Examples with PointSubDomain cbit.vcell.math.PointSubDomain used on opensource projects

Example 1 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class DiffEquMathMapping method addSpatialProcesses.

private void addSpatialProcesses(VariableHash varHash, ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts, ArrayList<MembraneSubdomainContext> membraneSubdomainContexts) throws MathException, MappingException, ExpressionException {
    if (simContext.getGeometry().getDimension() == 0) {
        return;
    }
    // 
    for (SpatialObject spatialObject : simContext.getSpatialObjects()) {
        if (spatialObject instanceof PointObject) {
            PointObject pointObject = (PointObject) spatialObject;
            // 
            // if true, have to solve for this category
            // 
            boolean bPosition = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointPosition);
            boolean bVelocity = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointVelocity);
            boolean bDirection = pointObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToPoint);
            boolean bDistance = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointDistanceMap);
            // 
            // either make a point subdomain, or just define functions.
            // 
            ArrayList<PointLocation> pointLocationProcesses = new ArrayList<PointLocation>();
            ArrayList<PointKinematics> pointKinematicsProcesses = new ArrayList<PointKinematics>();
            for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                if (spatialProcess instanceof PointLocation && ((PointLocation) spatialProcess).getPointObject() == pointObject) {
                    pointLocationProcesses.add((PointLocation) spatialProcess);
                }
                if (spatialProcess instanceof PointKinematics && ((PointKinematics) spatialProcess).getPointObject() == pointObject) {
                    pointKinematicsProcesses.add((PointKinematics) spatialProcess);
                }
            }
            if (pointLocationProcesses.size() == 1 && pointKinematicsProcesses.size() == 0 && !bVelocity) {
                GeometryClass gc = null;
                PointLocation pointLocation = pointLocationProcesses.get(0);
                if (bPosition) {
                    if (simContext.getGeometry().getDimension() == 1) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(posXExp, posXQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minus_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minus_X), new Expression(-1)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minus_X);
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 2) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                        LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
                        Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
                        Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                        LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
                        Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
                        Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
                        LocalParameter posZParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZParam, gc), getIdentifierSubstitutions(posZParam.getExpression(), posZParam.getUnitDefinition(), gc), gc));
                        Expression posZExp = new Expression(posZParam, pointLocation.getNameScope());
                        Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZQuantity, gc), getIdentifierSubstitutions(new Expression(posZParam, pointLocation.getNameScope()), posZQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                        Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
                        Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                } else {
                    throw new MappingException("PointLocation process defined for pointObject '" + pointObject.getName() + "' but Position not enabled");
                }
            } else if (pointLocationProcesses.size() == 0 && pointKinematicsProcesses.size() == 1) {
                GeometryClass gc = null;
                PointKinematics pointKinematics = pointKinematicsProcesses.get(0);
                if (bPosition && bVelocity) {
                    LocalParameter velXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityX);
                    LocalParameter iniPosXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionX);
                    SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                    SpatialQuantity velXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.X);
                    Expression posXExp = new Expression(posXQuantity, simContext.getNameScope());
                    Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                    Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                    LocalParameter velYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityY);
                    LocalParameter iniPosYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionY);
                    SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                    SpatialQuantity velYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Y);
                    Expression posYExp = new Expression(posYQuantity, simContext.getNameScope());
                    Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                    Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                    LocalParameter velZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityZ);
                    LocalParameter iniPosZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionZ);
                    SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
                    SpatialQuantity velZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Z);
                    Expression posZExp = new Expression(posZQuantity, simContext.getNameScope());
                    Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
                    Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
                    String pointSubdomainName = pointObject.getName();
                    Domain domain = new Domain(pointSubdomainName);
                    PointSubDomain pointSubdomain = new PointSubDomain(pointSubdomainName);
                    mathDesc.addSubDomain(pointSubdomain);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        PointVariable posXVar = new PointVariable(getMathSymbol(posXQuantity, gc), domain);
                        varHash.addVariable(posXVar);
                        Expression initXExp = getIdentifierSubstitutions(new Expression(iniPosXParam, pointKinematics.getNameScope()), iniPosXParam.getUnitDefinition(), gc);
                        Expression rateXExp = getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXParam.getUnitDefinition(), gc);
                        OdeEquation odeX = new OdeEquation(posXVar, initXExp, rateXExp);
                        pointSubdomain.addEquation(odeX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosXParam, gc), getIdentifierSubstitutions(new Expression(iniPosXParam.getExpression()), iniPosXParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, gc), getIdentifierSubstitutions(new Expression(velXParam.getExpression()), velXParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, gc), getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionX(getIdentifierSubstitutions(new Expression(posXQuantity, simContext.getNameScope()), posXQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        PointVariable posYVar = new PointVariable(getMathSymbol(posYQuantity, gc), domain);
                        varHash.addVariable(posYVar);
                        Expression initYExp = getIdentifierSubstitutions(new Expression(iniPosYParam, pointKinematics.getNameScope()), iniPosYParam.getUnitDefinition(), gc);
                        Expression rateYExp = getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYParam.getUnitDefinition(), gc);
                        OdeEquation odeY = new OdeEquation(posYVar, initYExp, rateYExp);
                        pointSubdomain.addEquation(odeY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosYParam, gc), getIdentifierSubstitutions(new Expression(iniPosYParam.getExpression()), iniPosYParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, gc), getIdentifierSubstitutions(new Expression(velYParam.getExpression()), velYParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, gc), getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionY(getIdentifierSubstitutions(new Expression(posYQuantity, simContext.getNameScope()), posYQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        PointVariable posZVar = new PointVariable(getMathSymbol(posZQuantity, gc), domain);
                        varHash.addVariable(posZVar);
                        Expression initZExp = getIdentifierSubstitutions(new Expression(iniPosZParam, pointKinematics.getNameScope()), iniPosZParam.getUnitDefinition(), gc);
                        Expression rateZExp = getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZParam.getUnitDefinition(), gc);
                        OdeEquation odeZ = new OdeEquation(posZVar, initZExp, rateZExp);
                        pointSubdomain.addEquation(odeZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosZParam, gc), getIdentifierSubstitutions(new Expression(iniPosZParam.getExpression()), iniPosZParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, gc), getIdentifierSubstitutions(new Expression(velZParam.getExpression()), velZParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, gc), getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionZ(getIdentifierSubstitutions(new Expression(posZQuantity, simContext.getNameScope()), posZQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() == 1) {
                        Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minux_X), new Expression(-1)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minux_X);
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 2) {
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
                        Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                } else {
                    throw new MappingException(pointKinematics.getDescription() + " process defined for pointObject '" + pointObject.getName() + "' but Position and Velocity not enabled");
                }
            } else {
                throw new MappingException("expecting 1 location or kinematics process for point '" + pointObject.getName() + "'");
            }
        } else if (spatialObject instanceof SurfaceRegionObject) {
            SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) spatialObject;
            SubVolume insideSubvolume = surfaceRegionObject.getInsideSubVolume();
            SubVolume outsideSubvolume = surfaceRegionObject.getOutsideSubVolume();
            SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubvolume, outsideSubvolume);
            MembraneSubdomainContext memSubdomainContext = null;
            for (MembraneSubdomainContext context : membraneSubdomainContexts) {
                if (context.surfaceClass == surfaceClass) {
                    memSubdomainContext = context;
                }
            }
            // 
            // if true, have to solve for this category
            // 
            boolean bNormal = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.Normal);
            boolean bVelocity = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity);
            boolean bDistance = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceDistanceMap);
            boolean bDirection = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
            boolean bSize = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceSize);
            if (bVelocity) {
                ArrayList<SurfaceKinematics> surfaceKinematicsList = new ArrayList<SurfaceKinematics>();
                for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                    if (spatialProcess instanceof SurfaceKinematics && ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject() == surfaceRegionObject) {
                        surfaceKinematicsList.add((SurfaceKinematics) spatialProcess);
                    }
                }
                if (surfaceKinematicsList.size() == 1) {
                    SurfaceKinematics surfaceKinematics = surfaceKinematicsList.get(0);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
                        LocalParameter velXParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, surfaceClass), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velXExp = new Expression(velXParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, surfaceClass), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.X);
                            Expression normXExp = new Expression(MathFunctionDefinitions.FUNCTION_normalX);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normXQuantity, surfaceClass), getIdentifierSubstitutions(normXExp, normXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
                        LocalParameter velYParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, surfaceClass), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velYExp = new Expression(velYParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Y);
                            Expression normYExp = new Expression(MathFunctionDefinitions.FUNCTION_normalY);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normYQuantity, surfaceClass), getIdentifierSubstitutions(normYExp, normYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                    if (simContext.getGeometry().getDimension() >= 3) {
                        SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
                        LocalParameter velZParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, surfaceClass), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velYExp = new Expression(velZParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Z);
                            // MathFunctionDefinitions.FUNCTION_normalZ);
                            Expression normZExp = new Expression("normalZ_not_implemented()");
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normZQuantity, surfaceClass), getIdentifierSubstitutions(normZExp, normZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                } else {
                    throw new MappingException("expecting 1 Surface Kinematics process for Surface Object '" + surfaceRegionObject.getName() + "'");
                }
            }
            if (bSize) {
                SpatialQuantity sizeQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceSize, QuantityComponent.Scalar);
                String funcName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
                Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + surfaceClass.getName() + "'") });
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, surfaceClass), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
            }
            if (bDirection) {
                SpatialQuantity directionXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.X);
                SpatialQuantity directionYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Y);
                SpatialQuantity directionZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Z);
                for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
                    Domain domain = new Domain(adjacentSubvolume);
                    CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
                    if (simContext.getGeometry().getDimension() >= 1) {
                        String name = adjacentSubvolume.getName() + "_dirX_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionXQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.X);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionXQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneX);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        String name = adjacentSubvolume.getName() + "_dirY_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionYQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Y);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionYQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneY);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        String name = adjacentSubvolume.getName() + "_dirZ_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionZQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Z);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionZQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneZ);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                }
            }
            if (bDistance) {
                SpatialQuantity distanceQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceDistanceMap, QuantityComponent.Scalar);
                for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
                    String name = adjacentSubvolume.getName() + "_distanceTo_" + memSubdomainContext.membraneSubdomain.getName();
                    LocalizedDistanceToMembraneQuantity localDistanceQuantity = addLocalizedDistanceToMembraneQuantity(name, surfaceClass, adjacentSubvolume);
                    CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
                    Domain domain = new Domain(adjacentSubvolume);
                    VolVariable distanceVar = new VolVariable(getMathSymbol(localDistanceQuantity, adjacentSubvolume), domain);
                    varHash.addVariable(distanceVar);
                    ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.distanceToMembrane);
                    membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                    compSubdomain.addEquation(membraneMetricEquation);
                }
            }
        } else if (spatialObject instanceof VolumeRegionObject) {
            VolumeRegionObject volumeRegionObject = (VolumeRegionObject) spatialObject;
            SubVolume subvolume = volumeRegionObject.getSubVolume();
            boolean bCentroid = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
            boolean bSize = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.VolumeSize);
            boolean bVelocity = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.InteriorVelocity);
            if (bVelocity) {
                ArrayList<VolumeKinematics> volumeKinematicsList = new ArrayList<VolumeKinematics>();
                for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                    if (spatialProcess instanceof VolumeKinematics && ((VolumeKinematics) spatialProcess).getVolumeRegionObject() == volumeRegionObject) {
                        volumeKinematicsList.add((VolumeKinematics) spatialProcess);
                    }
                }
                if (volumeKinematicsList.size() == 1) {
                    VolumeKinematics volumeKinematics = volumeKinematicsList.get(0);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        SpatialQuantity velXQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.X);
                        LocalParameter velXParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, subvolume), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velXExp = new Expression(velXParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, subvolume), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        SpatialQuantity velYQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Y);
                        LocalParameter velYParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, subvolume), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velYExp = new Expression(velYParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, subvolume), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        SpatialQuantity velZQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Z);
                        LocalParameter velZParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, subvolume), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velZExp = new Expression(velZParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, subvolume), getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                } else {
                    throw new MappingException("expecting 1 Volume Kinematics process for Volume Object '" + volumeRegionObject.getName() + "'");
                }
            }
            if (bSize) {
                SpatialQuantity sizeQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.VolumeSize, QuantityComponent.Scalar);
                String funcName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
                Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + subvolume.getName() + "'") });
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, subvolume), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), subvolume), subvolume));
            }
            if (bCentroid) {
                throw new MappingException(QuantityCategory.Centroid.description + " not yet implemented in math generation");
            }
        }
    }
}

Example 2 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    boolean bIsComsol = false;
    try {
        bIsComsol = isComsol();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    if (!bIsComsol) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !bIsComsol && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isWarnEnabled()) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (bIsComsol && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 3 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class XmlReader method getPointSubDomain.

private PointSubDomain getPointSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // get name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // *** create new pointSubDomain object ***
    PointSubDomain pointDomain = new PointSubDomain(name);
    // add OdeEquations
    Iterator<Element> iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            pointDomain.addEquation(getOdeEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e);
        }
    }
    String temp = param.getChildText(XMLTags.PositionXTag, vcNamespace);
    if (temp != null && temp.length() > 0) {
        pointDomain.setPositionX(unMangleExpression(temp));
    }
    temp = param.getChildText(XMLTags.PositionYTag, vcNamespace);
    if (temp != null && temp.length() > 0) {
        pointDomain.setPositionY(unMangleExpression(temp));
    }
    temp = param.getChildText(XMLTags.PositionZTag, vcNamespace);
    if (temp != null && temp.length() > 0) {
        pointDomain.setPositionZ(unMangleExpression(temp));
    }
    return pointDomain;
}

Example 4 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a SubDomain object type.
 * Creation date: (3/2/2001 1:13:30 PM)
 * @return Element
 * @param param cbit.vcell.math.SubDomain
 */
private Element getXML(SubDomain param) throws XmlParseException {
    Element e = null;
    if (param instanceof CompartmentSubDomain) {
        e = getXML((CompartmentSubDomain) param);
    } else if (param instanceof FilamentSubDomain) {
        e = getXML((FilamentSubDomain) param);
    } else if (param instanceof MembraneSubDomain) {
        e = getXML((MembraneSubDomain) param);
    } else if (param instanceof PointSubDomain) {
        e = getXML((PointSubDomain) param);
    }
    transcribeComments(param, e);
    return e;
}

Example 5 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class MovingBoundaryFileWriter method manageCompartment.

private void manageCompartment(Element e, SubDomain sd) {
    try {
        if (!sd.getEquationCollection().isEmpty()) {
            Element se = getXMLSubdomain(sd);
            if (sd instanceof CompartmentSubDomain || sd instanceof PointSubDomain) {
                for (Equation equation : sd.getEquationCollection()) {
                    System.out.println("add this: " + equation.getVariable().getName());
                    se.addContent(getSpecies(equation));
                }
                e.addContent(se);
            }
        }
    } catch (Exception exc) {
        throw new RuntimeException("error managing compartment", exc);
    }
}