Merge pull request #107 from NeuroML/experimental

Update to use of units in mod files

.github/workflows/ci.yml

@@ -21,9 +21,9 @@ jobs:
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.Java }}
         distribution: 'temurin'

.github/workflows/docs.yml

@@ -13,17 +13,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: nelonoel/[email protected]
 
     - name: Set up JDK 11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 11
         java-package: jdk
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
@@ -33,29 +33,29 @@ jobs:
         pip install ghp-import
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/NeuroML2
         ref: development
         path: NeuroML2
 
     - name: Checkout org.lemsml
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: LEMS/jLEMS
         ref: development
         path: jLEMS
 
 
     - name: Checkout org.neuroml.model.injectingplugin
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/org.neuroml.model.injectingplugin
         ref: development
         path: org.neuroml.model.injectingplugin
 
     - name: Checkout org.neuroml.model
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: NeuroML/org.neuroml.model
         ref: development

src/main/java/org/lemsml/export/sedml/SEDMLWriter.java

@@ -22,6 +22,7 @@
 import org.neuroml.export.utils.support.ModelFeature;
 import org.neuroml.model.util.NeuroMLException;
 import org.neuroml.export.utils.support.SupportLevelInfo;
+import org.neuroml.export.sbml.SBMLWriter;
 
 public class SEDMLWriter extends AXMLWriter
 {
@@ -274,24 +275,31 @@ public static void main(String[] args) throws Exception, ModelFeatureSupportExce
         ArrayList<File> lemsFiles = new ArrayList<File>();
 
 
-        lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_TwoCell.xml"));
+        //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_TwoCell.xml"));
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_ACNet.xml"));
 
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SpikingNet.xml"));
         //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SimpleNet.xml"));
         lemsFiles.add(new File("../neuroConstruct/osb/showcase/SBMLShowcase/NeuroML2/LEMS_NML2_Ex9_FN.xml"));
+        lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRose.xml"));
 
 
         SEDMLWriter nw;
         for(File lemsFile : lemsFiles)
         {
             Lems lems = Utils.readLemsNeuroMLFile(lemsFile.getAbsoluteFile()).getLems();
-            nw = new SEDMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sedml"), lemsFile.getName(), Format.SBML);
 
+            SBMLWriter sbmlw = new SBMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sbml"));
+            for(File genFile : sbmlw.convert())
+            {
+                System.out.println("Generated SBML: " + genFile.getAbsolutePath());
+            }
+
+            nw = new SEDMLWriter(lems, lemsFile.getParentFile(), lemsFile.getName().replaceAll(".xml", ".sedml"), lemsFile.getName(), Format.SBML);
             List<File> ff = nw.convert();
             for(File f : ff)
             {
-                System.out.println("Generated sed-ml: " + f.getCanonicalPath());
+                System.out.println("Generated SED-ML: " + f.getCanonicalPath());
             }
 
         }

src/main/java/org/neuroml/export/neuron/NRNUtils.java

@@ -37,7 +37,7 @@ public class NRNUtils implements UnitConverter
     final static String V_CURRENT_SUFFIX = "_I";
     final static String RATE_PREFIX = "rate_";
     final static String REGIME_PREFIX = "regime_";
-    final static String V_COPY_PREFIX = "copy_";
+    //final static String V_COPY_PREFIX = "copy_";
 
     final static String[] NON_NRN_STATE_VARS
         = new String[]{"weightFactor","isi","nextIsi","lastSpikeTime","nextSpikeTemp","nextSpike"};
@@ -51,18 +51,24 @@ public class NRNUtils implements UnitConverter
 
     static final int commentOffset = 40;
 
+    static final String LEN_UNIT = "cm";
+    static final float LEN_CONVERSION = 1e2f;
+
+
     static final String generalUnits = "\n(nA) = (nanoamp)\n"
         + "(uA) = (microamp)\n"
         + "(mA) = (milliamp)\n"
         + "(A) = (amp)\n"
         + "(mV) = (millivolt)\n"
         + "(mS) = (millisiemens)\n"
         + "(uS) = (microsiemens)\n"
+        + "(nF) = (nanofarad)\n"
         + "(molar) = (1/liter)\n"
         + "(kHz) = (kilohertz)\n"
         + "(mM) = (millimolar)\n"
         + "(um) = (micrometer)\n"
         + "(umol) = (micromole)\n"
+        + "(pC) = (picocoulomb)\n"
         + "(S) = (siemens)\n";
 
     static final String ghkUnits = ": bypass nrn default faraday const\n" + "FARADAY = 96485.3 (coulomb)\n" + "R = (k-mole) (joule/degC)\n";
@@ -342,7 +348,7 @@ else if (dimensionName.equals("conductance"))
         }
         else if (dimensionName.equals("capacitance"))
         {
-            return "(microfarads)";
+            return "(nF)";
         }
         else if (dimensionName.equals("specificCapacitance"))
         {
@@ -362,27 +368,31 @@ else if (dimensionName.equals("current"))
         }
         else if (dimensionName.equals("currentDensity"))
         {
-            return "(mA / cm2)";
+            return "(nA / cm2)";
         }
         else if (dimensionName.equals("current_per_time"))
         {
             return "(nA / ms)";
         }
         else if (dimensionName.equals("conductanceDensity"))
+        {
+            return "(uS / cm2)";
+        }
+        else if (dimensionName.equals("conductanceDensity_hoc"))
         {
             return "(S / cm2)";
         }
         else if (dimensionName.equals("length"))
         {
-            return "(um)";
+            return "("+LEN_UNIT+")";
         }
         else if (dimensionName.equals("area"))
         {
-            return "(um2)";
+            return "("+LEN_UNIT+"2)";
         }
         else if (dimensionName.equals("volume"))
         {
-            return "(um3)";
+            return "("+LEN_UNIT+"3)";
         }
         else if (dimensionName.equals("resistivity"))
         {
@@ -398,19 +408,19 @@ else if (dimensionName.equals("concentration"))
         }
         else if (dimensionName.equals("charge_per_mole"))
         {
-            return "(C / umol)";
+            return "(pC / umol)";
         }
         else if (dimensionName.equals("temperature"))
         {
             return "(K)";
         }
         else if (dimensionName.equals("idealGasConstantDims"))
         {
-            return "(millijoule / K / umol)";
+            return "(femtojoule / K / umol)";
         }
         else if (dimensionName.equals("rho_factor"))
         {
-            return "(mM m2 /A /s)";
+            return "(umol / cm / nA / ms)";
         }
         else if (dimensionName.equals("conductance_per_voltage"))
         {
@@ -474,7 +484,7 @@ else if (dimensionName.equals("conductance"))
         }
         else if (dimensionName.equals("capacitance"))
         {
-            return 1e6f;
+            return 1e9f;
         }
         else if (dimensionName.equals("specificCapacitance"))
         {
@@ -497,6 +507,10 @@ else if (dimensionName.equals("current_per_time"))
             return 1e6f;
         }
         else if (dimensionName.equals("conductanceDensity"))
+        {
+            return 1e2f;
+        }
+        else if (dimensionName.equals("conductanceDensity_hoc"))
         {
             return 1e-4f;
         }
@@ -506,15 +520,15 @@ else if (dimensionName.equals("time"))
         }
         else if (dimensionName.equals("length"))
         {
-            return 1000000f;
+            return LEN_CONVERSION;
         }
         else if (dimensionName.equals("area"))
         {
-            return 1e12f;
+            return LEN_CONVERSION * LEN_CONVERSION;
         }
         else if (dimensionName.equals("volume"))
         {
-            return 1e18f;
+            return LEN_CONVERSION * LEN_CONVERSION * LEN_CONVERSION;
         }
         else if (dimensionName.equals("resistance"))
         {
@@ -530,15 +544,15 @@ else if (dimensionName.equals("concentration"))
         }
         else if (dimensionName.equals("charge_per_mole"))
         {
-            return 1e-6f;
+            return 1e6f;
         }
         else if (dimensionName.equals("idealGasConstantDims"))
         {
-            return 0.001f;
+            return 1e9f;
         }
         else if (dimensionName.equals("rho_factor"))
         {
-            return 1f;
+            return 1e-8f;
         }
         else if (dimensionName.equals("conductance_per_voltage"))
         {
@@ -561,6 +575,10 @@ protected static String getDerivativeUnit(String dimensionName)
         {
             return "(/ms)";
         }
+        if (dimensionName.equals("voltage"))  // special case... for rate to calculate neuron voltage/current from abstract cell
+        {
+            return "(mV/ms)";
+        }
         else
         {
             return unit.replaceAll("\\)", "/ms)");