mat-io 0.7.0

A package for reading MATLAB .mat files, with support for MATLAB datatypes like table and string

Mat-IO Module

The mat-io module provides tools for loading and saving MAT-files, including MATLAB's classdef-based datatypes such as datetime, table and string. It supports almost all MATLAB object types, including user-defined objects and handle class objects. Additionally, it includes utilities to convert the following MATLAB datatypes into their respective Pythonic objects, and vice versa:

• string
• datetime, duration and calendarDuration
• table and timetable
• containers.Map and dictionary
• categorical
• Enumeration Instance Arrays

MAT-file versions v6, v7 and v7.3 are supported.

• Versions v6 and v7 uses a modified version of scipy.io under the hood
• Version v7.3 uses h5py to write in the HDF5 format.

Data is returned in the same format as scipy.io.loadmat does.

Installation

pip install mat-io

Usage

Loading MAT-files

from matio import load_from_mat

file_path = "path/to/your/file.mat"
data = load_from_mat(
    file_path,
    raw_data=False,
    add_table_attrs=False,
    mdict=None,
    variable_names=None,
)

• raw_data: If True, returns raw property maps of Opaque class objects.
• add_table_attrs: If True, adds custom Matlab Table or Timetable properties as pandas.DataFrame attributes.
• mdict: If provided, this dictionary will be updated with the data from a MAT-file.
• variable_names: A list of variable names to load from file.

Saving MAT-files

from matio import save_to_mat

file_path = "path/to/your/file.mat"
mdict = {"var1": data1, "var2": data2}
save_to_mat(
    file_path,
    mdict=mdict,
    version="v7.3",
    global_vars=None,
    oned_as="col",
    do_compression=True,
)

• file_path: The file to save data.
• mdict: A dictionary of {var_name: var_data} to write to MAT-files.
• version: The MAT-file version to save to. Supported versions are v7.3 and v7. Defaults to v7.3 which is based on the HDF5 format.
• global_vars: A list of variable names that are to be marked as global variables.
• saveobj_classes: A list of class names that implement saveobj methods.
• oned_as: The 2D shape to apply to unit numpy.ndarrays. Either row or col. Defaults to col.
• do_compression: If False, does not compress data when saving.

List variables in a MAT-file

from matio import whosmat

file_path = "path/to/your/file.mat"
vars = whosmat(file_path)
# Returns (variable_name, dims, datatype/classname)
print(vars)

Opaque Class Objects

Opaque class objects are what MATLAB calls object instances. Opaque objects have different types. The most common is MCOS, which is used for all user-defined classdefs, enumeration classes, as well as most MATLAB datatypes like string, datetime and table.

Opaque objects are returned as an instance of class MatlabOpaque with the following attributes:

• classname: The class name, including namespace qualifiers (if any).
• type_system: An interal MATLAB type identifier. Usually MCOS, but could also be java or handle.
• properties: A dictionary containing the property names and property values.
• class_alias: This is an optional attribute containing class aliases, if any.

If the raw_data parameter is set to False, then load_from_mat converts these objects into a corresponding Pythonic datatype, if available. For a list of conversion rules between MATLAB and Python datatypes, see the documentation.

When writing objects, matio tries to guess the class name of the object. For example, pandas.DataFrames could be read in as table or timetable. User-defined objects must contain a dictionary of property name, value pairs wrapped around a MatlabOpaque instance.

from matio import save_to_mat
from matio.utils import MatlabOpaque

prop_map = {"prop1": val1, "prop2": val2}
mat_obj = MatlabOpaque(properties=prop_map, classname="MyClass")
mdict = {"var1": mat_obj}
data = save_to_mat(file_path="temp.mat", mdict=mdict)

If the class implements a custom saveobj method, this can be specified in the saveobj_classes argument in save_to_mat. The property map for such classes must contain a single property called any. Typically, the value of this property would be in a format output by the saveobj method. This would be the input for the loadobj method in the class, if defined. More information here.

Wrapper Classes

This package uses wrapper classes to represent Matlab object data to help distinguish from basic datatypes. These are as follows:

• MatlabOpaque: A wrapper class for all opaque objects with three attributes: properties, classname, type_system. properties is a name-value pair dictionary for each property of the class saved to a MAT-file
• MatlabOpaqueArray: A wrapper class subclassed from numpy.ndarray to represent object arrays. Each item in this array is a MatlabOpaque object.
• MatlabEnumerationArray: A wrapper class subclassed from numpy.ndarray to represent enumeration instance arrays. Each item in this array is of type enum.Enum.
• MatlabContainerMap: A wrapper class subclassed from collections.UserDict to represent container.Map objects. During save, dictionaries are converted to a struct. Wrap dictionaries around MatlabContainerMap to write to container.Map instead.

To save these types to a MAT-file, data must be wrapped around the relevant wrapper class. These can be imported from matio.utils. An example is shown below:

# Save dictionary as container.Map
from matio.utils import MatlabContainerMap
from matio import save_to_mat

map = {"a": 1, "b": 2}
map = MatlabContainerMap(map)
var_dict = {"myVar": map}
save_to_mat("file.mat", var_dict)

Contribution

Feel free to create a PR if you'd like to add something, or open up an issue if you'd like to discuss!

Acknowledgement

Huge thanks to mahalex for their breakdown of MAT-files. A lot of this wouldn't be possible without it.