Add in the beginnings of an MCOS parser. (b10de602) · Commits · Matthew Dawson / JMatIO

MatlabClasses/SimpleEmpty.m

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		classdef SimpleEmpty
		%SIMPLEEMPTY A simple empty class definition.

		properties
		end

		methods
		end

		end

src/main/java/com/jmatio/io/MLObjectPlaceholder.java

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		/*
		* Copyright 2014 Matthew Dawson <matthew@mjdsystems.ca>
		*/
		package com.jmatio.io;

		import com.jmatio.types.MLArray;

		/**
		*
		* @author Matthew Dawson <matthew@mjdsystems.ca>
		*/
		class MLObjectPlaceholder extends MLArray {
		MLObjectPlaceholder( String name, String className, int[][] information )
		{
		super( name, new int[] {1, 1}, -1, 0 );
		this.className = className;
		this.information = information;
		}

		final String className;
		final int[][] information;
		}

src/main/java/com/jmatio/io/MatFileReader.java

+80 −26

Original line number	Diff line number	Diff line
		@@ -93,6 +93,15 @@ public class MatFileReader
		* Array name filter
		*/
		private MatFileFilter filter;
		/**
		* Whether or not we have found an MCOS type variable. Needed to know if further processing is needed.
		*/
		private boolean haveMCOS = false;
		/**
		* Holds the likely candidate for the MCOS extra data at the end of a MAT file.
		*/
		private MLUInt8 mcosData;

		/**
		* Creates instance of <code>MatFileReader</code> and reads MAT-file
		* from location given as <code>fileName</code>.
		@@ -360,10 +369,22 @@ public class MatFileReader
		//read in file header
		readHeader(buf);

		while ( buf.remaining() > 0 )
		{
		while ( buf.remaining() > 0 ) {
		readData( buf );
		}
		if ( haveMCOS ) {
		parseMCOS(mcosData);
		if ( data.get("@") == mcosData ) {
		data.remove("@");
		}
		for ( Map.Entry<String, MLArray> it : data.entrySet() ) {
		if ( it.getValue() == mcosData ) {
		data.remove(it.getKey());
		break;
		}
		}
		}
		mcosData = null;

		return getContent();
		}
		@@ -408,6 +429,25 @@ public class MatFileReader

		}

		private void parseMCOS(MLUInt8 mcosData) throws IOException
		{
		// First, parse back out the mcosData.
		ByteBuffer buffer = mcosData.getRealByteBuffer();
		ByteBufferInputStream dataStream = new ByteBufferInputStream(buffer, buffer.limit());

		Map<String, MLArray> mcosContent;

		mcosContent = (new MatFileReader(dataStream, MatFileType.ReducedHeader)).getContent();
		MLCell mcosInfo = (MLCell) ((MLStructure) mcosContent.get("@0")).getField("MCOS");

		for (Map.Entry<String, MLArray> it : data.entrySet()) {
		if ( it.getValue() instanceof MLObjectPlaceholder ) {
		MLObjectPlaceholder obj = (MLObjectPlaceholder) it.getValue();
		it.setValue(new MLObject(obj.name, obj.className, new MLStructure("", new int[]{1, 1})));
		}
		}
		}

		/**
		* Read a mat file from a stream. Internally this will read the stream fully
		* into memory before parsing it.
		@@ -804,6 +844,11 @@ public class MatFileReader
		(MLNumericArray<?>) mlArray );
		}

		// This might be the MCOS extra data. If there is no name, set it as the current set of data.
		if ( name.equals("") ) {
		mcosData = (MLUInt8) mlArray;
		}

		break;
		case MLArray.mxINT8_CLASS:
		mlArray = new MLInt8(name, dims, type, attributes);
		@@ -964,32 +1009,41 @@ public class MatFileReader
		// next tag should be miMatrix
		ISMatTag contentTag = new ISMatTag(buf);

		if ( contentTag.type == MatDataTypes.miMATRIX )
		{
		if ( contentTag.type == MatDataTypes.miMATRIX ) {
		if ( name.equals("java") ) {
		// should return UInt8
		MLUInt8 content = (MLUInt8) readMatrix(buf, false);

		// de-serialize object
		ObjectInputStream ois = new ObjectInputStream(
		new ByteBufferInputStream(content.getRealByteBuffer(),
		content.getRealByteBuffer().limit() ) );
		try
		{
		content.getRealByteBuffer().limit())
		);
		try {
		Object o = ois.readObject();
		mlArray = new MLJavaObject(arrName, className, o);
		}
		catch (Exception e)
		{
		} catch (Exception e) {
		throw new IOException(e);
		}
		finally
		{
		} finally {
		ois.close();
		}
		} else if ( name.equals("MCOS") ) {
		// FileWrapper__ is a special MATLAB internal name. Should never appear from users.
		if ( !className.equals("FileWrapper__") ) {
		MLUInt32 content = (MLUInt32) readMatrix(buf, false);
		int[][] t = content.getArray();
		mlArray = new MLObjectPlaceholder(arrName, className, t);
		haveMCOS = true;
		} else { // This is where we get the useful MCOS data. Only used on FileWrapper__ classes.
		mlArray = readMatrix(buf, false);
		}
		} else {
		throw new IOException("Unknown object type (" + name + ") found.");
		}
		}
		else
		{
		throw new IOException("Unexpected java object content");
		throw new IOException("Unexpected object content");
		}
		break;
		case MLArray.mxOBJECT_CLASS:

src/test/java/com/jmatio/test/MatlabMCOSTest.java

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		/*
		* Copyright 2014 Matthew Dawson <matthew@mjdsystems.ca>
		*/
		package com.jmatio.test;

		import com.jmatio.io.MatFileReader;
		import com.jmatio.types.MLArray;
		import com.jmatio.types.MLObject;
		import org.junit.Rule;
		import org.junit.Test;
		import org.junit.rules.TemporaryFolder;
		import org.junit.runner.RunWith;
		import org.junit.runners.JUnit4;

		import java.io.*;
		import java.util.Map;

		import static org.hamcrest.CoreMatchers.is;
		import static org.hamcrest.CoreMatchers.notNullValue;
		import static org.junit.Assert.assertThat;

		/**
		* This test verifies that ReducedHeader generated mat files work correctly.
		*
		* @author Matthew Dawson <matthew@mjdsystems.ca>
		*/
		@RunWith(JUnit4.class)
		public class MatlabMCOSTest {
		@Rule
		public TemporaryFolder folder = new TemporaryFolder();

		@Test
		public void testParsingSimpleEmptyMCOS() throws IOException
		{
		File file = fileFromStream("/mcos/simpleempty.mat");
		MatFileReader reader = new MatFileReader(file);
		Map<String, MLArray> content = reader.getContent();

		assertThat(content.size(), is(1));

		MLObject obj = (MLObject) content.get("obj");
		assertThat(obj, is(notNullValue()));

		assertThat(obj.getName(), is("obj"));
		assertThat(obj.getClassName(), is("SimpleEmpty"));
		assertThat(obj.getObject().getAllFields().size(), is(0));
		}

		private File fileFromStream(String location) throws IOException
		{
		String outname = location.replace("/", "_");
		File f = folder.newFile(outname);
		InputStream stream = MatlabMCOSTest.class.getResourceAsStream(location);
		OutputStream fos = new BufferedOutputStream(new FileOutputStream(f));
		byte[] buffer = new byte[1024];
		int read = 0;
		while ((read = stream.read(buffer)) != -1) {
		fos.write(buffer, 0, read);
		}
		fos.flush();
		fos.close();
		return f;
		}
		}

src/test/resources/mcos/simpleempty.mat

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