From 299d0f7b96fd6c41914a1b006dbcc6d18b370c84 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 14 Jan 2025 17:19:46 +0000
Subject: [PATCH 1/4] feat(utils): replace undetermined gates with standard
ones
Wherever possible.
Fixes #205
---
neuroml/utils.py | 57 ++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/neuroml/utils.py b/neuroml/utils.py
index af26761..1406531 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -472,6 +472,63 @@ def fix_external_morphs_biophys_in_cell(
return newdoc
+def create_new_typed_gate(gate):
+ """Convert an undetermined gate to a "determined" gate
+
+ :param gate: gate object of GateHHUndetermined type
+ :returns: new gate object, or None if the gate is not of a standard type
+ """
+ gates_name_map = {
+ "gateHHrates": "GateHHRates",
+ "gateHHratesTau": "GateHHRatesTau",
+ "gateHHratesInf": "GateHHRatesInf",
+ "gateHHratesTauInf": "GateHHRatesTauInf",
+ "gateHHtauInf": "GateHHTauInf",
+ "gateHHInstantaneous": "GateHHInstantaneous",
+ "gateFractional": "GateFractional",
+ "gateKS": "GateKS",
+ }
+ gate_type = getattr(gate, "type", None)
+ if gate_type:
+ try:
+ gate_class_type = gates_name_map[gate_type]
+ # if it isn't in our dict, it's non standard
+ except KeyError:
+ return None
+
+ new_gate = component_factory(component_type=gate_class_type, validate=False)
+ print(gate.__dict__)
+ new_gate.__dict__.update(gate.__dict__)
+ return new_gate
+
+
+def move_undetermined_gates_to_typed(nml2_doc):
+ """Replace gates of GateHHUndetermined type with their standard
+ counterparts where possible.
+
+ Note that this modifies the passed NeuroMLDocument object in-place.
+
+ :param nml2_doc: NeuroMLDocument object
+ :returns: None
+
+ """
+ all_channels = (
+ list(nml2_doc.ion_channel_hhs.__iter__())
+ + list(nml2_doc.ion_channel.__iter__())
+ + list(nml2_doc.ion_channel_v_shifts.__iter__())
+ )
+ for achannel in all_channels:
+ determined_gates = []
+ undetermined_gates = getattr(achannel, "gates", [])
+ for gate in undetermined_gates:
+ new_typed_gate = create_new_typed_gate(gate)
+ if new_typed_gate:
+ achannel.add(new_typed_gate)
+ determined_gates.append(gate)
+ for d_gate in determined_gates:
+ undetermined_gates.remove(d_gate)
+
+
def main():
if len(sys.argv) != 2:
print("Please specify the name of the NeuroML2 file...")
From 91269dbbe31efa77831398f75810b1b64a05e492 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 14 Jan 2025 17:21:12 +0000
Subject: [PATCH 2/4] feat(loader): move undetermined gates to standard ones
---
neuroml/loaders.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/neuroml/loaders.py b/neuroml/loaders.py
index 863ea5f..eb8d1f4 100644
--- a/neuroml/loaders.py
+++ b/neuroml/loaders.py
@@ -49,6 +49,7 @@ def __nml2_doc(cls, file_name: str) -> neuroml.NeuroMLDocument:
if supressGeneratedsWarnings:
warnings.simplefilter("ignore")
nml2_doc = nmlparse(file_name, silence=True)
+ utils.move_undetermined_gates_to_typed(nml2_doc)
if supressGeneratedsWarnings:
warnings.resetwarnings()
except Exception as e:
From 42424f3b48c4629e8a16f8f332fd07c787eab115 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 14 Jan 2025 17:30:35 +0000
Subject: [PATCH 3/4] feat(utils): improve type hints, docs
---
neuroml/utils.py | 42 +++++++++++++++++++++++++++++++++++++++---
1 file changed, 39 insertions(+), 3 deletions(-)
diff --git a/neuroml/utils.py b/neuroml/utils.py
index 1406531..f7bbff9 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -15,7 +15,20 @@
import networkx
import neuroml.nml.nml as schema
-from neuroml import BiophysicalProperties, Morphology, NeuroMLDocument
+from neuroml import (
+ BiophysicalProperties,
+ GateFractional,
+ GateHHInstantaneous,
+ GateHHRates,
+ GateHHRatesInf,
+ GateHHRatesTau,
+ GateHHRatesTauInf,
+ GateHHTauInf,
+ GateHHUndetermined,
+ GateKS,
+ Morphology,
+ NeuroMLDocument,
+)
from . import loaders
@@ -472,10 +485,24 @@ def fix_external_morphs_biophys_in_cell(
return newdoc
-def create_new_typed_gate(gate):
+def create_new_typed_gate(
+ gate: GateHHUndetermined,
+) -> Optional[
+ Union[
+ GateHHRates,
+ GateHHRatesTau,
+ GateHHRatesInf,
+ GateHHRatesTauInf,
+ GateHHTauInf,
+ GateHHInstantaneous,
+ GateFractional,
+ GateKS,
+ ]
+]:
"""Convert an undetermined gate to a "determined" gate
:param gate: gate object of GateHHUndetermined type
+ :type gate: GateHHUndetermined
:returns: new gate object, or None if the gate is not of a standard type
"""
gates_name_map = {
@@ -501,17 +528,26 @@ def create_new_typed_gate(gate):
new_gate.__dict__.update(gate.__dict__)
return new_gate
+ return None
-def move_undetermined_gates_to_typed(nml2_doc):
+
+def move_undetermined_gates_to_typed(nml2_doc: NeuroMLDocument):
"""Replace gates of GateHHUndetermined type with their standard
counterparts where possible.
Note that this modifies the passed NeuroMLDocument object in-place.
+ If `nml2_doc` is not a NeuroMLDocument, this function does nothing and
+ simply returns None.
+
:param nml2_doc: NeuroMLDocument object
+ :type nml2_doc: NeuroMLDocument
:returns: None
"""
+ if not isinstance(nml2_doc, NeuroMLDocument):
+ return None
+
all_channels = (
list(nml2_doc.ion_channel_hhs.__iter__())
+ list(nml2_doc.ion_channel.__iter__())
From 2e38e82ba5191e500b5e8e2d064f8cc5b0d0eb7b Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 14 Jan 2025 17:30:52 +0000
Subject: [PATCH 4/4] feat(loader): do gate tweaking after document is
correctly read
---
neuroml/loaders.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/neuroml/loaders.py b/neuroml/loaders.py
index eb8d1f4..7df336b 100644
--- a/neuroml/loaders.py
+++ b/neuroml/loaders.py
@@ -49,12 +49,12 @@ def __nml2_doc(cls, file_name: str) -> neuroml.NeuroMLDocument:
if supressGeneratedsWarnings:
warnings.simplefilter("ignore")
nml2_doc = nmlparse(file_name, silence=True)
- utils.move_undetermined_gates_to_typed(nml2_doc)
if supressGeneratedsWarnings:
warnings.resetwarnings()
except Exception as e:
raise Exception("Not a valid NeuroML 2 doc (%s): %s" % (file_name, e), e)
+ utils.move_undetermined_gates_to_typed(nml2_doc)
return nml2_doc