multielectrode_grasp/code/convert_to_nix.py

"""
This script loads a complete session in the blackrock format and converts it to a single nix file
"""
import os

import neo
from neo.test.tools import (assert_same_sub_schema,
                            assert_same_annotations,
                            assert_same_array_annotations)
from reachgraspio import reachgraspio


# Choose which session you want to convert into a nix file
# session = "l101210-001"
session = "i140703-001"

dataset_dir = '../datasets'
session_path = f'{dataset_dir}/{session}'

##### LOAD BLACKROCK FILES ############
session = reachgraspio.ReachGraspIO(
    filename=session_path,
    odml_directory=dataset_dir,
    verbose=False)

block = session.read_block(lazy=False, load_waveforms=True)


##### SAVE NIX FILE ###################
nix_filename = session_path + '.nix'
if os.path.exists(nix_filename):
    print('Nix file already exists and will not be overwritten.')
else:
    with neo.NixIO(nix_filename) as io:
        print(f'Saving nix file at {nix_filename}')
        io.write_block(block)

##### VALIDATION OF FILE CONTENT ######
with neo.NixIO(nix_filename, mode='ro') as io:
    blocks = io.read_all_blocks()
    assert len(blocks) == 1
    block_new = blocks[0]

    for seg_old, seg_new in zip(block.segments, block_new.segments):
        for anasig_old, anasig_new in zip(seg_old.analogsignals, seg_new.analogsignals):
            # ignoring differences in the file_origin attribute
            anasig_old.file_origin = anasig_new.file_origin
            # ignoring nix_name annotation generated by nix file
            anasig_new.annotations.pop('nix_name')

            assert_same_sub_schema(anasig_old, anasig_new)
            assert_same_annotations(anasig_old, anasig_new)
            assert_same_array_annotations(anasig_old, anasig_new)
            del anasig_old
        print(f'AnalogSignals are equivalent.')
        
        for st_old, st_new in zip(seg_old.spiketrains, seg_new.spiketrains):
            # ignoring differences in the file_origin attribute
            st_old.file_origin = st_new.file_origin
            # ignoring nix_name annotation generated by nix file
            st_new.annotations.pop('nix_name')

            assert_same_sub_schema(st_old, st_new)
            assert_same_annotations(st_old, st_new)
            assert_same_array_annotations(st_old, st_new)
            del st_old
        print(f'Spiketrains are equivalent.')
        
        for ev_old, ev_new in zip(seg_old.events, seg_new.events):
            # ignoring differences in the file_origin attribute
            ev_old.file_origin = ev_new.file_origin
            # ignoring nix_name annotation generated by nix file
            ev_new.annotations.pop('nix_name')
            # ignore list-array type changes
            if 'color_codes' in ev_old.annotations:
                ev_old.annotations['color_codes'] = list(ev_old.annotations['color_codes'])

            assert_same_sub_schema(ev_old, ev_new)
            assert_same_annotations(ev_old, ev_new)
            assert_same_array_annotations(ev_old, ev_new)
            del ev_old
        print(f'Events are equivalent.')
        
        for ep_old, ep_new in zip(seg_old.epochs, seg_new.epochs):
            # ignoring differences in the file_origin attribute
            ep_old.file_origin = ep_new.file_origin
            # ignoring nix_name annotation generated by nix file
            ep_new.annotations.pop('nix_name')

            assert_same_sub_schema(ep_old, ep_new)
            assert_same_annotations(ep_old, ep_new)
            assert_same_array_annotations(ep_old, ep_new)
            del ep_old
        print(f'Epochs are equivalent.')