hsupipeline / convnwb Goto Github PK

Currently the function save_units saves the h5 times files adding a ch before the channel name. However, because the channel names are already chan_\d\d\d, for example, the units spike times h5 files end up saved as times_chan_chan_\d\d\d_u\d.h5.

Note - ideas for 0.2.0 that were here became a bit outdated. Closing this.

Finalizing touches for a 0.1.0 release to tag:

• re-organize module
• describe base organization
• add changelog
• tag release

There are a couple dependencies that are only used for very specific things, and could be made optional, in order to keep with tool as something lightweight / easy to install.

Dependencies to make optional:

• pynwb
• sklearn

Need to reconcile / choose a strategy between the SDB object here, and the Paths definitions currently used in Convert T3 & TH.

I noticed that while create_session_directory supports the creation of subdirectories within a session, it does not currently support the creation of nested subfolders within those subdirectories.

For example, I am trying to adapt SESSION_FOLDERS to contain 00_origiSeshs, with subfolders origSesh00 to origSesh09, and each of these subfolders should contain additional subfolders named "behavior", "neural", and "audio". The current implementation creates the origSeshXX subfolders correctly but does not create the further nested folders.

I think this could be implemented by adding at the end of the function:

for nested_subfolder in nested_subfolders:
    make_folder(recordings_path / subject / experiment / session / subdir / subfolder / nested_subfolder)

As of scipy version 1.9.0, there is a new 'keepdims' argument in scipy.stats.mode that needs to be set for future-proofing, and will start to fail in scipy version 1.11.0: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mode.html

This relates to the use of scipy.stats.mode here:
https://github.com/HSUPipeline/convnwb/blob/main/convnwb/timestamps/align.py#L168

For future scipy usage, this could be updated to:
ixis_mode = stats.mode(ixis, keepdims=True)[0][0]

Or, equivalent updates:
ixis_mode = stats.mode(ixis, keepdims=True).mode[0]
ixis_mode = stats.mode(ixis, keepdims=False).mode

Basically - the fix is easy, but need to decide whether to enforce a specific version of scipy, and/or do a version check.

ToDo's for moving to 1.0 release version:

• rename to hsntools

Post 1.0 ready:

• release on PYPI
• recreate docs