public double elementSum() {
double sum = 0d;
MatrixCursor cursor = this.cursor();
while (cursor.next()) {
sum += cursor.val();
}
return sum;
}
/*
* simple generic implementation, can take advantage of sparsity structor
* of this matrix, but not the given one.
* @see org.genemania.engine.matricks.Matrix#elementMultiplySum(org.genemania.engine.matricks.Matrix)
*/
public double elementMultiplySum(Matrix m) {
double sum = 0d;
MatrixCursor cursor = this.cursor();
while (cursor.next()) {
sum += cursor.val() * m.get(cursor.row(), cursor.col());
}
return sum;
}
public Vector columnSums() throws MatricksException {
Vector sums = new DenseDoubleVector(numCols());
MatrixCursor cursor = cursor();
while (cursor.next()) {
sums.set(cursor.col(), cursor.val() + sums.get(cursor.col()));
}
return sums;
}
public void add(double a, Matrix B) throws MatricksException {
if (B.numRows() != this.numRows() && B.numCols() != this.numCols()) {
throw new MatricksException("incompatible size for addition");
}
MatrixCursor cursor = B.cursor();
while (cursor.next()) {
final int row = cursor.row();
final int col = cursor.col();
double v = a * cursor.val() + this.get(row, col);
this.set(row, col, v);
}
}
public Vector rowSums() throws MatricksException {
// TODO: can change this to a lower level interface,
// taking in an array of doubles and not allocating ... ?
Vector sums = new DenseDoubleVector(numRows());
// TODO: optimize out row() with local var? microopt, measure speed
MatrixCursor cursor = cursor();
while (cursor.next()) {
sums.set(cursor.row(), cursor.val() + sums.get(cursor.row()));
}
return sums;
}
/**
* a <- max(a,a')
*
* @param a
* @param b
*/
public void setToMaxTranspose() throws MatricksException {
// throw new RuntimeException("not implemented");
// TODO: bail if not square
MatrixCursor cursor = cursor();
while (cursor.next()) {
double u = cursor.val();
double v = get(cursor.col(), cursor.row());
if (u > v) {
set(cursor.col(), cursor.row(), u);
} else if (v > u) {
cursor.set(v);
}
}
}
public void mmwrite(String filename) throws IOException {
BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
try {
writer.write(MM_COORDINATE_MATRIX_HEADER + "\n");
int nnz = nnz();
writer.write(String.format("%d %d %d\n", numRows(), numCols(), nnz));
MatrixCursor cursor = cursor();
int total = 0;
while (cursor.next()) {
total += 1;
writer.write(String.format("%d %d %f\n", cursor.row() + 1, cursor.col() + 1, cursor.val()));
}
// safety check for internal data consistency
if (total != nnz) {
throw new MatricksException(
String.format("expected %d elements, only found %d", nnz, total));
}
} finally {
writer.close();
}
}
public void setAll(final double a) throws MatricksException {
MatrixCursor cursor = this.cursor();
while (cursor.next()) {
this.set(cursor.row(), cursor.col(), a);
}
}
/*
* A = A ./ (x*x')
*/
public void dotDivOuterProd(Vector x) {
MatrixCursor mCursor = cursor();
while (mCursor.next()) {
mCursor.set(mCursor.val() / (x.get(mCursor.row()) * x.get(mCursor.col())));
}
}