Add CellExplorerRecordingInterface

[garrettmflynn]

This PR attempts to add the CellExplorerRecordingInterface. However, an error on the standard test files blocks us from going further than the Source Data page:

Full Error

[main-process]: [2023-10-17 14:30:42,691] ERROR in app: Exception on /neuroconv/metadata [POST]
Traceback (most recent call last):
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/app.py", line 1484, in full_dispatch_request
rv = self.dispatch_request()
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/app.py", line 1469, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/flask_restx/api.py", line 404, in wrapper
resp = resource(*args, **kwargs)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/flask/views.py", line 109, in view
return current_app.ensure_sync(self.dispatch_request)(**kwargs)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/flask_restx/resource.py", line 46, in dispatch_request
resp = meth(*args, **kwargs)
File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/apis/neuroconv.py", line 77, in post
return get_metadata_schema(neuroconv_api.payload.get("source_data"), neuroconv_api.payload.get("interfaces"))
File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/manageNeuroconv/manage_neuroconv.py", line 205, in get_metadata_schema
converter = instantiate_custom_converter(source_data, interfaces)
File "/Users/garrettflynn/Documents/Github/nwb-guide/pyflask/manageNeuroconv/manage_neuroconv.py", line 168, in instantiate_custom_converter
return CustomNWBConverter(source_data)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 65, in init
self.data_interface_objects = {
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 66, in
name: data_interface(**source_data[name])
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py", line 304, in init
session_data = read_mat(filename=session_data_file_path, ignore_fields=ignore_fields)["session"]
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/pymatreader/pymatreader.py", line 87, in read_mat
mjv, _ = matfile_version(fid)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/scipy/io/matlab/_miobase.py", line 221, in matfile_version
return _get_matfile_version(fileobj)
File "/opt/anaconda3/envs/nwb-guide/lib/python3.9/site-packages/scipy/io/matlab/_miobase.py", line 243, in _get_matfile_version
maj_ind = int(tst_str[2] == b'I'[0])
IndexError: index out of range

[CodyCBakerPhD]

Weird, since that's the same one used in the tests: https://github.com/catalystneuro/neuroconv/blob/main/tests/test_on_data/test_recording_interfaces.py#L93C15-L93C15

Pinging @h-mayorquin since he put that interface together

[CodyCBakerPhD]

@h-mayorquin any ideas on this one?

[h-mayorquin]

It seems like a scipy version thing?

Which environment is used to run those tests?

[CodyCBakerPhD]

@h-mayorquin It varies by platform, for the most part is the same as NeuroConv, but in this case I assume it's the one from the following config file

https://github.com/NeurodataWithoutBorders/nwb-guide/blob/main/environments/environment-MAC.yml

[h-mayorquin]

I encountered this error locally. It seems to be a datalad / gin related thing. I just re-installed the gin data and it went away.

If you are using a similar structure for the tests as the ones in neuroconv I suggesty you renew your data from datalad. Following the instructions from the neuroconv documentation failed so I had to sort of do it manually:

(base) @h-laptop$ rm -rf ephy_testing_data/
(base) @h-laptop$ ls
behavior_testing_data  ophys_testing_data
(base) @h-laptop$ datalad clone https://gin.g-node.org/NeuralEnsemble/ephy_testing_data ephy_testing_data
CommandError: 'git -c diff.ignoreSubmodules=none cat-file blob git-annex:remote.log' failed with exitcode 128 under /home/heberto/neuroconv_testing_data/ephy_testing_data                                                                                                      
fatal: path 'remote.log' does not exist in 'git-annex'
(base) @h-laptop$ cd ephy_testing_data/
(base) @h-laptop$ datalad get .

[garrettmflynn]

@CodyCBakerPhD Just tested this and updating with datalad allows me to move forward. Looks like this'll be good then!