Serializing experiment objects

[benweinberg89]

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PLATFORM (Mac, PC, Linux, other):

Mac

OPERATING SYSTEM (eg OSX 10.7, Windows 8.1):

OS 12.5

SEVERITY (Critical? Major? Minor? Enhancement?):

Enhancement

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  I was wondering if there was a good way to serialize Experiment objects so that can be saved and re-opened later on (to avoid the slow import process). I have been trying to pickle them. Although I seemingly re-open them, something seems to happen after I apply() gaussian or threshold operations to them. I get an error that channels can't be found anymore even though I can see them before the operation using Experiment.channels.

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[benweinberg89]

This is what appears in the channels variable after trying to apply a 2d gaussian filter:
'Traceback (most recent call last):\n File "/Users/benweinberg/.vscode/extensions/ms-python.python-2023.4.0/pythonFiles/lib/python/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_resolver.py", line 189, in _get_py_dictionary\n attr = getattr(var, name)\n File "/Users/benweinberg/opt/anaconda3/envs/cf/lib/python3.8/site-packages/cytoflow/experiment.py", line 197, in _get_channels\n return sorted([x for x in self.data if self.metadata[x]['type'] == "channel"])\n File "/Users/benweinberg/opt/anaconda3/envs/cf/lib/python3.8/site-packages/cytoflow/experiment.py", line 197, in \n return sorted([x for x in self.data if self.metadata[x]['type'] == "channel"])\nKeyError: 'FSC-A'\n'

[CaRniFeXeR]

Can you maybe provide a jupyter notebook showing this problem?

[benweinberg89]

@CaRniFeXeR It will take me some time to do that. Perhaps I will try serializing some of the kiani data. Serializing could help address Issue #349.