Examples with FunctionInvocation cbit.vcell.parser.FunctionInvocation used on opensource projects

Example 6 with FunctionInvocation

use of cbit.vcell.parser.FunctionInvocation in project vcell by virtualcell.

the class AbstractMathMapping method getIdentifierSubstitutions.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected Expression getIdentifierSubstitutions(Expression origExp, VCUnitDefinition desiredExpUnitDef, GeometryClass geometryClass) throws ExpressionException, MappingException {
    String[] symbols = origExp.getSymbols();
    if (symbols == null) {
        return origExp;
    }
    VCUnitDefinition expUnitDef = null;
    try {
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(simContext.getModel().getUnitSystem());
        expUnitDef = unitEvaluator.getUnitDefinition(origExp);
        if (desiredExpUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', desiredUnits are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[null], observed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
        } else if (expUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', evaluated Units are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[null]", Issue.SEVERITY_WARNING));
        } else if (desiredExpUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        } else if (!desiredExpUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        }
    } catch (VCUnitException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (ExpressionException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    Expression newExp = new Expression(origExp);
    // 
    // flatten user-defined functions
    // 
    FunctionInvocation[] functionInvocations = newExp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return functionType == FunctionType.USERDEFINED;
        }
    });
    for (FunctionInvocation functionInvocation : functionInvocations) {
        if (functionInvocation.getSymbolTableFunctionEntry() instanceof Model.ModelFunction) {
            ModelFunction modelFunction = (ModelFunction) functionInvocation.getSymbolTableFunctionEntry();
            newExp.substituteInPlace(functionInvocation.getFunctionExpression(), modelFunction.getFlattenedExpression(functionInvocation));
        }
    }
    // 
    // then substitute Math symbols for Biological symbols.
    // 
    newExp.bindExpression(null);
    for (int i = 0; i < symbols.length; i++) {
        SymbolTableEntry ste = origExp.getSymbolBinding(symbols[i]);
        if (ste == null) {
            throw new ExpressionBindingException("symbol '" + symbols[i] + "' not bound");
        // ste = simContext.getGeometryContext().getModel().getSpeciesContext(symbols[i]);
        }
        if (ste != null) {
            String newName = getMathSymbol(ste, geometryClass);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 7 with FunctionInvocation

use of cbit.vcell.parser.FunctionInvocation in project vcell by virtualcell.

the class MathFunctionDefinitions method fixFunctionSyntax.

public static Expression fixFunctionSyntax(Expression exp) throws ExpressionException {
    FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return (functionName.equals(FunctionName_field_old) || functionName.equals(FunctionName_grad_old));
        }
    });
    for (int i = 0; functionInvocations != null && i < functionInvocations.length; i++) {
        Expression[] argExpressions = functionInvocations[i].getArguments();
        if (functionInvocations[i].getFunctionName().equals(FunctionName_field_old)) {
            if (argExpressions.length >= 2 && argExpressions.length <= 4) {
                StringBuffer functionBuffer = new StringBuffer(FieldFunctionDefinition.FUNCTION_name + "(");
                if (argExpressions[0].isIdentifier()) {
                    functionBuffer.append("'" + argExpressions[0].infix() + "'");
                } else {
                    throw new ExpressionException("unexpected function format '" + functionInvocations[i].getFunctionExpression() + "'");
                }
                functionBuffer.append(",");
                if (argExpressions[1].isIdentifier()) {
                    functionBuffer.append("'" + argExpressions[1].infix() + "'");
                } else {
                    throw new ExpressionException("unexpected function format '" + functionInvocations[i].getFunctionExpression() + "'");
                }
                functionBuffer.append(",");
                if (argExpressions.length >= 3) {
                    functionBuffer.append(argExpressions[2].infix());
                } else {
                    functionBuffer.append("0.0");
                }
                functionBuffer.append(",");
                if (argExpressions.length >= 4) {
                    if (argExpressions[3].isIdentifier()) {
                        VariableType varType = VariableType.getVariableTypeFromVariableTypeNameIgnoreCase(argExpressions[3].infix());
                        functionBuffer.append("'" + varType.getTypeName() + "'");
                    } else {
                        throw new ExpressionException("unexpected function format '" + functionInvocations[i].getFunctionExpression() + "'");
                    }
                } else {
                    functionBuffer.append("'" + VariableType.VOLUME.getTypeName() + "'");
                }
                functionBuffer.append(")");
                exp = exp.getSubstitutedExpression(functionInvocations[i].getFunctionExpression(), new Expression(functionBuffer.toString()));
            }
        } else if (functionInvocations[i].getFunctionName().equals(FunctionName_grad_old)) {
            if (argExpressions.length == 2 && !argExpressions[1].isLiteral()) {
                // grad(x,calcium) ==> vcGrad(calcium,'x') ... where x is [x y z m]
                StringBuffer functionBuffer = new StringBuffer(GradientFunctionDefinition.FUNCTION_name + "(");
                Expression componentArg = argExpressions[0];
                Expression variableArg = argExpressions[1];
                functionBuffer.append(variableArg.infix());
                functionBuffer.append(",");
                functionBuffer.append("'" + componentArg.infix() + "'");
                functionBuffer.append(")");
                exp = exp.getSubstitutedExpression(functionInvocations[i].getFunctionExpression(), new Expression(functionBuffer.toString()));
            }
        }
    }
    return exp;
}

Example 8 with FunctionInvocation

use of cbit.vcell.parser.FunctionInvocation in project vcell by virtualcell.

the class FiniteVolumeFileWriter method subsituteExpression.

/**
 * Insert the method's description here.
 * Creation date: (5/9/2005 2:52:48 PM)
 * @throws ExpressionException
 */
private Expression subsituteExpression(Expression exp, SymbolTable symbolTable, VariableDomain variableDomain) throws ExpressionException {
    Expression newExp = MathUtilities.substituteFunctions(exp, symbolTable).flatten();
    FieldFunctionArguments[] fieldFunctionArguments = FieldUtilities.getFieldFunctionArguments(newExp);
    if (fieldFunctionArguments != null && fieldFunctionArguments.length > 0) {
        if (uniqueFieldDataNSet != null && uniqueFieldDataNSet.size() > 0) {
            for (FieldDataNumerics fdn : uniqueFieldDataNSet) {
                newExp.substituteInPlace(new Expression(fdn.getFieldFunction()), new Expression(fdn.getNumericsSubsitute()));
            }
        } else {
            throw new RuntimeException("Didn't find field functions in simulation when preprocessing, but expression [" + exp.infix() + "] has field function " + newExp.infix() + " in it");
        }
    }
    if (bChomboSolver) {
        Set<FunctionInvocation> sizeFunctions = SolverUtilities.getSizeFunctionInvocations(newExp);
        if (sizeFunctions.size() > 0) {
            throw new ExpressionException("Size functions are not supported by " + simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel());
        }
    } else {
        newExp = SolverUtilities.substituteSizeAndNormalFunctions(newExp, variableDomain);
    }
    return newExp;
}

Example 9 with FunctionInvocation

use of cbit.vcell.parser.FunctionInvocation in project vcell by virtualcell.

the class TableCellEditorAutoCompletion method stopCellEditing.

@Override
public boolean stopCellEditing() {
    if (thisTable.getCellEditor() == null) {
        return true;
    }
    if (textFieldAutoCompletion.getSelectedIndex() >= 0) {
        return false;
    }
    final int editingRow = thisTable.getEditingRow();
    final int editingColumn = thisTable.getEditingColumn();
    textFieldAutoCompletion.stopEditing();
    boolean bExpressionValid = true;
    if (thisTable.getColumnClass(editingColumn).equals(ScopedExpression.class)) {
        if (textFieldAutoCompletion.getSymbolTable() != null) {
            ScopedExpression scopedExpression = (ScopedExpression) thisTable.getValueAt(editingRow, editingColumn);
            String text = textFieldAutoCompletion.getText();
            if (text.trim().length() > 0) {
                try {
                    Expression exp = new Expression(text);
                    exp.validateUnscopedSymbols();
                    if (scopedExpression == null || scopedExpression.isValidateFunctionBinding()) {
                        FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
                        for (FunctionInvocation functionInvocation : functionInvocations) {
                            String formalDefinition = functionInvocation.getFormalDefinition();
                            if (functionInvocation.getFunctionId() == FunctionType.USERDEFINED) {
                                SymbolTableFunctionEntry stfe = (SymbolTableFunctionEntry) textFieldAutoCompletion.getSymbolTable().getEntry(formalDefinition);
                                if (stfe == null) {
                                    // 
                                    // check for wrong number of arguments
                                    // 
                                    Map<String, SymbolTableEntry> entries = new HashMap<String, SymbolTableEntry>();
                                    textFieldAutoCompletion.getSymbolTable().getEntries(entries);
                                    System.out.println("available symbols");
                                    for (String symbol : entries.keySet()) {
                                        System.out.print(symbol + ",");
                                    }
                                    System.out.println("");
                                    throw new ExpressionBindingException("unknown function " + formalDefinition, formalDefinition);
                                }
                            } else {
                                // built in function, check arguments
                                FunctionType functionType = functionInvocation.getFunctionId();
                                String formalDefinitionBuiltin = ASTFuncNode.getFormalDefinition(functionType.getName(), functionType.getArgTypes());
                                if (!formalDefinition.equals(formalDefinitionBuiltin)) {
                                    throw new ExpressionBindingException("expecting " + formalDefinitionBuiltin, formalDefinition);
                                }
                            }
                        }
                    }
                    if (scopedExpression == null || scopedExpression.isValidateIdentifierBinding()) {
                        exp.bindExpression(textFieldAutoCompletion.getSymbolTable());
                    }
                } catch (ExpressionBindingException ex) {
                    ex.printStackTrace(System.out);
                    DialogUtils.showErrorDialog(thisTable.getParent(), ex.getMessage() + "\n\nUse 'Ctrl-Space' to see a list of available names in your model or 'Esc' to revert to the original expression.");
                    bExpressionValid = false;
                } catch (ExpressionException ex) {
                    ex.printStackTrace(System.out);
                    DialogUtils.showErrorDialog(thisTable.getParent(), ex.getMessage() + "\n\nUse 'Esc' to revert to the original expression.");
                    bExpressionValid = false;
                }
            }
        }
    }
    if (!bExpressionValid) {
        SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                thisTable.requestFocus();
                thisTable.setRowSelectionInterval(editingRow, editingRow);
                ((JComponent) getComponent()).setBorder(new LineBorder(Color.red));
                textFieldAutoCompletion.requestFocus();
            }
        });
        return false;
    }
    return super.stopCellEditing();
}

Example 10 with FunctionInvocation

use of cbit.vcell.parser.FunctionInvocation in project vcell by virtualcell.

the class DataSetControllerImpl method hasGradient.

private boolean hasGradient(Expression exp) {
    boolean hasGradient = false;
    FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
    for (FunctionInvocation fi : functionInvocations) {
        if (fi.getSymbolTableFunctionEntry() instanceof GradientFunctionDefinition) {
            hasGradient = true;
        }
    }
    return hasGradient;
}