def add_real_x(item):
"""fn to map over list of items returned by `get_groups_per_sweep`"""
i_res = item.copy()
abf = pyabf.ABF(item["fpath"])
time = abf.sweepX
peak_ints = db.str_list_to_list_ints(item["peaks"])
i_res["peak_times"] = time[peak_ints]
return i_res
def return_flat_list_of_treatment(dict_of_groups, treatment):
try:
abf = pyabf.ABF(dict_of_groups[0]["fpath"])
time = abf.sweepX
except TypeError as e:
print(f"ERROR! \n {dict_of_groups}\n")
target = [
db.str_list_to_list_ints(peaks["peaks"])
for peaks in dict_of_groups
if peaks["treatment"] == treatment
]
empty_less = [i for i in target if i]
flat = [item for sublist in empty_less for item in sublist]
x_time = time[flat]
return x_time, flat
def count_peaks_treatments(data_dict, treatment):
target = [
db.str_list_to_list_ints(peaks["peaks"])
for peaks in data_dict
if peaks["treatment"] == treatment
]
n_cells = len(target)
n_spikes = [len(i) for i in target]
mean_spikes = np.mean(n_spikes)
sd_spikes = np.std(n_spikes)
return {
"treatment": treatment,
"n_cells": n_cells,
"n_spikes": n_spikes,
"mean_spikes": mean_spikes,
"sd_spikes": sd_spikes,
}
def get_groups_per_sweep(sweep, include, query, db_path):
"""pulls out all the data in a sweep and structures it as a dict.
String of integers (`peaks`) is transformed into a list of ints or empty list."""
con = db.persistent_connection_to_db(db_path)
con.row_factory = sqlite3.Row
data = con.execute(query, (sweep, include))
extracted = [{
"fname": p["fname"],
"fpath": p["fpath"],
"mouse_id": p["mouse_id"],
"cell_side": p["cell_side"],
"cell_n": p["cell_n"],
"memb_potential": p["membrane_potential_uncorrected"],
"include": p["include"],
"protocol": p["protocol"],
"peaks": db.str_list_to_list_ints(p["peak_index"]),
"treatment": p["treatment_group"],
"sweep": sweep,
} for p in data]
con.close()
return extracted
def test_list_to_ints_and_back_empty_list():
list_empty = []
l_str = database.list_of_ints_to_str(list_empty)
decoded = database.str_list_to_list_ints(l_str)
assert list_empty == decoded
def test_assertion_throw_float_in_ints():
string_with_float = "1,2,3.5,4"
with pytest.raises(ValueError):
database.str_list_to_list_ints(string_with_float)
def test_list_to_ints_and_back():
list_ints = [1, 2, 3, 4]
l_str = database.list_of_ints_to_str(list_ints)
decoded = database.str_list_to_list_ints(l_str)
assert list_ints == decoded
def test_str_list_to_list_ints():
string_ints = "1,2,3,4"
converted = database.str_list_to_list_ints(string_ints)
assert [1, 2, 3, 4] == converted
def peaks_to_int_list(ditem):
"""helper to convert indicies from database to integers"""
ditem["peak_index"] = db.str_list_to_list_ints(ditem["peak_index"])
return ditem
