Geek Answers Handbook

An hfpy HDF5 file cannot be opened by h5py

I created the HDF5 file, apparently without problems, on Ubuntu 12.04 (32-bit), using Anaconda as a distribution and writing Python in ipython laptops. The main data is all numpy arrays. For example,

import numpy as np import h5py f = h5py.File('myfile.hdf5','w') group = f.create_group('a_group') group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')

If I try to open this file from a new iypthon laptop, I get an error message:

 f = h5py.File('myfile.hdf5', "r") --------------------------------------------------------------------------- IOError Traceback (most recent call last) <ipython-input-4-b64ac5089cd4> in <module>() ----> 1 f = h5py.File(file_name, "r") /home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/files.pyc in __init__(self, name, mode, driver, libver, userblock_size, **kwds) 220 221 fapl = make_fapl(driver, libver, **kwds) --> 222 fid = make_fid(name, mode, userblock_size, fapl) 223 224 Group.__init__(self, fid) /home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/files.pyc in make_fid(name, mode, userblock_size, fapl, fcpl) 77 78 if mode == 'r': ---> 79 fid = h5f.open(name, h5f.ACC_RDONLY, fapl=fapl) 80 elif mode == 'r+': 81 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) /home/sarah/anaconda/lib/python2.7/site-packages/h5py/h5f.so in h5py.h5f.open (h5py/h5f.c:1741)() IOError: Unable to open file (Unable to find a valid file signature)

Can you tell me what the missing file signature is? Did I miss something when I created the file?

+13
python numpy io hdf5 h5py
source share
2 answers

Since we solved the problem in the comments on my question, I write the results here to mark it as resolved.

The main problem was that I forgot to close the file after it was created. There would be two simple options:

 import numpy as np import h5py f = h5py.File('myfile.hdf5','w') group = f.create_group('a_group') group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip') f.close()

or, my favorite, because the file closes automatically:

 import numpy as np import h5py with h5py.File('myfile.hdf5','w') as f: group = f.create_group('a_group') group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')
+17
source share

I worked with https://github.com/matterport/Mask_RCNN and gave the same error:

  Traceback (most recent call last): File "detection.py", line 42, in <module> model.load_weights(model_path, by_name=True) File "/home/michael/Bachelor/important/Cable-detection/Mask_RCNN-2.1/samples/cable/mrcnn/model.py", line 2131, in load_weights f = h5py.File(filepath, mode='r') File "/home/michael/.local/lib/python3.6/site-packages/h5py/_hl/files.py", line 271, in __init__ fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr) File "/home/michael/.local/lib/python3.6/site-packages/h5py/_hl/files.py", line 101, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-s_7obrrg-build/h5py/_objects.c:2840) File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-s_7obrrg-build/h5py/_objects.c:2798) File "h5py/h5f.pyx", line 78, in h5py.h5f.open (/tmp/pip-s_7obrrg-build/h5py/h5f.c:2117) OSError: Unable to open file (Addr overflow, addr = 800, size=8336, eoa=2144) HDF5: infinite loop closing library D,T,F,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

The solution above worked for me too. I accidentally interrupted the workout, so the .hdf5 file .hdf5 not closed properly and could not be opened after that.

0
source share

More articles:


All Articles