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

Example 16 with Table

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

the class AttributeColumnsControllerImpl method importCSVToEdgesTable.

@Override
public void importCSVToEdgesTable(Graph graph, File file, Character separator, Charset charset, String[] columnNames, Class[] columnTypes, boolean createNewNodes) {
    if (columnNames == null || columnNames.length == 0) {
        return;
    }
    if (columnTypes == null || columnNames.length != columnTypes.length) {
        throw new IllegalArgumentException("Column names length must be the same as column types length");
    }
    CsvReader reader = null;
    graph.writeLock();
    try {
        //Prepare attribute columns for the column names, creating the not already existing columns:
        Table edgesTable = graph.getModel().getEdgeTable();
        Column weightColumn = edgesTable.getColumn("Weight");
        boolean isDynamicWeight = weightColumn.isDynamic();
        String idColumnHeader = null;
        String sourceColumnHeader = null;
        String targetColumnHeader = null;
        String typeColumnHeader = null;
        String weightColumnHeader = null;
        //Necessary because of column name case insensitivity, to map columns to its corresponding csv header.
        HashMap<Column, String> columnHeaders = new HashMap<>();
        for (int i = 0; i < columnNames.length; i++) {
            //Separate first id column found from the list to use as id. If more are found later, the will not be in the list and be ignored.
            if (columnNames[i].equalsIgnoreCase("id")) {
                if (idColumnHeader == null) {
                    idColumnHeader = columnNames[i];
                }
            } else if (columnNames[i].equalsIgnoreCase("source") && sourceColumnHeader == null) {
                //Separate first source column found from the list to use as source node id
                sourceColumnHeader = columnNames[i];
            } else if (columnNames[i].equalsIgnoreCase("target") && targetColumnHeader == null) {
                //Separate first target column found from the list to use as target node id
                targetColumnHeader = columnNames[i];
            } else if (columnNames[i].equalsIgnoreCase("type") && typeColumnHeader == null) {
                //Separate first type column found from the list to use as edge type (directed/undirected)
                typeColumnHeader = columnNames[i];
            } else if (edgesTable.hasColumn(columnNames[i])) {
                //Any other existing column:
                Column column = edgesTable.getColumn(columnNames[i]);
                columnHeaders.put(column, columnNames[i]);
                if (column.equals(weightColumn)) {
                    weightColumnHeader = columnNames[i];
                }
            } else {
                //New column:
                Column column = addAttributeColumn(edgesTable, columnNames[i], columnTypes[i]);
                if (column != null) {
                    columnHeaders.put(column, columnNames[i]);
                }
            }
        }
        Set<Column> columnList = columnHeaders.keySet();
        //Create edges:
        GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
        reader = new CsvReader(new FileInputStream(file), separator, charset);
        reader.setTrimWhitespace(false);
        reader.readHeaders();
        int recordNumber = 0;
        while (reader.readRecord()) {
            String id = null;
            Edge edge = null;
            String sourceId, targetId;
            Node source, target;
            String type;
            boolean directed;
            recordNumber++;
            sourceId = reader.get(sourceColumnHeader);
            targetId = reader.get(targetColumnHeader);
            if (sourceId == null || sourceId.trim().isEmpty() || targetId == null || targetId.trim().isEmpty()) {
                Logger.getLogger("").log(Level.WARNING, "Ignoring record number {0} due to empty source and/or target node ids", recordNumber);
                //No correct source and target ids were provided, ignore row
                continue;
            }
            source = graph.getNode(sourceId);
            if (source == null) {
                if (createNewNodes) {
                    //Create new nodes when they don't exist already and option is enabled
                    if (source == null) {
                        source = gec.createNode(null, sourceId, graph);
                    }
                } else {
                    //Ignore this edge row, since no new nodes should be created.
                    continue;
                }
            }
            target = graph.getNode(targetId);
            if (target == null) {
                if (createNewNodes) {
                    //Create new nodes when they don't exist already and option is enabled
                    if (target == null) {
                        target = gec.createNode(null, targetId, graph);
                    }
                } else {
                    //Ignore this edge row, since no new nodes should be created.
                    continue;
                }
            }
            if (typeColumnHeader != null) {
                type = reader.get(typeColumnHeader);
                //Undirected if indicated correctly, otherwise always directed:
                if (type != null) {
                    directed = !type.equalsIgnoreCase("undirected");
                } else {
                    directed = true;
                }
            } else {
                //Directed by default when not indicated
                directed = true;
            }
            //Prepare the correct edge to assign the attributes:
            if (idColumnHeader != null) {
                id = reader.get(idColumnHeader);
                if (id == null || id.trim().isEmpty()) {
                    //id null or empty, assign one
                    edge = gec.createEdge(source, target, directed);
                } else {
                    Edge edgeById = graph.getEdge(id);
                    if (edgeById == null) {
                        //Create edge because no edge with that id exists
                        edge = gec.createEdge(id, source, target, directed);
                    }
                }
            } else {
                if (findEdge(graph, null, source, target, directed) == null) {
                    //Only create if it does not exist
                    edge = gec.createEdge(source, target, directed);
                }
            }
            if (edge != null) {
                //Assign all attributes to the new edge:
                for (Column column : columnList) {
                    setAttributeValue(reader.get(columnHeaders.get(column)), edge, column);
                }
            } else {
                edge = findEdge(graph, id, source, target, directed);
                if (edge != null) {
                    //Increase non dynamic edge weight with specified weight (if specified), else increase by 1:
                    if (!isDynamicWeight) {
                        if (weightColumnHeader != null) {
                            String weight = reader.get(weightColumnHeader);
                            try {
                                Float weightFloat = Float.parseFloat(weight);
                                edge.setWeight(edge.getWeight() + weightFloat);
                            } catch (NumberFormatException numberFormatException) {
                                //Not valid weight, add 1
                                edge.setWeight(edge.getWeight() + 1);
                                Logger.getLogger("").log(Level.WARNING, "Could not parse weight {0}, adding 1", weight);
                            }
                        } else {
                            //Add 1 (weight not specified)
                            edge.setWeight(edge.getWeight() + 1);
                        }
                    }
                } else {
                    Logger.getLogger("").log(Level.WARNING, "Could not add edge [id = {0}, source = {1}, target = {2}, directed = {3}] to the graph and could not find the existing edge to add its weight. Skipping edge", new Object[] { id, source.getId(), target.getId(), directed });
                }
            }
        }
    } catch (FileNotFoundException ex) {
        Logger.getLogger("").log(Level.SEVERE, null, ex);
    } catch (IOException ex) {
        Logger.getLogger("").log(Level.SEVERE, null, ex);
    } finally {
        graph.readUnlockAll();
        graph.writeUnlock();
        if (reader != null) {
            reader.close();
        }
    }
}

Example 17 with Table

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

the class AttributeColumnsControllerImpl method importCSVToNodesTable.

@Override
public void importCSVToNodesTable(Graph graph, File file, Character separator, Charset charset, String[] columnNames, Class[] columnTypes, boolean assignNewNodeIds) {
    if (columnNames == null || columnNames.length == 0) {
        return;
    }
    if (columnTypes == null || columnNames.length != columnTypes.length) {
        throw new IllegalArgumentException("Column names length must be the same as column types length");
    }
    CsvReader reader = null;
    graph.writeLock();
    try {
        //Prepare attribute columns for the column names, creating the not already existing columns:
        Table nodesTable = graph.getModel().getNodeTable();
        String idColumn = null;
        //Necessary because of column name case insensitivity, to map columns to its corresponding csv header.
        HashMap<Column, String> columnHeaders = new HashMap<>();
        for (int i = 0; i < columnNames.length; i++) {
            //Separate first id column found from the list to use as id. If more are found later, the will not be in the list and be ignored.
            if (columnNames[i].equalsIgnoreCase("id")) {
                if (idColumn == null) {
                    idColumn = columnNames[i];
                }
            } else if (nodesTable.hasColumn(columnNames[i])) {
                Column column = nodesTable.getColumn(columnNames[i]);
                columnHeaders.put(column, columnNames[i]);
            } else {
                Column column = addAttributeColumn(nodesTable, columnNames[i], columnTypes[i]);
                if (column != null) {
                    columnHeaders.put(column, columnNames[i]);
                }
            }
        }
        Set<Column> columnList = columnHeaders.keySet();
        //Create nodes:
        GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
        String id;
        Node node;
        reader = new CsvReader(new FileInputStream(file), separator, charset);
        reader.setTrimWhitespace(false);
        reader.readHeaders();
        while (reader.readRecord()) {
            //Prepare the correct node to assign the attributes:
            if (idColumn != null) {
                id = reader.get(idColumn);
                if (id == null || id.isEmpty()) {
                    //id null or empty, assign one
                    node = gec.createNode(null, graph);
                } else {
                    node = graph.getNode(id);
                    if (node != null) {
                        //Node with that id already in graph
                        if (assignNewNodeIds) {
                            node = gec.createNode(null, graph);
                        }
                    } else {
                        //New id in the graph
                        node = gec.createNode(null, id, graph);
                    }
                }
            } else {
                node = gec.createNode(null);
            }
            //Assign attributes to the current node:
            for (Column column : columnList) {
                setAttributeValue(reader.get(columnHeaders.get(column)), node, column);
            }
        }
    } catch (FileNotFoundException ex) {
        Exceptions.printStackTrace(ex);
    } catch (IOException ex) {
        Exceptions.printStackTrace(ex);
    } finally {
        graph.readUnlockAll();
        graph.writeUnlock();
        if (reader != null) {
            reader.close();
        }
    }
}

Example 18 with Table

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

the class GraphElementsControllerImpl method copyNode.

private Node copyNode(Node node, Graph graph) {
    Node copy = buildNode(graph, node.getLabel());
    //Copy properties (position, size and color):
    copy.setX(node.x());
    copy.setY(node.y());
    copy.setZ(node.z());
    copy.setSize(node.size());
    copy.setR(node.r());
    copy.setG(node.g());
    copy.setB(node.b());
    copy.setAlpha(node.alpha());
    Table nodeTable = graph.getModel().getNodeTable();
    //Copy attributes:
    for (Column column : nodeTable) {
        if (!column.isReadOnly()) {
            copy.setAttribute(column, node.getAttribute(column));
        }
    }
    graph.addNode(copy);
    return copy;
}

Example 19 with Table

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

the class SearchReplaceControllerImpl method findOnNodes.

private SearchResult findOnNodes(SearchOptions searchOptions, int rowIndex, int columnIndex) {
    GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
    SearchResult result = null;
    Set<Integer> columnsToSearch = searchOptions.getColumnsToSearch();
    boolean searchAllColumns = columnsToSearch.isEmpty();
    Table table = Lookup.getDefault().lookup(GraphController.class).getGraphModel().getNodeTable();
    Node[] nodes = searchOptions.getNodesToSearch();
    Node row;
    Column column;
    Object value;
    TimeFormat timeFormat = table.getGraph().getModel().getTimeFormat();
    DateTimeZone timeZone = table.getGraph().getModel().getTimeZone();
    for (; rowIndex < nodes.length; rowIndex++) {
        if (!gec.isNodeInGraph(nodes[rowIndex])) {
            //Make sure node is still in graph when continuing a search
            continue;
        }
        row = nodes[rowIndex];
        for (; columnIndex < table.countColumns(); columnIndex++) {
            if (searchAllColumns || columnsToSearch.contains(columnIndex)) {
                column = table.getColumn(columnIndex);
                value = row.getAttribute(column);
                result = matchRegex(value, searchOptions, rowIndex, columnIndex, timeFormat, timeZone);
                if (result != null) {
                    result.setFoundNode(nodes[rowIndex]);
                    return result;
                }
            }
            //Start at the beginning for the next value
            searchOptions.setRegionStart(0);
        }
        //Start at the beginning for the next value
        searchOptions.setRegionStart(0);
        //Start at the first column for the next row
        columnIndex = 0;
    }
    return result;
}

Example 20 with Table

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

the class SearchReplaceControllerImpl method findOnEdges.

private SearchResult findOnEdges(SearchOptions searchOptions, int rowIndex, int columnIndex) {
    GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
    SearchResult result = null;
    Set<Integer> columnsToSearch = searchOptions.getColumnsToSearch();
    boolean searchAllColumns = columnsToSearch.isEmpty();
    Table table = Lookup.getDefault().lookup(GraphController.class).getGraphModel().getEdgeTable();
    Edge[] edges = searchOptions.getEdgesToSearch();
    Edge row;
    Column column;
    Object value;
    TimeFormat timeFormat = table.getGraph().getModel().getTimeFormat();
    DateTimeZone timeZone = table.getGraph().getModel().getTimeZone();
    for (; rowIndex < edges.length; rowIndex++) {
        if (!gec.isEdgeInGraph(edges[rowIndex])) {
            //Make sure edge is still in graph when continuing a search
            continue;
        }
        row = edges[rowIndex];
        for (; columnIndex < table.countColumns(); columnIndex++) {
            if (searchAllColumns || columnsToSearch.contains(columnIndex)) {
                column = table.getColumn(columnIndex);
                value = row.getAttribute(column);
                result = matchRegex(value, searchOptions, rowIndex, columnIndex, timeFormat, timeZone);
                if (result != null) {
                    result.setFoundEdge(edges[rowIndex]);
                    return result;
                }
            }
            //Start at the beginning for the next value
            searchOptions.setRegionStart(0);
        }
        //Start at the beginning for the next value
        searchOptions.setRegionStart(0);
        //Start at the first column for the next row
        columnIndex = 0;
    }
    return result;
}