I have a small (< 6Mb) .hdf file (obtained from the LAADS DAAC service). I have tried pandas and h5py to open it, to no avail (code shown below). I also tested the file with:
$ h5dump -n data.hdf
h5dump error: unable to open file "data.hdf"
and
$ h5debug data.hdf
cannot open file
This would all seem to point to a corrupt file, but the weird thing is that HDF View (v2.11) has absolutely no issues opening the same file.
What is going on here?
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'
I can reproduce the error message with:
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)
With the downloaded link (a 5M file):
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
Looks like the file is HDF4, not 5.
h5fromh4 -v ../Downloads/data.hdf
makes a data.h5 file with one dataset "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">
In hdfview I see the file is HDFEOS_V2.19
With pyhdf (and relevant HDF4 libraries) I can:
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),
...
And other datasets like those listed by HDFView.