CSMatIO: MAT-file I/O API for .NET 2.0

Package contains Matlab's MAT-File I/O API for .NET 2.0. Supports Matlab 5 MAT-file format.

Description

CSMatIO a .NET Library is a Matlab MAT-File I/O API for Microsoft's .NET 2.0 Architecture written entirely in C#. CSMatIO has the ability to read, write, and manipulate binary Level 5 MAT-Files.

Currently supported data types:
+ Double array
+ Single array
+ Char array
+ Structure
+ Cell array
+ Sparse array
+ Int8 array
+ UInt8 array
+ Int16 array
+ UInt16 array
+ Int32 array
+ UInt32 array
+ Int64 array
+ UInt64 array

Note:
The zlib.net.dll file is used to compress and decompress MAT-file data.

Acknowledgements

J Mat Io Matlab's Mat File I/O In Java inspired this file.

• MATLAB release: MATLAB 6.5 (R13)
• Other requirements: + .NET 2.0 (or later) Architecture to run assembly + Any application create with CSMatIO must include _both_ the csmatio.dll and the zlib.net.dll + Uses Visual Studio .NET 2005 for editing.

[Duc]

Hi, I found a bug in the library.
File MLArray.cs, line 103.
The Flags property should be
get{ return (int)((uint)(_type & mtFLAG_TYPE) | (uint)(_attributes & 0xFFFFFF00)); }

or it will make all the numberic data written as Double.

And thank you very much for creating this awesome library.
Regards.

[Jen]

Jayant,once you created the 3D array, then use: array.Set(value,row_ind,col_index). For example, your 3D array is m*n*3,for 1st dimension, use array.Set(value,row_ind,col_index);for 2nd dimension, use array.Set(value,row_ind,col_index+n);for 3rd dimension, use array.Set(value,row_ind,col_index+2n)

[Jayant]

How can we save a 3 dimensional array of type MLUInt8? I am able to create the array of 3 dimensions but I am not able to figure out how to populate the data inside it.

[Jen]

I took a look at inside of it and found the data types are little confusing. I will see what I can do, thanks for the trust. Let's solve this problem, everyone!

[Tobias Otto-Adamczak]

Hi Jen, thank you for sharing this. AFAIK David is currently not working on the code. Neither do I. But if you could make some improvements I would be glad to test your patches and update the code on sourceforge.

HTH, Tobias

[Jen]

one more thing, CSMatIO has no problem reading uint16/int8 files that is created by CSMatIO itself.
It only has problem when I tried Matlab "save()" function created mat files.
Thank you

[Jen]

It still doesn't work Tobias. I didn't make it very accurate in the last post: For uint16, error can be catched, saying "invalid binary MAT-file!"; For int8, the debugger stopped at ln386 in MatFileReader.cs and error message says "Additional information: Unable to cast object of type 'csmatio.types.MLInt8' to type'csmatio.types.MLNumericArray`1[System.Byte]'."
Has anyone tried on uint16 or int8 before?
Thank you for your reply.

[Tobias Otto-Adamczak]

Hi Jen, this might be due to one of the few shortcomings of Davids original code. Have a look at the latest version at sourceforge and tell me if it behaves the same way: https://sourceforge.net/projects/csmatio/files/

HTH, Tobias

[Jen]

I have no problem reading in Uint8 and Double.
But I couldn't read in "int8" and "uint16" type MAT file, debug stopped at Ln386 in "MatFileReader.cs", and error message says"Additional information: Unable to cast object of type 'csmatio.types.MLInt8' to type'csmatio.types.MLNumericArray`1[System.Byte]'."
What might be wrong? Thank you

[Tobias Otto-Adamczak]

Hello kushal, CSMatIO is about .NET, not Java. For Java consider JMatIO instead.

HTH, Tobias

[kushal]

suppose a mat file consist of multiple matrices and tensor,

how to read those matrices as it is in local java variable so as to perform the operations on those variables such as transpose etc.

e.g: say sample.mat contains
A(mxn),
B(m x n x k),
C(m x k),
D(n x k)

how to read these matrices in java and store them with their original dimensions as it is.

[Tobias Otto-Adamczak]

Hi Laurent, you can easily create a 3D double array as follows:

// init 3D double array (2x3x4 elements)
int[] dims = new int[] { 2, 3, 4 };
MLDouble array3Dim = new MLDouble("cube", dims);

HTH, Tobias

[Laurent]

Very nice and useful library.

A question for Tobias, which was asked (I quote) "How to read the content of a three-dimensional double array with this library."

My question is : how to create a 3D double array with this library ? Methods of MLDouble don't seem to enable that kind of thing...

Nice work anyway.

[M. Hakma]

 

[Tobias Otto-Adamczak]

Le me give you a basic example how to create nested matlab vars with this lib.

// suppose we have following C# struct

public struct Score
{
public string Name;
public double Value;
}

// initialize an struct object of that type

Score highscore;
highscore.Name = "David";
highscore.Value = 47.3;

// create a corresponding MATLAB structure

MLStructure structure = new MLStructure("highscore", new int[] { 1, 1 });

// create a MATLAB char and double variable and add it to the structure

MLChar scoreName = new MLChar("", highscore.Name);
MLDouble scoreValue = new MLDouble("", new double[] { highscore.Value }, 1);
structure["Name", 0] = scoreName;
structure["Value", 0] = scoreValue;

// save the structure as mat file using MatFileWriter

List<MLArray> mlList = new List<MLArray>();
mlList.Add(structure);
MatFileWriter mfw = new MatFileWriter("data.mat", mlList, false);

HTH, Tobias

[Ettore]

I need to write some nested vars in .mat file, like:
a.b.var1=10
a.b.var2=20

To my understanding, within the MatlabFileWriter, i can't do:
data.Add("a.b.var1", 10)

but I need to implement something like
- check if 'a' exists, create it if not
- check if 'b' exists under 'a', create it if not
- check if 'var' exists under 'b', create it if not
- set value and save

Is that correct?

[Tobias Otto-Adamczak]

Today I was asked how to read the content of a three-dimensional double array with this library. The same goes for arrays with four or more dimensions.

So lets assume we have a 220x180x33 double array called "cube" and we want to read what is in matlab syntax "cube(7,18,29)":

// get a reference to our matlab 'cube' double matrix
MLDouble mlCube = (mfr.Content["cube"] as MLDouble);
if (mlCube != null)
{
// calculate the index of our element
idx = 7-1 + (18-1)*220 + (29-1)*180*220;
// now get the double value
double value = mlCube.Get(idx);
}

HTH, Tobias

[Tobias Otto-Adamczak]

Hi all, I fixed some issues in this really useful libray. Have a look at https://sourceforge.net/projects/csmatio/files/

HTH, Tobias

[diiiego83]

ok good work David.
Ther's an error if you try to open a mat file with data of "single" class.
You forget the single case in MatFileReader.cs method ReadMatrix (Add this)

case MLArray.mxSINGLE_CLASS:
mlArray = new MLSingle(name, dims, type, attributes);
//read real
tag = new ISMatTag(buf);
tag.ReadToByteBuffer(((MLNumericArray<double>)mlArray).RealByteBuffer,
(ByteStorageSupport)mlArray);

// read complex
if (mlArray.IsComplex)
{
tag = new ISMatTag(buf);
tag.ReadToByteBuffer(((MLNumericArray<double>)mlArray).ImaginaryByteBuffer,
(ByteStorageSupport)mlArray);
}
break;

The keys in the internal structure has been saved with "\0". For Example in MlStructure.cs method ContentToString change :
sb.Append("\t" + key + " : " + this[key].ContentToString() + "\n");
with :
sb.Append("\t" + key.Replace("\0","") + " : " + this[key].ContentToString() + "\n");

;)

[Markus W]

Had problems reading mat-files with 2-dim arrays with larger number of elements. Saving the file with -v6 option solved the problem (so far).

[Tobias Otto-Adamczak]

Hi Qirong, I give you a very simple but more complete example. I tested this with Matlab R2006b and Visual Studio 2005.

Consider you created a "mydata.mat" file containing a 1x10 double matrix using matlab like this:

>> squares = [1:10].^2
>> save('mydata.mat', 'squares')

You can then use the following C# code to get this data into a .NET double-Array:

namespace csmatio_test
{
using System;
using csmatio.io;
using csmatio.types;

class Program
{
// this array receives the matlab data
static double[] squares;

static void Main(string[] args)
{
// create a reader for the file
MatFileReader mfr = new MatFileReader("mydata.mat");

// get a reference to out matlab 'squares' double matrix
MLDouble mlSquares = (mfr.Content["squares"] as MLDouble);
if (mlSquares != null)
{
// now get the double values
double[][] tmp = mlSquares.GetArray();
squares = tmp[0];
}
}
}
}

HTH, Tobias

[Tobias Otto-Adamczak]

Hi farid, csmatio uses zlib to compress/decompress matlab file data. There are several possibilities why zlib throws this exception; for example you might think of
(a) file format not supported (csmatio does not support all kinds of mat files)
(b) corrupt file content
(c) bug in csmatio
...

[Qirong]

So I know that the data is double array, how can I cast the MLArray type into MLDouble type? I tried

MatFileReader mfr = new MatFileReader(currentName);
foreach (MLArray mla in mfr.Data)
{
MLDouble da = mla;
}

But apparently this doesn't work...

[farid]

hi all.
I'm trying to read a mat file but i receive this error

==========================
Error in reading MAT-file 'initialize\matfile-1.mat':
csmatio.io.MatlabIOException: Could not decompress data: zlib.ZStreamException: inflating:
at zlib.ZOutputStream.Write(Byte[] b1, Int32 off, Int32 len)
at csmatio.io.MatFileReader.Inflate(Stream buf, Int32 numOfBytes)
at csmatio.io.MatFileReader.Inflate(Stream buf, Int32 numOfBytes)
at csmatio.io.MatFileReader.ReadData(Stream buf)
at csmatio.io.MatFileReader..ctor(String fileName, MatFileFilter filter)
==========================

what is the cause of this error message?
pleas help .... the situation is urgent!

[Tobias Otto-Adamczak]

First, you might want to get a reference to your matlab variable:

var mfr = new MatFileReader(fileName);
MLArray mlArrayRetrieved = mfr.GetMLArray("my_array");

Second, you need to find out of which type mlArrayRetrieved really is (as MLArray is only a base class) and you cast into the real type. Depending on the real type there are different Methods/Properties that represent the data.

HTH, Tobias

[Qirong]

How do I load data using this library? I followed the test application and it only uses the function MatFileReader.ContentToString() to access the content. Is that the only way I can access the data? And then parse the string to get the real data?

[Tobias Otto-Adamczak]

Really useful library. However it has some bugs (struct field access is buggy, writing empty strings doesn't work) und is somehow incomplete (unsupported data types). I try to provide some fixes in the next days.

[Markus W]

Easy to use an very helpful

Writing empty string seems to result in exception. Any workaround?

[Jörgen Ejr973jr]

Support for enumerations?

Any plans to add support for enumerations using declared as:
classdef(Enumeration) AdapRequestEnum < int32 ...

I have not found any description of the internal representation in MAT file format.

[Bart Ribbens]

Does there exist a binary Level 7 Mat fileformat?

In the latest document (MAT-File Format
Version 7) they still use the Level 5 binary.

[Lalit Parashar]

Any plans to upgrade it to manipulate binary Level 7 MAT-Files.

[Mike]

Writes to binary memory stream which runs out of memory at ~270 MB (.NET managed heap limitation, I believe) before being written to disk. Would be nice to have the option to take a performance hit but stream directly to disk, enabling creation of larger files.

[M D]

Missing cases MLArray.mxUINT16_CLASS, MLArray.mxINT16_CLASS, MLArray.mxUINT32_CLASS & MLArray.mxINT32_CLASS in the method ReadMatrix of MatFileReader class

[Pierluigi Fumi]

 

[Steffen S]

A bit tricky to get into. But once you got it its easy to use. Works stable.