Examples with Graph cbit.util.graph.Graph used on opensource projects

Example 1 with Graph

use of cbit.util.graph.Graph in project vcell by virtualcell.

the class SimpleGraphModel method setGraph.

/**
 * Sets the graph property (cbit.vcell.mapping.potential.Graph) value.
 * @param graph The new value for the property.
 * @see #getGraph
 */
public void setGraph(cbit.util.graph.Graph graph) {
    cbit.util.graph.Graph oldValue = fieldGraph;
    fieldGraph = graph;
    firePropertyChange("graph", oldValue, graph);
    refreshAll();
}

Example 2 with Graph

use of cbit.util.graph.Graph in project vcell by virtualcell.

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 3 with Graph

use of cbit.util.graph.Graph in project vcell by virtualcell.

the class PotentialMapping method determineLumpedEquations.

/**
 * Insert the method's description here.
 * Creation date: (2/20/2002 9:02:42 AM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param circuitGraph cbit.vcell.mapping.potential.Graph
 */
private void determineLumpedEquations(Graph graph, double temperatureKelvin) throws ExpressionException, MatrixException, MappingException, MathException {
    // 
    // traverses graph and calculates RHS expressions for all capacitive devices (dV/dt)
    // 
    // calculate dependent voltages as functions of independent voltages.
    // 
    // 
    Graph[] spanningTrees = graph.getSpanningForest();
    if (!bSilent) {
        System.out.println("spanning tree(s):");
        for (int i = 0; i < spanningTrees.length; i++) {
            System.out.println(i + ") " + spanningTrees[i]);
        }
    }
    Path[] fundamentalCycles = graph.getFundamentalCycles();
    if (!bSilent) {
        System.out.println("fundamental cycles:");
        for (int i = 0; i < fundamentalCycles.length; i++) {
            System.out.println("   " + fundamentalCycles[i]);
        }
    }
    // 
    // print out basic device information
    // 
    fieldEdges = graph.getEdges();
    // 
    if (!bSilent) {
        System.out.println("\n\n applying KVL to <<ALL>> fundamental cycles\n");
    }
    Path[] graphCycles = graph.getFundamentalCycles();
    RationalExpMatrix voltageMatrix = new RationalExpMatrix(graphCycles.length, graph.getNumEdges());
    for (int i = 0; i < graphCycles.length; i++) {
        Edge[] cycleEdges = graphCycles[i].getEdges();
        Node[] nodesTraversed = graphCycles[i].getNodesTraversed();
        Expression exp = new Expression(0.0);
        // 
        for (int j = 0; j < cycleEdges.length; j++) {
            int edgeIndex = graph.getIndex(cycleEdges[j]);
            Expression voltage = new Expression(((ElectricalDevice) cycleEdges[j].getData()).getVoltageSymbol(), fieldMathMapping.getNameScope());
            if (cycleEdges[j].getNode1().equals(nodesTraversed[j])) {
                // going same direction
                exp = Expression.add(exp, voltage);
                voltageMatrix.set_elem(i, edgeIndex, 1);
            } else {
                // going opposite direction
                exp = Expression.add(exp, Expression.negate(voltage));
                voltageMatrix.set_elem(i, edgeIndex, -1);
            }
        }
        if (!bSilent) {
            System.out.println(exp.flatten().infix() + " = 0.0");
        }
    }
    if (!bSilent) {
        voltageMatrix.show();
    }
    if (voltageMatrix.getNumRows() > 0) {
        RationalExpMatrix vPermutationMatrix = new RationalExpMatrix(voltageMatrix.getNumRows(), voltageMatrix.getNumRows());
        voltageMatrix.gaussianElimination(vPermutationMatrix);
        if (!bSilent) {
            System.out.println("reduced matrix");
            voltageMatrix.show();
        }
    } else {
        voltageMatrix = null;
    }
    // 
    // declare dependent voltages as functions of independent voltages
    // 
    // 1) Always use Voltage-Clamps as independent voltages
    // 2) Try to use Capacitive devices as independent voltages
    // 
    // solve for current-clamp voltages and redundant/constrained capacitive voltages as function of (1) and (2).
    // 
    Expression[] dependentVoltageExpressions = new Expression[fieldEdges.length];
    // 
    // make sure assumptions hold regarding edge ordering, otherwise wrong dependent voltages will be selected
    // 
    verifyEdgeOrdering();
    for (int i = 0; voltageMatrix != null && i < voltageMatrix.getNumRows(); i++) {
        // 
        // find first '1.0' element, this column is the next 'dependent' voltage
        // 
        int column = -1;
        for (int j = i; j < voltageMatrix.getNumCols(); j++) {
            RationalExp elem = voltageMatrix.get(i, j);
            if (elem.isConstant() && elem.getConstant().doubleValue() == 1.0) {
                column = j;
                break;
            }
        }
        if (column != -1) {
            // 
            // get electrical device of dependent voltage
            // 
            ElectricalDevice device = (ElectricalDevice) fieldEdges[column].getData();
            // 
            // form dependency expression
            // 
            StringBuffer buffer = new StringBuffer();
            for (int j = column + 1; j < graph.getNumEdges(); j++) {
                if (!voltageMatrix.get_elem(i, j).isZero()) {
                    ElectricalDevice colDevice = (ElectricalDevice) fieldEdges[j].getData();
                    Expression voltage = new Expression(colDevice.getVoltageSymbol(), fieldMathMapping.getNameScope());
                    buffer.append(" + " + voltageMatrix.get(i, j).minus().infixString() + '*' + voltage.infix());
                }
            }
            dependentVoltageExpressions[column] = (new Expression(buffer.toString())).flatten();
            dependentVoltageExpressions[column].bindExpression(device);
            device.setDependentVoltageExpression(dependentVoltageExpressions[column]);
        }
    }
    if (!bSilent) {
        for (int i = 0; i < dependentVoltageExpressions.length; i++) {
            System.out.println("dependentVoltageExpressions[" + i + "] = " + dependentVoltageExpressions[i]);
        }
    }
    // 
    if (!bSilent) {
        System.out.println("\n\nSOLVE FOR TOTAL CURRENTS IN TERMS OF APPLIED CURRENTS");
        System.out.println("\n\n  1)  applying KVL to all fundamental \"capacitive\" and Voltage-clamp cycles (after current-clamp edges are removed)\n");
    }
    Graph capacitorGraph = new Graph();
    for (int i = 0; i < fieldEdges.length; i++) {
        ElectricalDevice device = (ElectricalDevice) fieldEdges[i].getData();
        if (device.hasCapacitance() || device.isVoltageSource()) {
            capacitorGraph.addEdge(fieldEdges[i]);
        }
    }
    Path[] capacitorGraphCycles = capacitorGraph.getFundamentalCycles();
    RationalExpMatrix capacitorGraphVoltageMatrix = new RationalExpMatrix(capacitorGraphCycles.length, graph.getNumEdges());
    for (int i = 0; i < capacitorGraphCycles.length; i++) {
        Edge[] cycleEdges = capacitorGraphCycles[i].getEdges();
        Node[] nodesTraversed = capacitorGraphCycles[i].getNodesTraversed();
        Expression exp = new Expression(0.0);
        // 
        for (int j = 0; j < cycleEdges.length; j++) {
            int edgeIndex = graph.getIndex(cycleEdges[j]);
            Expression voltage = new Expression(((ElectricalDevice) cycleEdges[j].getData()).getVoltageSymbol(), fieldMathMapping.getNameScope());
            if (cycleEdges[j].getNode1().equals(nodesTraversed[j])) {
                // going same direction
                exp = Expression.add(exp, voltage);
                capacitorGraphVoltageMatrix.set_elem(i, edgeIndex, 1);
            } else {
                // going opposite direction
                exp = Expression.add(exp, Expression.negate(voltage));
                capacitorGraphVoltageMatrix.set_elem(i, edgeIndex, -1);
            }
        }
        if (!bSilent) {
            System.out.println(exp.flatten().infix() + " = 0.0");
        }
    }
    if (!bSilent) {
        capacitorGraphVoltageMatrix.show();
    }
    // 
    if (!bSilent) {
        System.out.println("\n\n  2)  applying KCL to all nodes (except one) .. n-1 nodes of full graph  --- CONSERVATION OF TOTAL CURRENT\n");
    }
    Node[] nodes = graph.getNodes();
    RationalExpMatrix kclMatrix = new RationalExpMatrix(graph.getNumNodes() - 1, graph.getNumEdges());
    for (int i = 0; i < nodes.length - 1; i++) {
        if (graph.getDegree(nodes[i]) > 0) {
            Edge[] adjacentEdges = graph.getAdjacentEdges(nodes[i]);
            Expression exp = new Expression(0.0);
            // 
            for (int j = 0; j < adjacentEdges.length; j++) {
                int edgeIndex = graph.getIndex(adjacentEdges[j]);
                Expression totalCurrent = new Expression(((ElectricalDevice) adjacentEdges[j].getData()).getTotalCurrentSymbol(), fieldMathMapping.getNameScope());
                if (adjacentEdges[j].getNode1().equals(nodes[i])) {
                    exp = Expression.add(exp, Expression.negate(totalCurrent));
                    kclMatrix.set_elem(i, edgeIndex, -1);
                } else {
                    exp = Expression.add(exp, totalCurrent);
                    kclMatrix.set_elem(i, edgeIndex, 1);
                }
            }
            if (!bSilent) {
                System.out.println(exp.flatten().infix() + " = 0.0");
            }
        } else {
            throw new MappingException("compartment '" + nodes[i].getName() + "' is electrically isolated, cannot generate ciruit equations for application '" + fieldSimContext.getName() + "'.  \n\nPlease specify electrical properties for all membranes (see Structures tab in Physiology).");
        }
    }
    if (!bSilent) {
        kclMatrix.show();
    }
    // 
    if (!bSilent) {
        System.out.println("\n\n  3)  form total 'current' matrix\n");
    }
    int numNonCapacitiveEdges = 0;
    for (int i = 0; i < fieldEdges.length; i++) {
        ElectricalDevice device = (ElectricalDevice) fieldEdges[i].getData();
        if (!device.hasCapacitance()) {
            numNonCapacitiveEdges++;
        }
    }
    int cmat_rows = kclMatrix.getNumRows() + capacitorGraphVoltageMatrix.getNumRows() + numNonCapacitiveEdges;
    RationalExpMatrix currentMatrix = new RationalExpMatrix(cmat_rows, 3 * graph.getNumEdges());
    // 
    // order edges for current elimination (unknown voltage-clamp currents as well as all total currents).
    // 
    int[] cIndex = new int[fieldEdges.length];
    int ci = 0;
    for (int i = 0; i < fieldEdges.length; i++) {
        if (((ElectricalDevice) fieldEdges[i].getData()).isVoltageSource()) {
            cIndex[ci++] = i;
        }
    }
    for (int i = 0; i < fieldEdges.length; i++) {
        if (!((ElectricalDevice) fieldEdges[i].getData()).isVoltageSource()) {
            cIndex[ci++] = i;
        }
    }
    if (ci != fieldEdges.length) {
        throw new RuntimeException("error computing current indexes");
    }
    if (!bSilent) {
        System.out.println("reordered devices for current matrix elimination");
        for (int i = 0; i < cIndex.length; i++) {
            Expression voltage = new Expression(((ElectricalDevice) fieldEdges[cIndex[i]].getData()).getVoltageSymbol(), fieldMathMapping.getNameScope());
            System.out.println(i + ") = device[" + cIndex[i] + "] = " + voltage.infix());
        }
    }
    int row = 0;
    // 
    for (int i = 0; i < kclMatrix.getNumRows(); i++) {
        for (int j = 0; j < kclMatrix.getNumCols(); j++) {
            // entry for i's
            currentMatrix.set_elem(row, j, kclMatrix.get(i, cIndex[j]));
        }
        row++;
    }
    // 
    for (int i = 0; i < fieldEdges.length; i++) {
        ElectricalDevice device = (ElectricalDevice) fieldEdges[cIndex[i]].getData();
        if (!device.hasCapacitance()) {
            currentMatrix.set_elem(row, i, 1);
            currentMatrix.set_elem(row, i + graph.getNumEdges(), -1);
            row++;
        }
    }
    // 
    // add current terms of (i - F)*1000/C form using KVL relationships from "capacitor graph"
    // 
    ModelUnitSystem modelUnitSystem = fieldMathMapping.getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition potentialUnit = modelUnitSystem.getVoltageUnit();
    VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
    for (int i = 0; i < capacitorGraphVoltageMatrix.getNumRows(); i++) {
        for (int j = 0; j < capacitorGraphVoltageMatrix.getNumCols(); j++) {
            ElectricalDevice device = (ElectricalDevice) fieldEdges[cIndex[j]].getData();
            RationalExp coefficient = capacitorGraphVoltageMatrix.get(i, cIndex[j]);
            if (device.hasCapacitance()) {
                // 
                // replace dVi/dt  with   1000/Ci * Ii  +  1000/Ci * Fi
                // 
                SymbolTableEntry capacitanceParameter = ((MembraneElectricalDevice) device).getCapacitanceParameter();
                Expression capacitance = new Expression(capacitanceParameter, fieldMathMapping.getNameScope());
                String Cname = capacitance.infix();
                VCUnitDefinition unitFactor = potentialUnit.divideBy(timeUnit).multiplyBy(capacitanceParameter.getUnitDefinition()).divideBy(device.getTotalCurrentSymbol().getUnitDefinition());
                RationalExp unitFactorExp = fieldMathMapping.getUnitFactorAsRationalExp(unitFactor);
                // entry for i's
                currentMatrix.set_elem(row, j, coefficient.mult(unitFactorExp.div(new RationalExp(Cname))));
                // entry for F's
                currentMatrix.set_elem(row, j + graph.getNumEdges(), coefficient.minus().mult(unitFactorExp).div(new RationalExp(Cname)));
            } else if (device.isVoltageSource()) {
                // 
                // directly insert "symbolic" dVi/dt into the new matrix
                // 
                currentMatrix.set_elem(row, j + 2 * graph.getNumEdges(), coefficient);
            }
        }
        row++;
    }
    if (!bSilent) {
        currentMatrix.show();
    }
    if (currentMatrix.getNumRows() > 0) {
        RationalExpMatrix cPermutationMatrix = new RationalExpMatrix(currentMatrix.getNumRows(), currentMatrix.getNumRows());
        currentMatrix.gaussianElimination(cPermutationMatrix);
        if (!bSilent) {
            System.out.println("reduced matrix");
            currentMatrix.show();
        }
    }
    // 
    if (!bSilent) {
        System.out.println("\n\n total currents for each device\n");
    }
    Expression[] totalCurrents = new Expression[fieldEdges.length];
    for (int i = 0; i < fieldEdges.length; i++) {
        ElectricalDevice device = (ElectricalDevice) fieldEdges[cIndex[i]].getData();
        StringBuffer buffer = new StringBuffer("0.0");
        // 
        for (int j = 0; j < graph.getNumEdges(); j++) {
            RationalExp coefficient = currentMatrix.get(i, j + graph.getNumEdges());
            if (!coefficient.isZero()) {
                ElectricalDevice colDevice = (ElectricalDevice) fieldEdges[cIndex[j]].getData();
                Expression source = new Expression(colDevice.getSourceSymbol(), fieldMathMapping.getNameScope());
                buffer.append(" + " + coefficient.minus() + "*" + source.infix());
            }
        }
        // 
        for (int j = 0; j < graph.getNumEdges(); j++) {
            RationalExp coefficient = currentMatrix.get(i, j + 2 * graph.getNumEdges());
            if (!coefficient.isZero()) {
                VoltageClampElectricalDevice colDevice = (VoltageClampElectricalDevice) fieldEdges[cIndex[j]].getData();
                Expression timeDeriv = colDevice.getVoltageClampStimulus().getVoltageParameter().getExpression().differentiate("t");
                timeDeriv = timeDeriv.flatten();
                timeDeriv.bindExpression(colDevice);
                timeDeriv.renameBoundSymbols(colDevice.getNameScope().getParent());
                buffer.append(" + " + coefficient.minus() + "*" + timeDeriv.infix());
            }
        }
        totalCurrents[cIndex[i]] = (new Expression(buffer.toString())).flatten();
        totalCurrents[cIndex[i]].bindExpression(device.getNameScope().getParent().getScopedSymbolTable());
        device.getParameterFromRole(ElectricalDevice.ROLE_TotalCurrent).setExpression(totalCurrents[cIndex[i]]);
    }
    if (!bSilent) {
        for (int i = 0; i < totalCurrents.length; i++) {
            System.out.println("totalCurrents[" + i + "] = " + totalCurrents[cIndex[i]].toString());
        }
    }
    // 
    if (!bSilent) {
        System.out.println("\n\n capacitive currents for each device\n");
    }
    Expression[] capacitiveCurrents = new Expression[fieldEdges.length];
    for (int i = 0; i < fieldEdges.length; i++) {
        ElectricalDevice device = (ElectricalDevice) fieldEdges[i].getData();
        if (device instanceof MembraneElectricalDevice) {
            MembraneElectricalDevice membraneElectricalDevice = (MembraneElectricalDevice) device;
            Expression source = new Expression(membraneElectricalDevice.getSourceSymbol(), fieldMathMapping.getNameScope());
            capacitiveCurrents[i] = Expression.add(totalCurrents[i], Expression.negate(source));
            capacitiveCurrents[i].bindExpression(membraneElectricalDevice);
        // membraneElectricalDevice.setCapacitiveCurrentExpression(capacitiveCurrents[i]);
        } else {
        // device.setCapacitiveCurrentExpression(new Expression(0.0));
        }
    }
    if (!bSilent) {
        for (int i = 0; i < capacitiveCurrents.length; i++) {
            System.out.println("capacitiveCurrents[" + i + "] = " + ((capacitiveCurrents[cIndex[i]] == null) ? "0.0" : capacitiveCurrents[cIndex[i]].infix()));
        }
    }
// 
// display equations for independent voltages.
// 
// if (!bSilent){
// for (int i = 0; i < graph.getNumEdges(); i++){
// ElectricalDevice device = (ElectricalDevice)graph.getEdges()[i].getData();
// //
// // membrane ode
// //
// if (device.hasCapacitance() && dependentVoltageExpressions[i]==null){
// Expression initExp = new Expression(0.0);
// System.out.println(device.getInitialVoltageFunction().getVCML());
// System.out.println((new cbit.vcell.math.OdeEquation(new cbit.vcell.math.VolVariable(device.getVName()),new Expression(device.getInitialVoltageFunction().getName()),new Expression(fieldCapacitiveCurrent[i].flatten().toString()+"*"+cbit.vcell.model.ReservedSymbol.KMILLIVOLTS.getName()+"/"+device.getCapName()))).getVCML());
// }
// //
// // membrane forced potential
// //
// if (device.hasCapacitance() && dependentVoltageExpressions[i]!=null){
// System.out.println((new Function(device.getVName(),dependentVoltageExpressions[i])).getVCML());
// System.out.println((new Function(device.getSourceName(),device.getCurrentSourceExpression()).getVCML()));
// }
// //
// // current clamp
// //
// if (!device.hasCapacitance() && !device.isVoltageSource()){
// System.out.println((new Function(device.getSourceName(),device.getCurrentSourceExpression()).getVCML()));
// System.out.println((new Function(device.getVName(),dependentVoltageExpressions[i])).getVCML());
// }
// //
// // voltage clamp
// //
// if (!device.hasCapacitance() && device.isVoltageSource()){
// System.out.println((new Function(device.getIName(),totalCurrents[i])).getVCML());
// System.out.println((new Function(device.getVName(),device.getInitialVoltageFunction().getExpression())).getVCML());
// }
// }
// }
}

Example 4 with Graph

use of cbit.util.graph.Graph in project vcell by virtualcell.

the class PotentialMapping method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
private static Graph getCircuitGraph(SimulationContext simContext, MathMapping_4_8 mathMapping_4_8) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping_4_8);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping_4_8);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    StructureTopology structTopology = simContext.getModel().getStructureTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            // if (!membraneMapping.getResolved()){
            Feature insideFeature = structTopology.getInsideFeature(membrane);
            Feature outsideFeature = structTopology.getOutsideFeature(membrane);
            if (insideFeature != null && outsideFeature != null) {
                Node insideNode = graph.getNode(insideFeature.getName());
                Node outsideNode = graph.getNode(outsideFeature.getName());
                // double capacitance = getTotalMembraneCapacitance(simContext,membrane).evaluateConstant();
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping_4_8);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping_4_8);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        // }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping_4_8);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 5 with Graph

use of cbit.util.graph.Graph in project vcell by virtualcell.

the class RegionImage method calculateRegions.

/**
 * Insert the method's description here.
 * Creation date: (3/28/2002 10:30:20 AM)
 * @param image cbit.image.VCImage
 */
private void calculateRegions(VCImage vcImage) throws cbit.image.ImageException {
    long time1 = System.currentTimeMillis();
    RegionMask[][] regionMasks = new RegionMask[numZ][];
    for (int k = 0; k < vcImage.getNumZ(); k++) {
        regionMasks[k] = calculateRegions3D(vcImage.getPixels(), k * numXY, numX, numY);
    }
    long time2 = System.currentTimeMillis();
    // time2 = System.currentTimeMillis();
    // RegionMask regionMasksFast[][] = new RegionMask[numZ][];
    // for (int k = 0; k < vcImage.getNumZ(); k++){
    // regionMasksFast[k] = calculateRegions3Dfaster(vcImage.getPixels(),k*numXY,numX,numY);
    // }
    // long time3 = System.currentTimeMillis();
    // System.out.println("4way recursive took "+((time2-time1)/1000.0)+" s, nonrecursive line took "+((time3-time2)/1000.0)+" s");
    // 
    // consolidate "off-plane contiguous" region indexes
    // build a graph of all 2D regions that touch
    // 
    // the final 3D regions are the set of nodes in each of the spanning trees.
    // 
    // 
    // build graph with 1 node per 2d region
    // 
    Graph connectionGraph = new Graph();
    for (int k = 0; k < numZ; k++) {
        for (int i = 0; i < regionMasks[k].length; i++) {
            Node node = new Node(k + "," + i, new org.vcell.util.ObjectReferenceWrapper(regionMasks[k][i]));
            connectionGraph.addNode(node);
        }
    }
    // 
    // add edges for any slice-slice touching of regions with same pixel value
    // 
    BitSet zeroBitSet = new BitSet();
    BitSet intersection = new BitSet(numXY);
    for (int k = 0; k < numZ - 1; k++) {
        for (int i = 0; i < regionMasks[k].length; i++) {
            Node node_i = connectionGraph.getNode(k + "," + i);
            for (int j = 0; j < regionMasks[k + 1].length; j++) {
                if (regionMasks[k][i].pixelValue == regionMasks[k + 1][j].pixelValue) {
                    // clear mask
                    intersection.and(zeroBitSet);
                    intersection.or(regionMasks[k][i].mask);
                    intersection.and(regionMasks[k + 1][j].mask);
                    if (!intersection.equals(zeroBitSet)) {
                        Node node_j = connectionGraph.getNode((k + 1) + "," + j);
                        connectionGraph.addEdge(new Edge(node_i, node_j));
                    }
                }
            }
        }
    }
    // 
    // get spanning forest, and for each spanning tree, assign a single regionID to each contained 2d mask
    // 
    Tree[] spanningForest = connectionGraph.getSpanningForest();
    regionInfos = new RegionInfo[spanningForest.length];
    for (int i = 0; i < spanningForest.length; i++) {
        Node[] nodes = spanningForest[i].getNodes();
        int pixelValue = -1;
        int numPixels = 0;
        BitSet fullMask = new BitSet(numXY * numZ);
        for (int j = 0; j < nodes.length; j++) {
            RegionMask regionMask = (RegionMask) ((ObjectReferenceWrapper) nodes[j].getData()).getObject();
            pixelValue = regionMask.pixelValue;
            for (int k = 0; k < numXY; k++) {
                if (regionMask.mask.get(k)) {
                    fullMask.set(regionMask.offset + k);
                    numPixels++;
                }
            }
        }
        regionInfos[i] = new RegionInfo(pixelValue, numPixels, i, fullMask);
    }
    long time3 = System.currentTimeMillis();
    System.out.println("4way recursive on slices took " + ((time2 - time1) / 1000.0) + " s, total RegionImage time " + ((time3 - time1) / 1000.0) + " s");
}