Example #1
0
  @SuppressWarnings("unchecked")
  public void addNode(int id, String label, Map attributes) {
    Node node = this.networkInfo.findNodeByOriginalID(id);
    Map annotatedAttributes = new HashMap();
    annotatedAttributes.putAll(attributes);

    if (node != null) {
      ArrayList nodeCommunities = node.getCommunities();

      for (int ii = 0; ii < nodeCommunities.size(); ii++) {
        String communityLevelAttributeName = BASE_COMMUNITY_LEVEL_ATTRIBUTE_NAME + ii;
        String communityName = BASE_COMMUNITY_LABEL + nodeCommunities.get(ii);
        annotatedAttributes.put(communityLevelAttributeName, communityName);
      }
    } else {
      // Isolate nodes would not have been added to our nodes list.
      for (int ii = 0; ii < this.networkInfo.getMaxCommunityLevel(); ii++) {
        String communityLevelAttributeName = BASE_COMMUNITY_LEVEL_ATTRIBUTE_NAME + ii;
        String communityName = BASE_ISOLATE_LABEL + this.isolateCount;
        annotatedAttributes.put(communityLevelAttributeName, communityName);
        this.isolateCount++;
      }
    }

    super.addNode(id, label, annotatedAttributes);
  }
Example #2
0
  @SuppressWarnings("unchecked") // Raw LinkedHashMap
  public void setNodeSchema(LinkedHashMap schema) {
    for (int ii = 0; ii < this.networkInfo.getMaxCommunityLevel(); ii++) {
      String communityLevelAttributeName = BASE_COMMUNITY_LEVEL_ATTRIBUTE_NAME + ii;
      schema.put(communityLevelAttributeName, NWBFileProperty.TYPE_STRING);
    }

    super.setNodeSchema(schema);
  }
  public static File writeCernColtMatrixToNWBFile(DoubleMatrix2D matrix) throws IOException {

    File nwbFile = NWBFileUtilities.createTemporaryNWBFile();

    NWBFileWriter nwbFileWriter = new NWBFileWriter(nwbFile);
    double[][] doubleMatrix = matrix.toArray();

    // Output node schema.

    nwbFileWriter.setNodeSchema(NWBFileWriter.getDefaultNodeSchema());

    // Output nodes and determine whether or not the matrix is directed.

    Map emptyAttributes = new HashMap();
    boolean hasDeterminedIfDirected = false;
    boolean isDirected = false;

    for (int ii = 0; ii < doubleMatrix.length; ii++) {
      int nodeID = ii + 1;
      nwbFileWriter.addNode(nodeID, "node" + nodeID, emptyAttributes);

      if (!hasDeterminedIfDirected) {
        for (int jj = 0; jj < doubleMatrix[ii].length; jj++) {
          if (doubleMatrix[ii][jj] != doubleMatrix[jj][ii]) {
            hasDeterminedIfDirected = true;
            isDirected = true;

            break;
          }
        }
      }
    }

    // Set the edge schema and output the edges.

    LinkedHashMap edgeSchema = NWBFileWriter.getDefaultEdgeSchema();

    if (isDirected) {
      nwbFileWriter.setDirectedEdgeSchema(edgeSchema);

      // This loop will iterate over every cell in the matrix.
      for (int ii = 0; ii < doubleMatrix.length; ii++) {
        for (int jj = 0; jj < doubleMatrix[ii].length; jj++) {
          double weight = doubleMatrix[ii][jj];

          if (weight != 0.0) {
            // Add a new edge.
            int sourceNodeID = ii + 1;
            int targetNodeID = jj + 1;
            HashMap attributes = new HashMap();
            attributes.put("weight", new Double(weight));

            nwbFileWriter.addDirectedEdge(sourceNodeID, targetNodeID, attributes);
          }
        }
      }
    } else {
      nwbFileWriter.setUndirectedEdgeSchema(edgeSchema);

      // This loop will only iterate over the upper half of the matrix.
      for (int ii = 0; ii < doubleMatrix.length; ii++) {
        for (int jj = ii; jj < doubleMatrix[ii].length; jj++) {
          double weight = doubleMatrix[ii][jj];

          if (weight != 0.0) {
            // Add a new edge.

            int sourceNodeID = ii + 1;
            int targetNodeID = jj + 1;
            HashMap attributes = new HashMap();
            attributes.put("weight", new Double(weight));

            nwbFileWriter.addUndirectedEdge(sourceNodeID, targetNodeID, attributes);
          }
        }
      }
    }

    nwbFileWriter.finishedParsing();

    return nwbFile;
  }