Error opening file in H5PY (File signature not found)

by

Usually the message File signature not found indicates either:

1. Your file is corrupted.

… is what I think is most likely. You said you’ve opened the files before. Maybe you forgot closing your file-handle which can corrupt the file.
Try checking the file with the HDF5 utility h5debug (available on command line if you’ve installed the hdf5 lib on your OS, check with dpkg -s libhdf5-dev on Linux).

2. The file is not in HDF5 format.

This is a known cause for your error message. But since you said you made sure, that this is the case and you’ve opened the files before, I’m giving this just for reference for others that may stumble here:

Since December 2015 (as of version 7.3), Matlab files use the HDF5 based format in their MAT-File Level 5 Containers (more doc). Earlier version MAT-files (v4 (Level 1.0), v6 and v7 to 7.2) are supported by and can be read with the scipy library:

import scipy.io
f = scipy.io.loadmat('dataset.mat')

Otherwise you may try other methods and see whether the error persists:

PyTables is an alternative to h5py and be found here.

import tables
file = tables.open_file('test.mat')

Install using

pip install tables

Python MATLAB Engine is an alternative to read MAT files, if you have matlab installed. Documentation is found here: MATLAB Engine API for Python.

import matlab.engine
mat = matlab.engine.start_matlab()
f = mat.load("dataset.mat", nargout=1)

More Related Contents:

  1. How to read a v7.3 mat file via h5py?
  2. read matlab v7.3 file into python list of numpy arrays via h5py
  3. Differences between return function in python and Matlab
  4. Need a python module for numerical and scientific computing other than NumPy and SciPy
  5. How I can convert this matlab code to python? [closed]
  6. Read .mat files in Python
  7. find length of sequences of identical values in a numpy array (run length encoding)
  8. A tool to convert MATLAB code to Python [closed]
  9. Calling MATLAB functions from python
  10. Python equivalent of MATLAB’s “ismember” function
  11. What is the equivalent of MATLAB’s repmat in NumPy
  12. pytables writes much faster than h5py. Why?
  13. MATLAB-style find() function in Python
  14. reading v 7.3 mat file in python
  15. “Converting” Numpy arrays to Matlab and vice versa
  16. Incremental writes to hdf5 with h5py
  17. Numpy loading csv TOO slow compared to Matlab
  18. Pandas can’t read hdf5 file created with h5py
  19. Performance: Matlab vs Python
  20. Selecting close matches from one array based on another reference array
  21. Why does numpy std() give a different result to matlab std()?
  22. How can I efficiently process a numpy array in blocks similar to Matlab’s blkproc (blockproc) function
  23. Input and output numpy arrays to h5py
  24. Access .mat file containing matlab classes in python
  25. What is the difference between the two ways of accessing the hdf5 group in SVHN dataset?
  26. Is MATLAB faster than Python?
  27. Procrustes Analysis with NumPy?
  28. 2D Convolution in Python similar to Matlab’s conv2
  29. Comparing Matlab and Numpy code that uses random number generation
  30. Why does numpy.histogram (Python) leave off one element as compared to hist in Matlab?

Leave a Comment