private static void saveDenseDoubleMatrix2D(OutputStream stream, DoubleMatrix2D matrix)
throws IOException {
BufferedWriter out = new BufferedWriter(new OutputStreamWriter(stream));
double[][] m = matrix.toArray();
for (double[] pu : m) {
for (int j = 0; j < pu.length; j++) {
out.write(Double.toString(pu[j]));
if (j < pu.length - 1) {
out.write('\t');
}
}
out.newLine();
}
out.flush();
}
/**
* @param x A Colt 2D matrix of doubles, not null
* @return An OG 2D matrix
*/
public static DoubleMatrix2D wrap(final cern.colt.matrix.DoubleMatrix2D x) {
Validate.notNull(x, "x");
return new DoubleMatrix2D(x.toArray());
}
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;
}