Analog Data
Processing with
BioProc3
Part One
Data Analysis and Smoothing
Introduction
• Download bpwin2.zip or bpwin2.exe from CSB website,
http://www.csb-scb.com
– go to Software and then to BioProc2
– BioProc2 is the free version
– BioProc3 may be obtained from the author
• http://www.health.uottawa.ca/biomech/csb/Software/bioproc2.htm
• installs all necessary device drivers
• only needs to be done once
• to get latest version use the Update from Internet item in the Help
menu of the program
Gait & Biomechanics Laboratory, University of Ottawa
Signal Generation
• click Generate Waveforms from Channels menu
• can generate sine waves, triangle waves, white noise etc. of any
sampling rate, duration or amplitude
• use Generate Fourier Series to generate a waveform with
multiple sinusoidal components
• can add several waveforms together to create test waveforms
using the Add Channels item
• can also multiply channels together or find the resultant
(hypotenuse) of several channels (2 or 3) e.g., three orthogonal
accelerometers
• use Duplicate Channels to make copies of a channel for testing
differences between processing or smoothing techniques
Gait & Biomechanics Laboratory, University of Ottawa
Graphically Displaying Data
• use View menu to select type of display
• choose Graph all Data on Single-axis Graph or Select Channels
for Multiaxis Graph
• can also press Graph or Multi-Axis buttons on right of screen
• right side of button will graph previously selected channels
• to view “epochs” enter a Duration in the Define Window area of
the form used to select channels
• for single-axis graphs this form is selected by pressing the
Channels button
• these forms may also be used to change the line colours
Gait & Biomechanics Laboratory, University of Ottawa
Digitally Displaying Data
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press the Table button
if too many data are present a form will request a range
width of columns may be modified or hidden
to change a value, double-click the cell and enter a new value
(caution, cannot be “undone” unless data are reloaded)
• only channels selected for graphical display will be included in
the table
Gait & Biomechanics Laboratory, University of Ottawa
Loading Data
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from main screen select drive, then directory or subdirectory
from Load data file list click to select a file
file extension filters are available below each list
use View data in text mode to preview an ASCII (text) file
double-click to load a file
single-click will allow you to delete a file using the File menu
after a file is selected by a single-click, press the right mouse
button to view file size information and OK to load the file
Gait & Biomechanics Laboratory, University of Ottawa
Scaling or Normalizing Data
• data may be scaled (multiplied by a constant) using the Scaling
item in the Analysis menu or normalized (divided by a constant)
using the Normalize Amplitude item
• the scaling factors can be reviewed by pressing the Setup
button from the main screen and examining the Gain column
• normalizing the amplitude also affects the gain column but the
factors used are divided into the gain
• you can normalize to the maximum for each channel or a known
factor, for example, body mass
• you can also change the normalization to percentages
Gait & Biomechanics Laboratory, University of Ottawa
Correlation and Regression
• often one needs to calibrate a new transducer against a known
standard or to determine the linearity or correlation of two
signals
• use the Pearson Correlation item in the Correlation menu
• select the two waveforms if the file has more than two signals
• a form will appear that shows the correlation and the regression
lines for X vs. Y and Y vs. X. The slopes and intercepts may
then be use to scale the data, if appropriate.
• you will be prompted to perform the regression
• plot the resulting data using the X−Y button on the main screen
• the Correlation menu also allows you to auto-correlate a
channel or cross-correlate two channels
Gait & Biomechanics Laboratory, University of Ottawa
Customization
• in the Options menu you can select your preferred text editor.
Choose from:
– Notepad, Notepad+, Write, Wordpad or your own choice
• You can also choose your preferred spreadsheet.
Choose from:
– Quattro Pro, Excel, the text editor or your own choice
• Select a User Level. Expert level reduces some annoying
prompts. Don’t switch to Expert too soon.
• Full-screen Graphics means that graphs are automatically
displayed in full-screen mode instead of windowed
• Multiaxis graphs selects this method instead of single-axis
Gait & Biomechanics Laboratory, University of Ottawa
Time Base Normalization
• to normalize the time base select the Time Base item from the
Analysis menu
• the time base can be percentage of the duration, a userselected unit, the item number (count) or by the default time in
seconds using the Units option
• the time base can be “resampled” using the powerful Shannon
reconstruction algorithm or by simple linear interpolation with
Normalize. The reconstruction algorithm can recover peak
values when the sampling rate was too low. Use it with caution.
• the time base can be Reversed and phase-shifted or rotated.
Phase-shifting adds zeros to the ends while rotation takes the
data from one end and concatenates it to the other end.
Gait & Biomechanics Laboratory, University of Ottawa
Mathematical Operations
• the Mathematical Functions item in the Analysis menu enables
various mathematical operations on single channels including:
– negation (-x)
– absolute value (|x|)
– squaring (x2)
– square-root (√x)
– integration over time (∫x dt)
– differentiation over time (dx/dt)
– inversion (1/x)
– path integration (1, 2 or 3 dimensionally)
– Root-mean-square (RMS) of residuals (differences between
two curves)
Gait & Biomechanics Laboratory, University of Ottawa
Moving Average, Median, RMS or Mean
Absolute Value
• select these from the Smoothing item in the Analysis menu
• Moving Median can be used to remove brief spikes from data
– width should be two data points longer than the duration of
the spike (i.e., 3 will remove single datum spikes)
• RMS Amplitude will compute root-mean-square values across
each interval (usually used with EMGs)
• Mean Absolute Value (MAV) and RMS are often used to smooth
EMG data
• Moving Average, RMS and MAV require durations or widths that
need to be determined empirically
Gait & Biomechanics Laboratory, University of Ottawa
Interpolation, Spline and Polynomial
Fitting
• to linearly interpolate across a section of the data
– graph the data in single-axis mode and press 2 for two cursors
– move the cursors to interval to be fitted then press Exit
– select Linear Interpolation from the Smoothing menu and then
select the curves to be interpolated
• to fit a curve to a polynomial or spline
– select Polynomial Fitting or Spline Fit an Interval
– spline fitting requires you to graph and select the interval
– enter the polynomial order for each curve to be fitted (zero
means don’t process the channel)
– polynomial fitting allows you to view the coefficients and fit the
interval or the whole data file to the polynomial
– spline fitting only fits an interval, not the whole duration
Gait & Biomechanics Laboratory, University of Ottawa
Digital Filtering
• High-pass Filter or Low-pass Filter may be selected from the
Analysis menu
• these routines use 4th-order, zero-lag, Butterworth filters
• select a non-zero cutoff frequency then press Process
• for other types of filters use either the Butterworth or Criticallydamped or Digital Filtering (various) items from Smoothing menu
• the Butterworth or Critically-Damped item allows selection of highor low-pass filters and zero-lag or non-zero-lag filters of various
orders
• up to 200 padding points may be added to both ends to remove
the need for leading and trailing data
• the padding points may be zeros, end-point averages or
reflexively mirrored data
Gait & Biomechanics Laboratory, University of Ottawa
Digital Filtering cont’d
• the Digital Filtering (various) item permits various types of nonzero-lag filters including Band-pass and Band-stop options
• Butterworth, critically-damped, elliptic, Chebyshev and inverse
Chebyshev are possible
• use the Filter Testing option to interactively try out different
Butterworth and critically-damped filter options without
permanently affecting the data
Gait & Biomechanics Laboratory, University of Ottawa