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Merge pull request #28 from pgleeson/main
Cells pages
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,201 @@ | ||
| from cect.Cells import ALL_PREFERRED_CELL_NAMES | ||
| from cect.Cells import GENERIC_CHEM_SYN | ||
| from cect.Cells import GENERIC_ELEC_SYN | ||
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| from cect.Cells import get_cell_notes | ||
| from cect.Cells import get_cell_internal_link | ||
| from cect.Cells import get_cell_wormatlas_link | ||
| from cect.Cells import get_cell_osbv1_link | ||
| from cect.Cells import are_bilateral_pair | ||
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| from cect import print_ | ||
| # from pprint import pprint | ||
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| import pandas as pd | ||
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| pd.options.plotting.backend = "plotly" | ||
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| def get_dataset_link(dataset): | ||
| # return dataset+'--' | ||
| dataset_text = dataset.replace("Herm", " Herm").replace("Male", " Male") | ||
| return f'<a href="../{dataset}_data">{dataset_text}</a>' | ||
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| def get_weight_table_markdown(w): | ||
| ww = {} | ||
| tot_conns = 0 | ||
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| for dataset in w: | ||
| # print(dataset) | ||
| # print(w[dataset].values()) | ||
| if ( | ||
| len(w[dataset]) > 0 | ||
| and sum(w[dataset].values()) > 0 | ||
| and "SSData" not in dataset | ||
| ): | ||
| ww[dataset] = w[dataset] | ||
| tot_conns += sum(w[dataset].values()) | ||
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| if tot_conns == 0: | ||
| return "No connections found!" | ||
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| sort_by = ( | ||
| get_dataset_link("Cook2019Herm") | ||
| if get_dataset_link("Cook2019Herm") in ww | ||
| else get_dataset_link("White_whole") | ||
| if get_dataset_link("White_whole") in ww | ||
| else get_dataset_link("Randi2023") | ||
| if get_dataset_link("Randi2023") in ww | ||
| else get_dataset_link("RipollSanchezShortRange") | ||
| if get_dataset_link("RipollSanchezShortRange") in ww | ||
| else list(ww.keys())[0] | ||
| ) | ||
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| # print_("Sorting the following data by %s" % sort_by) | ||
| # pprint(ww) | ||
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| df_all = pd.DataFrame(ww).fillna(0).sort_values(sort_by, ascending=False) | ||
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| if df_all is not None: | ||
| fig = df_all.plot( | ||
| labels=dict(index="Connection", value="Weight", variable="Dataset") | ||
| ) | ||
| fig.update_traces( | ||
| marker=dict(size=4), marker_symbol="circle", mode="lines+markers" | ||
| ) | ||
| indent = "" | ||
| fig_md = f"\n{indent}<br/>\n{indent}```plotly\n{indent}{fig.to_json()}\n{indent}```\n" | ||
| else: | ||
| fig_md = "" | ||
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| return "%s\n\n%s" % (df_all.to_markdown(), fig_md) | ||
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| def generate_cell_info_pages(connectomes): | ||
| for cell in ALL_PREFERRED_CELL_NAMES: | ||
| cell_info = '---\ntitle: "Cell: %s"\n---\n\n' % cell | ||
|
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| cell_info += "**%s**\n\n" % (get_cell_notes(cell)) | ||
| cell_info += "%s " % ( | ||
| get_cell_wormatlas_link(cell, text="Info on WormAtlas", button=True) | ||
| ) | ||
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| 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... | ||
|
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| for cds_name in connectomes: | ||
| cds = connectomes[cds_name] | ||
| for synclass in cds.connections: | ||
| if synclass not in all_synclasses: | ||
| all_synclasses.append(synclass) | ||
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| 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" | ||
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| cell_link = get_cell_internal_link( | ||
| cell, html=True, use_color=True, individual_cell_page=True | ||
| ) | ||
| header = "### %s connections %s %s { data-search-exclude }\n\n" % ( | ||
| synclass_info, | ||
| "from" if not synclass == GENERIC_ELEC_SYN else "from/to", | ||
| cell_link, | ||
| ) | ||
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| w = {} | ||
| for cds_name in connectomes: | ||
| r_name = get_dataset_link(cds_name) | ||
| w[r_name] = {} | ||
| cds = connectomes[cds_name] | ||
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| connection_symbol = "↔" if synclass == GENERIC_ELEC_SYN else "→" | ||
| if synclass in cds.connections: | ||
| conns = cds.get_connections_from(cell, synclass) | ||
| 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 % (cell_link, connection_symbol, cc)] = ( | ||
| conns[c] | ||
| ) | ||
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| w_md = get_weight_table_markdown(w) | ||
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| if "No connections" not in w_md: | ||
| cell_info += "%s\n%s\n\n" % (header, w_md) | ||
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| if not synclass == GENERIC_ELEC_SYN: | ||
| cell_link = get_cell_internal_link( | ||
| cell, html=True, use_color=True, individual_cell_page=True | ||
| ) | ||
| header = "### %s connections %s %s { data-search-exclude }\n\n" % ( | ||
| synclass_info, | ||
| "to", | ||
| cell_link, | ||
| ) | ||
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| w = {} | ||
| for cds_name in connectomes: | ||
| r_name = get_dataset_link(cds_name) | ||
| w[r_name] = {} | ||
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| cds = connectomes[cds_name] | ||
| if synclass in cds.connections: | ||
| conns = cds.get_connections_to(cell, synclass) | ||
| 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 % (cc, cell_link)] = conns[c] | ||
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| w_md = get_weight_table_markdown(w) | ||
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| if "No connections" not in w_md: | ||
| cell_info += "%s\n%s\n\n" % (header, w_md) | ||
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| 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) | ||
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| if __name__ == "__main__": | ||
| from cect.White_whole import get_instance | ||
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| cds_white = get_instance() | ||
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| from cect.WitvlietDataReader8 import get_instance | ||
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| cds_w8 = get_instance() | ||
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| connectomes = {"White_whole": cds_white, "Witvliet8": cds_w8} | ||
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| generate_cell_info_pages(connectomes) |
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