com.jmatio.io.MatFileWriter Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of jmatio Show documentation
Show all versions of jmatio Show documentation
Matlab's MAT-file I/O API in JAVA. Supports Matlab 5 MAT-flie format reading and writing. Written in pure JAVA.
The newest version!
package com.jmatio.io;
import java.io.ByteArrayOutputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.channels.WritableByteChannel;
import java.util.Collection;
import java.util.zip.Deflater;
import java.util.zip.DeflaterOutputStream;
import com.jmatio.common.MatDataTypes;
import com.jmatio.types.MLArray;
import com.jmatio.types.MLCell;
import com.jmatio.types.MLChar;
import com.jmatio.types.MLNumericArray;
import com.jmatio.types.MLSparse;
import com.jmatio.types.MLStructure;
/**
* MAT-file writer.
*
* Usage:
*
* //1. First create example arrays
* double[] src = new double[] { 1.0, 2.0, 3.0, 4.0, 5.0, 6.0 };
* MLDouble mlDouble = new MLDouble( "double_arr", src, 3 );
* MLChar mlChar = new MLChar( "char_arr", "I am dummy" );
*
* //2. write arrays to file
* ArrayList<MLArray> list = new ArrayList<MLArray>();
* list.add( mlDouble );
* list.add( mlChar );
*
* new MatFileWriter( "mat_file.mat", list );
*
*
* this is "equal" to Matlab commands:
*
* << double_arr = [ 1 2; 3 4; 5 6];
* << char_arr = 'I am dummy';
* <<
* << save('mat_file.mat', 'double_arr', 'char_arr');
*
*
* @author Wojciech Gradkowski ([email protected])
*/
public class MatFileWriter
{
// private static final Logger logger = Logger.getLogger(MatFileWriter.class);
/**
* Creates the new {@link MatFileWriter} instance
*/
public MatFileWriter()
{
super();
}
/**
* Writes MLArrays into file given by fileName.
*
* @param fileName - name of ouput file
* @param data - Collection of MLArray elements
* @throws IOException on underlying IOException
*/
public MatFileWriter(String fileName, Collection data) throws IOException
{
this( new File(fileName), data );
}
/**
* Writes MLArrays into File.
*
* @param file - an output File
* @param data - Collection of MLArray elements
* @throws IOException on underlying IOException
*/
public MatFileWriter(File file, Collection data) throws IOException
{
this( (new FileOutputStream(file)).getChannel(), data );
}
/**
* Writes MLArrays into OuputSteram.
*
* Writes MAT-file header and compressed data (miCOMPRESSED).
*
* @param channel channel
* @param data - Collection of MLArray elements
* @throws IOException on underlying IOExceptions
*/
public MatFileWriter(WritableByteChannel channel, Collection data) throws IOException
{
write(channel, data);
}
/**
* Writes MLArrays into file created from
* filepath.
*
* @param filepath the absolute file path of a MAT-file to which data is written
* @param data the collection of {@link MLArray} objects
* @throws IOException if error occurred during MAT-file writing
*/
public synchronized void write(String filepath, Collection data)
throws IOException
{
write(new File(filepath), data);
}
/**
* Writes MLArrays into File
*
* @param file the MAT-file to which data is written
* @param data the collection of {@link MLArray} objects
* @throws IOException if error occurred during MAT-file writing
*/
public synchronized void write(File file, Collection data)
throws IOException
{
FileOutputStream fos = new FileOutputStream(file);
try
{
write(fos.getChannel(), data);
}
catch ( IOException e )
{
throw e;
}
finally
{
fos.close();
}
}
/**
* Writes MLArrays into WritableByteChannel.
*
* @param channel the channel to write to
* @param data the collection of {@link MLArray} objects
* @throws IOException if writing fails
*/
private synchronized void write(WritableByteChannel channel,
Collection data) throws IOException
{
try
{
//write header
writeHeader(channel);
//write data
for ( MLArray matrix : data )
{
//prepare buffer for MATRIX data
ByteArrayOutputStream baos = new ByteArrayOutputStream();
DataOutputStream dos = new DataOutputStream( baos );
//write MATRIX bytes into buffer
writeMatrix( dos, matrix );
//compress data to save storage
Deflater compresser = new Deflater();
byte[] input = baos.toByteArray();
ByteArrayOutputStream compressed = new ByteArrayOutputStream();
DataOutputStream dout = new DataOutputStream(new DeflaterOutputStream(compressed, compresser));
dout.write(input);
dout.close();
compressed.close();
//write COMPRESSED tag and compressed data into output channel
byte[] compressedBytes = compressed.toByteArray();
ByteBuffer buf = ByteBuffer.allocateDirect(2 * 4 /* Int size */ + compressedBytes.length);
buf.putInt( MatDataTypes.miCOMPRESSED );
buf.putInt( compressedBytes.length );
buf.put( compressedBytes );
buf.flip();
channel.write( buf );
}
}
catch ( IOException e )
{
throw e;
}
finally
{
channel.close();
}
}
/**
* Writes MAT-file header into OutputStream
* @param channel channel
* @throws IOException on underlying IOException
*/
private void writeHeader(WritableByteChannel channel) throws IOException
{
//write descriptive text
MatFileHeader header = MatFileHeader.createHeader();
char[] dest = new char[116];
char[] src = header.getDescription().toCharArray();
System.arraycopy(src, 0, dest, 0, src.length);
byte[] endianIndicator = header.getEndianIndicator();
ByteBuffer buf = ByteBuffer.allocateDirect(dest.length * 2 /* Char size */ + 2 + endianIndicator.length);
for ( int i = 0; i < dest.length; i++ )
{
buf.put( (byte)dest[i] );
}
//write subsyst data offset
buf.position( buf.position() + 8);
//write version
int version = header.getVersion();
buf.put( (byte)(version >> 8) );
buf.put( (byte)version );
buf.put( endianIndicator );
buf.flip();
channel.write(buf);
}
/**
* Writes MATRIX into OutputStream.
*
* @param output DataOutputStream
* @param array - a MLArray
* @throws IOException on underlying IOException
*/
private void writeMatrix(DataOutputStream output, MLArray array) throws IOException
{
OSArrayTag tag;
ByteArrayOutputStream buffer;
DataOutputStream bufferDOS;
ByteArrayOutputStream baos = new ByteArrayOutputStream();
DataOutputStream dos = new DataOutputStream(baos);
//flags
writeFlags(dos, array);
//dimensions
writeDimensions(dos, array);
//array name
writeName(dos, array);
switch ( array.getType() )
{
case MLArray.mxCHAR_CLASS:
//write char data
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
Character[] ac = ((MLChar)array).exportChar();
for( int i = 0; i < ac.length; i++ )
{
String temp = new StringBuffer().append(ac[i].charValue()).toString();
bufferDOS.write(temp.getBytes("UTF-8"));
}
tag = new OSArrayTag(MatDataTypes.miUTF8, buffer.toByteArray() );
tag.writeTo( dos );
break;
case MLArray.mxDOUBLE_CLASS:
tag = new OSArrayTag(MatDataTypes.miDOUBLE,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miDOUBLE,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxSINGLE_CLASS:
tag = new OSArrayTag(MatDataTypes.miSINGLE,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miSINGLE,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxUINT8_CLASS:
tag = new OSArrayTag(MatDataTypes.miUINT8,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miUINT8,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxINT8_CLASS:
tag = new OSArrayTag(MatDataTypes.miINT8,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miINT8,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxINT16_CLASS:
tag = new OSArrayTag(MatDataTypes.miINT16,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miINT16,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxINT64_CLASS:
tag = new OSArrayTag(MatDataTypes.miINT64,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miINT64,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxUINT64_CLASS:
tag = new OSArrayTag(MatDataTypes.miUINT64,
((MLNumericArray)array).getRealByteBuffer() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
tag = new OSArrayTag(MatDataTypes.miUINT64,
((MLNumericArray)array).getImaginaryByteBuffer() );
tag.writeTo( dos );
}
break;
case MLArray.mxSTRUCT_CLASS:
//field name length
int itag = 4 << 16 | MatDataTypes.miINT32 & 0xffff;
dos.writeInt( itag );
dos.writeInt( ((MLStructure)array).getMaxFieldLenth() );
//get field names
tag = new OSArrayTag(MatDataTypes.miINT8, ((MLStructure)array).getKeySetToByteArray() );
tag.writeTo( dos );
for ( MLArray a : ((MLStructure)array).getAllFields() )
{
writeMatrix(dos, a);
}
break;
case MLArray.mxCELL_CLASS:
for ( MLArray a : ((MLCell)array).cells() )
{
writeMatrix(dos, a);
}
break;
case MLArray.mxSPARSE_CLASS:
int[] ai;
//write ir
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
ai = ((MLSparse)array).getIR();
for ( int i : ai )
{
bufferDOS.writeInt( i );
}
tag = new OSArrayTag(MatDataTypes.miINT32, buffer.toByteArray() );
tag.writeTo( dos );
//write jc
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
ai = ((MLSparse)array).getJC();
for ( int i : ai )
{
bufferDOS.writeInt( i );
}
tag = new OSArrayTag(MatDataTypes.miINT32, buffer.toByteArray() );
tag.writeTo( dos );
//write real
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
Double[] ad = ((MLSparse)array).exportReal();
for ( int i = 0; i < ad.length; i++ )
{
bufferDOS.writeDouble( ad[i].doubleValue() );
}
tag = new OSArrayTag(MatDataTypes.miDOUBLE, buffer.toByteArray() );
tag.writeTo( dos );
//write real imaginary
if ( array.isComplex() )
{
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
ad = ((MLSparse)array).exportImaginary();
for ( int i = 0; i < ad.length; i++ )
{
bufferDOS.writeDouble( ad[i].doubleValue() );
}
tag = new OSArrayTag(MatDataTypes.miDOUBLE, buffer.toByteArray() );
tag.writeTo( dos );
}
break;
default:
throw new MatlabIOException("Cannot write matrix of type: " + MLArray.typeToString( array.getType() ));
}
//write matrix
output.writeInt(MatDataTypes.miMATRIX); //matrix tag
output.writeInt( baos.size() ); //size of matrix
output.write( baos.toByteArray() ); //matrix data
}
/**
* Writes MATRIX flags into OutputStream.
*
* @param os - OutputStream
* @param array - a MLArray
* @throws IOException on underlying IOException
*/
private void writeFlags(DataOutputStream os, MLArray array) throws IOException
{
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
DataOutputStream bufferDOS = new DataOutputStream(buffer);
bufferDOS.writeInt( array.getFlags() );
if ( array.isSparse() )
{
bufferDOS.writeInt( ((MLSparse)array).getMaxNZ() );
}
else
{
bufferDOS.writeInt( 0 );
}
OSArrayTag tag = new OSArrayTag(MatDataTypes.miUINT32, buffer.toByteArray() );
tag.writeTo( os );
}
/**
* Writes MATRIX dimensions into OutputStream.
*
* @param os - OutputStream
* @param array - a MLArray
* @throws IOException on underlying IOException
*/
private void writeDimensions(DataOutputStream os, MLArray array) throws IOException
{
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
DataOutputStream bufferDOS = new DataOutputStream(buffer);
int[] dims = array.getDimensions();
for ( int i = 0; i < dims.length; i++ )
{
bufferDOS.writeInt(dims[i]);
}
OSArrayTag tag = new OSArrayTag(MatDataTypes.miINT32, buffer.toByteArray() );
tag.writeTo( os );
}
/**
* Writes MATRIX name into OutputStream.
*
* @param os - OutputStream
* @param array - a MLArray
* @throws IOException on underlying IOException
*/
private void writeName(DataOutputStream os, MLArray array) throws IOException
{
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
DataOutputStream bufferDOS = new DataOutputStream(buffer);
byte[] nameByteArray = array.getNameToByteArray();
buffer = new ByteArrayOutputStream();
bufferDOS = new DataOutputStream(buffer);
bufferDOS.write( nameByteArray );
OSArrayTag tag = new OSArrayTag(MatDataTypes.miINT8, buffer.toByteArray() );
tag.writeTo( os );
}
}