Don't use object as key, use id

Author: pgleeson

python/moose/neuroml2/reader.py

@@ -165,7 +165,10 @@ def __init__(self, verbose=False):
         self.verbose = verbose
         self.doc = None
         self.filename = None        
-        self.nml_to_moose = {} # NeuroML object to MOOSE object
+        self.nml_cells_to_moose = {} # NeuroML object to MOOSE object
+        self.nml_segs_to_moose = {} # NeuroML object to MOOSE object
+        self.nml_chans_to_moose = {} # NeuroML object to MOOSE object
+        self.nml_conc_to_moose = {} # NeuroML object to MOOSE object
         self.moose_to_nml = {} # Moose object to NeuroML object
         self.proto_cells = {} # map id to prototype cell in moose
         self.proto_chans = {} # map id to prototype channels in moose
@@ -252,7 +255,7 @@ def createCellPrototype(self, cell, symmetric=True):
         """To be completed - create the morphology, channels in prototype"""
         nrn = moose.Neuron('%s/%s' % (self.lib.path, cell.id))
         self.proto_cells[cell.id] = nrn
-        self.nml_to_moose[cell] = nrn
+        self.nml_cells_to_moose[cell.id] = nrn
         self.moose_to_nml[nrn] = cell
         self.createMorphology(cell, nrn, symmetric=symmetric)
         self.importBiophysics(cell, nrn)
@@ -297,7 +300,7 @@ def createMorphology(self, nmlcell, moosecell, symmetric=True):
             except AttributeError:
                 parent = None
             self.moose_to_nml[comp] = segment
-            self.nml_to_moose[segment] = comp            
+            self.nml_segs_to_moose[segment.id] = comp            
             p0 = segment.proximal            
             if p0 is None:
                 if parent:
@@ -356,15 +359,15 @@ def importCapacitances(self, nmlcell, moosecell, specificCapacitances):
         for specific_cm in specificCapacitances:
             cm = SI(specific_cm.value)
             for seg in sg_to_segments[specific_cm.segment_groups]:
-                comp = self.nml_to_moose[seg]
+                comp = self.nml_segs_to_moose[seg.id]
                 comp.Cm = sarea(comp) * cm
 
     def importInitMembPotential(self, nmlcell, moosecell, membraneProperties):
         sg_to_segments = self._cell_to_sg[nmlcell]
         for imp in membraneProperties.init_memb_potentials:
             initv = SI(imp.value)
             for seg in sg_to_segments[imp.segment_groups]:
-                comp = self.nml_to_moose[seg]
+                comp = self.nml_segs_to_moose[seg.id]
                 comp.initVm = initv 
 
     def importIntracellularProperties(self, nmlcell, moosecell, properties):
@@ -379,7 +382,7 @@ def importSpecies(self, nmlcell, properties):
                 continue
             segments = getSegments(nmlcell, species, sg_to_segments)
             for seg in segments:
-                comp = self.nml_to_moose[seg]    
+                comp = self.nml_segs_to_moose[seg.id]    
                 self.copySpecies(species, comp)
 
     def copySpecies(self, species, compartment):
@@ -405,7 +408,7 @@ def importAxialResistance(self, nmlcell, intracellularProperties):
         for r in intracellularProperties.resistivities:
             segments = getSegments(nmlcell, r, sg_to_segments)
             for seg in segments:
-                comp = self.nml_to_moose[seg]
+                comp = self.nml_segs_to_moose[seg.id]
                 setRa(comp, SI(r.value))     
 
     def isPassiveChan(self,chan):
@@ -461,14 +464,14 @@ def importChannelsToCell(self, nmlcell, moosecell, membrane_properties):
 
             if self.isPassiveChan(ionChannel):
                 for seg in segments:
-                    comp = self.nml_to_moose[seg]
-                    setRm(self.nml_to_moose[seg], condDensity)
-                    setEk(self.nml_to_moose[seg], erev)
+                    comp = self.nml_segs_to_moose[seg.id]
+                    setRm(comp, condDensity)
+                    setEk(comp, erev)
             else:
                 for seg in segments:
-                    self.copyChannel(chdens, self.nml_to_moose[seg], condDensity, erev)
-            '''moose.le(self.nml_to_moose[seg])
-            moose.showfield(self.nml_to_moose[seg], field="*", showtype=True)'''
+                    self.copyChannel(chdens, self.nml_segs_to_moose[seg.id], condDensity, erev)
+            '''moose.le(self.nml_segs_to_moose[seg.id])
+            moose.showfield(self.nml_segs_to_moose[seg.id], field="*", showtype=True)'''
 
     def copyChannel(self, chdens, comp, condDensity, erev):
         """Copy moose prototype for `chdens` condutcance density to `comp`
@@ -633,7 +636,7 @@ def importIonChannels(self, doc, vmin=-150e-3, vmax=100e-3, vdivs=5000):
                 mchan = self.createHHChannel(chan)
 
             self.id_to_ionChannel[chan.id] = chan
-            self.nml_to_moose[chan] = mchan
+            self.nml_chans_to_moose[chan.id] = mchan
             self.proto_chans[chan.id] = mchan
             if self.verbose:
                 print(self.filename, 'Created ion channel', mchan.path, 'for', chan.type, chan.id)
@@ -658,7 +661,7 @@ def createDecayingPoolConcentrationModel(self, concModel):
         ca.thick = SI(concModel.shellThickness)
         ca.B = 5.2e-6 # B = 5.2e-6/(Ad) where A is the area of the shell and d is thickness - must divide by shell volume when copying
         self.proto_pools[concModel.id] = ca
-        self.nml_to_moose[concModel.id] = ca
+        self.nml_concs_to_moose[concModel.id] = ca
         self.moose_to_nml[ca] = concModel
         logger.debug('Created moose element: %s for nml conc %s' % (ca.path, concModel.id))