Examples with NodeIterable org.gephi.graph.api.NodeIterable used on opensource projects

Example 21 with NodeIterable

use of org.gephi.graph.api.NodeIterable in project gephi by gephi.

the class ExporterGDF method exportData.

private void exportData(Graph graph, GraphModel graphModel) throws Exception {
    Progress.start(progressTicket);
    defaultNodeColumns(graph);
    defaultEdgeColumns(graph);
    Column[] nodeColumns = attributesNodeColumns(graphModel);
    Column[] edgeColumns = attributesEdgeColumns(graphModel);
    StringBuilder stringBuilder = new StringBuilder();
    // Node intro
    stringBuilder.append("nodedef> name VARCHAR,");
    // Default Node columns title
    for (NodeColumnsGDF c : defaultNodeColumnsGDFs) {
        if (c.isEnable()) {
            stringBuilder.append(c.getTitle());
            stringBuilder.append(" ");
            stringBuilder.append(c.getType().toString().toUpperCase());
            if (c.getDefaultValue() != null) {
                stringBuilder.append(" default ");
                stringBuilder.append(c.getDefaultValue().toString());
            }
            stringBuilder.append(",");
        }
    }
    // Attributes Node columns
    for (Column c : nodeColumns) {
        if (!c.isProperty()) {
            stringBuilder.append(c.getTitle());
            stringBuilder.append(" ");
            DataTypeGDF dataTypeGDF = getDataTypeGDF(c.getTypeClass());
            stringBuilder.append(dataTypeGDF.toString().toUpperCase());
            if (c.getDefaultValue() != null) {
                stringBuilder.append(" default ");
                stringBuilder.append(c.getDefaultValue().toString());
            }
            stringBuilder.append(",");
        }
    }
    // Remove last coma
    stringBuilder.setLength(stringBuilder.length() - 1);
    stringBuilder.append("\n");
    // Options
    if (normalize) {
        calculateMinMax(graph);
    }
    // Calculate progress units count
    int max = graph.getNodeCount() + graph.getEdgeCount();
    Progress.switchToDeterminate(progressTicket, max);
    // Node lines
    NodeIterable itr = graph.getNodes();
    for (Node node : itr) {
        if (cancel) {
            itr.doBreak();
            return;
        }
        // Id
        stringBuilder.append(node.getId());
        stringBuilder.append(",");
        // Default columns
        for (NodeColumnsGDF c : defaultNodeColumnsGDFs) {
            if (c.isEnable()) {
                c.writeData(stringBuilder, node);
                stringBuilder.append(",");
            }
        }
        // Attributes columns
        for (Column c : nodeColumns) {
            if (!c.isProperty()) {
                Object val = node.getAttribute(c, graph.getView());
                if (val != null) {
                    if (c.getTypeClass().equals(String.class) || c.getTypeClass().equals(String[].class)) {
                        String quote = !useQuotes ? "" : simpleQuotes ? "'" : "\"";
                        stringBuilder.append(quote);
                        stringBuilder.append(val.toString());
                        stringBuilder.append(quote);
                    } else {
                        stringBuilder.append(val.toString());
                    }
                }
                stringBuilder.append(",");
            }
        }
        // Remove last coma
        stringBuilder.setLength(stringBuilder.length() - 1);
        stringBuilder.append("\n");
        Progress.progress(progressTicket);
    }
    // Edge intro
    stringBuilder.append("edgedef> node1,node2,");
    // Edge settings helper
    for (Edge e : graph.getEdges()) {
        edgeColors = edgeColors || e.alpha() != 0;
        edgeLabels = edgeLabels || (e.getLabel() != null && !e.getLabel().isEmpty());
    }
    // Edge columns title
    for (EdgeColumnsGDF c : defaultEdgeColumnsGDFs) {
        if (c.isEnable()) {
            stringBuilder.append(c.getTitle());
            stringBuilder.append(" ");
            stringBuilder.append(c.getType().toString().toUpperCase());
            if (c.getDefaultValue() != null) {
                stringBuilder.append(" default ");
                stringBuilder.append(c.getDefaultValue().toString());
            }
            stringBuilder.append(",");
        }
    }
    // Attributes Edge columns
    for (Column c : edgeColumns) {
        if (!c.isProperty()) {
            stringBuilder.append(c.getTitle());
            stringBuilder.append(" ");
            DataTypeGDF dataTypeGDF = getDataTypeGDF(c.getTypeClass());
            stringBuilder.append(dataTypeGDF.toString().toUpperCase());
            if (c.getDefaultValue() != null) {
                stringBuilder.append(" default ");
                stringBuilder.append(c.getDefaultValue().toString());
            }
            stringBuilder.append(",");
        }
    }
    // Remove last coma
    stringBuilder.setLength(stringBuilder.length() - 1);
    stringBuilder.append("\n");
    // Edge lines
    EdgeIterable itrEdges = graph.getEdges();
    for (Edge edge : itrEdges) {
        if (cancel) {
            itrEdges.doBreak();
            return;
        }
        // Source & Target
        stringBuilder.append(edge.getSource().getId());
        stringBuilder.append(",");
        stringBuilder.append(edge.getTarget().getId());
        stringBuilder.append(",");
        // Default columns
        for (EdgeColumnsGDF c : defaultEdgeColumnsGDFs) {
            if (c.isEnable()) {
                c.writeData(stringBuilder, edge);
                stringBuilder.append(",");
            }
        }
        // Attributes columns
        for (Column c : edgeColumns) {
            if (!c.isProperty()) {
                Object val = edge.getAttribute(c, graph.getView());
                if (val != null) {
                    if (c.getTypeClass().equals(String.class) || c.getTypeClass().equals(String[].class)) {
                        String quote = !useQuotes ? "" : simpleQuotes ? "'" : "\"";
                        stringBuilder.append(quote);
                        stringBuilder.append(val.toString());
                        stringBuilder.append(quote);
                    } else {
                        stringBuilder.append(val.toString());
                    }
                }
                stringBuilder.append(",");
            }
        }
        // Remove last coma
        stringBuilder.setLength(stringBuilder.length() - 1);
        stringBuilder.append("\n");
        Progress.progress(progressTicket);
    }
    // Write StringBuilder
    if (!cancel) {
        writer.append(stringBuilder);
    }
    Progress.finish(progressTicket);
}

Example 22 with NodeIterable

use of org.gephi.graph.api.NodeIterable in project gephi by gephi.

the class ExporterVNA method exportNodeProperties.

/*
     * prints node properties as "id (x)? (y)? (size)? (color)? (shortlabel)?"
     */
private void exportNodeProperties(Graph graph) throws IOException {
    // header
    writer.append("*Node properties\n");
    writer.append("ID");
    if (exportCoords) {
        writer.append(" x y");
    }
    if (exportSize) {
        writer.append(" size");
    }
    if (exportColor) {
        writer.append(" color");
    }
    if (exportShortLabel) {
        writer.append(" shortlabel");
    }
    writer.append("\n");
    // body
    NodeIterable nodeIterable = graph.getNodes();
    for (Node node : nodeIterable) {
        Progress.progress(progressTicket);
        if (cancel) {
            nodeIterable.doBreak();
            return;
        }
        writer.append(node.getId().toString());
        if (exportCoords) {
            if (!normalize) {
                writer.append(" ").append(Float.toString(node.x())).append(" ").append(Float.toString(node.y()));
            } else {
                writer.append(" ").append(Double.toString((node.x() - minX) / (maxX - minX))).append(" ").append(Double.toString((node.y() - minY) / (maxY - minY)));
            }
        }
        if (exportSize) {
            if (!normalize) {
                writer.append(" ").append(Float.toString(node.size()));
            } else {
                writer.append(" ").append(Double.toString((node.size() - minSize) / (maxSize - minSize)));
            }
        }
        if (exportColor) {
            // [0..1] to [0..255]
            writer.append(" ").append(Integer.toString((int) (node.r() * 255f)));
        }
        if (exportShortLabel) {
            if (node.getLabel() != null) {
                writer.append(" ").append(printParameter(node.getLabel()));
            } else {
                writer.append(" ").append(printParameter(node.getId()));
            }
        }
        writer.append("\n");
    }
}

Example 23 with NodeIterable

use of org.gephi.graph.api.NodeIterable in project gephi by gephi.

the class NoverlapLayout method goAlgo.

@Override
public void goAlgo() {
    setConverged(true);
    this.graph = graphModel.getGraphVisible();
    graph.readLock();
    try {
        // Reset Layout Data
        for (Node n : graph.getNodes()) {
            if (n.getLayoutData() == null || !(n.getLayoutData() instanceof NoverlapLayoutData)) {
                n.setLayoutData(new NoverlapLayoutData());
            }
            NoverlapLayoutData layoutData = n.getLayoutData();
            layoutData.neighbours.clear();
            layoutData.dx = 0;
            layoutData.dy = 0;
        }
        // Get xmin, xmax, ymin, ymax
        this.xmin = Double.MAX_VALUE;
        this.xmax = Double.MIN_VALUE;
        this.ymin = Double.MAX_VALUE;
        this.ymax = Double.MIN_VALUE;
        for (Node n : graph.getNodes()) {
            float x = n.x();
            float y = n.y();
            float radius = n.size();
            // Get the rectangle occupied by the node
            double nxmin = x - (radius * ratio + margin);
            double nxmax = x + (radius * ratio + margin);
            double nymin = y - (radius * ratio + margin);
            double nymax = y + (radius * ratio + margin);
            // Update global boundaries
            this.xmin = Math.min(this.xmin, nxmin);
            this.xmax = Math.max(this.xmax, nxmax);
            this.ymin = Math.min(this.ymin, nymin);
            this.ymax = Math.max(this.ymax, nymax);
        }
        // Secure the bounds
        double xwidth = this.xmax - this.xmin;
        double yheight = this.ymax - this.ymin;
        double xcenter = (this.xmin + this.xmax) / 2;
        double ycenter = (this.ymin + this.ymax) / 2;
        double securityRatio = 1.1;
        this.xmin = xcenter - securityRatio * xwidth / 2;
        this.xmax = xcenter + securityRatio * xwidth / 2;
        this.ymin = ycenter - securityRatio * yheight / 2;
        this.ymax = ycenter + securityRatio * yheight / 2;
        SpatialGrid grid = new SpatialGrid();
        // Put nodes in their boxes
        for (Node n : graph.getNodes()) {
            grid.add(n);
        }
        // Build proximities
        for (int row = 0; row < grid.countRows() && !cancel; row++) {
            for (int col = 0; col < grid.countColumns() && !cancel; col++) {
                for (Node n : grid.getContent(row, col)) {
                    NoverlapLayoutData lald = n.getLayoutData();
                    // We search nodes that are in the boxes that are adjacent or the same.
                    for (int row2 = Math.max(0, row - 1); row2 <= Math.min(row + 1, grid.countRows() - 1); row2++) {
                        for (int col2 = Math.max(0, col - 1); col2 <= Math.min(col + 1, grid.countColumns() - 1); col2++) {
                            for (Node n2 : grid.getContent(row2, col2)) {
                                if (n2 != n && !lald.neighbours.contains(n2)) {
                                    lald.neighbours.add(n2);
                                }
                            }
                        }
                    }
                }
            }
        }
        // Proximities are built !
        // Apply repulsion force - along proximities...
        NodeIterable nodesIterable = graph.getNodes();
        for (Node n1 : nodesIterable) {
            NoverlapLayoutData lald = n1.getLayoutData();
            for (Node n2 : lald.neighbours) {
                float n1x = n1.x();
                float n1y = n1.y();
                float n2x = n2.x();
                float n2y = n2.y();
                float n1radius = n1.size();
                float n2radius = n2.size();
                // Check sizes (spheric)
                double xDist = n2x - n1x;
                double yDist = n2y - n1y;
                double dist = Math.sqrt(xDist * xDist + yDist * yDist);
                boolean collision = dist < (n1radius * ratio + margin) + (n2radius * ratio + margin);
                if (collision) {
                    setConverged(false);
                    // n1 repulses n2, as strongly as it is big
                    NoverlapLayoutData layoutData = n2.getLayoutData();
                    double f = 1. + n1.size();
                    if (dist > 0) {
                        layoutData.dx += xDist / dist * f;
                        layoutData.dy += yDist / dist * f;
                    } else {
                        // Same exact position, divide by zero impossible: jitter
                        layoutData.dx += 0.01 * (0.5 - Math.random());
                        layoutData.dy += 0.01 * (0.5 - Math.random());
                    }
                }
                if (cancel) {
                    break;
                }
            }
            if (cancel) {
                nodesIterable.doBreak();
                break;
            }
        }
        // apply forces
        for (Node n : graph.getNodes()) {
            NoverlapLayoutData layoutData = n.getLayoutData();
            if (!n.isFixed()) {
                layoutData.dx *= 0.1 * speed;
                layoutData.dy *= 0.1 * speed;
                float x = n.x() + layoutData.dx;
                float y = n.y() + layoutData.dy;
                n.setX(x);
                n.setY(y);
            }
        }
    } finally {
        graph.readUnlockAll();
    }
}