Analog Data Processing with BioProc3

1. Analog Data Processing withBioProc3 Part One Data Analysis and Smoothing

2. 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

3. 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

4. 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 orMulti-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

5. Digitally Displaying Data • 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

6. Loading Data • 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

7. 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

8. 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

9. 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

10. 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 user-selected 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

11. 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

12. 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

13. 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 LinearInterpolation 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

14. 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 Critically-damped or Digital Filtering (various) items from Smoothing menu • the Butterworth or Critically-Damped item allows selection of high- or 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

15. Digital Filtering cont’d • the Digital Filtering (various) item permits various types of non-zero-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