# MatFileHandler

This document briefly describes how to perform simple operations with .mat files using MatFileHandler.
If you have questions and/or ideas, you can [file a new issue](https://github.com/mahalex/MatFileHandler/issues/new) or contact me directly at <mahalex@gmail.com>.

## Reading a .mat file

```csharp
using MatFileHandler;
IMatFile matFile;
using (var fileStream = new System.IO.FileStream("example.mat", System.IO.FileMode.Open)) {
    var reader = new MatFileReader(fileStream);
    matFile = reader.Read();
}
```

After that, you can access the variables inside using the indexer
```csharp
IVariable variable = matFile["array"];
```
or iterating over all the variables:
```csharp
foreach (IVariable variable in matFile.Variables) {
    // Do stuff
}
```
(all of the interfaces and classes described in this text are in the `MatFileHandler` namespace).

Each `IVariable` has a name, a value, and a flag indicating if it's a “global” variable:
```csharp
public interface IVariable
{
    string Name { get; set; }
    IArray Value { get; }
    bool IsGlobal { get; }
}
```

The interesting part here is the `IArray` interface. This is a base interface, which is extended by other interfaces that provide access to more specific MATLAB arrays (numerical, cell, structure, char, etc.).
We can't do much with `IArray` itself: check for emptiness, get its dimensions and total number of elements in it, or try to convert it to an array of double (or complex) numbers:
```csharp
public interface IArray
{
    bool IsEmpty { get; }
    int[] Dimensions { get; }
    int Count { get; }
    double[] ConvertToDoubleArray();
    System.Numerics.Complex[] ConvertToDoubleArray();
}
```

Note that `Dimensions` is a list, since all arrays in MATLAB are (at least potentially) multi-dimensional. However, `ConvertToDoubleArray()` and `ConvertToDoubleArray()` return flat arrays, arranging all multi-dimensional data in columns (MATLAB-style). This functions return `null` if conversion failed (for example, if you tried to apply it to a structure array, or cell array). 

## Numerical and logical arrays

The simplest type of array is a numerical array, which implements the `IArrayOf<T>` interface, where `T` is a numerical type, i. e., one of `Int8`, `UInt8`, `Int16`, `UInt16`, `Int32`, `UInt32`, `Int64`, `UInt64`, `Single`, `Double`. Arrays can contain complex values, which are just pairs of ordinary numbers. These pairs of `Double`s are represented by `System.Numerics.Complex`, and pairs of other numerical types are represented by a simple `ComplexOf<T>` struct, which has two properties: 
```csharp
public struct ComplexOf<T> : IEquatable<ComplexOf<T>>
    where T : struct
{
    public T Real { get; }
    public T Imaginary { get; }
    // Some other stuff
}
```

All of this means that you can also have an `IArrayOf<T>` for `T` being `ComplexOf<Int8>`, `ComplexOf<UInt8>`, `ComplexOf<Int16>`, `ComplexOf<UInt16>`, `ComplexOf<Int32>`, `ComplexOf<UInt32>`, `ComplexOf<Int64>`, `ComplexOf<UInt64>`, `ComplexOf<Single>`, and, of course, `Complex` (note that we don't use `ComplexOf<Double>`). Finally, you can access a logical array as `IArrayOf<Boolean>`.

The `IArrayOf<T>` interface allows you to refer to a specific element by using a (multi-dimensional) indexer, or get all data at once as a flat array (multidimensional arrays get converted to flat using MATLAB conventions). Indexes start with 0 (note that in MATLAB they start with 1, so there is a shift in notation).
```csharp
public interface IArrayOf<T> : IArray
{
    T[] Data { get; }
    T this[params int[] list] { get; set; }
}
```
You can use a one-dimensional indexer or a multi-dimensional one, which is consistent with MATLAB notation. For example, a 2×3 array named `a` has elements `a[0, 0]`, `a[1, 0]` (first column), `a[0, 1]`, `a[1, 1]` (second column), `a[0, 2]`, `a[1, 2]` (third column), which can also be accessed as `a[0]`, `a[1]`, `a[2]`, `a[3]`, `a[4]`, and `a[5]`, respectively.

## Cell arrays

Cell array is just an array of arrays, so `ICellArray` implements `IArrayOf<IArray>`, and adds nothing to it. This means that you can refer to specific cells in a cell array by using the indexer, or by inspecting the `Data` array described in the previous section.

## Char arrays

Char arrays implement `IArrayOf<char>`, so you can refer to individual chars in it via an indexer. Often a char array is used to carry a string, so there is a property for that: 
```csharp
public interface ICharArray : IArrayOf<char>
{
    string String { get; }
}
```
This can be slightly weird for multi-dimensional arrays: the characters are stuffed into this string by columns (the same way the numerical array elements are flattened into a one-dimensional array). Moreover, each character array you read from a file actually implements either `IArrayOf<UInt8>`, or `IArrayOf<UInt16>`, depending on whether it was stored as a UTF-8 or UTF-16 encoded string. Characters arrays produced by MatFileHandler are always encoded as UTF-16.

## Structure arrays

Structure arrays have elements that are indexed not only by their positions in the array, but also by structure fields. For example, a 1×2 structure array `s` with fields `x` and `y` has four elements: `s(1).x`, `s(1).y`, `s(2).x`, `s(2).y` (in MATLAB notation). This means that if you only specify the numerical indices, you get a dictionary that maps `string` to `IArray`; in order to reach a specific element, you need to provide both the indices and the field name:
```csharp
public interface IStructureArray : IArrayOf<IReadOnlyDictionary<string, IArray>>
{
    IEnumerable<string> FieldNames { get; }
    IArray this[string field, params int[] list] { get; set; }
}
```
Here `FieldNames` gives you a list of all fields in the structure.

## Sparse arrays

Sparse array is like a numerical array, but not all of the values in it have to be specified; the rest are assumed to be 0.
```csharp
public interface ISparseArrayOf<T> : IArrayOf<T>
  where T : struct
{
    new IReadOnlyDictionary<(int, int), T> Data { get; }
}
```
Since `ISparseArrayOf<T>` implements `IArrayOf<T>`, you still can access all the elements in a sparse array (you'll get 0 when the element is not present). Alternatively, you can get a dictionary of all (possibly) non-zero elements. MATLAB only supports double, complex, and logical sparse arrays, so `T` here can be `Double`, `Complex` or `Boolean` (which, of course, uses `false` as the default value).

## Writing a .mat file

After reading a file into `IMatFile matFile`, you can alter some values using the described interfaces, and write the result to a new file:
```csharp
using (var fileStream = new System.IO.FileStream("output.mat", System.IO.FileMode.Create)) {
    var writer = new MatFileWriter(fileStream);
    writer.Write(matFile);
}
```

Another option is to create a file from scratch. You can do it with `DataBuilder` class:

```csharp
public class DataBuilder
{
    public IArrayOf<T> NewArray<T>(params int[] dimensions)
        where T : struct;
    public IArrayOf<T> NewArray<T>(T[] data, params int[] dimensions)
        where T : struct;
    public ICellArray NewCellArray(params int[] dimensions);
    public IStructureArray NewStructureArray(IEnumerable<string> fields, params int[] dimensions);
    public ICharArray NewCharArray(string contents);
    public ICharArray NewCharArray(string contents, params int[] dimensions);
    public IArray NewEmpty();
    public ISparseArrayOf<T> NewSparseArray<T>(params int[] dimensions)
      where T : struct;
    public IVariable NewVariable(string name, IArray value, bool isGlobal = false);
    public IMatFile NewFile(IEnumerable<IVariable> variables);
}
```
Numerical/logical arrays can be created with `NewArray<T>()` using the provided data; char arrays can be created with `NewCharArray()` using a string. All other types of arrays are created empty. Then you can wrap an array into a variable with `NewVariable()`, and put a bunch of variables into a file using `NewFile()`. The resulting file can be written to a stream using `MatFileWriter`, as shown above.