Python OSError: Unable to open file (File signature not found) – ( happens a lot with H5PY and Matlab ) is an error which occurs when you try using H5PY to open a MATLAB HDF5 file in python.
Today, I will explain in detail why this error is happening and how to fix it in the most efficient way possible.
Exploring the Python OSError: Unable to open file (File signature not found) – ( happens a lot with H5PY and Matlab )
This is an error which occurs when you try using H5PY to open a MATLAB HDF5 file in python.
Beware of mixing between different errors. Please make sure you are dealing with the same error.
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OSError: Unable to open file (File signature not found)
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I hope one of the methods bellow will help you solve the problem and get rid of the error for good.
Solution 1 : Use PyTables instead of using h5py
The first solution is to use PyTables as an alternative to h5py. PyTables is a package for managing hierarchical datasets and designed to efficiently cope with extremely large amounts of data.
You can use pip to install it
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pip install tables
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As for your code, instead of importing like this ( when using h5py )
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import h5py as h5py
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You can use this to import PyTables
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import tables
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Now, you do not have to use two lines in order to open the HDF5 file
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var='mydata.mat'
f=h5py.File(var, 'r')
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You can just use this line instead
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file = tables.open_file('mydata.mat')
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I hope this method solved your problem, thank you for reading this section, you can try the method bellow if you do not wish to use PyTables.
Solution 2 : Check if the HDF5 file is corrupted and correctly save an .h5 file in MATLAB
This method has two sections, in the first one I am going to talk about how you should save your .h5 file to avoid it being corrupted and in the second one we will talk about how you can check if your HDF5 file is corrupted or not.
First, let us talk about the best way to save an .h5 file, let us say you want to save a file named myfile.h5.
Select the checkbox next to myfile.h5 and then click download.
This method is way better than navigating to the file and right clicking on it and saving the link as …
That is one of the most popular causes of corrupted HDF5 files.
Second, here is how you can check if your HDF5 file is corrupted or not corrupted.
There is a HDF5 utility called h5debug. h5debug debugs existing HDF5 files at a low level
You can use the utility like this
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h5debug myfile.h5
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You cannot use the utility if you have not installed the hdf5 library on your system.
I hope the fixes above fixed your problem. Thank you so much for reading this entire blog post.
Summing-up :
This is the end of our post, I hope this has been helpful and helped you solve the error or at least pointed you in the right direction.
Thank you for reading my blog post to the end, If you want to learn more about the Python programming language, check out the official Python Documentation : https://docs.python.org/3/