how to read mat v7.3 files in python ？

I've created a small library to load MATLAB 7.3 files:

pip install mat73

To load a .mat 7.3 into Python as a dictionary:

import mat73
data_dict = mat73.loadmat('data.mat')

Try using h5py module

import h5py
with h5py.File('test.mat', 'r') as f:
   f.keys()

import h5py
import numpy as np
filepath = '/path/to/data.mat'
arrays = {}
f = h5py.File(filepath)
for k, v in f.items():
   arrays[k] = np.array(v)

Per Magu_'s answer on a related thread, check out the package hdf5storage which has convenience functions to read v7.3 matlab mat files; it is as simple as

import hdf5storage
mat = hdf5storage.loadmat('test.mat')

I had a look at this issue: https://github.com/h5py/h5py/issues/726. If you saved your mat file with -v7.3 option, you should generate the list of keys with (under Python 3.x):

import h5py
with h5py.File('test.mat', 'r') as file:
   print(list(file.keys()))

In order to access the variable a for instance, you have to use the same trick:

with h5py.File('test.mat', 'r') as file:
   a = list(file['a'])

So starting with (I think the [0][0] arises from Matlab giving everything to dimensions):

f = h5py.File('filename', 'r')
f['varname'][0][0]

Pass this reference to f again:

f[f['varname'][0][0]]

which gives an array: convert this to a numpy array and extract the value (or, recursively, another < HDF5 object reference > :

np.array(f[f['varname'][0][0]])[0][0]

Suggestion : 2

This library loads MATLAB 7.3 HDF5 files into a Python dictionary.,This library will only load mat 7.3 files. For older versions use scipy.io.loadmat,Load MATLAB 7.3 .mat files into Python.,Starting with MATLAB 7.3, .mat files have been changed to store as custom hdf5 files. This means they cannot be loaded by scipy.io.loadmat any longer and raise.

Starting with MATLAB 7.3, .mat files have been changed to store as custom hdf5 files. This means they cannot be loaded by scipy.io.loadmat any longer and raise.

NotImplementedError: Please use HDF reader
for matlab v7 .3 files

This library loads MATLAB 7.3 HDF5 files into a Python dictionary.

import mat73
data_dict = mat73.loadmat('data.mat')

By enabling use_attrdict=True you can even access sub-entries of structs as attributes, just like in MATLAB:

data_dict = mat73.loadmat('data.mat', use_attrdict = True)
struct = data_dict['structure'] # assuming a structure was saved in the.mat
struct[0].var1 == struct[0]['var1'] # it 's the same!

To install, run:

pip install mat73

Alternatively for most recent version:

pip install git + https: //github.com/skjerns/mat7.3

Suggestion : 3

I am trying to run afqbrowser-assemble on my AFQ output (output.mat) and I am seeing following error message.,We are starting to use 2017a, but I believe most of our apps still runs on 2016a. I will find out we can start storing our AFQ output in HDF5 format.,I am saving the AFQ output like following.,By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

$ ~/git/AFQ-Browser/bin/afqbrowser-assemble output.mat
Traceback (most recent call last):
File "/N/u/brlife/Karst/git/AFQ-Browser/bin/afqbrowser-assemble", line 19, in <module>
   afqb.assemble(args.source, args.target)
   File "/N/u/brlife/Karst/.local/lib/python2.7/site-packages/afqbrowser/browser.py", line 150, in assemble
   out_path=op.join(site_dir, 'client', 'data'))
   File "/N/u/brlife/Karst/.local/lib/python2.7/site-packages/afqbrowser/browser.py", line 43, in mat2tables
   afq = sio.loadmat(mat_file_name, squeeze_me=True)['afq']
   File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 135, in loadmat
   MR = mat_reader_factory(file_name, appendmat, **kwargs)
   File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/scipy/io/matlab/mio.py", line 65, in mat_reader_factory
   raise NotImplementedError('Please use HDF reader for matlab v7.3 files')
   NotImplementedError: Please use HDF reader for matlab v7.3 files

save('output.mat', 'fg_classified', 'classification', '-v7.3');

import mat73
data_dict = mat73.loadmat('data.mat')

import h5py
f = h5py.File('http.mat', 'r')
print(f.keys()) # <KeysViewHDF5 ['X', 'y' ]>
   print(f['X'][:])

Suggestion : 4

1 week ago save('test.mat', '-v7') Use the NumPy Module to Read mat Files in Python. It is discussed earlier how we cannot open files in MATLAB 7.3 using the scipy.io module in Python. It is worth noting that files in version 7.3 and above are hdf5 datasets, which means we can open them using the NumPy library. For this method to work, the h5py module needs to be installed, which requires … , These files can be read in Python using, for instance, the PyTables or h5py package. Reading Matlab structures in mat files does not seem supported at this point. Perhaps you could use Octave to re-save using the -vX flag. , 1 day ago Use the NumPy Module to Read mat Files in Python; Use the mat4py Module to Read mat Files in Python; Use the matlab.engine Module to Read mat Files in Python. MATLAB is a programming platform that is widely used these days for numerical computation, statistical analysis, and generating algorithms. It is a very flexible language and allows us to ... , 1 day ago By default, Python is not capable of reading .mat files. We need to import a library that knows how to handle the file format.

load digitStruct.mat
for i = 1: length(digitStruct) im = imread([digitStruct(i).name]);
for j = 1: length(digitStruct(i).bbox)[height, width] = size(im);
aa = max(digitStruct(i).bbox(j).top + 1, 1);
bb = min(digitStruct(i).bbox(j).top + digitStruct(i).bbox(j).height, height);
cc = max(digitStruct(i).bbox(j).left + 1, 1);
dd = min(digitStruct(i).bbox(j).left + digitStruct(i).bbox(j).width, width);
imshow(im(aa: bb, cc: dd,: ));
fprintf('%d\n', digitStruct(i).bbox(j).label);
pause;
end end