def make_montage_rasters(simulation):
"""Make montage of rasters.
:simulation: simulation to make montage for
:returns: nothing
"""
print("Generating raster montage for {}".format(simulation))
output_file = (
"{}-raster-lpz_c_E-p_lpz_E-montage.png".format(simulation)
)
f_glob = "{}-raster-lpz_c_E-p_lpz_E*.png".format(simulation)
file_list = natsorted(glob.glob(f_glob))
args = []
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
args += [
"-tile", "{}x{}".format(len(file_list), 1),
"-geometry", "+2+2",
output_file
]
make_montage(args, output_file)
def make_montage_totals(sim):
"""Make main total montages
:sim: simulation id
:returns: nothing
"""
print("Generating main structural plasticity graphs")
for nrn in ["E", "I"]:
# input conductances vs time from different regions
output_file = ("{}-structural-plasticity-{}-montage.png".format(
sim, nrn))
args = []
for i in range(0, 4):
fname = "{}-growth-curves-{}.png".format(sim, nrn)
args.append(fname)
for gps in [
"02-calcium",
"05-se-all-totals",
"05-se-all-means",
]:
for region in ["lpz_c", "lpz_b", "p_lpz", "o"]:
fname = "{}-{}-{}_{}.png".format(sim, gps, region, nrn)
args.append(fname)
args += ["-tile", "4x4", "-geometry", "+2+2", output_file]
make_montage(args, output_file)
def make_montage_grid_plots(simulation):
"""Make montage of firing rate grid plots.
:simulation: simulation to make montage for
:returns: nothing
"""
print("Generating firing rate grid plot montage for {}".format(simulation))
output_file = (
"{}-firing-rate-grid-plots-montage.png".format(simulation)
)
f_glob_E = "{}-firing-rates-grid-plot-E*.png".format(simulation)
f_glob_I = "{}-firing-rates-grid-plot-I*.png".format(simulation)
file_list_E = natsorted(glob.glob(f_glob_E))
file_list_I = natsorted(glob.glob(f_glob_I))
args = []
for afile in file_list_E + file_list_I:
if os.path.isfile(afile):
args.append(afile)
args += [
"-tile", "{}x{}".format(len(file_list_E), 2),
"-geometry", "+2+2",
output_file
]
make_montage(args, output_file)
def make_montages_hists(sim):
"""Make montage of snapshots: histograms
:sim: simulation to make montage of
:returns: TODO
"""
args = []
output_file = ("{}-02-calcium-hist-montage.png".format(sim))
for nrn in ["E", "I"]:
f_glob = ("{}-02-calcium-hist-{}-*.png".format(sim, nrn))
file_list = natsorted(glob.glob(f_glob))
if not file_list:
print("Component files not found. Skipping")
return
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
cols = len(args) / 2
args += [
"-tile", "{}x{}".format(int(cols), 2), "-geometry", "+2+2", output_file
]
make_montage(args, output_file)
def make_montages_hists(sim):
"""Make montage of snapshots: histograms
:sim: simulation to make montage of
:returns: TODO
"""
for nrn in ["E", "I"]:
for ty in ["all", "con"]:
args = []
output_file = ("{}-05-se-hist-{}-montage-{}.png".format(
sim, ty, nrn))
f_glob = ("{}-05-se-ax-hist-{}-{}*.png".format(sim, ty, nrn))
file_list = natsorted(glob.glob(f_glob))
if not file_list:
print("Component files not found. Skipping")
return
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
f_glob = ("{}-05-se-denE-hist-{}-{}*.png".format(sim, ty, nrn))
file_list = natsorted(glob.glob(f_glob))
if not file_list:
print("Component files not found. Skipping")
return
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
f_glob = ("{}-05-se-denI-hist-{}-{}*.png".format(sim, ty, nrn))
file_list = natsorted(glob.glob(f_glob))
if not file_list:
print("Component files not found. Skipping")
return
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
cols = len(args) / 3
args += [
"-tile", "{}x{}".format(int(cols), 3), "-geometry", "+2+2",
output_file
]
make_montage(args, output_file)
def make_montage_firng_rate_plots(simulation):
"""Make montage of firing rate vs time plots.
:simulation: simulation to make montage for
:returns: nothing
"""
print("Generating firing rate plots montage for {}".format(simulation))
output_file = (
"{}-firing-rate-E-I-montage.png".format(simulation)
)
args = []
args += [
"{}-mean-firing-rates-all-E-zoomed.png".format(simulation),
"{}-mean-firing-rates-all-I-zoomed.png".format(simulation),
"-tile", "1x2",
"-geometry", "+2+2",
output_file
]
if os.path.isfile(args[0]):
make_montage(args, output_file)
else:
print("Files not found. Skipping firing rate I-E montage.")
# regions
output_file = (
"{}-firing-rate-regions-montage.png".format(simulation)
)
args = []
args += [
"{}-mean-firing-rates-lpz_c_I-E-zoomed.png".format(simulation),
"{}-mean-firing-rates-lpz_b_I-E-zoomed.png".format(simulation),
"{}-mean-firing-rates-p_lpz_I-E-zoomed.png".format(simulation),
"{}-mean-firing-rates-o_I-E-zoomed.png".format(simulation),
"-tile", "1x4",
"-geometry", "+2+2",
output_file
]
if os.path.isfile(args[0]):
make_montage(args, output_file)
else:
print("Files not found. Skipping region montage.")
def make_montage_conductance_hists(sim):
"""Make montage of conductance time lapse histogram plots.
:sim: sim to make montage for
:returns: nothing
"""
print("Generating firing rate grid plot montage for {}".format(sim))
output_file = ("{}-08-conductance-hist-time-lapse-montage.png".format(sim))
args = []
for syn in ["EE", "IE", "EI", "II"]:
f_glob = "{}-08-conductance-hist-{}-*.png".format(sim, syn)
file_list = natsorted(glob.glob(f_glob))
for afile in file_list:
if os.path.isfile(afile):
args.append(afile)
cols = len(args) / 4
args += [
"-tile", "{}x{}".format(int(cols), 4), "-geometry", "+2+2", output_file
]
make_montage(args, output_file)
def make_montage_total_conductances(sim):
"""Make montages of total conductances to regions.
:sim: sim timestamp
:returns: nothing
"""
for nrn in ["E", "I"]:
# input conductances vs time from different regions
output_file = ("{}-75-conductances-{}-montage.png".format(sim, nrn))
args = []
for gps in [
"02-calcium", "08-total-conductances-E-to",
"08-total-conductances-I-to", "08-mean-conductances-E-to",
"08-mean-conductances-I-to"
]:
for region in ["lpz_c", "lpz_b", "p_lpz", "o"]:
fname = "{}-{}-{}_{}.png".format(sim, gps, region, nrn)
args.append(fname)
args += ["-tile", "4x5", "-geometry", "+2+2", output_file]
make_montage(args, output_file)
# input conductances from different regions: histograms
output_file = ("{}-75-conductances-histograms-{}-montage.png".format(
sim, nrn))
args = []
for gps in [
"02-calcium",
"081-conductance-clustered-histograms-E-to",
"081-conductance-clustered-histograms-I-to",
"081-conductance-rowstacked-histograms-E-to",
"081-conductance-rowstacked-histograms-I-to",
]:
for region in ["lpz_c", "lpz_b", "p_lpz", "o"]:
fname = "{}-{}-{}_{}.png".format(sim, gps, region, nrn)
args.append(fname)
args += ["-tile", "4x5", "-geometry", "+2+2", output_file]
make_montage(args, output_file)
# net conductances to different regions
output_file = ("{}-75-net-conductances-{}-montage.png".format(
sim, nrn))
args = []
for gps in [
"02-calcium", "08-net-regional-conductances-to",
"08-net-conductances-to", "08-net-conductances-slope-to"
]:
for region in ["lpz_c", "lpz_b", "p_lpz", "o"]:
fname = "{}-{}-{}_{}.png".format(sim, gps, region, nrn)
args.append(fname)
args += ["-tile", "4x4", "-geometry", "+2+2", output_file]
make_montage(args, output_file)
def neuron_metrics(simlist, timestamp):
"""Make the neuron metrics montage
:simlist: list of simulations
:timestamp: time at which montages are generated
:returns: nothing
"""
print("Generating neuron metrics montage")
# Each simulation gets a column
num_cols = len(simlist)
graphs = [
"02-calcium",
"05-se-all"
]
regions = ["lpz_c_E", "lpz_b_E", "p_lpz_E", "o_E"]
regions += ["lpz_c_I", "lpz_b_I", "p_lpz_I", "o_I"]
for region in regions:
output_file = (
"{}-multi-sim-neuron-metrics-{}-montage.png".format(
timestamp, region
)
)
print("Generating {}...".format(output_file))
args = []
# Add growth curves on top
gcs = ['growth-curves-E', 'growth-curves-I']
for gc in gcs:
for sim in simlist:
fname = (
os.path.join(sim, "{}-{}.png".format(
sim, gc
))
)
if os.path.isfile(fname):
args.append(fname)
else:
print(
"{}: file not found. Exiting.".format(
fname
),
file=sys.stderr
)
sys.exit(-2)
for graph in graphs:
for sim in simlist:
fname = (
os.path.join(sim, "{}-{}-{}.png".format(
sim, graph, region
))
)
if os.path.isfile(fname):
args.append(fname)
else:
print(
"{}: file not found. Exiting.".format(
fname
),
file=sys.stderr
)
sys.exit(-2)
# Final bits
args += [
"-title", "'{}'".format(
", ".join(str(sim) for sim in simlist)
),
"-tile", "{}x{}".format(num_cols, len(graphs) + len(gcs)),
"-pointsize", "28",
"-font", "OpenSans",
"-geometry", "+2+2",
output_file
]
make_montage(args, output_file)