fixed a bug in loading hd5py data

[dizcza]

The code to reproduce the bug:

import neo

# curl https://web.gin.g-node.org/INM-6/elephant-data/raw/master/dataset-1/dataset-1.h5 --output dataset-1.h5 --location
hdf5neo = neo.io.NeoHdf5IO("dataset-1.h5")
block = hdf5neo.read_block()

dataset.value threw a deprecation warning in h5py v2.x and became an error in v3.0.0. Now it works for both h5py v2 and v3.

Deprecation warning in v2.x:

.../site-packages/h5py/_hl/dataset.py:313: H5pyDeprecationWarning: 
"dataset.value has been deprecated. Use dataset[()] instead. Use dataset[()] instead.", H5pyDeprecationWarning)

Fixed error in v3.0.0

      1 hdf5neo = neo.io.NeoHdf5IO("dataset-1.h5")
----> 2 block = hdf5neo.read_block()

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in read_block(self, lazy, **kargs)
     87         """
     88         assert not lazy, 'Do not support lazy'
---> 89         return self.read_all_blocks(lazy=lazy)[0]
     90 
     91     def _read_block(self, node):

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in read_all_blocks(self, lazy, merge_singles, **kargs)
     79         for name, node in self._data.items():
     80             if "Block" in name:
---> 81                 blocks.append(self._read_block(node))
     82         return blocks
     83 

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in _read_block(self, node)
     97         for name, child_node in node['segments'].items():
     98             if "Segment" in name:
---> 99                 block.segments.append(self._read_segment(child_node, parent=block))
    100 
    101         if len(node['recordingchannelgroups']) > 0:

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in _read_segment(self, node, parent)
    172         for name, child_node in node['spiketrains'].items():
    173             if "SpikeTrain" in name:
--> 174                 spiketrains.append(self._read_spiketrain(child_node, parent=segment))
    175         segment.spiketrains = spiketrains
    176 

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in _read_spiketrain(self, node, parent)
    203     def _read_spiketrain(self, node, parent):
    204         attributes = self._get_standard_attributes(node)
--> 205         t_start = self._get_quantity(node["t_start"])
    206         t_stop = self._get_quantity(node["t_stop"])
    207         # todo: handle sampling_rate, waveforms, left_sweep

~/anaconda3/envs/temp/lib/python3.6/site-packages/neo/io/hdf5io.py in _get_quantity(self, node)
    312 
    313     def _get_quantity(self, node):
--> 314         value = node.value
    315         unit_str = [x for x in node.attrs.keys() if "unit" in x][0].split("__")[1]
    316         units = getattr(pq, unit_str)

AttributeError: 'Dataset' object has no attribute 'value'

[JuliaSprenger]

Hi @dizcza! Thanks for fixing the master branch.