README for data processing scripts:
average_new.m -> takes all of the .mot files listed in listfile, finds and  normalizes their gait cycles, computes their means and standard deviations, and saves the output.  No circshifting is currently implemented. Also saves files with GC data and mechanical variables. This is the averaging script that should be used on force plate treadmill data (specifically that from Harvard).  (1/18/12)

average_click.m -> takes all of the .mot files listed in listfile, finds and normalizes their gait cycles, computes their means and standard
deviations, and saves the output.  No circshifting is currently implemented. Also saves files with GC data and mechanical variables.
This script differs from average_new only in that GC removal is done via select_curves. (2/13/12)

compare_fp_heel.m ->  Plugs into average_new.m to allow one to check consistency of heel min vs. FP methods of detecting heel strike.  Typically find that heel min method is 1-2 samples behind FP method. (8/30/11)

fp_com -> performs the functions of average_new.m except on the files containing FP and COM data for walking trials.  (1/18/12)

getData.m ->  Reads in a group of SIMM .mot files and returns a data structure with the desired subset of motion capture data, force plate data, joint angles, joint torques, muscle lmtc's, muscle moment arms, subject initials, and leg with EMG electrodes.  (8/30/11)

getMuscleData.m ->  Reads the muscle parameters for a subject from a SIMM .msl file.  (8/30/11)

niceBars.m -> script for producing nice error bar plots.

plot_speeds.m ->  plots the average (with s.d.) of the mechanical  variables at the requested speed for the requested subject.  Only variables on the requested leg (usually that with the EMG sensors) are plotted. (8/30/11)

plot_subs.m ->  produces plots that compare the mechanical variables of different subjects during walking.  The plots include error bars and have the data for each requested subject on one plot. (9/1/11)

plot_train_test.m -> produces plots that compare the mechanical variables of the training, testing, and full data sets for each subject. (9/1/11)

readColData.m -> Reads in a data text file.  Has been modified so that only the file name and name of the first data column are needed as inputs.  If first column name is omitted script will assume it is "time."  Assumes that there is only one label line and that there are <= 1e5 columns in one group.  Can further modify if needed.  (5/22/11)

reduce_mot.m -> takes oversized SIMM _OUT files and discards some of the many columns unnecessary for analyses of walking.  Output is a much smaller _crit .mot file in the same directory. (8/30/11)

select_curves.m -> allows one to remove outlier data curves by clicking them on a plot.  It allows for multiple passes through
the plot, if necessary.  Upon entering data two plots are produced- one that tracks the curves selected in a given iteration and one that displays the remaining curves. When one concludes a pass through the plot they are prompted to declare whether they want to remove the selected curves and finish. If so, the selected curves are removed and the remaining data set is returned.  If not, the user can either keep (i.e. in the case of errant clicking) or remove the curves selected in his/her last iteration and continue until finished.  The indices of the removed curves and the remaining set are returned upon completion. (2/13/12)

train_test.m -> plug-in script for average_new.m that breaks total data set into training and testing data sets of approximately the same size.  Odd-numbered gait cycles go to the training set while even-numbered gait cycles go to the testing set. (8/30/11)

wrapper1.m -> wrapper for reduce_mot.m. (8/30/11)

wrapper2.m -> wrapper for average_new.m.  Currently configured to save plots to the Desktop.  (9/1/11)