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/*
* Copyright 2009 David Jurgens
*
* This file is part of the S-Space package and is covered under the terms and
* conditions therein.
*
* The S-Space package is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License version 2 as published
* by the Free Software Foundation and distributed hereunder to you.
*
* THIS SOFTWARE IS PROVIDED "AS IS" AND NO REPRESENTATIONS OR WARRANTIES,
* EXPRESS OR IMPLIED ARE MADE. BY WAY OF EXAMPLE, BUT NOT LIMITATION, WE MAKE
* NO REPRESENTATIONS OR WARRANTIES OF MERCHANT- ABILITY OR FITNESS FOR ANY
* PARTICULAR PURPOSE OR THAT THE USE OF THE LICENSED SOFTWARE OR DOCUMENTATION
* WILL NOT INFRINGE ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER
* RIGHTS.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see This class is thread-safe.
*
* @author David Jurgens
*/
public class MatlabSparseMatrixBuilder implements MatrixBuilder {
/**
* Logger for all the {@code MatlabSparseMatrixBuilder} instances
*/
private static final Logger LOGGER =
Logger.getLogger(MatlabSparseMatrixBuilder.class.getName());
/**
* The file to which the matrix will be written
*/
private final File matrixFile;
/**
* The writer used to add data to the matrix file
*/
private final PrintWriter matrixWriter;
/**
* Whether the inputted matrix columns should be transposed as rows in the
* final matrix data file.
*/
private final boolean transposeData;
/**
* Whether the builder has finished adding data to the matrix array
*/
private boolean isFinished;
/**
* The number of the column that will next be assigned
*/
private int curColumn;
/**
* Creates a builder for a matrix in the {@link
* MatrixIO.Format#MATLAB_SPARSE MATLAB_SPARSE} format to be stored in a
* temporary file.
*/
public MatlabSparseMatrixBuilder() {
this(getTempMatrixFile(), false);
}
/**
* Creates a builder for a matrix in the {@link
* MatrixIO.Format#MATLAB_SPARSE MATLAB_SPARSE} format to be stored in a
* temporary file.
*
* @param transposeData {@code true} if the input matrix columns should be
* tranposed in the backing matrix file
*/
public MatlabSparseMatrixBuilder(boolean transposeData) {
this(getTempMatrixFile(), transposeData);
}
/**
* Creates a builder for a matrix in the {@link
* MatrixIO.Format#MATLAB_SPARSE MATLAB_SPARSE} format, which will be stored
* in the specified file.
*
* @param backingFile the file to which the matrix should be written
*/
public MatlabSparseMatrixBuilder(File backingFile) {
this(backingFile, false);
}
/**
* Creates a builder for a matrix in the {@link
* MatrixIO.Format#MATLAB_SPARSE MATLAB_SPARSE} format, which will be stored
* in the specified file.
*
* @param backingFile the file to which the matrix should be written
* @param transposeData {@code true} if the input matrix columns should be
* tranposed in the backing matrix file
*/
public MatlabSparseMatrixBuilder(File backingFile, boolean transposeData) {
this.matrixFile = backingFile;
this.transposeData = transposeData;
curColumn = 0;
isFinished = false;
try {
matrixWriter = new PrintWriter(matrixFile);
} catch (IOException ioe) {
throw new IOError(ioe);
}
}
/**
* Returns a temporary file that will be deleted on JVM exit.
*'
* @return a temporary file used to store a matrix
*/
private static File getTempMatrixFile() {
File tmp = null;
try {
tmp = File.createTempFile("matlab-sparse-matrix", ".dat");
} catch (IOException ioe) {
throw new IOError(ioe);
}
tmp.deleteOnExit();
return tmp;
}
/**
* {@inheritDoc}
*/
public synchronized int addColumn(double[] column) {
if (isFinished)
throw new IllegalStateException(
"Cannot add rows to a MatrixBuilder that is finished");
for (int r = 0; r < column.length; ++r) {
if (column[r] != 0d) {
// NB: Matlab sparse format is in [col row val] format
//
// NOTE: Matlab indices start at 1, not 0, so update all the
// row and column values to be Matlab formatted.
addEntry(r + 1, curColumn + 1, column[r]);
}
}
return ++curColumn;
}
/**
* {@inheritDoc}
*/
public synchronized int addColumn(SparseArray column) {
if (isFinished)
throw new IllegalStateException(
"Cannot add columns to a MatrixBuilder that is finished");
for (int r : column.getElementIndices()) {
// NB: Matlab sparse format is in [row col val] format
//
// NOTE: Matlab indices start at 1, not 0, so update all the row
// and column values to be Matlab formatted.
addEntry(r + 1, curColumn + 1, column.get(r).doubleValue());
}
return ++curColumn;
}
/**
* {@inheritDoc}
*/
public synchronized int addColumn(Vector col) {
DoubleVector column = Vectors.asDouble(col);
if (isFinished)
throw new IllegalStateException(
"Cannot add columns to a MatrixBuilder that is finished");
if (column instanceof SparseVector) {
SparseVector s = (SparseVector)column;
for (int r : s.getNonZeroIndices()) {
// NB: Matlab sparse format is in [row col val] format
//
// NOTE: Matlab indices start at 1, not 0, so update all the
// column and column values to be Matlab formatted.
addEntry(r + 1, curColumn + 1, column.get(r));
}
}
else {
for (int r = 0; r < column.length(); ++r) {
double d = column.get(r);
if (d != 0d) {
// NOTE: Matlab indices start at 1, not 0, so update all
// the row and column values to be Matlab formatted.
addEntry(r + 1, curColumn + 1, d);
}
}
}
return ++curColumn;
}
private void addEntry(int row, int col, double value) {
if (transposeData)
matrixWriter.println(col + " " + row + " " + value);
else
matrixWriter.println(row + " " + col + " " + value);
}
/**
* {@inheritDoc} Once this method has been called, any subsequent calls will
* have no effect and will not throw an exception.
*/
public synchronized void finish() {
if (!isFinished) {
if (LOGGER.isLoggable(Level.FINE)) {
LOGGER.fine("Finished writing matrix in MATLAB_SPARSE format "
+ "with " + curColumn + " columns");
}
isFinished = true;
matrixWriter.close();
}
}
/**
* {@inheritDoc}
*/
public synchronized File getFile() {
if (!isFinished)
throw new IllegalStateException(
"Cannot access matrix file until finish has been called");
return matrixFile;
}
/**
* Returns {@link MatrixIO.Format#MATLAB_SPARSE MATLAB_SPARSE}.
*/
public Format getMatrixFormat() {
return MatrixIO.Format.MATLAB_SPARSE;
}
/**
* {@inheritDoc}
*/
public MatrixFile getMatrixFile() {
return new MatrixFile(getFile(), getMatrixFormat());
}
/**
* {@inheritDoc}
*/
public synchronized boolean isFinished() {
return isFinished;
}
}