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409 | def generate_cell_info_pages(connectomes):
"""Generates the individual cell pages
Args:
connectomes (list): The list of connectome readers to use
"""
cell_data = load_individual_neuron_info()
cell_classification = get_primary_classification()
all_cell_info = [["Cell name", "Type", "Name details", "Lineage", "Classification"]]
for cell in ALL_PREFERRED_CELL_NAMES:
print_("Generating individual cell page for: %s" % cell)
cell_info = '---\ntitle: "Cell: %s"\n---\n\n' % cell
cell_ref = (
cell
if not ((cell.startswith("CA") or cell.startswith("CP")) and cell[2] == "0")
else "%s%s" % (cell[:2], cell[-1])
) # CA04 -> CA4 etc.
# TODO: investigate DX1, DX2, DX3, EF1, EF2, EF3
if is_any_neuron(cell) and "DX" not in cell and "EF" not in cell:
acronym = cell_data[cell_ref][0]
lineage = cell_data[cell_ref][1]
desc = cell_data[cell_ref][2]
from_ = 0
for c in cell:
# print('Replacing %s (from %s) in %s'%(c,from_,acronym))
if c in acronym:
ii = acronym.index(c, from_)
acronym = "%s<u>%s</u>%s" % (
acronym[:ii],
acronym[ii],
acronym[ii + 1 :],
)
from_ = ii + 1
cell_info += '!!! question "**%s: %s**"\n\n' % (
cell,
acronym,
)
cell_info += (
' <p class="subtext"><b>%s</b> '
% (desc)
)
cell_info += "Lineage: <b>%s</b></p>\n\n" % (lineage)
all_cell_info.append(
[
cell,
get_cell_notes(cell),
cell_data[cell_ref][0],
lineage,
desc,
]
)
else:
cell_info += '!!! question "**%s: %s**"\n\n' % (cell, get_cell_notes(cell))
cc = cell_classification[cell]
all_cell_info.append(
[
cell,
get_cell_notes(cell),
cell_data[cell_ref][0]
if cell_ref in cell_data
else "- To be added... - ",
get_cell_notes(cell),
"- To be added... - ",
cc[0].upper() + cc[1:],
]
)
cell_info += (
' <p class="subtext"><a href="../Cook_2019">Cook 2019</a> classification: <b>%s</b> '
% (get_cell_notes(cell))
)
cc = cell_classification[cell]
color = get_standard_color(cell)
cell_info += (
'All cells of type: <a href="../Cells/#%s"><b><span style="color:%s">%s</span></b></a></p>\n\n'
% (
cc.lower().replace(" ", "-").replace("(", "").replace(")", ""),
color,
cc[0].upper() + cc[1:],
)
)
cell_info += " %s " % (
get_cell_wormatlas_link(cell, text="Info on WormAtlas", button=True)
)
cell_info += "%s\n\n" % get_cell_osbv1_link(
cell, text="View in 3D on Open Source Brain", button=True
)
all_synclasses = [
GENERIC_CHEM_SYN,
GENERIC_ELEC_SYN,
] # ensure these 2 are at the start...
for cds_name in connectomes:
cds = connectomes[cds_name]
for synclass in cds.connections:
if synclass not in all_synclasses:
all_synclasses.append(synclass)
cell_link = get_cell_internal_link(
cell, html=True, use_color=True, individual_cell_page=True
)
reference_cs = "Cook2019Male" if is_male_specific_cell(cell) else "Cook2019Herm"
reference_gj = reference_cs
reference_mono = "Bentley2016_MA"
reference_pep = "RipollSanchezShortRange"
reference_func = "Randi2023"
max_conn_cells = 5
conns_from_cs = "???"
conns_to_cs = "???"
conns_from_mono = "???"
conns_to_mono = "???"
conns_from_pep = "???"
conns_to_pep = "???"
conns_from_func = "???"
conns_to_func = "???"
conns_gj = "???"
tables_md = ""
for synclass in all_synclasses:
synclass_info = synclass
if synclass == GENERIC_CHEM_SYN:
synclass_info = "Chemical synaptic"
if synclass == GENERIC_ELEC_SYN:
synclass_info = "Electrical synaptic"
header = "### %s connections %s %s { data-search-exclude }\n\n" % (
synclass_info,
"to" if not synclass == GENERIC_ELEC_SYN else "from/to",
cell_link,
)
w = {}
for cds_name in connectomes:
r_name = get_dataset_link(cds_name)
w[r_name] = {}
cds = connectomes[cds_name]
connection_symbol = "↔" if synclass == GENERIC_ELEC_SYN else "→"
if synclass in cds.connections:
conns = cds.get_connections_to(cell, synclass)
if cds_name == reference_cs and synclass == GENERIC_CHEM_SYN:
conns_to_cs = _get_top_list(conns, max_conn_cells)
if cds_name == reference_gj and synclass == GENERIC_ELEC_SYN:
conns_gj = _get_top_list(conns, max_conn_cells)
if cds_name == reference_mono:
conns_to_mono = _get_top_list(conns, max_conn_cells)
if cds_name == reference_pep:
conns_to_pep = _get_top_list(conns, max_conn_cells)
if cds_name == reference_func:
conns_to_func = _get_top_list(conns, max_conn_cells)
for c in conns:
cc = get_cell_internal_link(
c, html=True, use_color=True, individual_cell_page=True
)
template = (
"<b><i>%s%s%s</i></b>"
if cell == c
else (
"<b>%s%s%s</b>"
if are_bilateral_pair(cell, c)
else "%s%s%s"
)
)
w[r_name][template % (cc, connection_symbol, cell_link)] = (
conns[c]
)
w_md = get_weight_table_markdown(w)
if "No connections" not in w_md:
tables_md += "%s\n%s\n\n" % (header, w_md)
if not synclass == GENERIC_ELEC_SYN:
header = "### %s connections %s %s { data-search-exclude }\n\n" % (
synclass_info,
"from",
cell_link,
)
w = {}
for cds_name in connectomes:
r_name = get_dataset_link(cds_name)
w[r_name] = {}
cds = connectomes[cds_name]
if synclass in cds.connections:
conns = cds.get_connections_from(cell, synclass)
if cds_name == reference_cs and synclass == GENERIC_CHEM_SYN:
conns_from_cs = _get_top_list(conns, max_conn_cells)
if cds_name == reference_mono:
conns_from_mono = _get_top_list(conns, max_conn_cells)
if cds_name == reference_pep:
conns_from_pep = _get_top_list(conns, max_conn_cells)
if cds_name == reference_func:
conns_from_func = _get_top_list(conns, max_conn_cells)
for c in conns:
cc = get_cell_internal_link(
c, html=True, use_color=True, individual_cell_page=True
)
template = (
"<b><i>%s→%s</i></b>"
if cell == c
else (
"<b>%s→%s</b>"
if are_bilateral_pair(cell, c)
else "%s→%s"
)
)
w[r_name][template % (cell_link, cc)] = conns[c]
w_md = get_weight_table_markdown(w)
if "No connections" not in w_md:
tables_md += "%s\n%s\n\n" % (header, w_md)
cell_info += f"""
### Summary of connections
<p class="subtext">Top {max_conn_cells} connections of specified types to/from this cell (based on {get_dataset_link(reference_cs)}, {get_dataset_link(reference_mono)}, {get_dataset_link(reference_pep)} & {get_dataset_link(reference_func)})</p>
<table style="width:700px">
<tr>
<td><b><a href="#chemical-synaptic-connections-to-{cell.lower()}">Chemical</a></b></td>
<td style="width:40%">{conns_to_cs}</td>
<td style="width:5%" style="vertical-align:bottom;text-align:center;">\u2198</td>
<td rowspan="4" style="vertical-align:middle;text-align:center;"><b>{cell_link}</b></td>
<td style="width:5%" style="vertical-align:bottom;text-align:center;">\u2197</td>
<td style="width:40%">{conns_from_cs}</td>
</tr><tr>
<td><b><a href="#monoaminergic-connections-to-{cell.lower()}">Monoaminergic</a></b></td><td>{conns_to_mono}</td><td align="middle">→</td><td align="middle">→</td><td>{conns_from_mono}</td>
</tr><tr>
<td><b><a href="#peptidergic-connections-to-{cell.lower()}">Peptidergic</a></b></td> <td>{conns_to_pep}</td><td align="middle">→</td><td align="middle">→</td><td>{conns_from_pep}</td>
</tr><tr>
<td><b><a href="#functional-connections-to-{cell.lower()}">Functional</a></b></td> <td>{conns_to_func}</td><td align="middle">\u2197</td><td align="middle">\u2198</td><td>{conns_from_func}</td>
</tr><tr>
<td> </td> <td colspan="5" align="middle">\u2195</td>
</tr><tr>
<td><b><a href="#electrical-synaptic-connections-fromto-{cell.lower()}">Electrical</a></b></td> <td colspan="5" align="middle">{conns_gj}</td>
</tr>
</table>
"""
cell_info += tables_md
cell_filename = "docs/%s.md" % cell
with open(cell_filename, "w") as cell_file:
print_(f"Writing info on cell {cell} to {cell_filename}")
cell_file.write(cell_info)
cell_info_filename = "cect/data/all_cell_info.csv"
with open(cell_info_filename, "w") as csv_file:
print_(f"Writing info on all cells to {cell_info_filename}")
csv_writer = csv.writer(csv_file, delimiter=",", quotechar='"')
for line in all_cell_info:
csv_writer.writerow(line)
|