def get_metric_details(path, timeshift, pathname_metadata=""):
metrics = load_pickle(path + "metrics_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
metrics_k = load_pickle(path + "metrics_k_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
nd = load_pickle(path + "nd_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
licks = load_pickle(path + "licks_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
lick_id_details = Lick_id_details()
lick_id_details.from_metrics(nd=nd,
metrics=metrics,
timeshift=timeshift,
licks=licks)
lick_id_details_k = []
for metric in metrics_k:
obj = Lick_id_details()
obj.from_metrics(nd=nd,
metrics=metric,
timeshift=timeshift,
licks=licks)
lick_id_details_k.append(obj)
# Calculate approximate accuracy
all_guesses = load_pickle(path + "all_guesses_timeshift=" +
str(timeshift) + pathname_metadata + ".pkl")
approximate_accuracy = np.zeros(
(len(lick_id_details.valid_licks), nd.num_wells))
for guess in all_guesses:
for evaluated_sample in guess:
i = evaluated_sample.lick_id - 1
prediction = evaluated_sample.prediction
approximate_accuracy[i][prediction - 1] += 1
second_highest_decoded = np.zeros(len(lick_id_details.valid_licks))
sum_highest = 0
sum_second = 0
sum_total = 0
for i, event in enumerate(approximate_accuracy):
# prints table of most frequent guesses by well
sum_highest += np.max(event)
sum_second += np.partition(event.flatten(), -2)[-2]
sum_total += np.sum(event)
second_largest_well = int(
np.where(event == np.partition(event.flatten(), -2)[-2])[0][0] +
1) # returns well of second largest value in list
if second_largest_well == licks[
i].target and lick_id_details.valid_licks[i] == 1:
second_highest_decoded[i] = 1
lick_id_details.second_highest_decoded = second_highest_decoded
print(sum_highest, sum_second, sum_total)
# generate all_guesses_k for standard deviation
return lick_id_details, lick_id_details_k
def load_position_network_output(path):
dict_files = glob.glob(path + "output/" + "*.pkl")
net_out = []
sorted_list = []
if len(dict_files) == 0:
raise OSError("Warning: network Directory is empty")
for i, file_path in enumerate(dict_files):
net_dict_i = load_pickle(file_path)
sorted_list.append([file_path, net_dict_i.net_data.time_shift])
sorted_list = sorted(sorted_list, key=lambda x: x[1])
dict_files = [i[0] for i in sorted_list]
for file_path in dict_files:
# print("processing", file_path)
net_dict_i = load_pickle(file_path)
net_out.append(net_dict_i)
return net_out
def print_table(paths):
data_collection = []
for path in paths:
data_collection.append(load_pickle(path)[0:56])
data_collection = np.transpose(data_collection)
for i, datarow in enumerate(data_collection):
print(i + 1, end=" & ")
for j, data in enumerate(datarow):
if j in [0, 1, 4, 5]: # which columns are ints (wells)
print(str(int(data)) + " & ", end="")
else:
print(format(float(data), ".1f") + " & ", end="")
print(" \ ")
def plot_accuracy_inside_phase(path,
shift,
title,
save_path,
color="darkviolet"):
# load accuracy data
metrics = load_pickle(path + "metrics_timeshift=" + str(shift) + ".pkl")
# plot chart
sample_counter = np.zeros(1000)
bin_values = []
accuracy_sum = np.zeros(1000)
position = 0
current_phase = metrics[0].phase
for i, lick in enumerate(metrics):
sample_counter[position] += 1
bin_values.append(position)
accuracy_sum[position] += lick.fraction_decoded
position += 1
if lick.phase != current_phase: # new phase
current_phase = lick.phase
position = 0
# remove trailing zeros and normalize phase
sample_counter = np.trim_zeros(sample_counter, 'b')
accuracy_sum = np.trim_zeros(accuracy_sum, 'b')
y = np.divide(accuracy_sum, sample_counter)
fig, ax = plt.subplots()
fontsize = 12
x = np.arange(0, len(y))
ax.plot(x, y, label='average', color=color, marker='.',
linestyle="None") # ,linestyle="None"
ax.legend()
ax.grid(c='k', ls='-', alpha=0.3)
ax.set_xlabel("Number of visits of well 1 inside phase")
ax.set_ylabel("Average fraction of samples decoded correctly")
ax.set_title(title)
ax_b = ax.twinx()
ax_b.set_ylabel("Phases with number of visits")
z = np.arange(0, 12)
ax_b.hist(bin_values, bins=z, facecolor='g', alpha=0.2)
# plt.show()
plt.savefig(save_path)
pass
def print_average_overlap(paths, filter_factor=0.0):
"""
:param paths: list of paths of the two neural activity output files produced by this module
:param filter_factor: keeps fraction of neurons with highest firing rate and filters out rest
:return:
"""
data_collection_i = []
for path in paths:
data_collection_i.append(load_pickle(path)[0:56])
data_collection = (list(zip(data_collection_i[0], data_collection_i[1])))
spikerate_collection = (data_collection_i[2] + data_collection_i[3])
sorted_collection = spikerate_collection.copy()
sorted_collection.sort() #
max_spikerate = sorted_collection[int(filter_factor *
len(spikerate_collection))]
counter = []
for i, data_row in enumerate(data_collection):
if spikerate_collection[i] > max_spikerate:
counter.append(data_row[0] == data_row[1])
print(np.average(counter))
return np.average(counter)
# speed_list_hc, spike_rate_list_hc = return_bar_values(nd, lickstart, lickstop, resolution)
# nd.filtered_data_path = "session_pfc_lw.pkl"
# speed_list_pfc, spike_rate_list_pfc = return_bar_values(nd, lickstart, lickstop, resolution)
#
# with open("speed_list_hc", 'wb') as f:
# pickle.dump(speed_list_hc, f)
# with open("spike_rate_list_hc", 'wb') as f:
# pickle.dump(spike_rate_list_hc, f)
#
# with open("speed_list_pfc", 'wb') as f:
# pickle.dump(speed_list_pfc, f)
# with open("spike_rate_list_pfc", 'wb') as f:
# pickle.dump(spike_rate_list_pfc, f)
speed_list_hc = load_pickle("speed_list_hc")
speed_list_pfc = load_pickle("speed_list_pfc")
spike_rate_list_hc = load_pickle("spike_rate_list_hc")
spike_rate_list_pfc = load_pickle("spike_rate_list_pfc")
# plot results
fig, ((ax1, ax3), (ax2, ax4)) = plt.subplots(2, 2)
ax1.plot(time_ind, speed_list_hc, color="b",
label="HC") # label="cv "+str(i+1)+"/10",
ax1.set_ylabel("speed [cm/s]", fontsize=fontsize)
ax1.xaxis.set_major_locator(plt.MaxNLocator(3))
ax1.yaxis.set_major_locator(plt.MaxNLocator(3))
ax1.legend(fontsize=fontsize)
ax2.plot(time_ind, spike_rate_list_hc,
color="b") # label="cv "+str(i+1)+"/10",
ax2.set_ylabel("spikes/s", fontsize=fontsize)
def print_metric_details(path, timeshift, pathname_metadata=""):
"""
:param path: directory of network files, should be filled
:param timeshift: +1 or - 1 for future or past decoding files
:param pathname_metadata: if there were multiple experiments in one directory, this can be used to distinguish this by appending to the end of the searched file names
:return: prints metric details and details by lick
"""
path = path + "output/"
# Create binary arrays for licks corresponding to each inspected filter
metrics = load_pickle(path + "metrics_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
nd = load_pickle(path + "nd_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
licks = load_pickle(path + "licks_timeshift=" + str(timeshift) +
pathname_metadata + ".pkl")
lick_id_details = Lick_id_details()
lick_id_details.from_metrics(nd=nd,
metrics=metrics,
timeshift=timeshift,
licks=licks)
latex_table = []
latex_table.append([
"event count", " correct guesses", "false guesses", "fraction correct",
"decoded next phase", "decoded last phase", "decoded current phase",
"fraction current phase", "decoded next lick", "decoded last lick"
])
top_row = [
"all licks", "correct licks", "false licks", "next well licked is 2",
"next well licked is 3", "next well licked is 4",
"next well licked is 5"
]
# print("Filter: all licks")
# latex_table.append(lick_id_details.print_details())
# print("Filter: correct licks")
# lick_id_details.filter = lick_id_details.target_lick_correct
# latex_table.append(lick_id_details.print_details())
# print("Filter: false licks")
# lick_id_details.filter = lick_id_details.target_lick_false
# latex_table.append(lick_id_details.print_details())
# # print("Filter: licks prior to switch")
# # lick_id_details.filter = lick_id_details.licks_prior_to_switch
# # latex_table.append(lick_id_details.print_details())
# # print("Filter: licks after switch")
# # lick_id_details.filter = lick_id_details.licks_after_switch
# # latex_table.append(lick_id_details.print_details())
# print("Filter: next well licked is 2")
# lick_id_details.filter = lick_id_details.next_well_licked_2
# latex_table.append(lick_id_details.print_details())
# print("Filter: next well licked is 3")
# lick_id_details.filter = lick_id_details.next_well_licked_3
# latex_table.append(lick_id_details.print_details())
# print("Filter: next well licked is 4")
# lick_id_details.filter = lick_id_details.next_well_licked_4
# latex_table.append(lick_id_details.print_details())
# print("Filter: next well licked is 5")
# lick_id_details.filter = lick_id_details.next_well_licked_5
# latex_table.append(lick_id_details.print_details())
# latex_table_2 = [[latex_table[j][i] for j in range(len(latex_table))] for i in range(len(latex_table[0]))] # transpose table
# for i,row in enumerate(latex_table_2):
# for j,item in enumerate(row):
# if j in [0]: # first column is string
# print(item ,end=" & ")
# else:
# if i in [0,1,2,4,5,6,8,9]:
# print(int(item),end= " & ")
# else:
# print(format(float(item), ".1f") ,end=" & ")
# print(" \ ")
print_lickwell_metrics(metrics, nd, licks)
only_phase_change_trials = False
by_sample = True
path = "C:/Users/NN/Desktop/Master/experiments/Lickwell_prediction/"
model_path_list = [
"C:/Users/NN/Desktop/Master/experiments/Experiments for thesis 2/well decoding/hc/"]
image_title_list = ["pfc","hc"]
fontsize = 24
rc('font',**{'family':'serif','serif':['Palatino']})
rc('text', usetex=True)
rc('xtick', labelsize=fontsize)
rc('ytick', labelsize=fontsize)
rc('axes', labelsize=fontsize)
if by_sample is False:
for timeshift in [1]:
for j,path in enumerate(model_path_list):
metrics = load_pickle(path + "output/metrics_timeshift=" + str(timeshift) + ".pkl")
metrics_k = load_pickle(path + "output/metrics_k_timeshift=" + str(timeshift) + ".pkl")
nd = load_pickle(path + "output/nd_timeshift=" + str(timeshift) + ".pkl")
licks = load_pickle(path + "output/licks_timeshift=" + str(timeshift) + ".pkl")
array = np.zeros((4,4))
metrics_flattened = [item for sublist in metrics_k for item in sublist]
# metrics_a = load_pickle(model_path_list[0] + "output/metrics_k_timeshift=" + str(timeshift) + ".pkl")
# metrics_b = load_pickle(model_path_list[1] + "output/metrics_k_timeshift=" + str(timeshift) + ".pkl")
# metrics_af = np.reshape(metrics_a,-1)
# metrics_bf = np.reshape(metrics_b,-1)
def init():
original = load_pickle("C:/Users/NN/AppData/Local/Temp/animation/target")
im.set_data(np.random.random((5, 5)))
return [im]