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

Example 6 with Node

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

the class RegionImage method sortSurfaceCollection.

public static void sortSurfaceCollection(SurfaceCollection surfCollection) {
    // Sort nodes
    Object[] nodeObjArr = new Object[surfCollection.getNodes().length];
    for (int i = 0; i < nodeObjArr.length; i++) {
        Object[] temp = new Object[2];
        temp[0] = new Integer(i);
        temp[1] = surfCollection.getNodes()[i];
        nodeObjArr[i] = temp;
    }
    Arrays.sort(nodeObjArr, new Comparator<Object>() {

        public int compare(Object obj1, Object obj2) {
            cbit.vcell.geometry.surface.Node o1 = (cbit.vcell.geometry.surface.Node) ((Object[]) obj1)[1];
            cbit.vcell.geometry.surface.Node o2 = (cbit.vcell.geometry.surface.Node) ((Object[]) obj2)[1];
            double xdiff = o1.getX() - o2.getX();
            double xmin = Math.min(Math.abs(o1.getX()), Math.abs(o2.getX()));
            double xlimit = (1e-12 * (xmin >= 1.0 ? (Math.pow(10, (int) Math.log10(xmin) + 1)) : 1));
            double ydiff = o1.getY() - o2.getY();
            double ymin = Math.min(Math.abs(o1.getY()), Math.abs(o2.getY()));
            double ylimit = (1e-12 * (ymin >= 1.0 ? (Math.pow(10, (int) Math.log10(ymin) + 1)) : 1));
            double zdiff = o1.getZ() - o2.getZ();
            double zmin = Math.min(Math.abs(o1.getZ()), Math.abs(o2.getZ()));
            double zlimit = (1e-12 * (zmin >= 1.0 ? (Math.pow(10, (int) Math.log10(zmin) + 1)) : 1));
            if (Math.abs(zdiff) < zlimit) {
                if (Math.abs(ydiff) < ylimit) {
                    return (int) Math.signum((Math.abs(xdiff) < xlimit ? 0 : xdiff));
                }
                return (int) Math.signum((Math.abs(ydiff) < ylimit ? 0 : ydiff));
            }
            return (int) Math.signum((Math.abs(zdiff) < zlimit ? 0 : zdiff));
        }
    });
    int[] remap = new int[nodeObjArr.length];
    Arrays.fill(remap, -1);
    cbit.vcell.geometry.surface.Node[] sortedNodes = new cbit.vcell.geometry.surface.Node[nodeObjArr.length];
    for (int i = 0; i < nodeObjArr.length; i++) {
        sortedNodes[i] = (cbit.vcell.geometry.surface.Node) ((Object[]) nodeObjArr[i])[1];
        if (remap[sortedNodes[i].getGlobalIndex()] == -1) {
            remap[sortedNodes[i].getGlobalIndex()] = i;
        } else {
            throw new RuntimeException("SORT error: duplicate nodes");
        }
    }
    // surfCollection.setNodes(sortedNodes);
    System.arraycopy(sortedNodes, 0, surfCollection.getNodes(), 0, sortedNodes.length);
    HashSet<cbit.vcell.geometry.surface.Node> remapHashSet = new HashSet<cbit.vcell.geometry.surface.Node>();
    for (int i = 0; i < surfCollection.getSurfaceCount(); i++) {
        Surface surf = surfCollection.getSurfaces(i);
        Polygon[] sortedPolygonArr = new Polygon[surf.getPolygonCount()];
        for (int j = 0; j < surf.getPolygonCount(); j++) {
            Polygon poly = surf.getPolygons(j);
            for (int k = 0; k < poly.getNodes().length; k++) {
                cbit.vcell.geometry.surface.Node node = poly.getNodes(k);
                if (!remapHashSet.contains(node)) {
                    node.setGlobalIndex(remap[node.getGlobalIndex()]);
                    remapHashSet.add(node);
                }
            }
            sortedPolygonArr[j] = poly;
        }
        Arrays.sort(sortedPolygonArr, new Comparator<Polygon>() {

            public int compare(Polygon obj1, Polygon obj2) {
                Coordinate o1 = ((Quadrilateral) obj1).calculateCentroid();
                Coordinate o2 = ((Quadrilateral) obj2).calculateCentroid();
                double xdiff = o1.getX() - o2.getX();
                double xmin = Math.min(Math.abs(o1.getX()), Math.abs(o2.getX()));
                double xlimit = (1e-12 * (xmin >= 1.0 ? (Math.pow(10, (int) Math.log10(xmin) + 1)) : 1));
                double ydiff = o1.getY() - o2.getY();
                double ymin = Math.min(Math.abs(o1.getY()), Math.abs(o2.getY()));
                double ylimit = (1e-12 * (ymin >= 1.0 ? (Math.pow(10, (int) Math.log10(ymin) + 1)) : 1));
                double zdiff = o1.getZ() - o2.getZ();
                double zmin = Math.min(Math.abs(o1.getZ()), Math.abs(o2.getZ()));
                double zlimit = (1e-12 * (zmin >= 1.0 ? (Math.pow(10, (int) Math.log10(zmin) + 1)) : 1));
                if (Math.abs(zdiff) < zlimit) {
                    if (Math.abs(ydiff) < ylimit) {
                        return (int) Math.signum((Math.abs(xdiff) < xlimit ? 0 : xdiff));
                    }
                    return (int) Math.signum((Math.abs(ydiff) < ylimit ? 0 : ydiff));
                }
                return (int) Math.signum((Math.abs(zdiff) < zlimit ? 0 : zdiff));
            }
        });
        OrigSurface sortedSurface = new OrigSurface(surf.getInteriorRegionIndex(), surf.getExteriorRegionIndex());
        for (int k = 0; k < sortedPolygonArr.length; k++) {
            int minGlobalIndex = sortedPolygonArr[k].getNodes(0).getGlobalIndex();
            // System.out.print("Surf "+i+" poly "+k+" nodeGI - ");
            for (int j = 0; j < sortedPolygonArr[k].getNodeCount(); j++) {
                if (sortedPolygonArr[k].getNodes(j).getGlobalIndex() < minGlobalIndex) {
                    minGlobalIndex = sortedPolygonArr[k].getNodes(j).getGlobalIndex();
                }
            // System.out.print(sortedPolygonArr[k].getNodes(j).getGlobalIndex()+" ");
            }
            while (sortedPolygonArr[k].getNodes(0).getGlobalIndex() != minGlobalIndex) {
                cbit.vcell.geometry.surface.Node lastNode = sortedPolygonArr[k].getNodes(sortedPolygonArr[k].getNodeCount() - 1);
                System.arraycopy(sortedPolygonArr[k].getNodes(), 0, sortedPolygonArr[k].getNodes(), 1, sortedPolygonArr[k].getNodeCount() - 1);
                sortedPolygonArr[k].getNodes()[0] = lastNode;
            }
            // System.out.println();
            sortedSurface.addPolygon(sortedPolygonArr[k]);
        }
        surfCollection.setSurfaces(i, sortedSurface);
    }
}

Example 7 with Node

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

the class ModelOptimizationSpec method calculateTimeDependentModelObjects.

/**
 * Insert the method's description here.
 * Creation date: (11/29/2005 5:10:51 PM)
 * @return cbit.vcell.parser.SymbolTableEntry[]
 */
public static SymbolTableEntry[] calculateTimeDependentModelObjects(SimulationContext simulationContext) {
    Graph digraph = new Graph();
    // 
    // add time
    // 
    Model model = simulationContext.getModel();
    Node timeNode = new Node("t", model.getTIME());
    digraph.addNode(timeNode);
    // 
    // add all species concentrations (that are not fixed with a constant initial condition).
    // 
    SpeciesContextSpec[] scs = simulationContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; scs != null && i < scs.length; i++) {
        SpeciesContextSpecParameter initParam = scs[i].getInitialConditionParameter();
        Expression iniExp = initParam == null ? null : initParam.getExpression();
        if (!scs[i].isConstant() || (iniExp != null && !iniExp.isNumeric())) {
            String speciesContextScopedName = scs[i].getSpeciesContext().getNameScope().getAbsoluteScopePrefix() + scs[i].getSpeciesContext().getName();
            Node speciesContextNode = new Node(speciesContextScopedName, scs[i].getSpeciesContext());
            digraph.addNode(speciesContextNode);
            digraph.addEdge(new Edge(speciesContextNode, timeNode));
        }
    }
    // 
    // add all model (global) parameters that are not simple constants
    // 
    ModelParameter[] modelParams = model.getModelParameters();
    for (int i = 0; modelParams != null && i < modelParams.length; i++) {
        Expression exp = modelParams[i].getExpression();
        if (exp != null) {
            String[] symbols = exp.getSymbols();
            if (symbols != null && symbols.length > 0) {
                // 
                // add parameter to graph as a node (if not already there).
                // 
                String parameterScopedName = modelParams[i].getNameScope().getAbsoluteScopePrefix() + modelParams[i].getName();
                Node parameterNode = digraph.getNode(parameterScopedName);
                if (parameterNode == null) {
                    parameterNode = new Node(parameterScopedName, modelParams[i]);
                    digraph.addNode(parameterNode);
                }
                // 
                for (int k = 0; symbols != null && k < symbols.length; k++) {
                    SymbolTableEntry ste = exp.getSymbolBinding(symbols[k]);
                    if (ste == null) {
                        throw new RuntimeException("Error, symbol '" + symbols[k] + "' not bound in parameter '" + modelParams[i].getName() + "'");
                    }
                    String symbolScopedName = ste.getNameScope().getAbsoluteScopePrefix() + ste.getName();
                    Node symbolNode = digraph.getNode(symbolScopedName);
                    if (symbolNode == null) {
                        symbolNode = new Node(symbolScopedName, ste);
                        digraph.addNode(symbolNode);
                    }
                    digraph.addEdge(new Edge(parameterNode, symbolNode));
                }
            }
        }
    }
    // 
    // add all reaction parameters that are not simple constants
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; reactionSteps != null && i < reactionSteps.length; i++) {
        Parameter[] parameters = reactionSteps[i].getKinetics().getKineticsParameters();
        for (int j = 0; parameters != null && j < parameters.length; j++) {
            Expression exp = parameters[j].getExpression();
            if (exp != null) {
                String[] symbols = exp.getSymbols();
                if (symbols != null && symbols.length > 0) {
                    // 
                    // add parameter to graph as a node (if not already there).
                    // 
                    String parameterScopedName = parameters[j].getNameScope().getAbsoluteScopePrefix() + parameters[j].getName();
                    Node parameterNode = digraph.getNode(parameterScopedName);
                    if (parameterNode == null) {
                        parameterNode = new Node(parameterScopedName, parameters[j]);
                        digraph.addNode(parameterNode);
                    }
                    // 
                    for (int k = 0; symbols != null && k < symbols.length; k++) {
                        SymbolTableEntry ste = exp.getSymbolBinding(symbols[k]);
                        if (ste == null) {
                            throw new RuntimeException("Error, symbol '" + symbols[k] + "' not bound in parameter '" + parameters[j].getName() + "'");
                        }
                        String symbolScopedName = ste.getNameScope().getAbsoluteScopePrefix() + ste.getName();
                        Node symbolNode = digraph.getNode(symbolScopedName);
                        if (symbolNode == null) {
                            symbolNode = new Node(symbolScopedName, ste);
                            digraph.addNode(symbolNode);
                        }
                        digraph.addEdge(new Edge(parameterNode, symbolNode));
                    }
                }
            }
        }
    }
    // 
    for (Structure structure : model.getStructures()) {
        if (structure instanceof Membrane && ((MembraneMapping) simulationContext.getGeometryContext().getStructureMapping(structure)).getCalculateVoltage()) {
            MembraneVoltage membraneVoltage = ((Membrane) structure).getMembraneVoltage();
            String membraneVoltageScopedName = membraneVoltage.getNameScope().getAbsoluteScopePrefix() + membraneVoltage.getName();
            Node membraneVoltageNode = digraph.getNode(membraneVoltageScopedName);
            if (membraneVoltageNode == null) {
                membraneVoltageNode = new Node(membraneVoltageScopedName, membraneVoltage);
                digraph.addNode(membraneVoltageNode);
            }
            digraph.addEdge(new Edge(membraneVoltageNode, timeNode));
        }
    }
    Node[] timeDependentNodes = digraph.getDigraphAttractorSet(timeNode);
    SymbolTableEntry[] steArray = new SymbolTableEntry[timeDependentNodes.length];
    for (int i = 0; i < steArray.length; i++) {
        steArray[i] = (SymbolTableEntry) timeDependentNodes[i].getData();
    }
    return steArray;
}

Example 8 with Node

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

the class StructureSorter method sortStructures.

public static Structure[] sortStructures(Model model) {
    Graph graph = new Graph();
    // add all structures to the graph
    for (Structure structure : model.getStructures()) {
        graph.addNode(new Node(structure.getName(), structure));
    }
    // add an edge
    for (Structure structure : model.getStructures()) {
        Structure parentStructure = null;
        if (structure.getSbmlParentStructure() != null) {
            parentStructure = structure.getSbmlParentStructure();
        } else if (model.getStructureTopology().getParentStructure(structure) != null) {
            parentStructure = model.getStructureTopology().getParentStructure(structure);
        }
        if (parentStructure != null) {
            int index1 = graph.getIndex(graph.getNode(structure.getName()));
            int index2 = graph.getIndex(graph.getNode(parentStructure.getName()));
            StructureRelationshipEdge edge = getStructureRelationshipEdge(graph, index1, index2);
            edge.bParentChild = true;
        }
    }
    for (ReactionStep rs : model.getReactionSteps()) {
        int index1 = graph.getIndex(graph.getNode(rs.getStructure().getName()));
        for (ReactionParticipant rp : rs.getReactionParticipants()) {
            if (rp.getStructure() != rs.getStructure()) {
                int index2 = graph.getIndex(graph.getNode(rp.getStructure().getName()));
                StructureRelationshipEdge edge = getStructureRelationshipEdge(graph, index2, index1);
                edge.numConnections++;
            }
        }
    }
    // remove edges such that all nodes have degree <= 2
    for (Node node : graph.getNodes()) {
        Edge[] adjacentEdges = graph.getAdjacentEdges(node);
        while (adjacentEdges.length > 2) {
            StructureRelationshipEdge lowestCostEdge = getLowestCostEdge(Arrays.asList(adjacentEdges));
            graph.remove(lowestCostEdge);
            adjacentEdges = graph.getAdjacentEdges(node);
        }
    }
    // for each dependency loop, remove edge with lowest cost
    Path[] fundamentalCycles = graph.getFundamentalCycles();
    while (fundamentalCycles.length > 0) {
        StructureRelationshipEdge lowestCostEdge = getLowestCostEdge(Arrays.asList(fundamentalCycles[0].getEdges()));
        graph.remove(lowestCostEdge);
        fundamentalCycles = graph.getFundamentalCycles();
    }
    // all graphs in the forest are linear now ... find path from first to last and line up all trees in list.
    Tree[] spanningForest = graph.getSpanningForest();
    ArrayList<Structure> structures = new ArrayList<Structure>();
    for (Tree tree : spanningForest) {
        if (tree.getNodes().length > 1) {
            Node start = null;
            Node end = null;
            for (Node node : tree.getNodes()) {
                if (tree.getDegree(node) == 1) {
                    if (start == null) {
                        start = node;
                    } else if (end == null) {
                        end = node;
                    } else {
                        break;
                    }
                }
            }
            Path path = tree.getTreePath(start, end);
            for (Node node : path.getNodesTraversed()) {
                structures.add((Structure) node.getData());
            }
        } else {
            structures.add((Structure) tree.getNodes()[0].getData());
        }
    }
    return structures.toArray(new Structure[structures.size()]);
}

Example 9 with Node

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

the class VariableHash method reorderVariables.

/**
 * Insert the method's description here.
 * Creation date: (4/12/2002 3:45:17 PM)
 * @return cbit.vcell.math.Variable[]
 * @param variables cbit.vcell.math.Variable[]
 */
private Variable[] reorderVariables(Variable[] variables) throws VariableHash.UnresolvedException {
    // 
    // add the nodes for each "Variable" (VolVariable, etc...) ... no dependencies
    // 
    Graph variableGraph = new Graph();
    Graph constantGraph = new Graph();
    Graph functionGraph = new Graph();
    for (int i = 0; i < variables.length; i++) {
        Node node = new Node(variables[i].getName(), variables[i]);
        if (variables[i] instanceof Constant) {
            constantGraph.addNode(node);
        } else if (variables[i] instanceof Function) {
            functionGraph.addNode(node);
        } else {
            variableGraph.addNode(node);
        }
    }
    // 
    // add an edge for each dependency of a Constant
    // 
    Node[] constantNodes = constantGraph.getNodes();
    for (int i = 0; i < constantNodes.length; i++) {
        Constant constant = (Constant) constantNodes[i].getData();
        String[] symbols = constant.getExpression().getSymbols();
        if (symbols != null) {
            for (int j = 0; j < symbols.length; j++) {
                // 
                // find node that this symbol references (it better find this in the Constants).
                // 
                Node symbolNode = constantGraph.getNode(symbols[j]);
                if (symbolNode == null) {
                    if (functionGraph.getNode(symbols[j]) != null) {
                        throw new RuntimeException("Constant " + constant.getName() + " references function '" + symbols[j] + "'");
                    } else if (variableGraph.getNode(symbols[j]) != null) {
                        throw new RuntimeException("Constant " + constant.getName() + " references variable '" + symbols[j] + "'");
                    } else {
                        throw new RuntimeException("Constant " + constant.getName() + " references unknown symbol '" + symbols[j] + "'");
                    }
                }
                Edge dependency = new Edge(constantNodes[i], symbolNode, constant.getName() + "->" + ((Variable) symbolNode.getData()).getName());
                constantGraph.addEdge(dependency);
            }
        }
    }
    Node[] sortedConstantNodes = constantGraph.topologicalSort();
    // 
    // add an edge for each dependency of a Function
    // 
    Node[] functionNodes = functionGraph.getNodes();
    for (int i = 0; i < functionNodes.length; i++) {
        Function function = (Function) functionNodes[i].getData();
        String[] symbols = function.getExpression().getSymbols();
        if (symbols != null) {
            for (int j = 0; j < symbols.length; j++) {
                // 
                // find node that this symbol references (better find it in FunctionGraph, ConstantGraph, or VariableGraph).
                // 
                Node symbolNode = functionGraph.getNode(symbols[j]);
                if (symbolNode != null) {
                    Edge dependency = new Edge(functionNodes[i], symbolNode, function.getName() + "->" + ((Variable) symbolNode.getData()).getName());
                    functionGraph.addEdge(dependency);
                } else if (ReservedMathSymbolEntries.getReservedVariableEntry(symbols[j]) == null && constantGraph.getNode(symbols[j]) == null && variableGraph.getNode(symbols[j]) == null) {
                    throw new VariableHash.UnresolvedException(symbols[j], "Unable to sort, unknown identifier " + symbols[j]);
                }
            }
        }
    }
    Node[] sortedFunctionNodes = functionGraph.topologicalSort();
    // 
    // reassemble in the proper order
    // Constants
    // Variables
    // Functions
    // 
    Vector newVariableOrder = new Vector();
    for (int i = 0; i < sortedConstantNodes.length; i++) {
        newVariableOrder.add(sortedConstantNodes[i].getData());
    }
    Node[] variableNodes = variableGraph.getNodes();
    for (int i = 0; i < variableNodes.length; i++) {
        Object var = variableNodes[i].getData();
        if (!(var instanceof InsideVariable) && !(var instanceof OutsideVariable)) {
            newVariableOrder.add(var);
        }
    }
    for (int i = 0; i < sortedFunctionNodes.length; i++) {
        newVariableOrder.add(sortedFunctionNodes[i].getData());
    }
    Variable[] sortedVars = new Variable[newVariableOrder.size()];
    newVariableOrder.copyInto(sortedVars);
    return sortedVars;
}

Example 10 with Node

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

the class MathSystemHash method getDependencyGraph.

/**
 * Insert the method's description here.
 * Creation date: (4/12/2002 3:45:17 PM)
 * @return cbit.vcell.math.Variable[]
 * @param variables cbit.vcell.math.Variable[]
 */
public Graph getDependencyGraph(Symbol[] symbols) throws MathSystemHash.UnresolvedException {
    // 
    // add the nodes for each "Symbol"
    // 
    Graph graph = new Graph();
    for (int i = 0; i < symbols.length; i++) {
        Node node = new Node(symbols[i].getName(), symbols[i]);
        graph.addNode(node);
    }
    // 
    // add an edge for each dependency of a Symbol (due to it's associated expression implied equation ... e.g. Rate, IC).
    // 
    Node[] nodes = graph.getNodes();
    for (int i = 0; i < nodes.length; i++) {
        Symbol symbol = (Symbol) nodes[i].getData();
        if (symbol.getExpression() != null) {
            String[] symbolNames = symbol.getExpression().getSymbols();
            for (int j = 0; symbolNames != null && j < symbolNames.length; j++) {
                // 
                // find node that this symbol references
                // 
                Node symbolNode = graph.getNode(symbolNames[j]);
                if (symbolNode == null) {
                    throw new RuntimeException("symbol " + symbol.getName() + " references unknown symbol '" + symbolNames[j] + "'");
                }
                Edge dependency = new Edge(nodes[i], symbolNode, symbol.getName() + "->" + ((Symbol) symbolNode.getData()).getName());
                graph.addEdge(dependency);
            }
        }
        if (symbol instanceof VariableReference) {
            VariableReference varRef = (VariableReference) symbol;
            Node referencingVarNode = graph.getNode(varRef.variable.getName());
            if (referencingVarNode == null) {
                throw new RuntimeException("symbol " + symbol.getName() + " references unknown variable '" + varRef.variable.getName() + "'");
            }
            Edge dependency = new Edge(referencingVarNode, nodes[i], varRef.variable.getName() + "->" + symbol.getName());
            graph.addEdge(dependency);
        }
    }
    return graph;
}