Automatic insertion of pre-computed LFP data from NWB (i.e. ImportedLFP)

[pauladkisson]

I have some LFP data in an NWB file that I would like to insert into spyglass. I see that lfp/lfp_imported.py has an ImportedLFP table, but its make() method is NotImplemented.

I tried to just directly insert into ImportedLFP, but had some trouble with the intricacies of the AnalysisNwbfile.

[samuelbray32]

In case you have time to take a stab at this before we do, here's steps for using the AnalysisNwbfile table:

1. Create a file and get its path on your system

lfp_file_name = AnalysisNwbfile().create(key["nwb_file_name"])
analysis_file_abspath = AnalysisNwbfile().get_abs_path(lfp_file_name)

2. Prepare whatever data you're inserting (in this case, load in the lfp data and timestamps
3. Make the nwb objects and write them into the file

  # Create dynamic table region and electrode series, write/close file
        with pynwb.NWBHDF5IO(
            path=analysis_file_abs_path, mode="a", load_namespaces=True
        ) as io:
            nwbf = io.read()

            # get the indices of the electrodes in the electrode table
            elect_ind = get_electrode_indices(nwbf, electrode_ids)

            electrode_table_region = nwbf.create_electrode_table_region(
                elect_ind, "filtered electrode table"
            )
            es = pynwb.ecephys.ElectricalSeries(
                name="filtered data",
                data=np.empty(tuple(output_shape_list), dtype=data_dtype),
                electrodes=electrode_table_region,
                timestamps=np.empty(output_shape_list[time_axis]),
                description=description,
            )
            if data_type == "LFP":
                ecephys_module = nwbf.create_processing_module(
                    name="ecephys", description=description
                )
                ecephys_module.add(pynwb.ecephys.LFP(electrical_series=es))
            else:
                nwbf.add_scratch(es)

            io.write(nwbf)

4. during that creation note the object_id of the added nwb object

lfp_object_id = es.object_id

5. Insert an entry into the AnalysisNwbfile table

AnalysisNwbfile().add(nwb_file_name, analysis_file_name)

6. Insert into the table you're populating

ImportedLFP.insert1(
    {
        "nwb_file_name": nwb_file_name,
        ---
        ---
        ---
        "lfp_object_id" : lfp_object_id,
        "analysis_file_name" : lfp_file_name
    }

• Example Code from LFPV1.make and FirFilterParameter.filter_data_nwb