trouble loading table with different shapes from h5py in pytables

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Mark Mikofski

Aug 7, 2018, 6:28:16 PM8/7/18
to pytables-users

I apologize if this has been answered previously. I have created an h5 table using h5py:

import numpy as np
import pvlib
import h5py

# create some data
= pvlib.pvsystem.singlediode(6.1, 1.2e-7, 0.012, 123, 1.23*60*0.026, 100)
= pvlib.pvsystem.singlediode(5.1, 1.2e-7, 0.012, 123, 1.23*60*0.026, 100)

# set the dtypes to use as a structured array
= np.dtype([
('i_l', float), ('i_0', float), ('r_s', float), ('r_sh', float), ('nNsVth', float),
('i_sc', float), ('v_oc', float), ('i_mp', float), ('v_mp', float),
('i', float, (1,100)), ('v', float, (1, 100))

# store the data in structured array, note that the IV curve is a nested
= np.array([
(6.1, 1.2e-7, 0.012, 123, 1.23*60*0.026,
['i_sc'], x['v_oc'], x['i_mp'], x['v_mp'], x['i'], x['v']),
(5.1, 1.2e-7, 0.012, 123, 1.23*60*0.026,
['i_sc'], y['v_oc'], y['i_mp'], y['v_mp'], y['i'], y['v'])
], my_dtype)

# pretend that this is a grid of IV curves for matrix of (E, T)
= np.copy(my_data)
# reshape my_data and your_data from (2,) to (1, 2),
# and concatentate to make fake grid
= np.concatenate([my_data.reshape(1,2), your_data.reshape(1,2)], axis=0)

# output to a file
with h5py.File('THIS_IS_A_TEST_FILE.H5', 'w') as f:
['data'] = all_data  # key "data" is arbitrary, choose as many groups as you need

I can reload the table in h5py and using hfdview or h5ls, but if I try to open the table in PyTables or ViTables, I get this error:

>>> f = tables.open_file('THIS_IS_A_TEST_FILE.H5')

File(filename=THIS_IS_A_TEST_FILE.H5, title='', mode='r', root_uep='/', filters=Filters(complevel=0, shuffle=False, bitshuffle=False, fletcher32=False, least_significant_digit=None))
/ (RootGroup) ''
/data (Table(2,)) ''
  description := {
  "i_l": Float64Col(shape=(), dflt=0.0, pos=0),
  "i_0": Float64Col(shape=(), dflt=0.0, pos=1),
  "r_s": Float64Col(shape=(), dflt=0.0, pos=2),
  "r_sh": Float64Col(shape=(), dflt=0.0, pos=3),
  "nNsVth": Float64Col(shape=(), dflt=0.0, pos=4),
  "i_sc": Float64Col(shape=(), dflt=0.0, pos=5),
  "v_oc": Float64Col(shape=(), dflt=0.0, pos=6),
  "i_mp": Float64Col(shape=(), dflt=0.0, pos=7),
  "v_mp": Float64Col(shape=(), dflt=0.0, pos=8),
  "i": Float64Col(shape=(1, 100), dflt=0.0, pos=9),
  "v": Float64Col(shape=(1, 100), dflt=0.0, pos=10)}
  byteorder := 'little'
  chunkshape := (39,)

>>> g = f.get_node('/data')

>>> g[0]

HDF5ExtError                              Traceback (most recent call last)
<ipython-input-8-73ec0726ff88> in <module>()
----> 1 g[0]

~\AppData\Local\Continuum\miniconda3\envs\py36\lib\site-packages\tables\ in __getitem__(self, key)
   2077                 key += self.nrows
   2078             (start, stop, step) = self._process_range(key, key + 1, 1)
-> 2079             return, stop, step)[0]
   2080         elif isinstance(key, slice):
   2081             (start, stop, step) = self._process_range(

~\AppData\Local\Continuum\miniconda3\envs\py36\lib\site-packages\tables\ in read(self, start, stop, step, field, out)
   1932                                                 warn_negstep=False)
-> 1934         arr = self._read(start, stop, step, field, out)
   1935         return internal_to_flavor(arr, self.flavor)

~\AppData\Local\Continuum\miniconda3\envs\py36\lib\site-packages\tables\ in _read(self, start, stop, step, field, out)
   1846             # This optimization works three times faster than
   1847             # the row._fill_col method (up to 170 MB/s on a pentium IV @ 2GHz)
-> 1848             self._read_records(start, stop - start, result)
   1849         # Warning!: _read_field_name should not be used until
   1850         # H5TBread_fields_name in tableextension will be finished

tables\tableextension.pyx in tables.tableextension.Table._read_records()

HDF5ExtError: HDF5 error back trace

  File "C:\ci\hdf5_1525883595717\work\src\H5Dio.c", line 216, in H5Dread
    can't read data
  File "C:\ci\hdf5_1525883595717\work\src\H5Dio.c", line 471, in H5D__read
    src and dest data spaces have different sizes

End of HDF5 error back trace

Problems reading records.

Curiously, if I index at the g[1] it returns that row. Also, it doesn't get the shape correct, it should be (2, 2), and so indexing by slice in PyTables also doesn't work.

>>> g.shape

If I open the file in vitables-2 or 3 it gives this message, which is irrelevant, since it's uncompressed, and if I change it to gzip, it says the same thing, even though zlib is already installed.

Error: problems reading records. The dataset seems to be compressed with the None library. Check that it is installed in your system, please.

ViTables properties shows the field names, their types and shapes correctly, but not the table size, which it says is (2, ) not surprising since it uses PyTables under the hood.

I have seen another similar post here "error selecting rows by list of indices in multidimensional array" from 2014 with @scopatz but it didn't seem exactly the same, and it was so old, so I didn't tag it.

I also search pytables issues on GitHub but I didn't find any similar, and didn't want to spam that if this is not a real issue.

Has anyone come across this issue or similar one? AFAICT HDF5 should handle multiple dimension tables with compound fields OK, and h5py, hdfview, and h5ls all can read them OK, but PyTables and ViTables can't. Why?


Francesc Alted

Aug 9, 2018, 2:44:26 AM8/9/18
to, pytables-users
Hi Mark,

Yes, multimensional tables are not supported in PyTables (only multimensional columns are).  Probably an `NotImplementedError` should be raised in this case.  Could you open a ticket please?


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Francesc Alted

Mark Mikofski

Aug 10, 2018, 1:53:59 PM8/10/18
to pytables-users
Hi Francesc, I've posted the issue here:

I've tried to follow the code base, to File class which is called by open_file, but no further, and it may some time before I can trouble shoot this more, but I will contribute what I can.

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