Add a system to deal with reduced header MAT files. (a132eb12) · Commits · Matthew Dawson / JMatIO

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

+40 −25

Original line number	Diff line number	Diff line
		@@ -73,6 +73,10 @@ public class MatFileReader
		public static final int DIRECT_BYTE_BUFFER = 2;
		public static final int HEAP_BYTE_BUFFER = 4;

		/**
		* Type of matlab mat file.
		*/
		private final MatFileType matType;
		/**
		* MAT-file header
		*/
		@@ -100,7 +104,7 @@ public class MatFileReader
		*/
		public MatFileReader(String fileName) throws FileNotFoundException, IOException
		{
		this ( new File(fileName), new MatFileFilter() );
		this ( new File(fileName), new MatFileFilter(), MatFileType.Regular);
		}
		/**
		* Creates instance of <code>MatFileReader</code> and reads MAT-file
		@@ -115,8 +119,9 @@ public class MatFileReader
		*/
		public MatFileReader(String fileName, MatFileFilter filter ) throws IOException
		{
		this( new File(fileName), filter );
		this( new File(fileName), filter, MatFileType.Regular);
		}

		/**
		* Creates instance of <code>MatFileReader</code> and reads MAT-file
		* from <code>file</code>.
		@@ -128,9 +133,10 @@ public class MatFileReader
		*/
		public MatFileReader(File file) throws IOException
		{
		this ( file, new MatFileFilter() );
		this ( file, new MatFileFilter(), MatFileType.Regular);

		}

		/**
		* Creates instance of <code>MatFileReader</code> and reads MAT-file from
		* <code>file</code>.
		@@ -148,15 +154,16 @@ public class MatFileReader
		* @throws IOException
		* when error occurred while processing the file.
		*/
		public MatFileReader(File file, MatFileFilter filter) throws IOException
		public MatFileReader(File file, MatFileFilter filter, MatFileType matType) throws IOException
		{
		this();
		this(matType);

		read(file, filter, MEMORY_MAPPED_FILE);
		}

		public MatFileReader()
		public MatFileReader(MatFileType matType)
		{
		this.matType = matType;
		filter = new MatFileFilter();
		data = new LinkedHashMap<String, MLArray>();
		}
		@@ -172,9 +179,9 @@ public class MatFileReader
		* @throws IOException
		* when error occurred while processing the file.
		*/
		public MatFileReader(InputStream stream) throws IOException
		public MatFileReader(InputStream stream, MatFileType type) throws IOException
		{
		this(stream, new MatFileFilter());
		this(stream, new MatFileFilter(), type);
		}

		/**
		@@ -196,9 +203,9 @@ public class MatFileReader
		* @throws IOException
		* when error occurred while processing the file.
		*/
		public MatFileReader(InputStream stream, MatFileFilter filter) throws IOException
		public MatFileReader(InputStream stream, MatFileFilter filter, MatFileType type) throws IOException
		{
		this();
		this(type);

		read(stream, filter);
		}
		@@ -1127,19 +1134,23 @@ public class MatFileReader
		int version;
		byte[] endianIndicator = new byte[2];

		// This part of the header is missing if the file isn't a regular mat file. So ignore.
		if (matType == MatFileType.Regular) {
		//descriptive text 116 bytes
		byte[] descriptionBuffer = new byte[116];
		buf.get(descriptionBuffer);

		description = zeroEndByteArrayToString(descriptionBuffer);

		if ( !description.matches("MATLAB 5.0 MAT-file.*") )
		{
		if (!description.matches("MATLAB 5.0 MAT-file.*")) {
		throw new MatlabIOException("This is not a valid MATLAB 5.0 MAT-file.");
		}

		//subsyst data offset 8 bytes
		buf.position(buf.position() + 8);
		} else {
		description = "Simulink generated MATLAB 5.0 MAT-file"; // Default simulink description.
		}

		byte[] bversion = new byte[2];
		//version 2 bytes
		@@ -1164,6 +1175,10 @@ public class MatFileReader
		buf.order( byteOrder );

		matFileHeader = new MatFileHeader(description, version, endianIndicator);

		// After the header, the next read must be aligned. Thus force the alignment. Only matters with reduced header data,
		// but apply it regardless for safety.
		buf.position((buf.position() + 7) & 0xfffffff8);
		}
		/**
		* TAG operator. Facilitates reading operations.

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

0 → 100644

+9 −0

Original line number	Diff line number	Diff line
		package com.jmatio.io;

		/** Describes the type of Mat file.
		* @author Matthew Dawson <matthew@mjdsystems.ca>
		*/
		public enum MatFileType {
		Regular,
		ReducedHeader
		}

src/test/java/com/jmatio/test/MatIOTest.java

+5 −8

Original line number	Diff line number	Diff line
		@@ -18,14 +18,11 @@ import java.util.Collection;
		import java.util.List;
		import java.util.Map;

		import com.jmatio.io.*;
		import org.junit.Rule;
		import org.junit.Test;
		import org.junit.rules.TemporaryFolder;

		import com.jmatio.io.MatFileFilter;
		import com.jmatio.io.MatFileIncrementalWriter;
		import com.jmatio.io.MatFileReader;
		import com.jmatio.io.MatFileWriter;
		import com.jmatio.types.MLArray;
		import com.jmatio.types.MLCell;
		import com.jmatio.types.MLChar;
		@@ -964,7 +961,7 @@ public class MatIOTest
		MLArray array = null;

		//try to read it
		MatFileReader reader = new MatFileReader();
		MatFileReader reader = new MatFileReader(MatFileType.Regular);
		reader.read(f, MatFileReader.MEMORY_MAPPED_FILE );
		array = reader.getMLArray("m1");
		assertEquals("Test if is correct file", array, m1);
		@@ -1022,7 +1019,7 @@ public class MatIOTest
		public void testBigSparseFile() throws IOException
		{
		//read array form file
		MatFileReader mfr = new MatFileReader();
		MatFileReader mfr = new MatFileReader(MatFileType.Regular);
		//reader crashes on reading this file
		//bug caused by sparse array allocation
		mfr.read( fileFromStream("/bigsparse.mat"), MatFileReader.DIRECT_BYTE_BUFFER );
		@@ -1051,12 +1048,12 @@ public class MatIOTest
		writer.write( filename, Arrays.asList( (MLArray)single) );

		//Test reading the MLSingle
		MatFileReader reader = new MatFileReader();
		MatFileReader reader = new MatFileReader(MatFileType.Regular);
		MLSingle readSingle = (MLSingle) reader.read( new File(filename) ).get( "arr" );

		assertEquals( single, readSingle );

		//Test reading the MLSingle generated natively by Matlab
		//Test reading the MLSingle generated natively by Regular
		MLSingle readSingleMatlabGenerated = (MLSingle) reader.read( fileFromStream("/single.mat") ).get( "arr" );

		assertEquals( single, readSingleMatlabGenerated );