Merge pull request #215 from DimitriPlotnikov/master

Improve model and symbol table infrastructure

models/ht_neuron.nestml

@@ -132,9 +132,18 @@ neuron ht_neuron_nestml:
     D_thresh real = -10.0
     D_slope real = 5.0;
     alias D_influx real = 1.0 / ( 1.0 + exp( -( V_m - D_thresh ) / D_slope ) );
+
+    alias I_Na real = -g_NaL * ( V_m - E_Na )
+    alias I_K real = -g_KL * ( V_m - E_K )
   end
 
   equations:
+    # delta V
+    V_m'  = ( I_Na + I_K + I_syn + I_NaP + I_KNa + I_T + I_h + I_stim ) / Tau_m + I_spike
+
+    # delta Theta
+    THETA' = -( THETA - Theta_eq ) / Tau_theta
+
     # equation modified from y[](1-D_eq) to (y[]-D_eq), since we'd not
     # be converging to equilibrium otherwise
     IKNa_D' = D_influx_peak * D_influx - ( IKNa_D  - KNa_D_EQ ) / tau_D

src/main/java/org/nest/nestml/_symboltable/NESTMLSymbolTableCreator.java

@@ -7,6 +7,7 @@
 
 import de.monticore.symboltable.*;
 import de.se_rwth.commons.Names;
+import de.se_rwth.commons.logging.Log;
 import org.nest.nestml._ast.*;
 import org.nest.nestml._visitor.NESTMLVisitor;
 import org.nest.ode._ast.ASTEquation;
@@ -82,7 +83,7 @@ public void visit(final ASTNESTMLCompilationUnit compilationUnitAst) {
   private List<ImportStatement> computeImportStatements(ASTNESTMLCompilationUnit compilationUnitAst) {
     final List<ImportStatement> imports = new ArrayList<>();
 
-    compilationUnitAst.getImports().stream().forEach(importStatement -> {
+    compilationUnitAst.getImports().forEach(importStatement -> {
       final String importAsString = Names.getQualifiedName(importStatement.getQualifiedName().getParts());
       imports.add(new ImportStatement(importAsString, importStatement.isStar()));
     });
@@ -115,6 +116,7 @@ public void visit(final ASTNeuron astNeuron) {
 
   public void endVisit(final ASTNeuron astNeuron) {
     addVariablesFromODEBlock(astNeuron.getBody());
+    assignOdeToVariables(astNeuron.getBody());
     removeCurrentScope();
     currentTypeSymbol = empty();
   }
@@ -135,12 +137,12 @@ private void addVariablesFromODEBlock(final ASTBody astBody) {
       astBody.getODEBlock().get().getODEs()
           .stream()
           .filter(ode -> ode.getLhs().getDifferentialOrder().size() > 1)
-          .forEach(this::addODEVariable);
+          .forEach(this::addDerivedVariable);
     }
 
   }
 
-  private void addODEVariable(final ASTEquation ode) {
+  private void addDerivedVariable(final ASTEquation ode) {
     final String variableName = convertToSimpleName(ode.getLhs());
 
     final TypeSymbol type = PredefinedTypes.getType("real");
@@ -151,6 +153,7 @@ private void addODEVariable(final ASTEquation ode) {
     var.setDeclaringType(currentTypeSymbol.get());
     var.setLoggable(true);
     var.setAlias(false);
+
     //var.setDeclaringExpression(ode.getRhs());
     var.setBlockType(VariableSymbol.BlockType.STATE);
 
@@ -159,6 +162,32 @@ private void addODEVariable(final ASTEquation ode) {
     trace("Adds new shape variable '" + var.getFullName() + "'.", LOGGER_NAME);
   }
 
+  private void assignOdeToVariables(final ASTBody astBody) {
+    if (astBody.getODEBlock().isPresent()) {
+      astBody.getODEBlock().get().getODEs()
+          .stream()
+          .forEach(this::addOdeToVariable);
+
+    }
+
+  }
+
+  private void addOdeToVariable(final ASTEquation ode) {
+    checkState(this.currentScope().isPresent());
+
+    final Scope scope = currentScope().get();
+    final String variableName = convertToSimpleName(ode.getLhs());
+    final Optional<VariableSymbol> stateVariable = scope.resolve(variableName, VariableSymbol.KIND);
+
+    if (stateVariable.isPresent()) {
+      stateVariable.get().setOdeDeclaration(ode.getRhs());
+    }
+    else {
+      Log.warn("NESTMLSymbolTableCreator: The left side of the ode is undefined. Cannot assign its definition: " + variableName);
+    }
+
+  }
+
   public void visit(final ASTComponent componentAst) {
     final NeuronSymbol componentSymbol = new NeuronSymbol(componentAst.getName(), COMPONENT);
     currentTypeSymbol = of(componentSymbol);

src/main/java/org/nest/symboltable/symbols/VariableSymbol.java

@@ -9,9 +9,7 @@
 import de.monticore.symboltable.Scope;
 import de.monticore.symboltable.SymbolKind;
 import org.nest.commons._ast.ASTExpr;
-import org.nest.nestml._ast.ASTInput;
 import org.nest.nestml._ast.ASTInputLine;
-import org.nest.nestml._ast.ASTInputType;
 import org.nest.utils.ASTUtils;
 
 import java.util.Objects;
@@ -33,6 +31,8 @@ public class VariableSymbol extends CommonSymbol {
 
   private ASTExpr declaringExpression = null;
 
+  private ASTExpr odeDeclaration = null;
+
   private TypeSymbol type;
 
   private NeuronSymbol declaringType;
@@ -49,12 +49,21 @@ public boolean isBuffer() {
     return blockType == BlockType.INPUT_BUFFER_CURRENT || blockType == BlockType.INPUT_BUFFER_SPIKE;
   }
 
+  @SuppressWarnings({"unused"}) // used in templates
   public boolean isLoggable() {
     // TODO: check whether the logic is correct. At the moment, the vector datatypes are not supported by the code
     // generator.
     return isLoggable && !isVector();
   }
 
+  public void setOdeDeclaration(final ASTExpr odeDeclaration) {
+    this.odeDeclaration = odeDeclaration;
+  }
+
+  public boolean definedByODE() {
+    return odeDeclaration != null;
+  }
+
   public void setLoggable(boolean loggable) {
     isLoggable = loggable;
   }
@@ -177,13 +186,15 @@ public void setBlockType(BlockType blockType) {
     this.blockType = blockType;
   }
 
+  @SuppressWarnings({"unused"}) // used in templates
   public boolean hasSetter() {
     checkState(getAstNode().isPresent(), "Symbol table must set the AST node.");
     checkArgument(getAstNode().get().getEnclosingScope().isPresent(), "Run symboltable creator.");
 
     return isSetterPresent(getName(), getType().getName(), getAstNode().get().getEnclosingScope().get());
   }
 
+  @SuppressWarnings({"unused"}) // used in templates
   public String printComment() {
     final StringBuffer output = new StringBuffer();
     if(getAstNode().isPresent()) {