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201 | class VarshneyDataReader(ConnectomeDataset):
"""Reader for Varshney et al. 2011 connectivity dataset"""
def __init__(self, include_nmj=False):
ConnectomeDataset.__init__(self)
self.typed_conns = {
SEND_SYN: [],
SEND_POLY_SYN: [],
RECEIVE_SYN: [],
RECEIVE_POLY_SYN: [],
SEND_ANY: set(),
RECEIVE_ANY: set(),
ELECT_JUNC_SYN: [],
NMJ_ENDPOINT: [],
}
self.include_nmj = include_nmj
cells, neuron_conns = self.read_data()
for conn in neuron_conns:
self.add_connection_info(
conn,
append_existing_connections=True,
check_overwritten_connections=True,
fail_on_any_repeated_connection=False,
)
def _check_valid_synapse_type(self, syn_type):
if syn_type not in self.typed_conns:
raise ValueError(
f"Synapse type '{syn_type}' not recognized for {NAME}. Valid types are: {list(self.typed_conns.keys())}"
)
return syn_type
def read_data(self):
cells = []
conns = []
if filename.endswith(".xls"):
from xlrd import open_workbook
wb = open_workbook(filename)
rows = []
sheet = wb.sheet_by_index(0)
for row in range(1, sheet.nrows):
rows.append(
(
str(sheet.cell(row, 0).value),
str(sheet.cell(row, 1).value),
str(sheet.cell(row, 2).value),
int(sheet.cell(row, 3).value),
)
)
else:
wb = load_workbook(filename)
sheet = wb.worksheets[0]
rows = sheet.iter_rows(min_row=2, values_only=True)
print_("Opened the Excel file: " + filename)
for row in rows: # Assuming data starts from the second row
pre = str(row[0])
post = str(row[1])
pre = _remove_leading_index_zero(pre)
post = _remove_leading_index_zero(post)
if post == NMJ_ENDPOINT:
post = UNSPECIFIED_BODY_WALL_MUSCLE
syntype_here = self._check_valid_synapse_type(str(row[2]))
num = int(row[3])
self.typed_conns[syntype_here].append(f"{pre}_{post}_{num}")
if syntype_here in [SEND_SYN, SEND_POLY_SYN]:
self.typed_conns[SEND_ANY].add(f"{pre}_{post}")
elif syntype_here in [RECEIVE_SYN, RECEIVE_POLY_SYN]:
self.typed_conns[RECEIVE_ANY].add(f"{pre}_{post}")
if syntype_here != NMJ_ENDPOINT or self.include_nmj:
synclass = (
GENERIC_ELEC_SYN_CLASS
if syntype_here == ELECT_JUNC_SYN
else GENERIC_CHEM_SYN_CLASS
if (syntype_here == SEND_POLY_SYN or syntype_here == SEND_SYN)
else GENERIC_CHEM_SYN_CLASS
if (syntype_here == NMJ_ENDPOINT)
else None
)
if syntype_here == ELECT_JUNC_SYN:
syntype = ELECTRICAL_SYN_TYPE
else:
syntype = CHEMICAL_SYN_TYPE
if synclass is not None:
conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
if pre not in cells:
cells.append(pre)
if post not in cells:
cells.append(post)
else:
if not (
syntype_here == RECEIVE_SYN or syntype_here == RECEIVE_POLY_SYN
):
raise ValueError(
f"Warning: Unrecognized synapse type '{syntype_here}' for connection {pre} -> {post} for {NAME}."
)
total = 0
for syn_type, conn_list in self.typed_conns.items():
total += len(conn_list)
info = ""
if syn_type in [SEND_SYN, SEND_POLY_SYN, RECEIVE_SYN, RECEIVE_POLY_SYN]:
info = f"\t({', '.join(conn_list[:5])}..., {conn_list[-1]})"
print_(
f" {syn_type}: {len(conn_list)} connections\t({len(set(conn_list))} unique) {info}"
)
print_(f" Total: {total} connections (half: {total / 2})")
s_tot = len(self.typed_conns[SEND_SYN]) + len(self.typed_conns[SEND_POLY_SYN])
r_tot = len(self.typed_conns[RECEIVE_SYN]) + len(
self.typed_conns[RECEIVE_POLY_SYN]
)
print_(
f" Total chemical synapses: {s_tot} (send) + {r_tot} (receive) = {s_tot + r_tot}"
)
gj = len(self.typed_conns[ELECT_JUNC_SYN])
print_(f" Total electrical synapses: {gj}, half: {gj / 2}")
return cells, conns
def read_muscle_data(self):
conns = []
neurons = []
muscles = []
return neurons, muscles, conns
|