matrixvectorreader.java

另一个功能更强大的矩阵运算软件开源代码

/*
 * Copyright (C) 2003-2006 Bjørn-Ove Heimsund
 * 
 * This file is part of MTJ.
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by the
 * Free Software Foundation; either version 2.1 of the License, or (at your
 * option) any later version.
 * 
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
 * for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */

package no.uib.cipr.matrix.io;

import java.io.BufferedReader;
import java.io.EOFException;
import java.io.IOException;
import java.io.Reader;
import java.io.StreamTokenizer;
import java.util.LinkedList;
import java.util.List;

/**
 * Reads matrices and vectors
 */
public class MatrixVectorReader extends BufferedReader {

    /**
     * Reads the entries of the matrix or vector
     */
    private StreamTokenizer st;

    /**
     * Constructor for MatrixVectorReader
     * 
     * @param in
     *            A Reader
     */
    public MatrixVectorReader(Reader in) {
        super(in);
        setup();
    }

    /**
     * Constructor for MatrixVectorReader
     * 
     * @param in
     *            A Reader
     * @param sz
     *            Input buffer size
     */
    public MatrixVectorReader(Reader in, int sz) {
        super(in, sz);
        setup();
    }

    /**
     * Sets up the stream tokenizer
     */
    private void setup() {
        st = new StreamTokenizer(this);
        st.resetSyntax();
        st.eolIsSignificant(false);
        st.lowerCaseMode(true);

        // Parse numbers as words
        st.wordChars('0', '9');
        st.wordChars('-', '.');

        // Characters as words
        st.wordChars('\u0000', '\u00FF');

        // Skip comments
        st.commentChar('%');

        // Skip whitespace and newlines
        st.whitespaceChars(' ', ' ');
        st.whitespaceChars('\u0009', '\u000e');
    }

    /**
     * Shifts the indices. Useful for converting between 0- and 1-based
     * indicing.
     * 
     * @param num
     *            Added to every index
     * @param indices
     *            Indices to shift
     */
    public void add(int num, int[] indices) {
        for (int i = 0; i < indices.length; ++i)
            indices[i] += num;
    }

    /**
     * Reads a line, and trims it of surrounding whitespace
     * 
     * @throws IOException
     *             If either I/O errors occur, or there was nothing to read
     */
    private String readTrimmedLine() throws IOException {
        String line = readLine();
        if (line != null)
            return line.trim();
        else
            throw new EOFException();
    }

    /**
     * Reads the matrix info for the Matrix Market exchange format. The line
     * must consist of exactly 5 space-separated entries, the first being
     * "%%MatrixMarket"
     */
    public MatrixInfo readMatrixInfo() throws IOException {
        String[] component = readTrimmedLine().split(" +");
        if (component.length != 5)
            throw new IOException(
                    "Current line unparsable. It must consist of 5 tokens");

        // Read header
        if (!component[0].equalsIgnoreCase("%%MatrixMarket"))
            throw new IOException("Not in Matrix Market exchange format");

        // This will always be "matrix"
        if (!component[1].equalsIgnoreCase("matrix"))
            throw new IOException("Expected \"matrix\", got " + component[1]);

        // Sparse or dense?
        boolean sparse = false;
        if (component[2].equalsIgnoreCase("coordinate"))
            sparse = true;
        else if (component[2].equalsIgnoreCase("array"))
            sparse = false;
        else
            throw new IOException("Unknown layout " + component[2]);

        // Dataformat
        MatrixInfo.MatrixField field = null;
        if (component[3].equalsIgnoreCase("real"))
            field = MatrixInfo.MatrixField.Real;
        else if (component[3].equalsIgnoreCase("integer"))
            field = MatrixInfo.MatrixField.Integer;
        else if (component[3].equalsIgnoreCase("complex"))
            field = MatrixInfo.MatrixField.Complex;
        else if (component[3].equalsIgnoreCase("pattern"))
            field = MatrixInfo.MatrixField.Pattern;
        else
            throw new IOException("Unknown field specification " + component[3]);

        // Matrix pattern
        MatrixInfo.MatrixSymmetry symmetry = null;
        if (component[4].equalsIgnoreCase("general"))
            symmetry = MatrixInfo.MatrixSymmetry.General;
        else if (component[4].equalsIgnoreCase("symmetric"))
            symmetry = MatrixInfo.MatrixSymmetry.Symmetric;
        else if (component[4].equalsIgnoreCase("skew-symmetric"))
            symmetry = MatrixInfo.MatrixSymmetry.SkewSymmetric;
        else if (component[4].equalsIgnoreCase("Hermitian"))
            symmetry = MatrixInfo.MatrixSymmetry.Hermitian;
        else
            throw new IOException("Unknown symmetry specification "
                    + component[4]);

        // Pack together. This also verifies the format
        return new MatrixInfo(sparse, field, symmetry);
    }

    /**
     * Reads the vector info for the Matrix Market exchange format. The line
     * must consist of exactly 4 space-separated entries, the first being
     * "%%MatrixMarket"
     */
    public VectorInfo readVectorInfo() throws IOException {
        String[] component = readTrimmedLine().split(" +");
        if (component.length != 4)
            throw new IOException(
                    "Current line unparsable. It must consist of 4 tokens");

        // Read header
        if (!component[0].equalsIgnoreCase("%%MatrixMarket"))
            throw new IOException("Not in Matrix Market exchange format");

        // This will always be "vector"
        if (!component[1].equalsIgnoreCase("vector"))
            throw new IOException("Expected \"vector\", got " + component[1]);

        // Sparse or dense?
        boolean sparse = false;
        if (component[2].equalsIgnoreCase("coordinate"))
            sparse = true;
        else if (component[2].equalsIgnoreCase("array"))
            sparse = false;
        else
            throw new IOException("Unknown layout " + component[2]);

        // Dataformat
        VectorInfo.VectorField field = null;
        if (component[3].equalsIgnoreCase("real"))
            field = VectorInfo.VectorField.Real;
        else if (component[3].equalsIgnoreCase("integer"))
            field = VectorInfo.VectorField.Integer;
        else if (component[3].equalsIgnoreCase("complex"))
            field = VectorInfo.VectorField.Complex;
        else if (component[3].equalsIgnoreCase("pattern"))
            field = VectorInfo.VectorField.Pattern;
        else
            throw new IOException("Unknown field specification " + component[3]);

        // Pack together. This also verifies the format
        return new VectorInfo(sparse, field);
    }

    /**
     * Checks if a Matrix Market header is present ("%%MatrixMarket")
     * 
     * @return True if a header was found, else false
     * @throws IOException
     */
    public boolean hasInfo() throws IOException {
        // Read a line, then skip back
        mark(1024);
        String[] component = readTrimmedLine().split(" +");
        reset();

        return component[0].equalsIgnoreCase("%%MatrixMarket");
    }

    /**
     * Reads all the comments (lines starting with '%'). Positions the reader at
     * the first non-comment line. Can only be called after reading the matrix
     * or vector info. The comments read does not include '%' or the newline
     */
    public String[] readComments() throws IOException {
        List<String> list = new LinkedList<String>();
        while (true) {
            mark(1024); // Line length equal 1024 at most
            String line = readTrimmedLine();
            if (line.length() > 0)
                if (line.charAt(0) != '%') {
                    reset();
                    break;
                } else
                    list.add(line.substring(1));
        }
        return list.toArray(new String[list.size()]);
    }

    /**
     * Reads in the size of a matrix. Skips initial comments
     */
    public MatrixSize readMatrixSize(MatrixInfo info) throws IOException {
        // Always read the matrix size
        int numRows = getInt(), numColumns = getInt();

        // For coordinate matrices we also read the number of entries
        if (info.isDense())
            return new MatrixSize(numRows, numColumns, info);
        else {
            int numEntries = getInt();
            return new MatrixSize(numRows, numColumns, numEntries);
        }
    }

    /**
     * Reads in the size of an array matrix. Skips initial comments
     */
    public MatrixSize readArraySize() throws IOException {
        int numRows = getInt(), numColumns = getInt();

        return new MatrixSize(numRows, numColumns, numRows * numColumns);
    }

    /**
     * Reads in the size of a coordinate matrix. Skips initial comments
     */
    public MatrixSize readCoordinateSize() throws IOException {
        int numRows = getInt(), numColumns = getInt(), numEntries = getInt();

        return new MatrixSize(numRows, numColumns, numEntries);
    }

    /**
     * Reads in the size of a vector. Skips initial comments
     */
    public VectorSize readVectorSize(VectorInfo info) throws IOException {
        // Always read the vector size
        int size = getInt();

        // For coordinate vectors we also read the number of entries
        if (info.isDense())
            return new VectorSize(size);
        else {
            int numEntries = getInt();
            return new VectorSize(size, numEntries);
        }
    }

    /**
     * Reads in the size of a dense vector. Skips initial comments
     */
    public VectorSize readVectorArraySize() throws IOException {
        int size = getInt();

        return new VectorSize(size);
    }

    /**
     * Reads in the size of a coordinate vector. Skips initial comments
     */
    public VectorSize readVectorCoordinateSize() throws IOException {
        int size = getInt(), numEntries = getInt();

        return new VectorSize(size, numEntries);
    }

    /**
     * Reads the array data
     */
    public void readArray(double[] data) throws IOException {
        int size = data.length;
        for (int i = 0; i < size; ++i)