protected synchronized ArrayAccess implGetTransposedArray(
int mode, int startColumn, int columns, int rows) throws ApfloatRuntimeException {
int width = (int) (getSize() / rows);
if (columns != (columns & -columns)
|| rows != (rows & -rows)
|| startColumn + columns > width) {
throw new ApfloatInternalException("Invalid size");
}
int blockSize = columns * rows, b = columns;
ArrayAccess arrayAccess =
new TransposedMemoryArrayAccess(mode, new double[blockSize], startColumn, columns, rows);
if ((mode & READ) != 0) {
// Read the data from the input file in b x b blocks
long readPosition = startColumn;
for (int i = 0; i < rows; i += b) {
int writePosition = i;
for (int j = 0; j < b; j++) {
readToArray(readPosition, arrayAccess, writePosition, b);
readPosition += width;
writePosition += rows;
}
// Transpose the b x b block
ArrayAccess subArrayAccess = arrayAccess.subsequence(i, blockSize - i);
DoubleMatrix.transposeSquare(subArrayAccess, b, rows);
}
}
return arrayAccess;
}
// Write the data back to the same location in file as retrieved with getTransposedArray()
private synchronized void setTransposedArray(
ArrayAccess arrayAccess, int startColumn, int columns, int rows)
throws ApfloatRuntimeException {
int width = (int) (getSize() / rows);
int blockSize = arrayAccess.getLength(), b = columns;
long writePosition = startColumn;
for (int i = 0; i < rows; i += b) {
int readPosition = i;
// Transpose the b x b block
ArrayAccess subArrayAccess = arrayAccess.subsequence(i, blockSize - i);
DoubleMatrix.transposeSquare(subArrayAccess, b, rows);
for (int j = 0; j < b; j++) {
writeFromArray(arrayAccess, readPosition, writePosition, b);
readPosition += rows;
writePosition += width;
}
}
}
private void writeFromArray(
ArrayAccess arrayAccess, int readPosition, long writePosition, int length)
throws ApfloatRuntimeException {
ArrayAccess writeArrayAccess = getArray(WRITE, writePosition, length);
System.arraycopy(
arrayAccess.getData(),
arrayAccess.getOffset() + readPosition,
writeArrayAccess.getData(),
writeArrayAccess.getOffset(),
length);
writeArrayAccess.close();
}
private void readToArray(
long readPosition, ArrayAccess arrayAccess, int writePosition, int length)
throws ApfloatRuntimeException {
ArrayAccess readArrayAccess = getArray(READ, readPosition, length);
System.arraycopy(
readArrayAccess.getData(),
readArrayAccess.getOffset(),
arrayAccess.getData(),
arrayAccess.getOffset() + writePosition,
length);
readArrayAccess.close();
}