Error when reading NWB file in MatNWB, but not PyNWB

[amadaabrego]

Hi!

I have a dataset from a collaborator in NWB format. I can upload it using pynwb, but when I try to do it in matlab, I get the following error

read_nwbfile = nwbRead('sub-TA525_task-places_ieeg.nwb')

Error using types.core.ElectricalSeries/validate_data_unit_
Unable to set the 'data_unit' property of class 'ElectricalSeries' because it is read-only.

Error in types.core.TimeSeries/set.data_unit (line 94)
obj.data_unit = obj.validate_data_unit(val);

Error in types.core.TimeSeries (line 61)
obj.data_unit = p.Results.data_unit;

Error in types.core.ElectricalSeries (line 22)
obj = [email protected](varargin{:});

Error in io.parseGroup (line 85)
parsed = eval([Type.typename '(kwargs{:})']);

Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);

Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);

Error in nwbRead (line 79)
nwb = io.parseGroup(filename, h5info(filename), Blacklist);

For what it's worth, the dataset was written in Matlab. And it was generated years ago. Collaborator never had any issues with it, so they think it might be something in a newer update.

I'm not sure what is the best way to address this. I have gone through all the functions, and have not found a way to fix it. Any ideas?

[CodyCBakerPhD]

attn @lawrence-mbf or @bendichter

[lawrence-mbf]

@amadaabrego what is the version of the schema for the file? You can run util.getSchemaVersion(<filename>) to get a file's schema version. FWIW, ElectricalSeries in 2.6.0 does not have the data_unit validation defined, just a default setter in the constructor.

[ehennestad]

If you change the commit you are using, you might also need to run generateCore again before opening the file.

[ehennestad]

@amadaabrego Just to confirm, the value for the unit is different than volts, right? Is it a question of casing being different, or is it another unit altogether like millivolts?

[amadaabrego]

@ehennestad Our collaborator shared with me the script they use to make the NWB files - our lab is going to adapt it, so I'm using that to base ours, but I'm trying to get familiarized with the dataset right now. In their script, they have their units as 'V'. I'm not sure if that might be the issue

I did not have any issues with reading the file into Python. I was able to extract the data matrix and everything. And, I'm trying to make this work with Matlab because we will be using Brainstorm for some ECoG data visualization

[ehennestad]

Yes, the issue is setting the value to "V".

The NWB schemas specify that the unit for ElectricalSeries data should be "volts".
https://github.com/NeurodataWithoutBorders/nwb-schema/blob/d65d42257003543c569ea7ac0cd6d7aee01c88d6/core/nwb.ecephys.yaml#L35-L42

I was using matnwb and I realised that I could set the unit to whatever and I therefore proposed a fix to make this property read-only in matnwb to adhere to the schema. Apparently such a limitation does not exist in pynwb.

Maybe @oruebel @rly or @bendichter could comment on this, whether this is a bug in pynwb or if I am misunderstanding the schema definition?

[ehennestad]

@amadaabrego

I would suggest that you do not fill in the value of units, i.e skip setting unit to "V". It should by default be set to volts. If you still need to read in files in MATLAB which are created earlier with python and has the unit set to "V", let me know, and I will propose a fix where instead of erroring, there will be a warning instead.

[ehennestad]

@ehennestad if there is a better way to resolve this, that would be good too.

@lawrence-mbf
It might be better to throw a warning rather than an error.

And I guess it is best to throw a warning and keep the value from the file, not enforce volts.

Another question is then whether this deviation from schema is also present in pynwb?

[oruebel]

Another question is then whether this deviation from schema is also present in pynwb?

In PyNWB, the unit for ElectricalSeries is set to a fixed value here:

https://github.com/NeurodataWithoutBorders/pynwb/blob/65b2a7d0ea642132a7a5fcb5a5199b675f092e0b/src/pynwb/ecephys.py#L93

[ehennestad]

This makes it fixed in the constructor, but it does not stop anyone from overwriting the value after an electrical series is created, like in the example below:

raw_data = np.random.randn(50, 12)
raw_electrical_series = ElectricalSeries(
    name="ElectricalSeries",
    data=raw_data,
    electrodes=all_table_region,
    starting_time=0.0,  # timestamp of the first sample in seconds relative to the session start time
    rate=20000.0,  # in Hz
)

# Set the unit for the electrical series
raw_electrical_series.unit = "V"