Method for extract metada from nwb to make our round trip testing more complete

[h-mayorquin]

Right now, our ecephys tests with data, the ones in test_gin_ecephys mainly compare the traces as written from the recording extractors.

nwb-conversion-tools/tests/test_on_data/test_gin_ecephys.py

Lines 197 to 220 in a875b40

	check_recordings_equal(RX1=recording, RX2=nwb_recording, check_times=False, return_scaled=False)
	check_recordings_equal(RX1=recording, RX2=nwb_recording, check_times=False, return_scaled=True)
	# Technically, check_recordings_equal only tests a snippet of data. Above tests are for metadata mostly.
	# For GIN test data, sizes should be OK to load all into RAM even on CI
	npt.assert_array_equal(
	x=recording.get_traces(return_scaled=False), y=nwb_recording.get_traces(return_scaled=False)
	)
	else:
	# Spikeinterface behavior is to load the electrode table channel_name property as a channel_id
	nwb_recording = NwbRecordingExtractorSI(file_path=nwbfile_path)
	if "channel_name" in recording.get_property_keys():
	renamed_channel_ids = recording.get_property("channel_name")
	else:
	renamed_channel_ids = recording.get_channel_ids().astype("str")
	recording = recording.channel_slice(
	channel_ids=recording.get_channel_ids(), renamed_channel_ids=renamed_channel_ids
	)
	check_recordings_equal_si(RX1=recording, RX2=nwb_recording, return_scaled=False)
	# This can only be tested if both gain and offest are present
	if recording.has_scaled_traces() and nwb_recording.has_scaled_traces():
	check_recordings_equal_si(RX1=recording, RX2=nwb_recording, return_scaled=True)

Whereas the corresponding tests for sorting extractor mainly compares the output of the sorting object:

nwb-conversion-tools/tests/test_on_data/test_gin_ecephys.py

Lines 284 to 289 in a875b40

	sf = sorting.get_sampling_frequency()
	if sf is None: # need to set dummy sampling frequency since no associated acquisition in file
	sf = 30000
	sorting.set_sampling_frequency(sf)
	nwb_sorting = NwbSortingExtractor(file_path=nwbfile_path, sampling_frequency=sf)
	check_sortings_equal(SX1=sorting, SX2=nwb_sorting)

That is, of the components of the nwb_file, our test cover mostly the effects of the recording extractors and sorters ignoring the metadata.

I am wondering on whether it would be a good idea to create a method get_metadata for nwb files so we can also compare the get_metadata method of the interface with the data as it is written in the nwb file.

Does this makes sense? is there some obvious hurdle that I am not seeing or something that I am missing?

[bendichter]

are you able to follow the form here?

[CodyCBakerPhD]

(a) Yes, we need many more tests for checking metadata, that is true. Follow Bens established format for the Neuralynx/Neuroscope.

(b) Getting a metadata dict that matches our schema but constructed from a written NWBFile could indeed be nice, but I wouldn't put it at a high priority. For the tests Ben mentioned, it's so few items that doing manual direct assertions are fine for now.

(c) Why is this issue in the buzsaki repo? Let me see if I can do a fancy issue transfer.

[h-mayorquin]

are you able to follow the form here?

Yes, that's the one I am trying to follow right now.
I am thinking thought that the tests that we are adding over there test that the functions produce the right output.

The idea that I have on mind is to make the round-trip more complete by testing that the metadata is written as expected.

I don't know why I opened this on Buzsaki. A lapse, thanks @CodyCBakerPhD for writing in the right place.

[bendichter]

The problem is that metadata is pretty unique per input data type so it's tough to put in one big parallel structure