error in foraging.data_to_change_detection_core #563
Description
session_id: 855711263
experiment: 856123117
(mesoscope session ; The workflow for the experiment is QC).
I get the error below when running the convert code. Any thoughts?
File "", line 2, in
ophys_data = convert_level_1_to_level_2(experiment_id, cache_dir) #, plot_roi_validation=False);
File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/ophys/io/convert_level_1_to_level_2.py", line 976, in convert_level_1_to_level_2
core_data = get_core_data(pkl, timestamps_stimulus)
File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/ophys/io/convert_level_1_to_level_2.py", line 415, in get_core_data
core_data = foraging.data_to_change_detection_core(pkl, time=timestamps_stimulus)
File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/translator/foraging/init.py", line 40, in data_to_change_detection_core
handler = ListHandler(log_messages)
File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/utilities.py", line 174, in init
super(ListHandler, self).init()
TypeError: super(type, obj): obj must be an instance or subtype of type
Activity
nickponvert commentedon May 21, 2019
@farznaj this looks like the same error you were getting after you switched to the
fix/issue533branch to try and debug #562, is this still on that same branch?farznaj commentedon May 21, 2019
@nickponvert I know... no I am not ... I'm on feature/ production
nickponvert commentedon May 21, 2019
Ok I'm going to try and reproduce it.
farznaj commentedon May 21, 2019
I am getting this error for more sessions now:
session_id: 850894918
One point that might be helpful is that this session is just fixed by LIMS folks in service now .....
what's going on? is it about pkl files?
farznaj commentedon May 21, 2019
@nickponvert Same error with two experiments (from session_id: 851428829) that had issues with motion correction, and just got fixed by LIMS people....
farznaj commentedon May 21, 2019
@jeromelecoq @nickponvert I am in a python environment, after I check out a new git branch, for the codes to take effect, do I need to restart my python session? I am just surprised that why I used to get a platform_info error on feature/production ... and a type error on fix/issue533 .... but I am not back to feature branch , however I am getting the same error as in fix branch ....
there is something, I am up to date with new git changes (did git pull very recently) ... I cant remember if the platform error was before I did git pull or after .... is there a chance that feature codes are updated to what was in fix branch, and hence I am getting a similar type of error now on feature branch?
or is it that somehow I am not running feature branch code, even though I am in it (based on git branch start indication)....
jeromelecoq commentedon May 21, 2019
Yes, I usually restart my kernel when I update a package.
You can also use the reload function
https://www.geeksforgeeks.org/reloading-modules-python/
nickponvert commentedon May 21, 2019
@farznaj that fix branch hasn't yet been merged into production analysis, so that shouldn't be the issue. Would you copy/paste the code you are running to get the error? It would be helpful for me to debug the other issue in the fix branch too
farznaj commentedon May 21, 2019
I found this that might be helpful:
https://thomas-cokelaer.info/blog/2011/09/382/
The error happens on super function below: (I've already sent the exact files).
class ListHandler(logging.Handler):
"""docstring for ListHandler."""
def init(self, log_list):
super(ListHandler, self).init()
self.log_list = log_list
farznaj commentedon May 21, 2019
thanks @jeromelecoq
@nickponvert after restarting the kernel, now the error changes back to platform_info .... the interesting thing is that all these sessions that just got fixed by lims folks (which initially had segmentation problems), are now failing due to this platform error....
farznaj commentedon May 21, 2019
@nickponvert update: after restarting the kernel, the newly fixed sessions (by lims folks) are working... the only failed sessions are the ones that I originally sent you about the platform error:
session_id:
845444695
846652517
nickponvert commentedon Jan 22, 2020
@farznaj since the feature/production_analysis branch got merged into master (master should now be the default branch for all analysis) could we re-check this issue to see if it is still a problem?