Better way to handle soma

Author: pgleeson

CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml

@@ -6834,7 +6834,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="dend_11"/>
                 <include segmentGroup="dend_10"/>
             </segmentGroup>
-            <segmentGroup id="soma">
+            <segmentGroup id="ModelViewParmSubset_1">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="dend">
@@ -6876,7 +6876,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="axon_0"/>
                 <include segmentGroup="axon_1"/>
             </segmentGroup>
-            <segmentGroup id="OneSecGrp_SectionRef_1">
+            <segmentGroup id="soma">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="soma_group">

CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml

@@ -24388,7 +24388,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="apic_11"/>
                 <include segmentGroup="apic_10"/>
             </segmentGroup>
-            <segmentGroup id="soma">
+            <segmentGroup id="ModelViewParmSubset_9">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="ModelViewParmSubset_10">
@@ -24626,7 +24626,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="apic_11"/>
                 <include segmentGroup="apic_10"/>
             </segmentGroup>
-            <segmentGroup id="OneSecGrp_SectionRef_289">
+            <segmentGroup id="soma">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="soma_group">

CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml

@@ -21025,7 +21025,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="apic_38"/>
                 <include segmentGroup="apic_37"/>
             </segmentGroup>
-            <segmentGroup id="soma">
+            <segmentGroup id="ModelViewParmSubset_23">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="ModelViewParmSubset_24">
@@ -21265,7 +21265,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="axon_0"/>
                 <include segmentGroup="axon_1"/>
             </segmentGroup>
-            <segmentGroup id="OneSecGrp_SectionRef_1193">
+            <segmentGroup id="soma">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="soma_group">

CellTypesDatabase/models/NeuroML2/Cell_497233223.cell.nml

@@ -6914,7 +6914,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <include segmentGroup="axon_0"/>
                 <include segmentGroup="axon_1"/>
             </segmentGroup>
-            <segmentGroup id="OneSecGrp_SectionRef_1">
+            <segmentGroup id="soma">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="soma_group">

CellTypesDatabase/models/ParseAll.py

@@ -147,7 +147,7 @@
         print("PA >> Found group: %s"%sg.id)
         if (sg.id.startswith('ModelViewParm')) and len(sg.members)==0:
             replace = {}
-            replace['soma_'] = 'soma'
+            #replace['soma_'] = 'soma'
             replace['axon_'] = 'axon'
             replace['apic_'] = 'apic'
             replace['dend_'] = 'dend'
@@ -157,9 +157,16 @@
                     #print inc
                     all_match = all_match and inc.segment_groups.startswith(prefix)
                 if all_match:
-                    print("Replacing group named %s with %s"%(sg.id,replace[prefix]))
+                    print("PA >>    1) Replacing group named %s with %s"%(sg.id,replace[prefix]))
                     sg.id = replace[prefix]
 
+        if (sg.id.startswith('OneSecGrp')) and len(sg.includes)==1:
+            if sg.includes[0].segment_groups == "soma_0":
+                rep = 'soma'
+                print("PA >>    2) Replacing group named %s with %s"%(sg.id,rep))
+                sg.id = rep
+
+
     cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="soma_group", includes=[neuroml.Include("soma")]))
     cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="axon_group", includes=[neuroml.Include("axon")]))
     cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="dendrite_group", includes=[neuroml.Include("dend")]))