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MatFileRW - Read and write .mat files

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/*
 * Code licensed under new-style BSD (see LICENSE).
 * All code up to tags/original: Copyright (c) 2006, Wojciech Gradkowski
 * All code after tags/original: Copyright (c) 2015, DiffPlug
 */
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.DataFormatException;
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 list = new ArrayList();
 * 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 {

	/**
	 * A hack stolen from Greg Wilkins of Mortbay.
	 * A {@link ByteArrayOutputStream} with revealed internals so there is no more wasteful
	 * copying when calling {@link ByteArrayOutputStream#toByteArray()}
	 * @author ss
	 *
	 */
	static class ByteArrayOutputStream2 extends ByteArrayOutputStream {
		public ByteArrayOutputStream2() {
			super();
		}

		public byte[] getBuf() {
			return buf;
		}

		public int getCount() {
			return count;
		}
	}
	//    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
	 * @throws DataFormatException
	 */
	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
	 * @throws DataFormatException
	 */
	@SuppressWarnings("resource")
	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 output - OutputStream
	 * @param data - Collection of MLArray elements
	 * @throws IOException
	 */
	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) {
				//compress data to save storage
				Deflater compresser = new Deflater();

				ByteArrayOutputStream2 compressed = new ByteArrayOutputStream2();
				DataOutputStream dout = new DataOutputStream(new DeflaterOutputStream(compressed, compresser));

				writeMatrix(dout, matrix);
				dout.flush();
				dout.close();

				//write COMPRESSED tag and compressed data into output channel

				int compressedSize = compressed.getCount();
				ByteBuffer buf = ByteBuffer.allocateDirect(2 * 4 /* Int size */ + compressedSize);
				buf.putInt(MatDataTypes.miCOMPRESSED);

				buf.putInt(compressedSize);
				buf.put(compressed.getBuf(), 0, compressedSize);

				buf.flip();
				channel.write(buf);
			}
		} catch (IOException e) {
			throw e;
		} finally {
			channel.close();
		}
	}

	/**
	 * Writes MAT-file header into OutputStream
	 * @param os OutputStream
	 * @throws 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 os - OutputStream
	 * @param array - a MLArray
	 * @throws 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.mxINT32_CLASS:
			tag = new OSArrayTag(MatDataTypes.miINT32,
					((MLNumericArray) array).getRealByteBuffer());
			tag.writeTo(dos);

			if (array.isComplex()) {
				tag = new OSArrayTag(MatDataTypes.miINT32,
						((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
	 */
	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
	 */
	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
	 */
	private void writeName(DataOutputStream os, MLArray array) throws IOException {
		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
		DataOutputStream bufferDOS = new DataOutputStream(buffer);

		byte[] nameByteArray = array.getNameToByteArray();
		bufferDOS.write(nameByteArray);
		OSArrayTag tag = new OSArrayTag(MatDataTypes.miINT8, buffer.toByteArray());
		tag.writeTo(os);
	}

}




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