Fixed loading point cell params from legacy models (iincl. ssue 607)

suny-downstate-medical-center · Oct 1, 2023 · b75c109 · b75c109
1 parent 5bbafa1
commit b75c109
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,11 @@
+# Version in development
+
+**New features**
+
+**Bug fixes**
+
+- Fixed loading point cell params from legacy models (issue 607)
+
 # Version 1.0.5
 
 **New features**

diff --git a/netpyne/cell/compartCell.py b/netpyne/cell/compartCell.py
@@ -88,6 +88,13 @@ def create(self, createNEURONObj=None):
 
         # apply cell rules
         for propLabel, prop in sim.net.params.cellParams.items():  # for each set of cell properties
+
+            # Try to catch a bug where the cell is designed to be PointCell but misclassfied as CompartCell in Pop._setCellClass()
+            # (may happen if .mod not compiled or mech name misspelled)
+            assert 'secs' in prop, \
+                f"""Cell rule labeled '{propLabel}' is a compartment cell, but it doesn't have required entry 'secs'.
+If this cell is excpected to be a point cell instead, make sure the correspondent mechanism is included and compiled."""
+
             conditionsMet = 1
             if 'conds' in prop and len(prop['conds']) > 0:
                 for (condKey, condVal) in prop['conds'].items():  # check if all conditions are met

diff --git a/netpyne/cell/pointCell.py b/netpyne/cell/pointCell.py
@@ -66,6 +66,8 @@ def __init__(self, gid, tags, create=True, associateGid=True):
         if 'params' in self.tags:
             dictParams = sim.replaceDictODict(self.tags.pop('params'))
             self.params = deepcopy(dictParams)
+        else:
+            self.params = {}
 
         if create and sim.cfg.createNEURONObj:
             self.createNEURONObj()  # create cell

diff --git a/netpyne/network/pop.py b/netpyne/network/pop.py
@@ -498,39 +498,48 @@ def _setCellClass(self):
 
         else:
             # set cell class: CompartCell for compartmental cells of PointCell for point neurons (NetStims, IntFire1,...)
-            try:  # check if cellModel corresponds to an existing point process mechanism; if so, use PointCell
-                tmp = getattr(h, cellModel)
+            if cellModel and hasattr(h, cellModel):
+                # check if cellModel corresponds to an existing point process mechanism; if so, use PointCell
                 self.cellModelClass = sim.PointCell
-                excludeTags = [
-                    'pop',
-                    'cellModel',
-                    'cellType',
-                    'numCells',
-                    'density',
-                    'cellsList',
-                    'gridSpacing',
-                    'xRange',
-                    'yRange',
-                    'zRange',
-                    'xnormRange',
-                    'ynormRange',
-                    'znormRange',
-                    'vref',
-                    'spkTimes',
-                    'dynamicRates',
-                ]
-                params = {k: v for k, v in self.tags.items() if k not in excludeTags}
-                self.tags['params'] = params
-                for k in self.tags['params']:
-                    self.tags.pop(k)
+
+                if 'params' in self.tags and isinstance(self.tags['params'], dict):
+                    # in some cases, params for point cell may already be grouped in the nested 'params' dict.
+                    params = self.tags['params']
+                else:
+                    # otherwise, try extracting them from the top level of tags dict
+                    excludeTags = [
+                        'pop',
+                        'cellModel',
+                        'cellType',
+                        'numCells',
+                        'density',
+                        'cellsList',
+                        'gridSpacing',
+                        'xRange',
+                        'yRange',
+                        'zRange',
+                        'xnormRange',
+                        'ynormRange',
+                        'znormRange',
+                        'vref',
+                        'spkTimes',
+                        'dynamicRates',
+                    ]
+                    params = {k: v for k, v in self.tags.items() if k not in excludeTags}
+                    self.tags['params'] = params
+                    for k in self.tags['params']:
+                        self.tags.pop(k)
                 sim.net.params.popTagsCopiedToCells.append('params')
 
                 # if point cell params defined directly in pop params, need to scan them for string functions
                 if len(params):
                     from ..specs.netParams import CellParams
 
                     CellParams.updateStringFuncsWithPopParams(self.tags['pop'], params)
-            except:
+            else:
+                # otherwise assume has sections and some cellParam rules apply to it; use CompartCell
+                self.cellModelClass = sim.CompartCell
+
                 if getattr(self.tags, 'cellModel', None) in [
                     'NetStim',
                     'DynamicNetStim',
@@ -543,9 +552,6 @@ def _setCellClass(self):
                         'Warning: could not find %s point process mechanism required for population %s'
                         % (cellModel, self.tags['pop'])
                     )
-                self.cellModelClass = (
-                    sim.CompartCell
-                )  # otherwise assume has sections and some cellParam rules apply to it; use CompartCell
 
     def calcRelativeSegCoords(self):
         """Calculate segment coordinates from 3d point coordinates