Transcript BioProc2 - University of Ottawa

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
Analog Data
Processing with
BioProc3
Part Two
EMG Analysis Techniques
Bias Removal
• high-pass filtering with a Butterworth filter is usually best
• use Autozero, Drift and Autozero or Mean from Bias Removal
menu
• for an AC signal, using the means can be effective
• once the biases have been determined they can be saved for
later use
• autozeroing is used for piezoelectric signals such as signals
from Kistler force platforms or accelerometers
Gait & Biomechanics Laboratory, School of Human Kinetics
Notch Filtering of Line Frequency
• use a Buttterworth band-stop filter from the Digital Filtering
(various) item in the Smoothing menu
• set the low-pass frequency to 59.5 Hz and the high-pass
frequency to 60.5 Hz
• note that any 60 Hz EMG data will also be removed
Gait & Biomechanics Laboratory, School of Human Kinetics
Linear Envelope, RMS or MAV
• root-mean-square (RMS) and mean-absolute-values (MAV) are
in the data smoothing menu
• linear-envelope detection rectifies (absolute values) the signal
and then passes the data through a low-pass filter (usually not
zero-lag)
raw EMG
MAV – 0.1 s
RMS – 0.1 s
LE fc=5 Hz
Gait & Biomechanics Laboratory, School of Human Kinetics
Integration
• definite integration (scalar) can be done within the graphics
mode by pressing “I” or “E” or selecting Statistics | All data or
Between Cursors and then Integration stats. or EMG stats.
– use the value under the column labeled Abs. Integ’l
• integration by epoch allows for repetitive definite integrals for
selected durations called epochs
– this option is selected from the EMG Analysis item in the
Analysis menu
– a graph of the results is presented and may be stored
– use the absolute integral or RMS results
– results may be sent to Notepad, Quattro Pro or Excel
• use Integrate and Reset item to integrate over set time intervals
• use Rectify and Integrate for an indefinite integral
Gait & Biomechanics Laboratory, School of Human Kinetics
EMG Onset Detection
• first use a Butterworth high-pass filter to remove any drift or bias
or movement artifacts (5–10 Hz cutoff)
• next use a critically-damped low-pass filter with the checkbox
Rectify signal(s) for Linear Envel. checked (< 5 Hz)
• graph the data in multiaxis mode, one curve per graph
• press 2 to get cursors then select an area of resting EMGs
• press Threshold then Calculate Thresholds
• click on a curve to change a threshold then press “T” to set it
• move cursors to an area then press Onsets from the Cursor
menu
Gait & Biomechanics Laboratory, School of Human Kinetics
EMG Onset Detection
• first use a Butterworth high-pass filter to remove any drift or bias
or movement artifacts (5–10 Hz cutoff)
• next use a critically-damped low-pass filter with the checkbox
Rectify signal(s) for Linear Envel. checked (< 5 Hz)
• graph the data in multiaxis mode, one curve per graph
• press 2 to get cursors then select an area of resting EMGs
• press Threshold then Calculate Thresholds
• click on a curve to change a threshold then press “T” to set it
• move cursors to an area then press Onsets from the Cursor
menu
Gait & Biomechanics Laboratory, School of Human Kinetics
EMG Onset Detection
• first use a Butterworth high-pass filter to remove any drift or bias
or movement artifacts (5–10 Hz cutoff)
• next use a critically-damped low-pass filter with the checkbox
Rectify signal(s) for Linear Envel. checked (< 5 Hz)
• graph the data in multiaxis mode, one curve per graph
• press 2 to get cursors then select an area of resting EMGs
• press Threshold then Calculate Thresholds
• click on a curve to change a threshold then press “T” to set it
• move cursors to an area then press Onsets from the Cursor
menu
Gait & Biomechanics Laboratory, School of Human Kinetics
Event Tracking
• press F9 to start event tracking then double-click each curve or
right-click to record events for all waveforms
• press Insert button to create a second set of events
• press Delete button to delete the last set of events
• press F10 to save the events in a file (.bpv)
• the file will record the times of both the left and right cursors and
each waveforms’ associated amplitudes
• the file can be viewed in a spreadsheet or test editor (Notepad)
Gait & Biomechanics Laboratory, School of Human Kinetics
Event Tracking
• press F9 to start event tracking then double-click each curve or
right-click to record events for all waveforms
• press Insert button to create a second set of events
• press Delete button to delete the last set of events
• press F10 to save the events in a file (.bpv)
• the file will record the times of both the left and right cursors and
each waveforms’ associated amplitudes
• the file can be viewed in a spreadsheet or test editor (Notepad)
Gait & Biomechanics Laboratory, School of Human Kinetics
Event Tracking
• press F9 to start event tracking then double-click each curve or
right-click to record events for all waveforms
• press Insert button to create a second set of events
• press Delete button to delete the last set of events
• press F10 to save the events in a file (.bpv)
• the file will record the times of both the left and right cursors and
each waveforms’ associated amplitudes
• the file can be viewed in a spreadsheet or test editor (Notepad)
Gait & Biomechanics Laboratory, School of Human Kinetics
Event Tracking
• press F9 to start event tracking then double-click each curve or
right-click to record events for all waveforms
• press Insert button to create a second set of events
• press Delete button to delete the last set of events
• press F10 to save the events in a file (.bpv)
• the file will record the times of both the left and right cursors and
each waveforms’ associated amplitudes
• the file can be viewed in a spreadsheet or test editor (Notepad)
Gait & Biomechanics Laboratory, School of Human Kinetics
Fourier Analysis
• use Harmonic Regression or Fast Fourier Transform from the
Fourier Analysis menu
• FFT usually requires a windowing technique (e.g., Hamming,
Blackwood, Cosine Tapered, etc. Rectangular means no
windowing). Select the windowing technique, then press the
Power Spectrum (FFT) option
• Harmonic Regression is slower but has more features and fewer
restrictions than an FFT
– check which channels to analyze and enter the maximum
number of harmonics to be computed
– results may be graphed or tabulated and saved for later use
including signal reconstruction (.FTF format)
Gait & Biomechanics Laboratory, School of Human Kinetics
Fatigue Analysis
• fatigue analysis is a series of sequential Fourier analyses
• press Fatigue Analysis from the EMG Analysis menu
• select FFT or Harmonic Regression (FFT is faster)
– if FFT select window width as a power of 2
– if Harmonic Analysis select duration and maximum number
of harmonics
• you can interleave the data to create greater resolution
• press Select Channel to process one channel at a time
• table will appear of the results
• press Graph button to view data two dimensionally
• use checkboxes to select which data are displayed graphically
• press 3D to view a three-dimensional graph
Gait & Biomechanics Laboratory, School of Human Kinetics
Ensemble or EMG Signal Averaging
• this is a powerful tool for averaging a series of cyclical data
• for EMG data signals must first be rectified by using moving
RMS or MAV averaging or using a linear-envelope detector
• the software will average multiple waveforms, simultaneously,
for example a group of EMG signals from the same person
• it can average multiple trials of the same person or average
across a group of subjects
• select Ensemble Averaging from the Analysis menu
• data should be cropped so that each cycle is in a single file
• (new) cycles can be selected graphically and saved
• use high and low pass filtering as necessary
• amplitude normalize as needed
Gait & Biomechanics Laboratory, School of Human Kinetics
Steps for Ensemble Averaging
1. enter a filename to hold the results
2. select a “mask” that can be used to create the filenames of the
input data
3. enter the number of intervals for the time-base normalization
usually 100 is used to get “cycle percentage”
4. select the first file to be averaged this step determines the
number of channels that will be averaged
5. button 5 allows you to change your channel selection
6. press button 6 to start the averaging process
7. use button 7 to add other files and use 8 to remove the last file
8. press the Graph Last File button to view files as they are added
9. press button 9 to compute the ensemble average and SDs
Gait & Biomechanics Laboratory, School of Human Kinetics
Steps for Ensemble Averaging
1. enter a filename to hold the results
2. select a “mask” that can be used to create the filenames of the
input data
3. enter the number of intervals for the time-base normalization
usually 100 is used to get “cycle percentage”
4. select the first file to be averaged this step determines the
number of channels that will be averaged
5. button 5 allows you to change your channel selection
6. press button 6 to start the averaging process
7. use button 7 to add other files and use 8 to remove the last file
8. press the Graph Last File button to view files as they are added
9. press button 9 to compute the ensemble average and SDs
Gait & Biomechanics Laboratory, School of Human Kinetics
Steps for Ensemble Averaging
1. enter a filename to hold the results
2. select a “mask” that can be used to create the filenames of the
input data
3. enter the number of intervals for the time-base normalization
usually 100 is used to get “cycle percentage”
4. select the first file to be averaged this step determines the
number of channels that will be averaged
5. button 5 allows you to change your channel selection
6. press button 6 to start the averaging process
7. use button 7 to add other files and use 8 to remove the last file
8. press the Graph Last File button to view files as they are added
9. press button 9 to compute the ensemble average and SDs
Gait & Biomechanics Laboratory, School of Human Kinetics
Results from Ensemble Averaging
• list at right shows the filenames that have been added or
removed and the actual time durations of each file
• coefficients of variation for each channel are calculated
• press Graph Results to view the means and standard deviations
for each channel. The data are paired in multiaxis graphs.
Dashed lines are the SDs.
• press button 10 to save the ensemble averages in .BPB
(BioProc2 Binary) format
• press Export to Excel or Quattro to view the data in spreadsheet
format
• to change from Excel to Quattro Pro use the Options menu from
the main screen
Gait & Biomechanics Laboratory, School of Human Kinetics
Results from Ensemble Averaging
• list at right shows the filenames that have been added or
removed and the actual time durations of each file
• coefficients of variation for each channel are calculated
• press Graph Results to view the means and standard deviations
for each channel. The data are paired in multiaxis graphs.
Dashed lines are the SDs.
• press button 10 to save the ensemble averages in .BPB
(BioProc2 Binary) format
• press Export to Excel or Quattro to view the data in spreadsheet
format
• to change from Excel to Quattro Pro use the Options menu from
the main screen
Gait & Biomechanics Laboratory, School of Human Kinetics
Analog Data
Processing with
BioProc3
Part Three
Impact, Work and Force
Analysis Techniques
Force Transducer Calibration or
EMG to Isometric Force Relationships
• use Pearson Correlation from Correlation menu
• after correlation and regression coefficients are computed you
are prompted to apply one of the regression equations to the
original data
• plot relationship with X-Y plot
• use Scaling menu from Analysis menu to scale data to any
units`
force
raw
EMG
LEEMG
Force platform analyses
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use submenu Analyze Force Plate Data from Analysis menu
two plates can be combined (Combine Two Plates)
impulse computed (from integration statistics)
changes in centres of gravity estimated (Centre of Gravity)
Centre of gravity calculations
• requires subject to have static initial conditions
• subject’s feet must be on one force platform or the data from two
force platforms must be combined
• can compute 2D or 3D takeoff velocities, height after takeoff,
work done, power and lowest and highest positions during
stance period
• high-pass filtering reduces drift for horizontal dimensions
Angular Impulse
• use Work or Angular Impulse Analysis from Integration Statics
submenu of Analysis menu
• requires data file that contains moments (from Vicon or
Visual3D ASCII export)
• moments must be in the first half of the data file, second half
may contain powers
External, Internal and Total Work
• use Work or Angular Impulse Analysis from Integration Statics
submenu of Analysis menu
• requires data file that contains moment powers (from Vicon or
Visual3D ASCII export)
• powers must be in first half or all of the data file
• average work, sum of positive and negative work and external,
internal and total mechanical work done are computed for each
axis
• sums for each axis and total for all axes are also computed
• calculates percent contributions for each moment
Moment Power Analysis (Work Bursts)
• use Moment Power Analysis from Integration Statics submenu
of Analysis menu
• requires data file that contains moment powers (from Vicon or
Visual3D ASCII export)
• computes work bursts and peak moments and powers
whenever power changes from positive to negative or moment
changes from positive to negative
• set a threshold to eliminate small bursts of power
Impact (GSI and HIC) Analyses
• use GSI and HIC (Impacts) from Integration Statics submenu of
Analysis menu
• needs one channel of acceleration data scaled to g’s or m/s2
• second channel may contain triggering information (no longer
used)
• computes Gadd Severity Index for head impacts only (i.e., uses
a2.5)
• average acceleration, A-3 and HIC, integral, delta g and time to
peak acceleration
• HIC is only done for the maximum allowable time interval