//****************************************************************************** // // File: DoubleMatrixFile.java // Package: edu.rit.io // Unit: Class edu.rit.io.DoubleMatrixFile // // This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights // reserved. For further information, contact the author, Alan Kaminsky, at // ark@cs.rit.edu. // // This Java source file is part of the Parallel Java Library ("PJ"). PJ is free // software; you can redistribute it and/or modify it under the terms of the GNU // General Public License as published by the Free Software Foundation; either // version 3 of the License, or (at your option) any later version. // // PJ 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 General Public License for more details. // // Linking this library statically or dynamically with other modules is making a // combined work based on this library. Thus, the terms and conditions of the // GNU General Public License cover the whole combination. // // As a special exception, the copyright holders of this library give you // permission to link this library with independent modules to produce an // executable, regardless of the license terms of these independent modules, and // to copy and distribute the resulting executable under terms of your choice, // provided that you also meet, for each linked independent module, the terms // and conditions of the license of that module. An independent module is a // module which is not derived from or based on this library. If you modify this // library, you may extend this exception to your version of the library, but // you are not obligated to do so. If you do not wish to do so, delete this // exception statement from your version. // // A copy of the GNU General Public License is provided in the file gpl.txt. You // may also obtain a copy of the GNU General Public License on the World Wide // Web at http://www.gnu.org/licenses/gpl.html. // //****************************************************************************** package edu.rit.io; import edu.rit.util.Range; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.DataInputStream; import java.io.DataOutputStream; import java.io.EOFException; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; /** * Class DoubleMatrixFile provides an object for reading or writing a double * matrix from or to a file. The matrix containing the data to read or write is * a separate object, specified as an argument to the constructor or the * setMatrix() method. *

* To write the matrix to a file, call the prepareToWrite() method, * specifying the output stream to write. The prepareToWrite() method * returns an instance of class {@linkplain DoubleMatrixFile.Writer}. Call the * methods of the writer object to write the matrix, or sections of the matrix, * to the output stream. When finished, close the writer. *

* To read the matrix from a file, call the prepareToRead() method, * specifying the input stream to read. The prepareToRead() method * returns an instance of class {@linkplain DoubleMatrixFile.Reader}. Call the * methods of the reader object to read the matrix, or sections of the matrix, * from the input stream. When finished, close the reader. *

* Class DoubleMatrixFile includes a main program to combine a group of double * matrix files into one double matrix file. You might use this main program * when the processes of a parallel program have computed slices of a matrix and * stored the slices in separate files, and you want to combine the slices * together into one file. *

* Double Matrix File Format *

* A double matrix file is a binary file containing the following items. Each * primitive item is written as though by java.io.DataOutput (int, four * bytes; double, eight bytes; most significant byte first). *

*

* Each segment contains the following items. *

* * @author Alan Kaminsky * @version 06-Jan-2008 */ public class DoubleMatrixFile { // Hidden data members. private static final long BYTES_PER_ELEMENT = 8L; private int R = -1; private int C = -1; private double[][] myMatrix; // Exported constructors. /** * Construct a new double matrix file object. The matrix's number of rows * and number of columns are uninitialized. Before using the matrix file, * specify the number of rows and the number of columns by calling the * setMatrix() method or by reading the matrix file from an input * stream. */ public DoubleMatrixFile() { } /** * Construct a new double matrix file object with the given number of rows, * number of columns, and underlying matrix. * * @param R Number of rows. * @param C Number of columns. * @param theMatrix Underlying matrix. * * @exception NullPointerException * (unchecked exception) Thrown if theMatrix is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if R < 0. Thrown if * C < 0. Thrown if theMatrix.length does not * equal R. */ public DoubleMatrixFile (int R, int C, double[][] theMatrix) { setMatrix (R, C, theMatrix); } // Exported operations. /** * Returns the number of rows in this matrix file. * * @return Number of rows R, or -1 if not initialized. */ public int getRowCount() { return R; } /** * Returns the number of columns in this matrix file. * * @return Number of columns, C, or -1 if not initialized. */ public int getColCount() { return C; } /** * Obtain this matrix file's underlying matrix. * * @return Underlying matrix, or null if not initialized. */ public double[][] getMatrix() { return myMatrix; } /** * Set this matrix file's number of rows, number of columns, and underlying * matrix. * * @param R Number of rows. * @param C Number of columns. * @param theMatrix Underlying matrix. * * @exception NullPointerException * (unchecked exception) Thrown if theMatrix is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if R < 0. Thrown if * C < 0. Thrown if theMatrix.length does not * equal R. */ public void setMatrix (int R, int C, double[][] theMatrix) { setRC (R, C); if (theMatrix.length != R) { throw new IllegalArgumentException ("DoubleMatrixFile.setMatrix(): theMatrix.length (= " + theMatrix.length + ") does not equal R (= " + R + ")"); } myMatrix = theMatrix; } /** * Prepare to write this matrix file to the given output stream. The number * of rows and the number of columns in this matrix file are written to the * output stream at this time. To write this matrix file's elements, call * methods on the returned writer, then close the writer. *

* For improved performance, specify an output stream with buffering, such * as an instance of class java.io.BufferedOutputStream. * * @param theStream Output stream. * * @return Writer object with which to write this matrix file. * * @exception IllegalStateException * (unchecked exception) Thrown if this matrix file object is * uninitialized. * @exception NullPointerException * (unchecked exception) Thrown if theStream is null. * @exception IOException * Thrown if an I/O error occurred. */ public Writer prepareToWrite (OutputStream theStream) throws IOException { if (myMatrix == null) { throw new IllegalStateException ("DoubleMatrixFile.prepareToWrite(): Not initialized"); } return new Writer (theStream); } /** * Prepare to read this matrix file from the given input stream. The number * of rows and the number of columns are read from the input stream at this * time. If this matrix file object is uninitialized, it becomes initialized * with the given number of rows and columns, and storage is allocated for * the underlying matrix's row references; call the getMatrix() * method to obtain the underlying matrix. If this matrix file object is * already initialized, the number of rows and columns read from the input * stream must match those of this matrix file object, otherwise an * exception is thrown. To read this matrix file's elements, call methods on * the returned reader, then close the reader. *

* For improved performance, specify an input stream with buffering, such * as an instance of class java.io.BufferedInputStream. * * @param theStream Input stream. * * @return Reader object with which to read this matrix file. * * @exception NullPointerException * (unchecked exception) Thrown if theStream is null. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents were * invalid. */ public Reader prepareToRead (InputStream theStream) throws IOException { return new Reader (theStream); } /** * Main program to combine a group of double matrix files into one double * matrix file. The program reads all the given input files into a matrix, * then writes the entire matrix to the given output file as a single * segment. Each input file must be for a matrix with the same number of * rows and columns. There must be sufficient main memory to hold the entire * matrix. *

* You might use this main program when the processes of a parallel program * have computed slices of a matrix and stored the slices in separate files, * and you want to combine the slices together into one file. *

* Usage: java edu.rit.io.DoubleMatrixFile outfile infile1 * [ infile2 . . . ] */ public static void main (String[] args) throws Exception { // Validate command line arguments. if (args.length < 2) { System.err.println ("Usage: java edu.rit.io.DoubleMatrixFile [ ...]"); System.exit (1); } // Double matrix file object. DoubleMatrixFile dmf = new DoubleMatrixFile(); // Read each input file. for (int i = 1; i < args.length; ++ i) { DoubleMatrixFile.Reader reader = dmf.prepareToRead (new BufferedInputStream (new FileInputStream (args[i]))); reader.read(); reader.close(); } // Write output file. DoubleMatrixFile.Writer writer = dmf.prepareToWrite (new BufferedOutputStream (new FileOutputStream (args[0]))); writer.write(); writer.close(); } // Exported helper classes. /** * Class DoubleMatrixFile.Writer provides an object with which to write a * {@linkplain DoubleMatrixFile} to an output stream. *

* When a writer is created, the number of rows and number of columns are * written to the output stream. Each time the write(), * writeRowSlice(), writeColSlice(), or * writePatch() method is called, one segment of matrix elements is * written to the output stream. When finished, call the close() * method. *

* Note: Class DoubleMatrixFile.Writer is not multiple thread safe. * * @author Alan Kaminsky * @version 06-Jan-2008 */ public class Writer { // Hidden data members. private OutputStream myOs; private DataOutputStream myDos; // Hidden constructors. /** * Construct a new double matrix file writer. * * @param theStream Output stream. * * @exception NullPointerException * (unchecked exception) Thrown if theStream is null. * @exception IOException * Thrown if an I/O error occurred. */ private Writer (OutputStream theStream) throws IOException { if (theStream == null) { throw new NullPointerException ("DoubleMatrixFile.Writer(): theStream is null"); } myOs = theStream; myDos = new DataOutputStream (theStream); myDos.writeInt (R); // Number of matrix rows myDos.writeInt (C); // Number of matrix columns } // Exported operations. /** * Write all rows and columns of the matrix to the output stream. * * @exception IOException * Thrown if an I/O error occurred. */ public void write() throws IOException { write (0, R-1, 0, C-1); } /** * Write the given row slice of the matrix to the output stream. * Elements in the given range of rows and in all columns are written. *

* Note: theRowRange's stride must be 1. * * @param theRowRange Range of matrix rows. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. * @exception IOException * Thrown if an I/O error occurred. */ public void writeRowSlice (Range theRowRange) throws IOException { if (theRowRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Writer.writeRowSlice(): theRowRange stride > 1"); } int RL = theRowRange.lb(); int RU = theRowRange.ub(); if (0 > RL || RL + theRowRange.length() > R) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Writer.writeRowSlice(): theRowRange = " + theRowRange + " out of bounds"); } write (RL, RU, 0, C-1); } /** * Write the given column slice of the matrix to the output stream. * Elements in all rows and in the given range of columns are written. *

* Note: theColRange's stride must be 1. * * @param theColRange Range of matrix columns. * * @exception NullPointerException * (unchecked exception) Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theColRange * is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. */ public void writeColSlice (Range theColRange) throws IOException { if (theColRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Writer.writeColSlice(): theColRange stride > 1"); } int CL = theColRange.lb(); int CU = theColRange.ub(); if (0 > CL || CL + theColRange.length() > C) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Writer.writeColSlice(): theColRange = " + theColRange + " out of bounds"); } write (0, R-1, CL, CU); } /** * Write the given patch of the matrix to the output stream. Elements in * the given range of rows and in the given range of columns are * written. *

* Note: theRowRange's stride must be 1. * theColRange's stride must be 1. * * @param theRowRange Range of matrix rows. * @param theColRange Range of matrix columns. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. Thrown if any index in * theColRange is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. */ public void writePatch (Range theRowRange, Range theColRange) throws IOException { if (theRowRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Writer.writePatch(): theRowRange stride > 1"); } if (theColRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Writer.writePatch(): theColRange stride > 1"); } int RL = theRowRange.lb(); int RU = theRowRange.ub(); if (0 > RL || RL + theRowRange.length() > R) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Writer.writePatch(): theRowRange = " + theRowRange + " out of bounds"); } int CL = theColRange.lb(); int CU = theColRange.ub(); if (0 > CL || CL + theColRange.length() > C) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Writer.writePatch(): theColRange = " + theColRange + " out of bounds"); } write (RL, RU, CL, CU); } /** * Close the output stream. * * @exception IOException * Thrown if an I/O error occurred. */ public void close() throws IOException { myDos.close(); } // Hidden operations. /** * Write the given rows and columns of the matrix to the output stream. * * @param RL Segment lower row index. * @param RU Segment upper row index. * @param CL Segment lower column index. * @param CU Segment upper column index. * * @exception IOException * Thrown if an I/O error occurred. */ private void write (int RL, int RU, int CL, int CU) throws IOException { myDos.writeInt (RL); // Segment lower row index myDos.writeInt (CL); // Segment lower column index myDos.writeInt (RU-RL+1); // Number of rows in segment myDos.writeInt (CU-CL+1); // Number of columns in segment for (int r = RL; r <= RU; ++ r) { double[] myMatrix_r = myMatrix[r]; for (int c = CL; c <= CU; ++ c) { myDos.writeDouble (myMatrix_r[c]); } } } } /** * Class DoubleMatrixFile.Reader provides an object with which to read a * {@linkplain DoubleMatrixFile} from an input stream. *

* When a reader is created, the number of rows and number of columns are * read from the input stream. If the matrix file object is uninitialized, * it becomes initialized with the given number of rows and columns, and * storage is allocated for the underlying matrix's row references. If the * matrix file object is already initialized, the number of rows and columns * read from the input stream must match those of the matrix file object, * otherwise an exception is thrown. *

* To read the matrix element segments one at a time, first call the * getRowRange() and getColRange() methods to obtain the * range of rows and columns in the next segment. At this point, allocate * storage for the rows and columns in the underlying matrix if necessary. * Then call the readSegment() method to read the actual matrix * elements. Repeat these steps if there are additional segments. *

* To read all the matrix element segments (or all the remaining segments), * call the read() method. *

* Methods are also provided to read the current segment, or all the * remaining segments, through a filter. As the segment(s) are read, * only those matrix elements within a given row range, a given column * range, or a given row and column range are actually stored in the * underlying matrix. *

* When finished, call the close() method. *

* Note: Class DoubleMatrixFile.Reader is not multiple thread safe. * * @author Alan Kaminsky * @version 07-Jan-2008 */ public class Reader { // Hidden data members. private InputStream myIs; private DataInputStream myDis; private Range myRowRange; private Range myColRange; // Hidden constructors. /** * Construct a new double matrix file reader. * * @param theStream Input stream. * * @exception NullPointerException * (unchecked exception) Thrown if theStream is null. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ private Reader (InputStream theStream) throws IOException { if (theStream == null) { throw new NullPointerException ("DoubleMatrixFile.Reader(): theStream is null"); } myIs = theStream; myDis = new DataInputStream (theStream); int R = myDis.readInt(); // Number of matrix rows int C = myDis.readInt(); // Number of matrix columns if (myMatrix == null) { setRC (R, C); myMatrix = new double [R] []; } else if (DoubleMatrixFile.this.R != R) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader(): Number of rows from stream (" + R + ") != number of rows in this matrix file (" + DoubleMatrixFile.this.R + ")"); } else if (DoubleMatrixFile.this.C != C) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader(): Number of columns from stream (" + C + ") != number of columns in this matrix file (" + DoubleMatrixFile.this.C + ")"); } getNextSegment(); } // Exported operations. /** * Read all matrix element segments from the input stream. If some * segments have already been read, the read() method reads all * remaining segments. If there are no more segments, the * read() method does nothing. If storage is not already * allocated in the underlying matrix for the matrix elements, the * read() method allocates the necessary storage. * * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void read() throws IOException { while (myRowRange != null) readSegment(); } /** * Read all matrix element segments from the input stream, storing only * the matrix elements in the given row slice. If some segments have * already been read, the readRowSlice() method reads all * remaining segments. If there are no more segments, the * readRowSlice() method does nothing. If storage is not * already allocated in the underlying matrix for the matrix elements, * the readRowSlice() method allocates the necessary storage. * * @param theRowRange Row range. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readRowSlice (Range theRowRange) throws IOException { while (myRowRange != null) { readSegmentRowSlice (theRowRange); } } /** * Read all matrix element segments from the input stream, storing only * the matrix elements in the given column slice. If some segments have * already been read, the readColSlice() method reads all * remaining segments. If there are no more segments, the * readColSlice() method does nothing. If storage is not * already allocated in the underlying matrix for the matrix elements, * the readColSlice() method allocates the necessary storage. * * @param theColRange Column range. * * @exception NullPointerException * (unchecked exception) Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theColRange * is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readColSlice (Range theColRange) throws IOException { while (myRowRange != null) { readSegmentColSlice (theColRange); } } /** * Read all matrix element segments from the input stream, storing only * the matrix elements in the given patch. If some segments have already * been read, the readPatch() method reads all remaining * segments. If there are no more segments, the readPatch() * method does nothing. If storage is not already allocated in the * underlying matrix for the matrix elements, the readPatch() * method allocates the necessary storage. * * @param theRowRange Row range. * @param theColRange Column range. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. Thrown if any index in * theColRange is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readPatch (Range theRowRange, Range theColRange) throws IOException { while (myRowRange != null) { readSegmentPatch (theRowRange, theColRange); } } /** * Obtain the row range of the next matrix element segment in the input * stream. If there are no more segments, null is returned. * * @return Row range, or null. */ public Range getRowRange() { return myRowRange; } /** * Obtain the column range of the next matrix element segment in the * input stream. If there are no more segments, null is returned. * * @return Column range, or null. */ public Range getColRange() { return myColRange; } /** * Read the next matrix element segment from the input stream. If there * are no more segments, the readSegment() method does nothing. * If storage is not already allocated in the underlying matrix for the * matrix elements, the readSegment() method allocates the * necessary storage. * * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readSegment() throws IOException { readSegment (0, R-1, 0, C-1); } /** * Read the next matrix element segment from the input stream, storing * only the matrix elements in the given row slice. If there are no more * segments, the readSegmentRowSlice() method does nothing. If * storage is not already allocated in the underlying matrix for the * matrix elements, the readSegmentRowSlice() method allocates * the necessary storage. * * @param theRowRange Row range. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readSegmentRowSlice (Range theRowRange) throws IOException { if (theRowRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Reader.readSegmentRowSlice(): theRowRange stride > 1"); } int RL = theRowRange.lb(); int RU = theRowRange.ub(); if (0 > RL || RL + theRowRange.length() > R) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Reader.readSegmentRowSlice(): theRowRange = " + theRowRange + " out of bounds"); } readSegment (RL, RU, 0, C-1); } /** * Read the next matrix element segment from the input stream, storing * only the matrix elements in the given column slice. If there are no * more segments, the readSegmentRowSlice() method does * nothing. If storage is not already allocated in the underlying matrix * for the matrix elements, the readSegmentRowSlice() method * allocates the necessary storage. * * @param theColRange Column range. * * @exception NullPointerException * (unchecked exception) Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theColRange * is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readSegmentColSlice (Range theColRange) throws IOException { if (theColRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Reader.readSegmentColSlice(): theColRange stride > 1"); } int CL = theColRange.lb(); int CU = theColRange.ub(); if (0 > CL || CL + theColRange.length() > C) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Reader.readSegmentColSlice(): theColRange = " + theColRange + " out of bounds"); } readSegment (0, R-1, CL, CU); } /** * Read the next matrix element segment from the input stream, storing * only the matrix elements in the given patch. If there are no more * segments, the readSegmentPatch() method does nothing. If * storage is not already allocated in the underlying matrix for the * matrix elements, the readSegmentPatch() method allocates the * necessary storage. * * @param theRowRange Row range. * @param theColRange Column range. * * @exception NullPointerException * (unchecked exception) Thrown if theRowRange is null. * Thrown if theColRange is null. * @exception IllegalArgumentException * (unchecked exception) Thrown if theRowRange's stride is * greater than 1. Thrown if theColRange's stride is * greater than 1. * @exception IndexOutOfBoundsException * (unchecked exception) Thrown if any index in theRowRange * is outside the range 0 .. R-1. Thrown if any index in * theColRange is outside the range 0 .. C-1. * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ public void readSegmentPatch (Range theRowRange, Range theColRange) throws IOException { if (theRowRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Reader.readSegmentPatch(): theRowRange stride > 1"); } int RL = theRowRange.lb(); int RU = theRowRange.ub(); if (0 > RL || RL + theRowRange.length() > R) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Reader.readSegmentPatch(): theRowRange = " + theRowRange + " out of bounds"); } if (theColRange.stride() != 1) { throw new IllegalArgumentException ("DoubleMatrixImage.Reader.readSegmentPatch(): theColRange stride > 1"); } int CL = theColRange.lb(); int CU = theColRange.ub(); if (0 > CL || CL + theColRange.length() > C) { throw new IndexOutOfBoundsException ("DoubleMatrixImage.Reader.readSegmentPatch(): theColRange = " + theColRange + " out of bounds"); } readSegment (RL, RU, CL, CU); } /** * Close the input stream. * * @exception IOException * Thrown if an I/O error occurred. */ public void close() throws IOException { myDis.close(); } // Hidden operations. /** * Read the bounds of the next segment from the input stream and store * them in myRowRange and myColRange. * * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ private void getNextSegment() throws IOException { try { int RL = myDis.readInt(); // Segment lower row index int CL = myDis.readInt(); // Segment lower column index int M = myDis.readInt(); // Number of rows in segment int N = myDis.readInt(); // Number of columns in segment if (RL < 0) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader.getNextSegment(): Invalid segment lower row index (" + RL + ")"); } if (CL < 0) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader.getNextSegment(): Invalid segment lower column index (" + CL + ")"); } if (M < 0 || RL + M > R) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader.getNextSegment(): Invalid numer of rows in segment (" + M + ")"); } if (N < 0 || CL + N > C) { throw new InvalidMatrixFileException ("DoubleMatrixFile.Reader.getNextSegment(): Invalid numer of columns in segment (" + N + ")"); } myRowRange = new Range (RL, RL+M-1); myColRange = new Range (CL, CL+N-1); } catch (EOFException exc) { myRowRange = null; myColRange = null; } } /** * Read the next matrix element segment from the input stream, storing * only the matrix elements within the given row and column index * bounds. If there are no more segments, the readSegment() * method does nothing. If storage is not already allocated in the * underlying matrix for the matrix elements, the readSegment() * method allocates the necessary storage. * * @param RL Lower row index. * @param RU Upper row index. * @param CL Lower column index. * @param CU Upper column index. * * @exception IOException * Thrown if an I/O error occurred. * @exception InvalidMatrixFileException * (subclass of IOException) Thrown if the input stream's contents * were invalid. */ private void readSegment (int RL, int RU, int CL, int CU) throws IOException { // Early return if no more segments. if (myRowRange == null) return; // Get row and column bounds of segment. int SRL = myRowRange.lb(); int SRU = myRowRange.ub(); int SCL = myColRange.lb(); int SCU = myColRange.ub(); // Number of bytes in an entire row. long rowBytes = BYTES_PER_ELEMENT * myColRange.length(); // First row to read. int firstRow = Math.max (RL, SRL); // Last row to read. int lastRow = Math.min (RU, SRU); // Number of rows (bytes) to skip at the beginning of the segment. int preSkipRows = firstRow - SRL; long preSkipRowBytes = preSkipRows * rowBytes; // Number of rows (bytes) to skip at the end of the segment. int postSkipRows = SRU - lastRow; long postSkipRowBytes = postSkipRows * rowBytes; // First column to read. int firstCol = Math.max (CL, SCL); // Last column to read. int lastCol = Math.min (CU, SCU); // Number of columns (bytes) to skip at the beginning of the row. int preSkipCols = firstCol - SCL; long preSkipColBytes = preSkipCols * BYTES_PER_ELEMENT; // Number of columns (bytes) to skip at the end of the row. int postSkipCols = SCU - lastCol; long postSkipColBytes = postSkipCols * BYTES_PER_ELEMENT; // Skip rows at beginning of segment. skipFully (preSkipRowBytes); // Read rows. for (int r = firstRow; r <= lastRow; ++ r) { // Allocate storage for row if necessary. double[] myMatrix_r = myMatrix[r]; if (myMatrix_r == null) { myMatrix_r = new double [C]; myMatrix[r] = myMatrix_r; } // Skip columns at beginning of row. skipFully (preSkipColBytes); // Read columns. for (int c = firstCol; c <= lastCol; ++ c) { myMatrix_r[c] = myDis.readDouble(); } // Skip columns at end of row. skipFully (postSkipColBytes); } // Skip rows at end of segment. skipFully (postSkipRowBytes); getNextSegment(); } /** * Skip over the given number of bytes in the input stream. * * @param n Number of bytes to skip. * * @exception IOException * Thrown if an I/O error occurred. */ private void skipFully (long n) throws IOException { while (n > 0L) n -= myDis.skip (n); } } // Hidden operations. /** * Set this matrix file's number of rows and number of columns. * * @param R Number of rows. * @param C Number of columns. * * @exception IllegalArgumentException * (unchecked exception) Thrown if R < 0. Thrown if * C < 0. */ void setRC (int R, int C) { if (R < 0) { throw new IllegalArgumentException ("DoubleMatrixFile.setHeightAndWidth(): R = " + R + " illegal"); } if (C < 0) { throw new IllegalArgumentException ("DoubleMatrixFile.setHeightAndWidth(): C = " + C + " illegal"); } this.R = R; this.C = C; } }