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registering new actions #63
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Thanks for reporting this @mariapfj Will push a fix tomorrow morning. The problem is that the widgets part is not tested because it requires user input, so there was probably an unspotted naming issue |
side note: tried running kilosort on the registered (no depth) data, which failed. Pasting the entire error below as there's a couple of things that might need debugging (dubious ownership?) Spike sorting with kilosort2 using installed sorter
Usage: which [options] [--] COMMAND [...] --version, -[vV] Print version and exit successfully. Recommended use is to write the output of (alias; declare -f) to standard If the options --read-alias and/or --read-functions are specified then the Report bugs to [email protected]. Spike sorting failed. You can inspect the runtime trace in /projects/ec109/maria/novel-env-nwb/actions/158-290224-1/data/spikeinterface/kilosort2/spikesorting/spikeinterface_log.json. During handling of the above exception, another exception occurred: Traceback (most recent call last): Spike sorting error trace: Spike sorting failed. You can inspect the runtime trace in /projects/ec109/maria/novel-env-nwb/actions/158-290224-1/data/spikeinterface/kilosort2/spikesorting/spikeinterface_log.json. |
The registration is fixed on Educloud. To run KS2, you need to run this command (once):
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@mariapfj can you confirm this is fixed? |
@alejoe91 the cinpla kernel is back to crashing every time we run a simple command, if you sort this i'll get right to testing out the registration |
Hey, I can't access educloud at the moment..what is the error? still some permission issues? |
the cinpla kernel crashes when running any cell, even a simple print() function. we've had this issue previously when you were just setting up the kernel, but not sure if it's a permission error or something else |
we've also had issues simply logging onto educloud on demand this week, not sure if that's connected in any way |
hold up I found it: |
thanks, I'll check |
@lepmik did you modify the environment? Can you give group permissions? |
Same error on my side |
Sorry, I forgot... Should work now |
seems like its partly working now, was able to register a surgery and adjustment, but got an error when registering a recording specifically when I wanted to register the depth/adjustment (works fine without), see error below. AttributeError Traceback (most recent call last) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/widgets/register.py:104, in register_openephys_view..on_register(change) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/register.py:142, in register_openephys_recording(project, action_id, openephys_path, probe_path, depth, overwrite, include_events, entity_id, user, session, location, message, tags, delete_raw_data, correct_depth_answer, register_depth) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/utils.py:132, in register_depth(project, action, depth, answer, overwrite) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/utils.py:118, in get_depth_from_adjustment(project, action, entity_id) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/utils.py:118, in get_depth_from_adjustment..(x) File /fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/utils.py:50, in deltadate(adjustdate, regdate) AttributeError: type object 'datetime.datetime' has no attribute 'timedelta' |
Will push a fix soon! |
@mariapfj the error should be fixed and I added logs for the missing tabs! You might need to restart the kernel ;) |
Tried to register actions in educloud, but it couldn't find depth measurements (would cause issues in downstream scripts and is used to separate different experiments in the same animal). The raw data and the probe are both available in my folder, as is entity data from the nwb conversion. Surgery and adjustment folders cause issues when converting the project, but I tried copying them into the new action folder just in case it was able to get depth data from there (it was not). It seems to work fine when registering without depth.
I then tried to register the surgery and the entity, both giving similar error messages (see under). I've also tried converting the actions directly from exdir but unsuccessfully (with a previous version of expipe-plugin-cinpla the latter returned av error message about 'processing' not existing, but current version simply skips unsuccessful attempts). Any clue what's causing these errors?
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