File IO (scipy.io) — SciPy v1.15.3 Manual (original) (raw)

MATLAB files#

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:

This is the package from which loadmat, savemat, and whosmatare 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 {'header': b'MATLAB 5.0 MAT-file, written by Octave 3.2.3, 2010-05-30 02:13:40 UTC', 'version': '1.0', 'globals': [], 'a': array([[[ 1., 4., 7., 10.], [ 2., 5., 8., 11.], [ 3., 6., 9., 12.]]])} 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 {'header': b'MATLAB 5.0 MAT-file, written by Octave 3.2.3, 2010-05-30 02:00:26 UTC', 'version': '1.0', 'globals': [], 'my_struct': array([[(array([[1.]]), array([[2.]]))]], dtype=[('field1', 'O'), ('field2', 'O')]) }

oct_struct = mat_contents['my_struct'] oct_struct.shape (1, 1) val = oct_struct[0, 0] val np.void((array([[1.]]), array([[2.]])), dtype=[('field1', 'O'), ('field2', 'O')]) 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 "", line 1, in 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})

loaded as:

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=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#

Matrix Market files#

Wav sound files (scipy.io.wavfile)#

Arff files (scipy.io.arff)#

Netcdf#

Allows reading of NetCDF files (version of pupynere package)