Import SLEAP H5 files

Importing a directory of .SLP files into a SimBA project. The .SLP files has been created by joining several .SLP files.

NOTE I: Use simba-uw-tf-dev version >=1.70.5

NOTE II: The .SLP files has to have been joined in the same order. E.g., all .SLP files has to have been left joined on Dam. There should not be some files which has been left joined on Nest, and some on Dam.

import os
from simba.mixins.config_reader import ConfigReader
from simba.utils.read_write import find_files_of_filetypes_in_directory, write_df
from simba.utils.data import slp_to_df_convert
from simba.utils.read_write import get_fn_ext
from simba.data_processors.interpolation_smoothing import Smooth, Interpolate

# DEFINE THE DIRECTORY CONTAINING YOUR SLEAP DATA IN H5 FORMAT AND THE PATH TO YOUR SIMBA PROJECT CONFIG
DATA_DIR = '/Users/simon/Desktop/envs/troubleshooting/sleap_dam_roi/data'
CONFIG_PATH = '/Users/simon/Desktop/envs/troubleshooting/sleap_dam_roi/project_folder/project_config.ini'

#SPECIFY SMOOTHING AND INTERPOLATION SETTINGS
interpolation_method = 'Body-parts: Nearest' # Set to "None" if interpolation should be skipped
smoothing_method = {'Method': 'Savitzky Golay', 'Parameters': {'Time_window': '200'}}

# READ IN THE SIMBA PROJECT CONFIG AND FIND THE H5 PATHS INSIDE THE DATA_DIR
config = ConfigReader(config_path=CONFIG_PATH, read_video_info=False)
data_files = find_files_of_filetypes_in_directory(directory=DATA_DIR, extensions=['.h5'], raise_error=True)

FOR EVERY H5 FILE FOUND IN THE DATA_DIR, WE (i) CONVERT IT TO A DATAFRAME AND APPEND THE HEADERS AS DEFINED IN THE SIMBA PROJECT, AND (ii) SAVE THE DATAFRAME IN THE SIMBA PROJECT project_folder/csv/input_csv directory.

Note: We pass joined_tracks=True to slp_to_df_convert to specify that the .SLP files has been created by joining several .SLP files.

for file_path in data_files:
    _, video_name, _ = get_fn_ext(filepath=file_path)
    print(f'Importing {video_name}...')
    df = slp_to_df_convert(file_path=file_path, headers=config.bp_col_names, joined_tracks=True)
    save_path = os.path.join(config.input_csv_dir, f'{video_name}.csv')
    write_df(df=df, file_type='csv', save_path=save_path, multi_idx_header=True)

    #Run interpolation if `interpolation_method` is not "None"
    if interpolation_method != 'None':
        Interpolate(input_path=save_path,
                    config_path=CONFIG_PATH,
                    method=interpolation_method,
                    initial_import_multi_index=True)

    # Run smoothing if `smoothing_method['Method']` is not "None"
    if smoothing_method['Method'] != 'None':
        Smooth(config_path=CONFIG_PATH,
               input_path=save_path,
               time_window=int(smoothing_method['Parameters']['Time_window']),
               smoothing_method=smoothing_method['Method'],
               initial_import_multi_index=True)

    print(f'Complete: {video_name}...')

Importing LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 50597 Dam_Nose_1 body-parts for animal Dam in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 1653 Dam_Head_1 body-parts for animal Dam in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 298 Dam_Body_1 body-parts for animal Dam in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 34014 Dam_Tail_1 body-parts for animal Dam in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 251 Nest_First_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 8 Nest_Second_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 139 Nest_Third_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 177 Nest_Fourth_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 1551 Nest_Fifth_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 1056 Nest_Sixth_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Interpolating 23041 Nest_Sevent_corner_2 body-parts for animal Nest in video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...
Video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c interpolated (elapsed time 5.4641) ...
SIMBA COMPLETE: 1 data file(s) interpolated) (elapsed time: 5.47s)      complete
Video LBNL4b_LBN_P05_3_2022-01-17_19-48-06c smoothed (Savitzky Golay: 200ms) (elapsed time 4.3516)...
SIMBA COMPLETE: 1 data file(s) smoothened (elapsed time: 4.3593s)       complete
Complete: LBNL4b_LBN_P05_3_2022-01-17_19-48-06c...