load HTK files about ecogvis HOT 14 CLOSED

def elecs_to_electrode_table(nwb_file, elecspath):
    """
    Takes an NWB file and the elecs .mat file path, loads the anatomical and
    location information for each electrode,
    and writes this information to the NWB file.
    Parameters:
    -----------
    nwbfile : object
        An NWB file object.
    elecspath : str
        Path to the TDT_elecs_all.mat file for this subject. First, second,
        and third columns of the key 'elecmatrix'
        should be x, y, and z coordinates, respectively. For the 'anatomy'
        field, second column should be the full electrode label and the
        fourth column should be the anatomical location name.
    Returns:
    --------
    nwb_file : object
        The edited NWB file with the added electrode information.
    ecog_channels : 1d array of ints
        Indices of electrodes channels that were not labeled NaN.
    """

    # Get anatomical and location information for electrodes.
    elec_mat = sio.loadmat(elecspath)
    labels = elec_mat['anatomy'][:, 1]
    location = elec_mat['anatomy'][:, 3]
    x = elec_mat['elecmatrix'][:, 0]
    y = elec_mat['elecmatrix'][:, 1]
    z = elec_mat['elecmatrix'][:, 2]

    # Get MNI warped electrode coordinates.
    try:
        elec_mat_warped = sio.loadmat(elecspath.split('.')[0] + '_warped.mat')
        x_warped = elec_mat_warped['elecmatrix'][:, 0]
        y_warped = elec_mat_warped['elecmatrix'][:, 1]
        z_warped = elec_mat_warped['elecmatrix'][:, 2]
    except FileNotFoundError:
        print('No warped electrode information found...filling with zeros.')
        x_warped = np.zeros_like(x)
        y_warped = np.zeros_like(y)
        z_warped = np.zeros_like(z)

    # Define electrode device label names.
    group_labels = []
    for current_group in labels:
        group_labels.append(current_group[0].rstrip('0123456789'))

    # Get the list of unique electrode device label names
    unique_group_indexes = np.unique(group_labels, return_index=True)[1]
    unique_group_labels = [group_labels[f] for f in
                           sorted(unique_group_indexes)]

    # Add additional columns to the electodes table.
    nwb_file.add_electrode_column('label', 'label of electrode')
    nwb_file.add_electrode_column('bad', 'electrode identified as too noisy')
    nwb_file.add_electrode_column('x_warped',
                                  'x warped onto cvs_avg35_inMNI152')
    nwb_file.add_electrode_column('y_warped',
                                  'y warped onto cvs_avg35_inMNI152')
    nwb_file.add_electrode_column('z_warped',
                                  'z warped onto cvs_avg35_inMNI152')

    for group_label in unique_group_labels:

        if group_label != 'NaN':

            # Get region name and device label for the group.
            if 'Depth' in group_label:
                group_label_split = group_label.split('Depth')
            elif 'Strip' in group_label:
                group_label_split = group_label.split('Strip')
            elif 'Grid' in group_label:
                group_label_split = group_label.split('Grid')
            elif 'Pole' in group_label:
                group_label_split = group_label.split('Pole')

            # Get general group region
            brain_area = group_label_split[0]

            # Create electrode device (same as the group).
            device = nwb_file.create_device(group_label)

            # Create electrode group with name, description, device object,
            # and general location.
            electrode_group = nwb_file.create_electrode_group(
                name='{} electrodes'.format(group_label),
                description='{}'.format(group_label),
                device=device,
                location=str(brain_area))

            # Loop through the number of electrodes in this electrode group
            elec_nums = np.where(np.array(group_labels) == group_label)[0]
            for elec_num in elec_nums:

                # Add the electrode information to the table.
                elec_location = location[elec_num]
                if len(elec_location) == 0:
                    # If no label is recorded for this electrode, set it to
                    # nan.
                    elec_location = 'nan'
                else:
                    elec_location = elec_location[0]

                nwb_file.add_electrode(
                    x=x[elec_num],
                    y=y[elec_num],
                    z=z[elec_num],
                    imp=np.nan,
                    x_warped=x_warped[elec_num],
                    y_warped=y_warped[elec_num],
                    z_warped=z_warped[elec_num],
                    location=str(elec_location),
                    filtering='filtering',
                    group=electrode_group,
                    label=str(labels[elec_num][0]),
                    bad=False)

    # Get the electrodes that were recorded into the file.
    ecog_channels = np.where(np.array(group_labels) != 'NaN')[0]

    # # Create electrode table region that includes all the recorded
    # electrodes.
    # all_table_region = nwb_file.create_electrode_table_region(
    #     list(range(len(ecog_channels))), 'all electrodes')

    return nwb_file, ecog_channels