpar["stimtype"], sesspar["plane"],
stimpar["visflow_dir"],stimpar["visflow_size"], stimpar["gabk"])
dendstr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"])
datatype = extrapar["datatype"]
datastr = sess_str_util.datatype_par_str(datatype)
if datatype == "roi":
label_str = sess_str_util.fluor_par_str(
analyspar["fluor"], str_type="print")
full_label_str = u"{}, {} across ROIs".format(
label_str, analyspar["stats"])
elif datatype == "run":
label_str = datastr
full_label_str = datastr
lab_app = (f" ({analyspar['stats']} over "
f"{stimpar['pre']}/{stimpar['post']} sec)")
logger.info(f"Plotting pupil vs {datastr} changes.")
delta = "\u0394"
# extract some info from sess_info
keys = ["mouse_ns", "sess_ns", "lines", "planes"]
[mouse_ns, sess_ns, lines, planes] = [sess_info[key] for key in keys]
n_sess = len(mouse_ns)
nroi_strs = sess_str_util.get_nroi_strs(
sess_info, empty=(datatype!="roi"), style="comma"
)
if figpar is None:
figpar = sess_plot_util.init_figpar()
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
figpar["init"]["sharex"] = False
figpar["init"]["sharey"] = False
figpar["init"]["ncols"] = n_sess
fig, ax = plot_util.init_fig(2 * n_sess, **figpar["init"])
suptitle = (f"Relationship between pupil diam. and {datastr} changes, "
"locked to unexpected events")
for i, sess_diffs in enumerate(corr_data["diffs"]):
sub_axs = ax[:, i]
title = (f"Mouse {mouse_ns[i]} - {stimstr_pr}, " +
u"{}".format(statstr_pr) + f"\n(sess {sess_ns[i]}, {lines[i]} "
f"{planes[i]}{dendstr_pr}{nroi_strs[i]})")
# top plot: correlations
corr = f"Corr = {corr_data['corrs'][i]:.2f}"
sub_axs[0].plot(
sess_diffs[0], sess_diffs[1], marker=".", linestyle="None",
label=corr)
sub_axs[0].set_title(title, y=1.01)
sub_axs[0].set_xlabel(u"{} pupil diam.{}".format(delta, lab_app))
if i == 0:
sub_axs[0].set_ylabel(u"{} {}\n{}".format(
delta, full_label_str, lab_app))
sub_axs[0].legend()
# bottom plot: differences across occurrences
data_lab = u"{} {}".format(delta, label_str)
pup_lab = u"{} pupil diam.".format(delta)
cols = []
scaled = []
for d, lab in enumerate([pup_lab, data_lab]):
scaled.append(math_util.scale_data(
np.asarray(sess_diffs[d]), sc_type="min_max")[0])
art, = sub_axs[1].plot(scaled[-1], marker=".")
cols.append(sub_axs[-1].lines[-1].get_color())
if i == n_sess - 1: # only for last graph
art.set_label(lab)
sub_axs[1].legend()
sub_axs[1].set_xlabel("Unexpected event occurrence")
if i == 0:
sub_axs[1].set_ylabel(
u"{} response locked\nto unexpected onset (scaled)".format(delta))
# shade area between lines
plot_util.plot_btw_traces(
sub_axs[1], scaled[0], scaled[1], color=cols, alpha=0.4)
fig.suptitle(suptitle, fontsize="xx-large", y=1)
if savedir is None:
savedir = Path(
figpar["dirs"][datatype],
figpar["dirs"]["pupil"])
savename = f"{datatype}_diff_corr_{sessstr}{dendstr}"
fulldir = plot_util.savefig(fig, savename, savedir, **figpar["save"])
return fulldir, savename
def plot_pup_roi_stim_corr(analyspar, sesspar, stimpar, extrapar,
sess_info, corr_data, figpar=None, savedir=None):
"""
plot_pup_roi_stim_corr(analyspar, sesspar, stimpar, extrapar,
sess_info, corr_data)
From dictionaries, plots correlation between unexpected-locked changes in
pupil diameter and each ROI, for gabors versus visual flow responses for
each session.
Required args:
- analyspar (dict) : dictionary with keys of AnalysPar namedtuple
- sesspar (dict) : dictionary with keys of SessPar namedtuple
- stimpar (dict) : dictionary with keys of StimPar namedtuple
- extrapar (dict) : dictionary containing additional analysis
parameters
["analysis"] (str): analysis type (e.g., "r")
["datatype"] (str): datatype (e.g., "roi")
- sess_info (dict) : dictionary containing information from each
session
["mouse_ns"] (list) : mouse numbers
["sess_ns"] (list) : session numbers
["lines"] (list) : mouse lines
["planes"] (list) : imaging planes
["nrois"] (list) : number of ROIs in session
- corr_data (dict) : dictionary containing data to plot:
["stim_order"] (list): ordered list of stimtypes
["roi_corrs"] (list) : nested list of correlations between pupil
and ROI responses changes locked to
unexpected, structured as
session x stimtype x ROI
["corrs"] (list) : list of correlation between stimtype
correlations for each session
Optional args:
- figpar (dict) : dictionary containing the following figure parameter
dictionaries
default: None
["init"] (dict): dictionary with figure initialization parameters
["save"] (dict): dictionary with figure saving parameters
["dirs"] (dict): dictionary with additional figure parameters
- savedir (Path): path of directory in which to save plots.
default: None
Returns:
- fulldir (Path): final path of the directory in which the figure is
saved (may differ from input savedir, if datetime
subfolder is added.)
- savename (str): name under which the figure is saved
"""
stimstr_prs = []
for stimtype in corr_data["stim_order"]:
stimstr_pr = sess_str_util.stim_par_str(
stimtype, stimpar["visflow_dir"], stimpar["visflow_size"],
stimpar["gabk"], "print")
stimstr_pr = stimstr_pr[:-1] if stimstr_pr[-1] == "s" else stimstr_pr
stimstr_prs.append(stimstr_pr)
dendstr_pr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"], "print")
sessstr = f"sess{sesspar['sess_n']}_{sesspar['plane']}"
dendstr = sess_str_util.dend_par_str(
analyspar["dend"], sesspar["plane"], extrapar["datatype"])
label_str = sess_str_util.fluor_par_str(
analyspar["fluor"], str_type="print")
lab_app = (f" ({analyspar['stats']} over "
f"{stimpar['pre']}/{stimpar['post']} sec)")
logger.info("Plotting pupil-ROI difference correlations for "
"{} vs {}.".format(*corr_data["stim_order"]))
# extract some info from sess_info
keys = ["mouse_ns", "sess_ns", "lines", "planes"]
[mouse_ns, sess_ns, lines, planes] = [sess_info[key] for key in keys]
n_sess = len(mouse_ns)
nroi_strs = sess_str_util.get_nroi_strs(sess_info, style="comma")
if figpar is None:
figpar = sess_plot_util.init_figpar()
figpar = copy.deepcopy(figpar)
if figpar["save"]["use_dt"] is None:
figpar["save"]["use_dt"] = gen_util.create_time_str()
figpar["init"]["sharex"] = True
figpar["init"]["sharey"] = True
fig, ax = plot_util.init_fig(n_sess, **figpar["init"])
suptitle = (u"Relationship between pupil diam. and {} changes, locked to "
"unexpected events\n{} for each ROI ({} vs {})".format(
label_str, lab_app, *corr_data["stim_order"]))
for i, sess_roi_corrs in enumerate(corr_data["roi_corrs"]):
sub_ax = plot_util.get_subax(ax, i)
title = (f"Mouse {mouse_ns[i]} (sess {sess_ns[i]}, {lines[i]} "
f"{planes[i]}{dendstr_pr}{nroi_strs[i]})")
# top plot: correlations
corr = f"Corr = {corr_data['corrs'][i]:.2f}"
sub_ax.plot(
sess_roi_corrs[0], sess_roi_corrs[1], marker=".", linestyle="None",
label=corr)
sub_ax.set_title(title, y=1.01)
if sub_ax.is_last_row():
sub_ax.set_xlabel(f"{stimstr_prs[0].capitalize()} correlations")
if sub_ax.is_first_col():
sub_ax.set_ylabel(f"{stimstr_prs[1].capitalize()} correlations")
sub_ax.legend()
plot_util.turn_off_extra(ax, n_sess)
fig.suptitle(suptitle, fontsize="xx-large", y=1)
if savedir is None:
savedir = Path(
figpar["dirs"]["roi"],
figpar["dirs"]["pupil"])
savename = f"roi_diff_corrbyroi_{sessstr}{dendstr}"
fulldir = plot_util.savefig(fig, savename, savedir, **figpar["save"])
return fulldir, savename
