htk --> nwb conversion

[jthermiz]

@jihyun.bak@gmail.com @VBaratham I looked for an existing nwb from htk and I couldn't find one. Does one exist?

I also tried to create one, but I ran into a roadblock. The NWBBuilder requires a MetadataManager object, but I couldn't find how to create one for an htk dataset. Am I missing something trivial?

[jihyunbak]

Hi @jthermiz, could you try running scripts/generate_nwb.py, replacing with the line that has use_htk=True option in the build() step?

[jthermiz]

@jihyunbak I did notice that keyword agrument and set it to True, but the error happens before I call nwb_bulder.build. The constructor NWBBuilder fails bc I'm not feeding a a required keyword agrument, nwb_metadata: MetadataManager. Here's my test case and the error message that's thrown.

Should we modify the NWBBuilder to make nwb_metadata an optional arg or have an use_htk argument for nwb_builder?

def test_build_nwb_case3_htk(self):
        ''' build NWB but do not write file to disk '''
        animal_name = 'R56'
        block = 'B13'
        block_name = '{}_{}'.format(animal_name, block)

        # create a builder for the block
        nwb_builder = NWBBuilder( # <------ Error happens here!
                        animal_name=animal_name,
                        block=block,
                        data_path=self.data_path,
                        out_path=self.out_path
                        )
        # build the NWB file content
        nwb_content = nwb_builder.build(use_htk=True, process_stim=False)

Error Message

Traceback (most recent call last): File "/home/jhermiz/software/nsds_lab_to_nwb/tests/test_build_nwb.py", line 76, in test_build_nwb_case3_htk nwb_builder = NWBBuilder( TypeError: init() missing 1 required positional argument: 'nwb_metadata'

[jihyunbak]

Hi John, the metadata is actually essential for the builder, so we need it for an end-to-end test. Can you add a few lines that creates nwb_metadata and pass it to the builder? Maybe something like this...

    def test_build_nwb_case3_old_htk(self):
        ''' build NWB but do not write file to disk '''
        animal_name = 'R56'
        block = 'B13'
        block_name = '{}_{}'.format(animal_name, block)
        # link to metadata files
        block_metadata_path = os.path.join(PWD, f'../yaml/{animal_name}/{animal_name}_{block}.yaml')
        library_path = os.path.join(USER_HOME, 'Src/NSDSLab-NWB-metadata/')
        # collect metadata needed to build the NWB file
        nwb_metadata = MetadataManager(block_name=block_name,
                                       block_metadata_path=block_metadata_path,
                                       library_path=library_path)
        # create a builder for the block
        nwb_builder = NWBBuilder(
                        animal_name=animal_name,
                        block=block,
                        data_path=self.data_path,
                        out_path=self.out_path,
                        nwb_metadata=nwb_metadata
                        )
        # build the NWB file content
        nwb_content = nwb_builder.build()

Note that block_name is a new optional input to MetadataManager, required for the new pipeline (the old pipeline will also accept the input but ignore it).