Getting started with the analysis of nvg data

This notebook assumes that data exists in a database in the hdf5 format. For instructions how to set up the database with data see [../readme.md].

The approximate orientation of the IMUs

The IMUs has its local z-axis pointing out of the box, and its local x-axis pointing in the long direction. The IMUs were strapped to the body with the positive local x-direction pointing downwards along the main axis of the segment. The z-axis was approximately pointing outwards from the body, normal to the sagittal plane.

Import modules



In [1]:

    
import numpy as np
import matplotlib.pyplot as plt
import nvg.ximu.ximudata as ximudata
%matplotlib notebook

Load the database



In [2]:

    
reload(ximudata)
dbfilename = "/home/kjartan/Dropbox/Public/nvg201209.hdf5"
db = ximudata.NVGData(dbfilename);

Explore contents of the database file



In [3]:

    
dbfile = db.hdfFile;
print "Subjects: ",  dbfile.keys()
print "Trials: ", dbfile['S5'].keys()
print "IMUs: ", dbfile['S5/B'].keys()
print "Attributes of example trial", dbfile['S5/B'].attrs.keys()
print "Shape of example IMU data entry", dbfile['S5/B/N'].shape









    



Subjects:  [u'S10', u'S11', u'S12', u'S2', u'S3', u'S4', u'S5', u'S6', u'S7', u'S8', u'S9']
Trials:  [u'B', u'D', u'M', u'N']
IMUs:  [u'B', u'LA', u'LH', u'LT', u'N', u'RA', u'RH', u'RT']
Attributes of example trial [u'PNAtICLA', u'PNAtICRA', u'PNAtCycleEvents', u'cycleFrequency', u'verticalDisplacement']
Shape of example IMU data entry (87243, 10)

The content of the raw IMU file

The columns of the IMU data contain:

Packet number
Gyroscope X (deg/s)
Gyroscope Y (deg/s)
Gyroscope Z (deg/s)
Accelerometer X (g)
Accelerometer Y (g)
Accelerometer Z (g)
Magnetometer X (G)
Magnetometer Y (G)
Magnetometer Z (G)

Plot example data



In [5]:

    
db.plot_imu_data("S12", "D", "RA")









    














    











    Out[5]:





<HDF5 dataset "RA": shape (84223, 10), type "<f8">

Implemented analysis methods



In [ ]:

    
print [s for s in dir(db) if s.startswith("get")]

Try an analysis



In [3]:

    
db.get_angle_to_vertical_markers(subject="S4")









    



2012-09-19 11:30:58.122000
2012-09-19, 09:53:12.302938






    Out[3]:





[]



In [ ]:

    
res = db.apply_to_all_trials(db.get_RoM_angle_to_vertical, {'imu':'LH'},
                                           subjlist=['S4', 'S6'], triallist=['B', 'N'])



In [ ]:

    
res = db.apply_to_all_trials(db.get_angle_to_vertical_markers, {'imu':'LH'},
                                           subjlist=['S4', 'S6'], triallist=['B', 'N'])



In [ ]: