'Segment' object has no attribute 'imagesequences' (neo 0.8.0)

[dizcza]

Dear neos,

I have a problem while filtering a block with neo 0.8.0. Previously, with neo 0.7.2, I don't have such a problem. The data is resting state if it makes any sense for you.

    fpath = os.path.join(DATA_DIR, "block_rst.pkl")
    f = neo.io.PickleIO(fpath)
    block = f.read_block()
    analog_signals = block.filter(objects="AnalogSignal")

Traceback

  File "/home/ulianych/PycharmProjects/elephant/examples/granger_example.py", line 207, in granger_example_resting_state
    analog_signals = block.filter(objects="AnalogSignal")
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 426, in filter
    children.extend(self.data_children_recur)
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/block.py", line 115, in data_children_recur
    return tuple(unique_objs(super(Block, self).data_children_recur))
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 350, in data_children_recur
    self.container_children]
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 349, in <listcomp>
    childs = [list(child.data_children_recur) for child in
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 351, in data_children_recur
    return self.data_children + tuple(sum(childs, []))
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 321, in data_children
    self._data_child_containers]
  File "/home/ulianych/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/core/container.py", line 320, in <listcomp>
    childs = [list(getattr(self, attr)) for attr in
AttributeError: 'Segment' object has no attribute 'imagesequences'

[samuelgarcia]

Andrew ? any idea ?

[JuliaSprenger]

@dizcza Did you generate the file with Neo version 0.7.2 or 0.8.x?

[dizcza]

The file was generated with neo 0.7.2

[dizcza]

The reason why I used PickleIO is because NixIO threw exceptions when I tried to save it. Don't remember which exceptions they were and I've not checked if NixIO is improved since then.

[apdavison]

We could in principle handle this, but PickleIO is not expected to work across different versions, and I don't think we should encourage its use.

The docstring for PickleIO says:

"Note that files in this format may not be readable if using a different version
of Neo to that used to create the file. It should therefore not be used for
long-term storage, but rather for intermediate results in a pipeline."

Having said that, if you have a lot of 0.7.2 files in this format @dizcza we could provide a temporary solution to migrate them to 0.8.0. Please let us know.

[dizcza]

I would like to see a version control check while loading a file in neo using a file format that is not cross-version compatible.
If the current version of neo does not match with the neo version of the file I'm loading, show a warning.
In particular for PickleIO.

[apdavison]

That's a good idea. I've created a ticket: #856