@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);
}
@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;
}