org.knowceans.util
Class ArrayIo

java.lang.Object
  org.knowceans.util.ArrayIo

public class ArrayIo
extends java.lang.Object

MatrixIo provides methods to load and save matrices and vectors to file, which automatic compression if the file extension given is ".zip". The standard methods are load/saveBinaryMatrix that load/save a double[][] with the protocol rows,cols,foreach(row): foreach(col): double[row][col] :end :end.

Custom protocols for more complex data can be easily constructed by opening a stream using one of the open*Stream() methods, using the methods of the Data*Stream classes and read/write* methods of this class for matrices and vectors and then closing the stream using the close*Stream methods in this class (provided for symmetry) or the close() methods in the Data*Stream classes.

TODO: The binary methods could be considered for change to a subclass of DataInputStream and DataOutputStream.

Author:

gregor

Constructor Summary

ArrayIo()

Method Summary

static void	closeInputStream(java.io.DataInputStream dis) Close the input stream
static void	closeOutputStream(java.io.DataOutputStream dos) Close the data output, which results in flushing the write buffer and closing the file.
static java.lang.String	formatDouble(double d)
static double[][]	loadAscii(java.lang.String filename)
static int[][]	loadBinaryIntMatrix(java.lang.String filename) Loads an integer matrix from a binary file, optionally a zip file.
static double[][]	loadBinaryMatrix(java.lang.String filename) Loads a matrix from a binary file, optionally a zip file.
static java.io.DataInputStream	openInputStream(java.lang.String filename) Opens a data input stream with optional zip compression.
static java.io.DataOutputStream	openOutputStream(java.lang.String filename) Opens a data output stream with optional zip compression.
static java.lang.String	padSpace(java.lang.String s, int length)
static java.lang.Object	read(java.io.DataInputStream is, java.lang.Object type) generic method that calls the methods according to the type of the argument Object
static double[][]	readDoubleMatrix(java.io.DataInputStream bw) Read matrix from file.
static double[][][]	readDoubleTensor(java.io.DataInputStream bw)
static double[]	readDoubleVector(java.io.DataInputStream bw) Read vector from file.
static float[][]	readFloatMatrix(java.io.DataInputStream bw) Read matrix from file.
static float[]	readFloatVector(java.io.DataInputStream bw) Read vector from file.
static int[][]	readIntMatrix(java.io.DataInputStream bw) Read matrix from file.
static int[]	readIntVector(java.io.DataInputStream bw) Read vector from file.
static void	saveAscii(java.lang.String filename, double[][] a)
static void	saveBinaryIntMatrix(java.lang.String filename, int[][] a) Writes integer matrix to binary file.
static void	saveBinaryMatrix(java.lang.String filename, double[][] a) Writes matrix to binary file.
static void	saveShades(java.lang.String filename, double[][] a) Save a matrix as shaded values using MayaShades.
static void	saveTransposedAscii(java.lang.String filename, double[][] a)
static void	saveTransposedShades(java.lang.String filename, double[][] a) Save a transposed matrix as shaded values using MayaShades.
static void	write(java.io.DataOutputStream os, java.lang.Object data) generic write method that calls the respective method of the type of data
static void	writeDoubleMatrix(java.io.DataOutputStream bw, double[][] matrix) Writes a double matrix in the format rows,cols1,a11,a12,a1...,cols2,a21,...
static void	writeDoubleTensor(java.io.DataOutputStream bw, double[][][] tensor) Writes a double tensor (here = 3d matrix).
static void	writeDoubleVector(java.io.DataOutputStream bw, double[] vector) Writes a double vector in the format size,v1,v2,...
static void	writeFloatMatrix(java.io.DataOutputStream bw, float[][] matrix) Writes a float matrix in the format rows,cols,a11,a12,a1...,a21,...
static void	writeFloatVector(java.io.DataOutputStream bw, float[] vector) Writes a float vector in the format size,v1,v2,...
static void	writeIntMatrix(java.io.DataOutputStream bw, int[][] matrix) Writes an integer matrix in the format rows,cols1,a11,a12,a1...,cols2,a21,...
static void	writeIntVector(java.io.DataOutputStream bw, int[] vector) Writes an integer vector in the format size,v1,v2,...

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayIo

public ArrayIo()

Method Detail

loadBinaryIntMatrix

public static int[][] loadBinaryIntMatrix(java.lang.String filename)

Loads an integer matrix from a binary file, optionally a zip file. The method actually reads a float matrix.

Parameters:

filename -

Returns:

loadBinaryMatrix

public static double[][] loadBinaryMatrix(java.lang.String filename)

Loads a matrix from a binary file, optionally a zip file. The method actually reads a float matrix.

Parameters:

filename -

Returns:

saveBinaryIntMatrix

public static void saveBinaryIntMatrix(java.lang.String filename,
                                       int[][] a)

Writes integer matrix to binary file. If the file name ends with zip, the output is zipped. Note: The method actually saves float values.

Parameters:

filename -

a -

saveBinaryMatrix

public static void saveBinaryMatrix(java.lang.String filename,
                                    double[][] a)

Writes matrix to binary file. If the file name ends with zip, the output is zipped. Note: The method actually saves float values.

Parameters:

filename -

a -

read

public static java.lang.Object read(java.io.DataInputStream is,
                                    java.lang.Object type)
                             throws java.io.IOException

generic method that calls the methods according to the type of the argument Object

Parameters:

is -

type -

Returns:

Throws:

java.io.IOException

readIntMatrix

public static int[][] readIntMatrix(java.io.DataInputStream bw)
                             throws java.io.IOException

Read matrix from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

readIntVector

public static int[] readIntVector(java.io.DataInputStream bw)
                           throws java.io.IOException

Read vector from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

readDoubleTensor

public static double[][][] readDoubleTensor(java.io.DataInputStream bw)
                                     throws java.io.IOException

Throws:

java.io.IOException

readDoubleMatrix

public static double[][] readDoubleMatrix(java.io.DataInputStream bw)
                                   throws java.io.IOException

Read matrix from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

readDoubleVector

public static double[] readDoubleVector(java.io.DataInputStream bw)
                                 throws java.io.IOException

Read vector from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

readFloatMatrix

public static float[][] readFloatMatrix(java.io.DataInputStream bw)
                                 throws java.io.IOException

Read matrix from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

readFloatVector

public static float[] readFloatVector(java.io.DataInputStream bw)
                               throws java.io.IOException

Read vector from file.

Parameters:

bw -

Returns:

Throws:

java.io.IOException

write

public static void write(java.io.DataOutputStream os,
                         java.lang.Object data)
                  throws java.io.IOException

generic write method that calls the respective method of the type of data

Parameters:

writer -

data - object

Throws:

java.io.IOException

writeIntMatrix

public static void writeIntMatrix(java.io.DataOutputStream bw,
                                  int[][] matrix)
                           throws java.io.IOException

Writes an integer matrix in the format rows,cols1,a11,a12,a1...,cols2,a21,... This way, matrices can be stored that have variable row lengths.

Parameters:

bw -

matrix -

Throws:

java.io.IOException

writeIntVector

public static void writeIntVector(java.io.DataOutputStream bw,
                                  int[] vector)
                           throws java.io.IOException

Writes an integer vector in the format size,v1,v2,...

Parameters:

bw -

vector -

Throws:

java.io.IOException

writeDoubleTensor

public static void writeDoubleTensor(java.io.DataOutputStream bw,
                                     double[][][] tensor)
                              throws java.io.IOException

Writes a double tensor (here = 3d matrix).

Parameters:

bw -

tensor -

Throws:

java.io.IOException

writeDoubleMatrix

public static void writeDoubleMatrix(java.io.DataOutputStream bw,
                                     double[][] matrix)
                              throws java.io.IOException

Writes a double matrix in the format rows,cols1,a11,a12,a1...,cols2,a21,...

Parameters:

bw -

matrix -

Throws:

java.io.IOException

writeDoubleVector

public static void writeDoubleVector(java.io.DataOutputStream bw,
                                     double[] vector)
                              throws java.io.IOException

Writes a double vector in the format size,v1,v2,...

Parameters:

bw -

vector -

Throws:

java.io.IOException

writeFloatMatrix

public static void writeFloatMatrix(java.io.DataOutputStream bw,
                                    float[][] matrix)
                             throws java.io.IOException

Writes a float matrix in the format rows,cols,a11,a12,a1...,a21,...

Parameters:

bw -

matrix -

Throws:

java.io.IOException

writeFloatVector

public static void writeFloatVector(java.io.DataOutputStream bw,
                                    float[] vector)
                             throws java.io.IOException

Writes a float vector in the format size,v1,v2,...

Parameters:

bw -

vector -

Throws:

java.io.IOException

padSpace

public static java.lang.String padSpace(java.lang.String s,
                                        int length)

formatDouble

public static java.lang.String formatDouble(double d)

Parameters:

d -

Returns:

loadAscii

public static double[][] loadAscii(java.lang.String filename)

saveAscii

public static void saveAscii(java.lang.String filename,
                             double[][] a)

Parameters:

filename -

a -

saveTransposedAscii

public static void saveTransposedAscii(java.lang.String filename,
                                       double[][] a)

Parameters:

filename -

a - matrix (with equal columns for each row)

openOutputStream

public static java.io.DataOutputStream openOutputStream(java.lang.String filename)
                                                 throws java.io.FileNotFoundException,
                                                        java.io.IOException

Opens a data output stream with optional zip compression. The returned DataOutputStream can be written to and must be closed using closeStream(DataOutputStream dos) or dos.close().

Parameters:

filename -

Returns:

Throws:

java.io.FileNotFoundException

java.io.IOException

closeOutputStream

public static void closeOutputStream(java.io.DataOutputStream dos)
                              throws java.io.IOException

Close the data output, which results in flushing the write buffer and closing the file.

Parameters:

dos -

Throws:

java.io.IOException

openInputStream

public static java.io.DataInputStream openInputStream(java.lang.String filename)
                                               throws java.io.IOException,
                                                      java.io.FileNotFoundException

Opens a data input stream with optional zip compression. The returned DataInputStream can be read from and must be closed using closeStream(DataOutputStream dos) or dos.close().

Parameters:

filename -

Returns:

Throws:

java.io.FileNotFoundException

java.io.IOException

closeInputStream

public static void closeInputStream(java.io.DataInputStream dis)
                             throws java.io.IOException

Close the input stream

Parameters:

dis -

Throws:

java.io.IOException

saveShades

public static void saveShades(java.lang.String filename,
                              double[][] a)

Save a matrix as shaded values using MayaShades. The values are normalised on the maximum.

Parameters:

filename -

a -

saveTransposedShades

public static void saveTransposedShades(java.lang.String filename,
                                        double[][] a)

Save a transposed matrix as shaded values using MayaShades. The values are normalised on the maximum.

Parameters:

filename -

a - matrix with equal cols in each row