OSError: Невозможно открыть файл (не найдена подпись файла) / Обратное завершение ошибки HDF5

Question

У меня небольшой (<6Mb) файл <code>.hdf (полученный из сервиса LAADS DAA C). Я пытался pandas и h5py открыть его, но безрезультатно (код показан ниже). Я также проверил файл с:

$ h5dump -n data.hdf
h5dump error: unable to open file "data.hdf"

и

$ h5debug data.hdf  
cannot open file

Казалось бы, все это указывает на поврежденный файл, но странная вещь в том, что HDF View (v2.11) имеет абсолютно никаких проблем с открытием этого файла .

Что здесь происходит?

---

1.

import h5py
data = h5py.File(filename, 'r')

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/h5py/_hl/files.py", line 394, in __init__
    swmr=swmr)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/h5py/_hl/files.py", line 170, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 85, in h5py.h5f.open
OSError: Unable to open file (file signature not found)

2.

import pandas as pd
data = pd.io.pytables.read_hdf(filename)

Traceback (most recent call last):
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 603, in open
    self._handle = tables.open_file(self._path, self._mode, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/tables/file.py", line 320, in open_file
    return File(filename, mode, title, root_uep, filters, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/tables/file.py", line 784, in __init__
    self._g_new(filename, mode, **params)
  File "tables/hdf5extension.pyx", line 492, in tables.hdf5extension.File._g_new
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "H5F.c", line 511, in H5Fopen
    unable to open file
  File "H5Fint.c", line 1604, in H5F_open
    unable to read superblock
  File "H5Fsuper.c", line 413, in H5F__super_read
    file signature not found

End of HDF5 error back trace

Unable to open/create file 'data.hdf'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 368, in read_hdf
    store = HDFStore(path_or_buf, mode=mode, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 488, in __init__
    self.open(mode=mode, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 636, in open
    raise IOError(str(e))
OSError: HDF5 error back trace

  File "H5F.c", line 511, in H5Fopen
    unable to open file
  File "H5Fint.c", line 1604, in H5F_open
    unable to read superblock
  File "H5Fsuper.c", line 413, in H5F__super_read
    file signature not found

End of HDF5 error back trace

Unable to open/create file 'data.hdf'

3.

import pandas as pd
data = pd.HDFStore(filename, mode='r')

Traceback (most recent call last):
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 603, in open
    self._handle = tables.open_file(self._path, self._mode, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/tables/file.py", line 320, in open_file
    return File(filename, mode, title, root_uep, filters, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/tables/file.py", line 784, in __init__
    self._g_new(filename, mode, **params)
  File "tables/hdf5extension.pyx", line 492, in tables.hdf5extension.File._g_new
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "H5F.c", line 511, in H5Fopen
    unable to open file
  File "H5Fint.c", line 1604, in H5F_open
    unable to read superblock
  File "H5Fsuper.c", line 413, in H5F__super_read
    file signature not found

End of HDF5 error back trace

Unable to open/create file 'data.hdf'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 488, in __init__
    self.open(mode=mode, **kwargs)
  File "/home/gabriel/miniconda3/envs/py3/lib/python3.7/site-packages/pandas/io/pytables.py", line 636, in open
    raise IOError(str(e))
OSError: HDF5 error back trace

  File "H5F.c", line 511, in H5Fopen
    unable to open file
  File "H5Fint.c", line 1604, in H5F_open
    unable to read superblock
  File "H5Fsuper.c", line 413, in H5F__super_read
    file signature not found

End of HDF5 error back trace

Unable to open/create file 'data.hdf'

Answer 1

Я могу воспроизвести сообщение об ошибке с:

In [88]: h5py.File('echo.py','r')                                                              
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-88-4c05cde6b6ff> in <module>
----> 1 h5py.File('echo.py','r')

/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, **kwds)
    406                 fid = make_fid(name, mode, userblock_size,
    407                                fapl, fcpl=make_fcpl(track_order=track_order),
--> 408                                swmr=swmr)
    409 
    410             if isinstance(libver, tuple):

/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
    171         if swmr and swmr_support:
    172             flags |= h5f.ACC_SWMR_READ
--> 173         fid = h5f.open(name, flags, fapl=fapl)
    174     elif mode == 'r+':
    175         fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5f.pyx in h5py.h5f.open()

OSError: Unable to open file (file signature not found)

С загруженной ссылкой (файл 5M):

1614:~/mypy$ h5debug ../Downloads/data.hdf 
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 139633948224384:
  #000: ../../../src/H5F.c line 579 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: ../../../src/H5Fint.c line 1208 in H5F_open(): unable to read superblock
    major: File accessibilty
    minor: Read failed
  #002: ../../../src/H5Fsuper.c line 273 in H5F__super_read(): file signature not found
    major: File accessibilty
    minor: Not an HDF5 file
cannot open file

---

Похоже, файл HDF4, а не 5.

h5fromh4 -v ../Downloads/data.hdf 

создает файл data.h5 с одним набором данных "data"

In [3]: f = h5py.File('../Downloads/data.h5','r')                                              
In [4]: f                                                                                      
Out[4]: <HDF5 file "data.h5" (mode r+)>
In [5]: list(f.keys())                                                                         
Out[5]: ['data']
In [9]: f['data']                                                                              
Out[9]: <HDF5 dataset "data": shape (680, 451), type "<f8">

В hdfview Я вижу, что файл HDFEOS_V2.19

С pyhdf (и соответствующими HDF4 библиотеками) я могу:

In [3]: from pyhdf.SD import SD, SDC                                                           
In [5]: f = SD('../Downloads/data.hdf', SDC.READ)                                              
In [6]: f.datasets()                                                                           
Out[6]: 
{'Longitude': (('Cell_Along_Swath:mod04', 'Cell_Across_Swath:mod04'),
  (680, 451),
  5,
  0),
...

и другие наборы данных, подобные перечисленным в HDFView.