From af097ee8b80524beb2b41a56501d87a7fdaa15d8 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 9 Apr 2024 14:26:31 +0100
Subject: [PATCH] wip: KC

---
 NeuroML2/postprocess_cells.py | 128 ++++++++++++++++++++++++++++++++++
 1 file changed, 128 insertions(+)
 create mode 100644 NeuroML2/postprocess_cells.py

diff --git a/NeuroML2/postprocess_cells.py b/NeuroML2/postprocess_cells.py
new file mode 100644
index 0000000..b7cad54
--- /dev/null
+++ b/NeuroML2/postprocess_cells.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python3
+"""
+Post process and add biophysics to cells.
+
+We make any updates to the morphology, and add biophysics.
+
+File: NeuroML2/postprocess_cells.py
+
+Copyright 2022 Ankur Sinha
+Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
+"""
+
+
+import random
+
+import neuroml
+from neuroml.loaders import read_neuroml2_file
+from pyneuroml.pynml import write_neuroml2_file
+from neuroml.utils import component_factory
+
+random.seed(1412)
+
+
+def load_and_setup_cell(cellname: str):
+    """Load a cell, and clean it to prepare it for further modifications.
+
+    These operations are common for all cells.
+
+    :param cellname: name of cell.
+        the file containing the cell should then be <cell>.morph.cell.nml
+    :returns: document with cell
+    :rtype: neuroml.NeuroMLDocument
+
+    """
+    celldoc = read_neuroml2_file(
+        f"{cellname}.morph.cell.nml"
+    )  # type: neuroml.NeuroMLDocument
+    cell = celldoc.cells[0]  # type: neuroml.Cell
+    celldoc.networks = []
+    cell.id = cellname
+    cell.notes = cell.notes.replace("GGN_20170309_sc_0_0", cellname)
+    cell.notes += ". Reference: Subhasis Ray, Zane N Aldworth, Mark A Stopfer (2020) Feedback inhibition and its control in an insect olfactory circuit eLife 9:e53281."
+
+    [
+        default_all_group,
+        default_soma_group,
+        default_dendrite_group,
+        default_axon_group,
+    ] = cell.setup_default_segment_groups(
+        use_convention=True,
+        default_groups=["all", "soma_group", "dendrite_group", "axon_group"],
+    )
+
+    # populate default groups
+    for sg in cell.morphology.segment_groups:
+        if "soma" in sg.id and sg.id != "soma_group":
+            default_soma_group.add(neuroml.Include(segment_groups=sg.id))
+        if "axon" in sg.id and sg.id != "axon_group":
+            default_axon_group.add(neuroml.Include(segment_groups=sg.id))
+        if "dend" in sg.id and sg.id != "dendrite_group":
+            default_dendrite_group.add(neuroml.Include(segment_groups=sg.id))
+
+    cell.optimise_segment_groups()
+
+    return celldoc
+
+
+def postprocess_GGM():
+    """Post process GGM and add biophysics."""
+    cellname = "GGM"
+    celldoc = load_and_setup_cell(cellname)
+    cell = celldoc.cells[0]  # type: neuroml.Cell
+
+    # biophysics
+    # all
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="pas",
+        ion_channel="pas",
+        cond_density="0.00003 S_per_cm2",
+        erev="-51 mV",
+        group_id="all",
+        ion="non_specific",
+        ion_chan_def_file="channels/pas.channel.nml",
+    )
+    cell.set_resistivity("0.1 kohm_cm", group_id="all")
+    cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
+    cell.set_init_memb_potential("-80mV")
+
+    # L1 validation
+    # cell.validate(recursive=True)
+    cell.summary(morph=False, biophys=True)
+    # use pynml writer to also run L2 validation
+    write_neuroml2_file(celldoc, f"{cellname}.cell.nml")
+
+
+def postprocess_KC():
+    """Manually create KC and add biophysics."""
+    celldoc = component_factory("NeuroMLDocument", id="KC_doc")  # type: neuroml.NeuroMLDocument
+    cell = celldoc.add("Cell", id="KC", validate=False)  # type: neuroml.Cell
+    cell.setup_nml_cell()
+    cell.add_segment([0, 0, 0, 20], [0, 0, 6.366, 20], seg_type="soma")
+
+    # biophysics
+    # all
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="pas",
+        ion_channel="pas",
+        cond_density=".0000975 S_per_cm2",
+        erev="-70 mV",
+        group_id="all",
+        ion="non_specific",
+        ion_chan_def_file="channels/pas.channel.nml",
+    )
+    cell.set_resistivity("35.4 ohm_cm", group_id="all")
+    cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
+    cell.set_init_memb_potential("-80mV")
+
+    # L1 validation
+    # cell.validate(recursive=True)
+    cell.summary(morph=False, biophys=True)
+    # use pynml writer to also run L2 validation
+    write_neuroml2_file(celldoc, "KC.cell.nml")
+
+
+if __name__ == "__main__":
+    postprocess_GGM()