def main(dir):
container = NDataContainer(load_on_fly=True)
container.add_axona_files_from_dir(dir, recursive=True)
container.setup()
print(container.string_repr(True))
nca.place_cell_summary(
container, dpi=200, out_dirname="nc_spat_plots", output_format="pdf",
burst_thresh=6, isi_bin_length=1, filter_place_cells=False)
def main(dir, bin_size, bin_bound):
container = NDataContainer(load_on_fly=True)
container.add_axona_files_from_dir(dir, recursive=True)
container.setup()
print(container.string_repr(True))
event = NEvent()
last_stm_name = None
dict_list = []
for i in range(len(container)):
try:
result_dict = OrderedDict()
data_index, _ = container._index_to_data_pos(i)
stm_name = container.get_file_dict("STM")[data_index][0]
data = container[i]
# Add extra keys
spike_file = data.spike.get_filename()
spike_dir = os.path.dirname(spike_file)
spike_name = os.path.basename(spike_file)
spike_name_only, spike_ext = os.path.splitext(spike_name)
spike_ext = spike_ext[1:]
result_dict["Dir"] = spike_dir
result_dict["Name"] = spike_name_only
result_dict["Tet"] = int(spike_ext)
result_dict["Unit"] = data.spike.get_unit_no()
# Do analysis
if last_stm_name != stm_name:
event.load(stm_name, 'Axona')
last_stm_name = stm_name
graph_data = event.psth(data.spike, bins=bin_size, bound=bin_bound)
spike_count = data.get_unit_spikes_count()
result_dict["Num_Spikes"] = spike_count
# Bin renaming
for (b, v) in zip(graph_data["all_bins"][:-1], graph_data["psth"]):
result_dict[str(b)] = v
dict_list.append(result_dict)
# Do plotting
name = (spike_name_only + "_" + spike_ext + "_" +
str(result_dict["Unit"]) + ".png")
plot_name = os.path.join(dir, "psth_results", name)
make_dir_if_not_exists(plot_name)
plot_psth(graph_data, plot_name)
print("Saved psth to {}".format(plot_name))
except Exception as e:
log_exception(e, "During stimulation batch at {}".format(i))
dict_list.append(result_dict)
fname = os.path.join(dir, "psth_results", "psth.csv")
save_dicts_to_csv(fname, dict_list)
print("Saved results to {}".format(fname))
def main(dir):
container = NDataContainer(load_on_fly=True)
container.add_axona_files_from_dir(dir, recursive=True)
container.setup()
print(container.string_repr(True))
nca.place_cell_summary(container, dpi=200, out_dirname="nc_spat_plots")