def get_accel(synapse_table,
              row,
              column_name,
              start=0,
              device_motion=True,
              out_path='.',
              username='',
              password=''):
    """
    Read accelerometer json data from Synapse table row.

    Calls ::
        from mhealthx.xio import read_file_from_synapse_table
        from mhealthx.xio import read_accel_json

    Parameters
    ----------
    synapse_table : string or Schema
        a synapse ID or synapse table Schema object
    row : pandas Series or string
        row of a Synapse table converted to a Series or csv file
    column_name : string
        name of file handle column
    start : integer
        starting index (remove beginning)
    device_motion : Boolean
        use deviceMotion vs. accelerometer json file?
    out_path : string or None
        a local path in which to store downloaded files.
        If None, stores them in (~/.synapseCache)
    username : string
        Synapse username (only needed once on a given machine)
    password : string
        Synapse password (only needed once on a given machine)

    Returns
    -------
    t : list
        time points for accelerometer data
    ax : list
        x-axis acceleration
    ay : list
        y-axis acceleration
    az : list
        z-axis acceleration
    gx : list
        x-axis gravity acceleration
    gy : list
        y-axis gravity acceleration
    gz : list
        z-axis gravity acceleration
    rx : list
        x-axis rotationRate
    ry : list
        y-axis rotationRate
    rz : list
        z-axis rotationRate
    uw : list
        w of attitude quaternion
    ux : list
        x of attitude quaternion
    uy : list
        y of attitude quaternion
    uz : list
        z of attitude quaternion
    sample_rate : float
        sample rate
    duration : float
        duration of time series
    row : pandas Series
        same as passed in: row of a Synapse table as a file or Series
    file_path : string
        path to accelerometer file

    Examples
    --------
    >>> from mhealthx.xio import extract_synapse_rows, read_file_from_synapse_table, get_accel
    >>> import synapseclient
    >>> syn = synapseclient.Synapse()
    >>> syn.login()
    >>> synapse_table = 'syn4590866'
    >>> row_series, row_files = extract_synapse_rows(synapse_table, save_path='.', limit=3, username='', password='')
    >>> column_name = 'deviceMotion_walking_outbound.json.items'
    >>> device_motion = True
    >>> start = 150
    >>> out_path = None
    >>> username = ''
    >>> password = ''
    >>> for i in range(1):
    >>>     row = row_series[i]
    >>>     row, filepath = read_file_from_synapse_table(synapse_table, row,
    >>>         column_name, out_path, username, password)
    >>>     print(row)
    >>>     t, ax, ay, az, gx, gy, gz, rx, ry, rz, uw, ux, uy, uz, sample_rate, duration, row, file_path = get_accel(synapse_table,
    >>>                                       row, column_name,
    >>>                                       start, device_motion,
    >>>                                       out_path, username, password)

    """
    from mhealthx.xio import read_file_from_synapse_table, read_accel_json

    # Load row data and accelerometer json file (full path):
    row, file_path = read_file_from_synapse_table(synapse_table, row,
                                                  column_name, out_path,
                                                  username, password)
    # Read accelerometer json file:
    t, axyz, gxyz, wxyz, rxyz, sample_rate, \
    duration, = read_accel_json(file_path, start, device_motion)

    ax, ay, az = axyz
    gx, gy, gz = gxyz
    rx, ry, rz = rxyz
    uw, ux, uy, uz = wxyz

    return t, ax, ay, az, gx, gy, gz, rx, ry, rz, uw, ux, uy, uz, \
           sample_rate, duration, row, file_path
コード例 #2
0
ファイル: xio.py プロジェクト: Sandy4321/mhealthx
def get_accel(synapse_table, row, column_name, start=0, device_motion=True,
              out_path='.', username='', password=''):
    """
    Read accelerometer json data from Synapse table row.

    Calls ::
        from mhealthx.xio import read_file_from_synapse_table
        from mhealthx.xio import read_accel_json

    Parameters
    ----------
    synapse_table : string or Schema
        a synapse ID or synapse table Schema object
    row : pandas Series or string
        row of a Synapse table converted to a Series or csv file
    column_name : string
        name of file handle column
    start : integer
        starting index (remove beginning)
    device_motion : Boolean
        use deviceMotion vs. accelerometer json file?
    out_path : string or None
        a local path in which to store downloaded files.
        If None, stores them in (~/.synapseCache)
    username : string
        Synapse username (only needed once on a given machine)
    password : string
        Synapse password (only needed once on a given machine)

    Returns
    -------
    t : list
        time points for accelerometer data
    ax : list
        x-axis acceleration
    ay : list
        y-axis acceleration
    az : list
        z-axis acceleration
    gx : list
        x-axis gravity acceleration
    gy : list
        y-axis gravity acceleration
    gz : list
        z-axis gravity acceleration
    rx : list
        x-axis rotationRate
    ry : list
        y-axis rotationRate
    rz : list
        z-axis rotationRate
    uw : list
        w of attitude quaternion
    ux : list
        x of attitude quaternion
    uy : list
        y of attitude quaternion
    uz : list
        z of attitude quaternion
    sample_rate : float
        sample rate
    duration : float
        duration of time series
    row : pandas Series
        same as passed in: row of a Synapse table as a file or Series
    file_path : string
        path to accelerometer file

    Examples
    --------
    >>> from mhealthx.xio import extract_synapse_rows, read_file_from_synapse_table, get_accel
    >>> import synapseclient
    >>> syn = synapseclient.Synapse()
    >>> syn.login()
    >>> synapse_table = 'syn4590866'
    >>> row_series, row_files = extract_synapse_rows(synapse_table, save_path='.', limit=3, username='', password='')
    >>> column_name = 'deviceMotion_walking_outbound.json.items'
    >>> device_motion = True
    >>> start = 150
    >>> out_path = None
    >>> username = ''
    >>> password = ''
    >>> for i in range(1):
    >>>     row = row_series[i]
    >>>     row, filepath = read_file_from_synapse_table(synapse_table, row,
    >>>         column_name, out_path, username, password)
    >>>     print(row)
    >>>     t, ax, ay, az, gx, gy, gz, rx, ry, rz, uw, ux, uy, uz, sample_rate, duration, row, file_path = get_accel(synapse_table,
    >>>                                       row, column_name,
    >>>                                       start, device_motion,
    >>>                                       out_path, username, password)

    """
    from mhealthx.xio import read_file_from_synapse_table, read_accel_json

    # Load row data and accelerometer json file (full path):
    row, file_path = read_file_from_synapse_table(synapse_table, row,
                                                  column_name, out_path,
                                                  username, password)
    # Read accelerometer json file:
    t, axyz, gxyz, wxyz, rxyz, sample_rate, \
    duration, = read_accel_json(file_path, start, device_motion)

    ax, ay, az = axyz
    gx, gy, gz = gxyz
    rx, ry, rz = rxyz
    uw, ux, uy, uz = wxyz

    return t, ax, ay, az, gx, gy, gz, rx, ry, rz, uw, ux, uy, uz, \
           sample_rate, duration, row, file_path
コード例 #3
0
    import numpy as np

    from mhealthx.xio import read_accel_json
    from mhealthx.extractors.dead_reckon import velocity_from_acceleration,\
        position_from_velocity
    from mhealthx.utilities import plotxyz

    #-------------------------------------------------------------------------
    # Load accelerometer x,y,z values (and clip beginning from start):
    #-------------------------------------------------------------------------
    #input_file = '/Users/arno/DriveWork/mhealthx/mpower_sample_data/accel_walking_outbound.json.items-6dc4a144-55c3-4e6d-982c-19c7a701ca243282023468470322798.tmp'
    #device_motion = False
    input_file = '/Users/arno/DriveWork/mhealthx/mpower_sample_data/deviceMotion_walking_outbound.json.items-5981e0a8-6481-41c8-b589-fa207bfd2ab38771455825726024828.tmp'
    device_motion = True
    start = 150
    t, axyz, gxyz, uxyz, rxyz, sample_rate, duration = read_accel_json(
        input_file, start, device_motion)
    ax, ay, az = axyz

    #-------------------------------------------------------------------------
    # De-mean accelerometer readings:
    #-------------------------------------------------------------------------
    ax -= np.mean(ax)
    ay -= np.mean(ay)
    az -= np.mean(az)

    plotxyz(ax, ay, az, t, 'Acceleration')

    #-------------------------------------------------------------------------
    # Estimate velocity:
    #-------------------------------------------------------------------------
    vx, vy, vz = velocity_from_acceleration(ax, ay, az, t)
コード例 #4
0
ファイル: dead_reckon.py プロジェクト: Sandy4321/mhealthx
    import numpy as np

    from mhealthx.xio import read_accel_json
    from mhealthx.extractors.dead_reckon import velocity_from_acceleration,\
        position_from_velocity
    from mhealthx.utilities import plotxyz

    #-------------------------------------------------------------------------
    # Load accelerometer x,y,z values (and clip beginning from start):
    #-------------------------------------------------------------------------
    #input_file = '/Users/arno/DriveWork/mhealthx/mpower_sample_data/accel_walking_outbound.json.items-6dc4a144-55c3-4e6d-982c-19c7a701ca243282023468470322798.tmp'
    #device_motion = False
    input_file = '/Users/arno/DriveWork/mhealthx/mpower_sample_data/deviceMotion_walking_outbound.json.items-5981e0a8-6481-41c8-b589-fa207bfd2ab38771455825726024828.tmp'
    device_motion = True
    start = 150
    t, axyz, gxyz, uxyz, rxyz, sample_rate, duration = read_accel_json(input_file, start, device_motion)
    ax, ay, az = axyz

    #-------------------------------------------------------------------------
    # De-mean accelerometer readings:
    #-------------------------------------------------------------------------
    ax -= np.mean(ax)
    ay -= np.mean(ay)
    az -= np.mean(az)
    
    plotxyz(ax, ay, az, t, 'Acceleration')
    
    #-------------------------------------------------------------------------
    # Estimate velocity:
    #-------------------------------------------------------------------------
    vx, vy, vz = velocity_from_acceleration(ax, ay, az, t)