# File IO (`scipy.io`)#

## MATLAB files#

 `loadmat`(file_name[, mdict, appendmat]) Load MATLAB file. `savemat`(file_name, mdict[, appendmat, ...]) Save a dictionary of names and arrays into a MATLAB-style .mat file. `whosmat`(file_name[, appendmat]) List variables inside a MATLAB file.

### The basic functions#

We’ll start by importing `scipy.io` and calling it `sio` for convenience:

```>>> import scipy.io as sio
```

If you are using IPython, try tab-completing on `sio`. Among the many options, you will find:

```sio.loadmat
sio.savemat
sio.whosmat
```

These are the high-level functions you will most likely use when working with MATLAB files. You’ll also find:

```sio.matlab
```

This is the package from which `loadmat`, `savemat`, and `whosmat` are imported. Within `sio.matlab`, you will find the `mio` module This module contains the machinery that `loadmat` and `savemat` use. From time to time you may find yourself re-using this machinery.

### How do I start?#

You may have a `.mat` file that you want to read into SciPy. Or, you want to pass some variables from SciPy / NumPy into MATLAB.

To save us using a MATLAB license, let’s start in Octave. Octave has MATLAB-compatible save and load functions. Start Octave (`octave` at the command line for me):

```octave:1> a = 1:12
a =

1   2   3   4   5   6   7   8   9  10  11  12

octave:2> a = reshape(a, [1 3 4])
a =

ans(:,:,1) =

1   2   3

ans(:,:,2) =

4   5   6

ans(:,:,3) =

7   8   9

ans(:,:,4) =

10   11   12

octave:3> save -6 octave_a.mat a % MATLAB 6 compatible
octave:4> ls octave_a.mat
octave_a.mat
```

Now, to Python:

```>>> mat_contents = sio.loadmat('octave_a.mat')
>>> mat_contents
{'a': array([[[  1.,   4.,   7.,  10.],
[  2.,   5.,   8.,  11.],
[  3.,   6.,   9.,  12.]]]),
'__version__': '1.0',
'__header__': 'MATLAB 5.0 MAT-file, written by
Octave 3.6.3, 2013-02-17 21:02:11 UTC',
'__globals__': []}
>>> oct_a = mat_contents['a']
>>> oct_a
array([[[  1.,   4.,   7.,  10.],
[  2.,   5.,   8.,  11.],
[  3.,   6.,   9.,  12.]]])
>>> oct_a.shape
(1, 3, 4)
```

Now let’s try the other way round:

```>>> import numpy as np
>>> vect = np.arange(10)
>>> vect.shape
(10,)
>>> sio.savemat('np_vector.mat', {'vect':vect})
```

Then back to Octave:

```octave:8> load np_vector.mat
octave:9> vect
vect =

0  1  2  3  4  5  6  7  8  9

octave:10> size(vect)
ans =

1   10
```

If you want to inspect the contents of a MATLAB file without reading the data into memory, use the `whosmat` command:

```>>> sio.whosmat('octave_a.mat')
[('a', (1, 3, 4), 'double')]
```

`whosmat` returns a list of tuples, one for each array (or other object) in the file. Each tuple contains the name, shape and data type of the array.

### MATLAB structs#

MATLAB structs are a little bit like Python dicts, except the field names must be strings. Any MATLAB object can be a value of a field. As for all objects in MATLAB, structs are, in fact, arrays of structs, where a single struct is an array of shape (1, 1).

```octave:11> my_struct = struct('field1', 1, 'field2', 2)
my_struct =
{
field1 =  1
field2 =  2
}

octave:12> save -6 octave_struct.mat my_struct
```

We can load this in Python:

```>>> mat_contents = sio.loadmat('octave_struct.mat')
>>> mat_contents
{'my_struct': array([[([[1.0]], [[2.0]])]],
dtype=[('field1', 'O'), ('field2', 'O')]), '__version__': '1.0', '__header__': 'MATLAB 5.0 MAT-file, written by Octave 3.6.3, 2013-02-17 21:23:14 UTC', '__globals__': []}
>>> oct_struct = mat_contents['my_struct']
>>> oct_struct.shape
(1, 1)
>>> val = oct_struct[0,0]
>>> val
([[1.0]], [[2.0]])
>>> val['field1']
array([[ 1.]])
>>> val['field2']
array([[ 2.]])
>>> val.dtype
dtype([('field1', 'O'), ('field2', 'O')])
```

In the SciPy versions from 0.12.0, MATLAB structs come back as NumPy structured arrays, with fields named for the struct fields. You can see the field names in the `dtype` output above. Note also:

```>>> val = oct_struct[0,0]
```

and:

```octave:13> size(my_struct)
ans =

1   1
```

So, in MATLAB, the struct array must be at least 2-D, and we replicate that when we read into SciPy. If you want all length 1 dimensions squeezed out, try this:

```>>> mat_contents = sio.loadmat('octave_struct.mat', squeeze_me=True)
>>> oct_struct = mat_contents['my_struct']
>>> oct_struct.shape
()
```

Sometimes, it’s more convenient to load the MATLAB structs as Python objects rather than NumPy structured arrays - it can make the access syntax in Python a bit more similar to that in MATLAB. In order to do this, use the `struct_as_record=False` parameter setting to `loadmat`.

```>>> mat_contents = sio.loadmat('octave_struct.mat', struct_as_record=False)
>>> oct_struct = mat_contents['my_struct']
>>> oct_struct[0,0].field1
array([[ 1.]])
```

`struct_as_record=False` works nicely with `squeeze_me`:

```>>> mat_contents = sio.loadmat('octave_struct.mat', struct_as_record=False, squeeze_me=True)
>>> oct_struct = mat_contents['my_struct']
>>> oct_struct.shape # but no - it's a scalar
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: 'mat_struct' object has no attribute 'shape'
>>> type(oct_struct)
<class 'scipy.io.matlab.mio5_params.mat_struct'>
>>> oct_struct.field1
1.0
```

Saving struct arrays can be done in various ways. One simple method is to use dicts:

```>>> a_dict = {'field1': 0.5, 'field2': 'a string'}
>>> sio.savemat('saved_struct.mat', {'a_dict': a_dict})
```

```octave:21> load saved_struct
octave:22> a_dict
a_dict =

scalar structure containing the fields:

field2 = a string
field1 =  0.50000
```

You can also save structs back again to MATLAB (or Octave in our case) like this:

```>>> dt = [('f1', 'f8'), ('f2', 'S10')]
>>> arr = np.zeros((2,), dtype=dt)
>>> arr
array([(0.0, ''), (0.0, '')],
dtype=[('f1', '<f8'), ('f2', 'S10')])
>>> arr[0]['f1'] = 0.5
>>> arr[0]['f2'] = 'python'
>>> arr[1]['f1'] = 99
>>> arr[1]['f2'] = 'not perl'
>>> sio.savemat('np_struct_arr.mat', {'arr': arr})
```

### MATLAB cell arrays#

Cell arrays in MATLAB are rather like Python lists, in the sense that the elements in the arrays can contain any type of MATLAB object. In fact, they are most similar to NumPy object arrays, and that is how we load them into NumPy.

```octave:14> my_cells = {1, [2, 3]}
my_cells =
{
[1,1] =  1
[1,2] =

2   3

}

octave:15> save -6 octave_cells.mat my_cells
```

Back to Python:

```>>> mat_contents = sio.loadmat('octave_cells.mat')
>>> oct_cells = mat_contents['my_cells']
>>> print(oct_cells.dtype)
object
>>> val = oct_cells[0,0]
>>> val
array([[ 1.]])
>>> print(val.dtype)
float64
```

Saving to a MATLAB cell array just involves making a NumPy object array:

```>>> obj_arr = np.zeros((2,), dtype=np.object)
>>> obj_arr[0] = 1
>>> obj_arr[1] = 'a string'
>>> obj_arr
array([1, 'a string'], dtype=object)
>>> sio.savemat('np_cells.mat', {'obj_arr':obj_arr})
```
```octave:16> load np_cells.mat
octave:17> obj_arr
obj_arr =
{
[1,1] = 1
[2,1] = a string
}
```

## IDL files#

 `readsav`(file_name[, idict, python_dict, ...]) Read an IDL .sav file.

## Matrix Market files#

 `mminfo`(source) Return size and storage parameters from Matrix Market file-like 'source'. `mmread`(source) Reads the contents of a Matrix Market file-like 'source' into a matrix. `mmwrite`(target, a[, comment, field, ...]) Writes the sparse or dense array a to Matrix Market file-like target.

## Wav sound files (`scipy.io.wavfile`)#

 `read`(filename[, mmap]) Open a WAV file. `write`(filename, rate, data) Write a NumPy array as a WAV file.

## Netcdf#

 `netcdf_file`(filename[, mode, mmap, version, ...]) A file object for NetCDF data.

Allows reading of NetCDF files (version of pupynere package)