Read mat files in Python

Question

Is it possible to read binary MATLAB  mat files in Python   I ve seen that SciPy has alleged support for reading  mat files  but I m unsuccessful with it  I installed SciPy version 0 7 0  and I can t find the loadmat   method

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An import is required  import scipy io     import scipy io mat   scipy io loadmat  file mat

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First save the  mat file as   save  test mat    -v7     After that  in Python  use the usual loadmat function   import scipy io as sio test   sio loadmat  test mat

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Reading the file  import scipy io mat   scipy io loadmat file name    Inspecting the type of MAT variable  print type mat    OUTPUT -  lt class  dict  gt    The keys inside the dictionary are MATLAB variables  and the values are the objects assigned to those variables

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There is a nice package called mat4py which can easily be installed using  pip install mat4py   It is straightforward to use  from the website    Load data from a MAT-file  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  Numeric and cell arrays are converted to row-ordered nested lists  Arrays are squeezed to eliminate arrays with only one element  The resulting data structure is composed of simple types that are compatible with the JSON format   Example  Load a MAT-file into a Python data structure   from mat4py import loadmat  data   loadmat  datafile mat     The variable data is a dict with the variables and values contained in the MAT-file   Save a Python data structure to a MAT-file  Python data can be saved to a MAT-file  with the function savemat  Data has to be structured in the same way as for loadmat  i e  it should be composed of simple data types  like dict  list  str  int  and float   Example  Save a Python data structure to a MAT-file   from mat4py import savemat  savemat  datafile mat   data    The parameter data shall be a dict with the variables

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There is also the MATLAB Engine for Python by MathWorks itself  If you have MATLAB  this might be worth considering  I haven t tried it myself but it has a lot more functionality than just reading MATLAB files   However  I don t know if it is allowed to distribute it to other users  it is probably not a problem if those persons have MATLAB  Otherwise  maybe NumPy is the right way to go     Also  if you want to do all the basics yourself  MathWorks provides  if the link changes  try to google for matfile format pdf or its title MAT-FILE Format  a detailed documentation on the structure of the file format  It s not as complicated as I personally thought  but obviously  this is not the easiest way to go  It also depends on how many features of the  mat-files you want to support   I ve written a  small   about 700 lines  Python script which can read some basic  mat-files  I m neither a Python expert nor a beginner and it took me about two days to write it  using the MathWorks documentation linked above   I ve learned a lot of new stuff and it was quite fun  most of the time   As I ve written the Python script at work  I m afraid I cannot publish it    But I can give some advice here    First read the documentation  Use a hex editor  such as HxD  and look into a reference  mat-file you want to parse  Try to figure out the meaning of each byte by saving the bytes to a  txt file and annotate each line  Use classes to save each data element  such as miCOMPRESSED  miMATRIX  mxDOUBLE  or miINT32  The  mat-files  structure is optimal for saving the data elements in a tree data structure  each node has one class and subnodes

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To read mat file to pandas dataFrame with mixed data types mat sio loadmat  file mat    load mat-file mdata   mat  myVar      variable in mat file  ndata    n  mdata n  0 0  for n in mdata dtype names  Columns    n for n  v in ndata items   if v size    1  d dict  c  ndata c  0   for c in Columns  df pd DataFrame from dict d  display df

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from os path import dirname  join as pjoin import scipy io as sio data dir   pjoin dirname sio   file      matlab    tests    data   mat fname   pjoin data dir   testdouble 7 4 GLNX86 mat   mat contents   sio loadmat mat fname    You can use above code to read the default saved  mat file in Python

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Neither scipy io savemat  nor scipy io loadmat work for MATLAB arrays version 7 3  But the good part is that MATLAB version 7 3 files are hdf5 datasets  So they can be read using a number of tools  including NumPy   For Python  you will need the h5py extension  which requires HDF5 on your system   import numpy as np import h5py f   h5py File  somefile mat   r   data   f get  data variable1   data   np array data    For converting to a NumPy array

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Having MATLAB 2014b or newer installed  the MATLAB engine for Python could be used   import matlab engine eng   matlab engine start matlab   content   eng load  example mat   nargout 1

[python] Read .mat files in Python

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