Bases: ConnectomeDataset
Reader for datasets from Brittin et al. 2021
Source code in cect/readers/BrittinDataReader.py
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136 | class BrittinDataReader(ConnectomeDataset):
"""Reader for datasets from [Brittin et al. 2021](../../Brittin_2021.md)"""
verbose = False
def __init__(self, reference_graph):
ConnectomeDataset.__init__(self)
self.reference_graph = reference_graph
cells, neuron_conns = self.read_data()
for conn in neuron_conns:
self.add_connection_info(
conn,
check_overwritten_connections=True,
append_existing_connections=False,
fail_on_any_repeated_connection=True,
)
def read_data(self):
cells = []
conns = []
wb = load_workbook(filename)
sheet = wb.get_sheet_by_name(self.reference_graph)
bilaterals = []
single_cells = []
print_("Opened sheet %s in Excel file: %s" % (sheet, filename))
# print(dir(sheet))
DELTA_VALUE_4 = 4
for row in sheet.rows:
# print(row[0].value)
if "cell_1" not in row[0].value:
delta = int(row[3].value)
if delta == DELTA_VALUE_4:
A = row[0].value
B = row[1].value
contact_area = float(row[2].value)
add_pair_of_contact_conns(conns, A, B, contact_area)
if A not in cells:
cells.append(A)
if B not in cells:
cells.append(B)
A_c = get_contralateral_cell(A)
B_c = get_contralateral_cell(B)
if not A_c == B:
add_pair_of_contact_conns(conns, A_c, B_c, contact_area)
if A_c not in cells:
cells.append(A_c)
if B_c not in cells:
cells.append(B_c)
for cell in cells:
if is_one_of_bilateral_pair(cell):
bilaterals.append(cell)
else:
single_cells.append(cell)
print_(
"Finished processing %i cells, %i bilateral and %i single cells: %s"
% (len(cells), len(bilaterals), len(single_cells), sorted(single_cells))
)
return cells, conns
|