Improved conditions for closing nwb when using hdf5 backend#3150
Merged
alejoe91 merged 2 commits intoSpikeInterface:mainfrom Jul 8, 2024
Merged
Improved conditions for closing nwb when using hdf5 backend#3150alejoe91 merged 2 commits intoSpikeInterface:mainfrom
alejoe91 merged 2 commits intoSpikeInterface:mainfrom
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alejoe91
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Jul 5, 2024
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| def _close_hdf5_file(self): | ||
| has_hdf5_backend = hasattr(self, "_file") | ||
| if has_hdf5_backend: | ||
| import h5py | ||
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| main_file_id = self._file.id | ||
| open_object_ids_main = h5py.h5f.get_obj_ids(main_file_id, types=h5py.h5f.OBJ_ALL) | ||
| for object_id in open_object_ids_main: | ||
| object_name = h5py.h5i.get_name(object_id).decode("utf-8") | ||
| try: | ||
| object_id.close() | ||
| except: | ||
| import warnings | ||
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| warnings.warn(f"Error closing object {object_name}") |
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since this is the same function as the Sorting object, why not making a separate unique function?
def _close_hdf5_file(extraxctor):
has_hdf5_backend = hasattr(extraxctor, "_file")
....
then you would just call it in the __del__ with _close_hdf5_file(self)
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You are right that this repetition is unecessary but I wanted to use self, check out the latest commit. I implemented a mixing class that should hold the methods that need the state of the nwb extractor and are common to both recording and sorting.
h-mayorquin
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alejoe91
approved these changes
Jul 8, 2024
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So we have been battling this for a while. Our access pattern of nwb when using the hdf5 backend directly (instead of the pynwb API) leaves files references dangling.
When looking a this, I see that we are keeping references to some groups and datasets even after closing the main reference. I am not sure if it is the weak reference or the way we access some properties were we don't copy at read.
At some point I have to look deeply into this but meanwhile this should alleviate some of the problems. This uses the low level API of h5py to access all the references to a particular id and tries to close them when calling del. It did solve my issue that I was facing but I am too skeptical to think this is the final nail on the coffin.