Source code for biomechzoo.conversion.mvnx2zoo_data

import numpy as np
from biomechzoo.mvn.load_mvnx import load_mvnx
from biomechzoo.mvn.mvn import JOINTS, SEGMENTS
from biomechzoo.utils.set_zoosystem import set_zoosystem



def mvnx2zoo_data(fl):
    """ loads mvnx file from xsens"""

    mvnx_file = load_mvnx(fl)

    # create zoo data dict
    data = {'zoosystem': set_zoosystem()}
    # extract joint angle data (All JOINTS may not exist in a given dataset)
    for key, val in JOINTS.items():
        try:
            r = mvnx_file.get_joint_angle(joint=key)
            data[val] = {
                'line': np.array(r),
                'event': {}
            }
            data['zoosystem']['Video']['Channels'].append(val)

        except KeyError:
            print('joint {} does not exist, skipping'.format(val))

    # extract segment orientations (All SEGMENTS may not exist in a given dataset)
    for key, val in SEGMENTS.items():
        try:
            r = mvnx_file.get_sensor_ori(segment=key)

            data[val] = {
                'line': np.array(r),
                'event': {}
            }
            data['zoosystem']['Video']['Channels'].append(val)

        except KeyError:
            print('segment {} does not exist, skipping'.format(val))

    # get foot strike events
    data = _get_foot_strike_events(mvnx_file, data)

    # add meta information
    data = _get_meta_info(fl, mvnx_file, data)

    return data





def is_valid_for_zoo(val):
    """
    Returns True if the value is valid for a MATLAB-compatible zoo structure.
    """
    if val is None:
        return False
    if isinstance(val, list) and len(val) == 0:
        return False
    if isinstance(val, np.ndarray) and val.size == 0:
        return False
    return True



def _get_meta_info(fl, mvnx_file, data):
    # todo: add more, see mvnx_file object
    data['zoosystem']['Video']['Freq'] = int(mvnx_file.frame_rate)
    data['zoosystem']['mvnx_version'] = mvnx_file.version
    data['zoosystem']['mvnx_configuration'] = mvnx_file.configuration
    data['zoosystem']['recording_date'] = mvnx_file.recording_date
    data['zoosystem']['original_file_name'] = mvnx_file.original_file_name
    data['zoosystem']['frame_count'] = mvnx_file.frame_count
    return data


def _get_foot_strike_events(mvnx_file, data):
    RHeel = np.zeros(mvnx_file.frame_count)
    LHeel = np.zeros(mvnx_file.frame_count)

    for n in range(mvnx_file.frame_count):
        list_contact = mvnx_file.get_foot_contacts(n)
        for contact in list_contact:
            if contact['segment_index'] == 17:
                RHeel[n] = True
            elif contact['segment_index'] == 21:
                LHeel[n] = True

    hs_r = []
    hs_l = []
    for i in range(1, len(LHeel)):  # Start from 1 to avoid i-1 out-of-range
        if RHeel[i - 1] == 0 and RHeel[i] == 1:
            hs_r.append(i)
        if LHeel[i - 1] == 0 and LHeel[i] == 1:
            hs_l.append(i)

    # add to event branch of any channel
    if 'jL5S1' in data:
        ch = 'jL5S1'
    else:
        ch = next(iter(data))

    if hs_r:
        for i, rHS in enumerate(hs_r):
            data[ch]['event']['R_FS' + str(i + 1)] = [rHS, 0, 0]
    if hs_l:
        for i, lHS in enumerate(hs_l):
            data[ch]['event']['L_FS' + str(i + 1)] = [lHS, 0, 0]

    return data


if __name__ == '__main__':
    """ testing """
    import os
    from biomechzoo.processing.split_trial_data import split_trial_data
    # -------TESTING--------
    project_root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
    fl = os.path.join(project_root, 'data', 'other', 'Flat001.mvnx')
    fl_zoo = fl.replace('.mvnx', '.zoo')
    data = mvnx2zoo_data(fl)