From ff939da9abdfd8f2faf8f60dc517fcabf10f2854 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 14 May 2024 12:49:57 +0100
Subject: [PATCH] Regenerated nets

---
 NeuroML2/BC1_StimNet.net.nml |  4 ++--
 NeuroML2/BC2_StimNet.net.nml |  4 ++--
 NeuroML2/BC6_StimNet.net.nml |  4 ++--
 NeuroML2/CreateNetwork.py    |  4 ++--
 NeuroML2/LEMS_Test_BC1.xml   | 35 +++++++++++++++++------------------
 NeuroML2/LEMS_Test_BC2.xml   | 35 +++++++++++++++++------------------
 NeuroML2/LEMS_Test_BC6.xml   | 35 +++++++++++++++++------------------
 7 files changed, 59 insertions(+), 62 deletions(-)

diff --git a/NeuroML2/BC1_StimNet.net.nml b/NeuroML2/BC1_StimNet.net.nml
index 63d0b3b..bdacb7a 100644
--- a/NeuroML2/BC1_StimNet.net.nml
+++ b/NeuroML2/BC1_StimNet.net.nml
@@ -1,10 +1,10 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta5.xsd" id="BC1_StimNet">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="BC1_StimNet">
     <include href="BC1_na_k.cell.nml"/>
     <pulseGenerator id="stim0" delay="50ms" duration="200ms" amplitude="0.5nA"/>
     <network id="BC1_StimNet">
         <population id="BC" component="BC1_na_k" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim0_input" population="BC" component="stim0">
diff --git a/NeuroML2/BC2_StimNet.net.nml b/NeuroML2/BC2_StimNet.net.nml
index 040761d..5febe2c 100644
--- a/NeuroML2/BC2_StimNet.net.nml
+++ b/NeuroML2/BC2_StimNet.net.nml
@@ -1,10 +1,10 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta5.xsd" id="BC2_StimNet">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="BC2_StimNet">
     <include href="BC2_na_k.cell.nml"/>
     <pulseGenerator id="stim0" delay="50ms" duration="200ms" amplitude="0.5nA"/>
     <network id="BC2_StimNet">
         <population id="BC" component="BC2_na_k" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim0_input" population="BC" component="stim0">
diff --git a/NeuroML2/BC6_StimNet.net.nml b/NeuroML2/BC6_StimNet.net.nml
index ffd0fde..9430852 100644
--- a/NeuroML2/BC6_StimNet.net.nml
+++ b/NeuroML2/BC6_StimNet.net.nml
@@ -1,10 +1,10 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta5.xsd" id="BC6_StimNet">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="BC6_StimNet">
     <include href="BC6_na_k.cell.nml"/>
     <pulseGenerator id="stim0" delay="50ms" duration="200ms" amplitude="0.5nA"/>
     <network id="BC6_StimNet">
         <population id="BC" component="BC6_na_k" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim0_input" population="BC" component="stim0">
diff --git a/NeuroML2/CreateNetwork.py b/NeuroML2/CreateNetwork.py
index 2e7751a..4ef2dfa 100644
--- a/NeuroML2/CreateNetwork.py
+++ b/NeuroML2/CreateNetwork.py
@@ -75,8 +75,8 @@ def create_network_for_cell(cell_ref):
     to_save = {'%s_voltages.dat'%cell_id:[]}
 
     for seg_id in interesting_seg_ids:
-        to_plot.values()[0].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
-        to_save.values()[0].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
+        to_plot['Some_voltages'].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
+        to_save['%s_voltages.dat'%cell_id].append('%s/0/%s/%s/v'%(pop.id, pop.component,seg_id))
 
     generate_lems_file_for_neuroml(sim_id, 
                                    nml_file, 
diff --git a/NeuroML2/LEMS_Test_BC1.xml b/NeuroML2/LEMS_Test_BC1.xml
index 66dfa89..55f366d 100644
--- a/NeuroML2/LEMS_Test_BC1.xml
+++ b/NeuroML2/LEMS_Test_BC1.xml
@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.3.14 (libNeuroML v0.2.45)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.12 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="Test"/>
 
@@ -13,29 +13,28 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="BC1_StimNet.net.nml"/>
     <Include file="BC1_na_k.cell.nml"/>
     <Include file="pas.channel.nml"/>
     <Include file="channelConvert/Na_BC.channel.nml"/>
     <Include file="channelConvert/K_BC.channel.nml"/>
-   
-    <Simulation id="Test" length="400ms" step="0.025ms" target="BC1_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
-        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.0" ymin="-80" ymax="40">
-            <Line id="BC_0_BC1_na_k_0_v" quantity="BC/0/BC1_na_k/0/v" scale="1mV" color="#6aa799" timeScale="1ms"/>
-            <Line id="BC_0_BC1_na_k_1000_v" quantity="BC/0/BC1_na_k/1000/v" scale="1mV" color="#029a72" timeScale="1ms"/>
-            <Line id="BC_0_BC1_na_k_2000_v" quantity="BC/0/BC1_na_k/2000/v" scale="1mV" color="#d340bb" timeScale="1ms"/>
-            <Line id="BC_0_BC1_na_k_10000_v" quantity="BC/0/BC1_na_k/10000/v" scale="1mV" color="#4c73a9" timeScale="1ms"/>
+
+    <Simulation id="Test" length="400.0ms" step="0.025ms" target="BC1_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.00000000000006" ymin="-80" ymax="40">
+            <Line id="BC_0_BC1_na_k_0_v" quantity="BC/0/BC1_na_k/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
+            <Line id="BC_0_BC1_na_k_1000_v" quantity="BC/0/BC1_na_k/1000/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="BC_0_BC1_na_k_2000_v" quantity="BC/0/BC1_na_k/2000/v" scale="1mV" color="#98e752" timeScale="1ms"/>
+            <Line id="BC_0_BC1_na_k_10000_v" quantity="BC/0/BC1_na_k/10000/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="BC1_na_k_voltages_dat" fileName="BC1_na_k_voltages.dat">
-            <OutputColumn id="BC_0_BC1_na_k_0_v" quantity="BC/0/BC1_na_k/0/v"/> 
-            <OutputColumn id="BC_0_BC1_na_k_1000_v" quantity="BC/0/BC1_na_k/1000/v"/> 
-            <OutputColumn id="BC_0_BC1_na_k_2000_v" quantity="BC/0/BC1_na_k/2000/v"/> 
-            <OutputColumn id="BC_0_BC1_na_k_10000_v" quantity="BC/0/BC1_na_k/10000/v"/> 
+            <OutputColumn id="BC_0_BC1_na_k_0_v" quantity="BC/0/BC1_na_k/0/v"/>
+            <OutputColumn id="BC_0_BC1_na_k_1000_v" quantity="BC/0/BC1_na_k/1000/v"/>
+            <OutputColumn id="BC_0_BC1_na_k_2000_v" quantity="BC/0/BC1_na_k/2000/v"/>
+            <OutputColumn id="BC_0_BC1_na_k_10000_v" quantity="BC/0/BC1_na_k/10000/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NeuroML2/LEMS_Test_BC2.xml b/NeuroML2/LEMS_Test_BC2.xml
index a3a4619..1bd399b 100644
--- a/NeuroML2/LEMS_Test_BC2.xml
+++ b/NeuroML2/LEMS_Test_BC2.xml
@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.3.14 (libNeuroML v0.2.45)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.12 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="Test"/>
 
@@ -13,29 +13,28 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="BC2_StimNet.net.nml"/>
     <Include file="BC2_na_k.cell.nml"/>
     <Include file="pas.channel.nml"/>
     <Include file="channelConvert/Na_BC.channel.nml"/>
     <Include file="channelConvert/K_BC.channel.nml"/>
-   
-    <Simulation id="Test" length="400ms" step="0.025ms" target="BC2_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
-        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.0" ymin="-80" ymax="40">
-            <Line id="BC_0_BC2_na_k_0_v" quantity="BC/0/BC2_na_k/0/v" scale="1mV" color="#6aa799" timeScale="1ms"/>
-            <Line id="BC_0_BC2_na_k_1000_v" quantity="BC/0/BC2_na_k/1000/v" scale="1mV" color="#029a72" timeScale="1ms"/>
-            <Line id="BC_0_BC2_na_k_2000_v" quantity="BC/0/BC2_na_k/2000/v" scale="1mV" color="#d340bb" timeScale="1ms"/>
-            <Line id="BC_0_BC2_na_k_10000_v" quantity="BC/0/BC2_na_k/10000/v" scale="1mV" color="#4c73a9" timeScale="1ms"/>
+
+    <Simulation id="Test" length="400.0ms" step="0.025ms" target="BC2_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.00000000000006" ymin="-80" ymax="40">
+            <Line id="BC_0_BC2_na_k_0_v" quantity="BC/0/BC2_na_k/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
+            <Line id="BC_0_BC2_na_k_1000_v" quantity="BC/0/BC2_na_k/1000/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="BC_0_BC2_na_k_2000_v" quantity="BC/0/BC2_na_k/2000/v" scale="1mV" color="#98e752" timeScale="1ms"/>
+            <Line id="BC_0_BC2_na_k_10000_v" quantity="BC/0/BC2_na_k/10000/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="BC2_na_k_voltages_dat" fileName="BC2_na_k_voltages.dat">
-            <OutputColumn id="BC_0_BC2_na_k_0_v" quantity="BC/0/BC2_na_k/0/v"/> 
-            <OutputColumn id="BC_0_BC2_na_k_1000_v" quantity="BC/0/BC2_na_k/1000/v"/> 
-            <OutputColumn id="BC_0_BC2_na_k_2000_v" quantity="BC/0/BC2_na_k/2000/v"/> 
-            <OutputColumn id="BC_0_BC2_na_k_10000_v" quantity="BC/0/BC2_na_k/10000/v"/> 
+            <OutputColumn id="BC_0_BC2_na_k_0_v" quantity="BC/0/BC2_na_k/0/v"/>
+            <OutputColumn id="BC_0_BC2_na_k_1000_v" quantity="BC/0/BC2_na_k/1000/v"/>
+            <OutputColumn id="BC_0_BC2_na_k_2000_v" quantity="BC/0/BC2_na_k/2000/v"/>
+            <OutputColumn id="BC_0_BC2_na_k_10000_v" quantity="BC/0/BC2_na_k/10000/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NeuroML2/LEMS_Test_BC6.xml b/NeuroML2/LEMS_Test_BC6.xml
index 54a445a..eba7643 100644
--- a/NeuroML2/LEMS_Test_BC6.xml
+++ b/NeuroML2/LEMS_Test_BC6.xml
@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.3.14 (libNeuroML v0.2.45)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.12 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="Test"/>
 
@@ -13,29 +13,28 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="BC6_StimNet.net.nml"/>
     <Include file="BC6_na_k.cell.nml"/>
     <Include file="pas.channel.nml"/>
     <Include file="channelConvert/Na_BC.channel.nml"/>
     <Include file="channelConvert/K_BC.channel.nml"/>
-   
-    <Simulation id="Test" length="400ms" step="0.025ms" target="BC6_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
-        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.0" ymin="-80" ymax="40">
-            <Line id="BC_0_BC6_na_k_0_v" quantity="BC/0/BC6_na_k/0/v" scale="1mV" color="#6aa799" timeScale="1ms"/>
-            <Line id="BC_0_BC6_na_k_1000_v" quantity="BC/0/BC6_na_k/1000/v" scale="1mV" color="#029a72" timeScale="1ms"/>
-            <Line id="BC_0_BC6_na_k_2000_v" quantity="BC/0/BC6_na_k/2000/v" scale="1mV" color="#d340bb" timeScale="1ms"/>
-            <Line id="BC_0_BC6_na_k_10000_v" quantity="BC/0/BC6_na_k/10000/v" scale="1mV" color="#4c73a9" timeScale="1ms"/>
+
+    <Simulation id="Test" length="400.0ms" step="0.025ms" target="BC6_StimNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="Some_voltages" title="Plots of Some_voltages" timeScale="1ms" xmin="-40.0" xmax="440.00000000000006" ymin="-80" ymax="40">
+            <Line id="BC_0_BC6_na_k_0_v" quantity="BC/0/BC6_na_k/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
+            <Line id="BC_0_BC6_na_k_1000_v" quantity="BC/0/BC6_na_k/1000/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="BC_0_BC6_na_k_2000_v" quantity="BC/0/BC6_na_k/2000/v" scale="1mV" color="#98e752" timeScale="1ms"/>
+            <Line id="BC_0_BC6_na_k_10000_v" quantity="BC/0/BC6_na_k/10000/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="BC6_na_k_voltages_dat" fileName="BC6_na_k_voltages.dat">
-            <OutputColumn id="BC_0_BC6_na_k_0_v" quantity="BC/0/BC6_na_k/0/v"/> 
-            <OutputColumn id="BC_0_BC6_na_k_1000_v" quantity="BC/0/BC6_na_k/1000/v"/> 
-            <OutputColumn id="BC_0_BC6_na_k_2000_v" quantity="BC/0/BC6_na_k/2000/v"/> 
-            <OutputColumn id="BC_0_BC6_na_k_10000_v" quantity="BC/0/BC6_na_k/10000/v"/> 
+            <OutputColumn id="BC_0_BC6_na_k_0_v" quantity="BC/0/BC6_na_k/0/v"/>
+            <OutputColumn id="BC_0_BC6_na_k_1000_v" quantity="BC/0/BC6_na_k/1000/v"/>
+            <OutputColumn id="BC_0_BC6_na_k_2000_v" quantity="BC/0/BC6_na_k/2000/v"/>
+            <OutputColumn id="BC_0_BC6_na_k_10000_v" quantity="BC/0/BC6_na_k/10000/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>