Load Mat File With Python

You may have a mat file that you want to read into scipy.

Load mat file with python.

Start octave octave at the command line for me. Starting with matlab 7 3 mat files have been changed to store as custom hdf5 files. V4 level 1 0 v6 and v7 to 7 2 matfiles are supported. Arrays are squeezed to eliminate arrays with only one element.

To save us using a matlab license let s start in octave. These files can be read in python using for instance the pytables or h5py package. After reading a structure called e g. You can get the file used in this post here.

Octave has matlab compatible save and load functions. Dictionary with variable names as keys and loaded matrices as values. Beginning at release 7 3 of matlab mat files are actually saved using the hdf5 format by default except if you use the vx flag at save time see help save in matlab. Scipy is a really popular python library used for scientific computing and quite naturally they have a method which lets you read in mat files.

If filename has no extension that is no text after a period load looks for a file named filename mat if filename has an extension other than mat the load function treats. Load data from mat file. This file contains gene expression data from the albeck lab at uc davis. Filename can include a file extension and a full or partial path.

Coming from the academia the annotations for the dataset was in the mat format. Matlab up to 7 1 mat files created with matlab up to version 7 1 can be read using the mio module part of scipy io reading structures and arrays of structures is supported elements are accessed with the same syntax as in matlab. In this exercise you ll figure out how to load a matlab file using scipy io loadmat and you ll discover what python datatype it yields. You will need an hdf5 python library to read matlab 7 3 format mat files.

Please use hdf reader for matlab v7. Name of file specified as a character vector or string scalar. Or you want to pass some variables from scipy numpy into matlab. If you do not specify filename the load function searches for a file named matlab mat.

This means they cannot be loaded by scipy io loadmat any longer and raise. Reading matlab structures in mat files does not seem supported at this point. Reading them in is definitely the easy part. Numeric and cell arrays are converted to row ordered nested lists.

You can find the data and some great documentation here. This library loads matlab 7 3 hdf5 files into a python dictionary. Because scipy does not supply one we do not implement the hdf5 7 3 interface here. The file albeck gene expression mat is in your working directory.

The function loadmat loads all variables stored in the mat file into a simple python data structure using only python s dict and list objects.