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getEvents.m
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% Retrieve Key Events from a gait cycle in c3d format
% Tim Dorn
% Last Updated: September 2010
%
% ----------------------------------------------------------------------
% Usage: C3Dkey = getEvents(c3dFile, direction*, FP_order*, FP_sequence*)
% ----------------------------------------------------------------------
%
% Inputs: c3dFile = the name of the c3d file
%
% direction* = the direction of travel in VICON COORDINATES.
% (required for marker extraction)
% 1 = X ; -1 = -X
% 2 = Y ; -2 = -Y
%
% FP_order* = Vector containing the order of force plate numbers
% stepped on during the trial. This parameter can be
% neglected if the trial is NOT a dynamic general
% trial (i.e (static trial or EMG/kinematics only trial) but
% otherwise it must be included.
% e.g. Walking on FP3, FP2, FP1 --> FP_order = [3 2 1]
% e.g. Running on FP1, FP3 (FP2 is skipped due to the
% large stride length --> FP_order = [1 3]
%
% FP_sequence* = For gait, the sequence of force plates to be used for the left
% and right foot during each event interval is automatically detected.
% However this can be manually overridden by specifying this matrix.
% It must have two columns (1 = rightfoot, 2 = leftfoot)
% Each row corresponds to an event interval (area between two events)
% The value is the force plate number that is active.
% i.e. FP_sequence(3,1) = 2 means: In the 3rd event
% interval, the RIGHT foot is on force plate #2.
%
% Note: direction and FP_order are required here if you will
% be processing kinetics using this toolbox.
%
% e.g. keyDyn = getEvents(c3dFileDynamic, -2, [4 5 1], [4 5; 0 5; 1 5;1 0]);
%
%
%
%
%
% Outputs: C3Dkey is a structure which contains key information about the trial
%
% C3Dkey.transform.FPMODEL{i}: transform matrix from FP coords -> Model coords for force plate i
% C3Dkey.transform.VICMODEL: transform matrix from Vicon coords -> Model coords
% C3Dkey.transform.FPVICON{i}: transform matrix from FP coords -> Vicon coords for force plate i
%
% C3Dkey.transform.MODELFP{i}: transform matrix from Model coords -> FP coords for force plate i
% C3Dkey.transform.MODELVIC: transform matrix from Model coords -> Vicon coords
% C3Dkey.transform.VICONFP{i}: transform matrix from Vicon coords -> FP coords for force plate i
%
% C3Dkey.name: subject name
% C3Dkey.markerSet: marker set used for the trial
% C3Dkey.c3dFile: c3d file name
% C3Dkey.c3dFile: c3d file path
% C3Dkey.direction: direction of forward facing value
% C3Dkey.aFreq: analog frequency
% C3Dkey.vFreq: video (VICON) frequency
% C3Dkey.r: video/analog frequency ratio
% C3Dkey.mass: subject mass (SIMPLE TRIAL ONLY)
%
% C3Dkey.numFrames.uncroppedV: number of total video frames in the trial
% C3Dkey.numFrames.uncroppedA: number of total analog frames in the trial
% C3Dkey.numFrames.croppedV = number of cropped frames (video)
% C3Dkey.numFrames.croppedA = number of cropped frames (analog)
%
% C3Dkey.event.txt: label of events
% C3Dkey.event.times: times of events
% C3Dkey.event.percent: percentage of cycle that events occur
% C3Dkey.event.Vframe: video frames of events
% C3Dkey.event.Aframe: analog frames of events
% C3Dkey.event.Vframe0: video frames of events (starting at frame 1)
% C3Dkey.event.Aframe0: analog frames of events (starting at frame 1)
% C3Dkey.event.times0: times of events (starting at time 0)
%
% C3Dkey.interval.txt: txt interval of events
% C3Dkey.interval.time: time interval of events
% C3Dkey.interval.Vframe: video frame interval of events
% C3Dkey.interval.Aframe: analog frame interval of events
% C3Dkey.interval.time0: time interval of events (starting at time 0)
% C3Dkey.interval.Vframe0: video frame interval of events (starting at frame 1)
% C3Dkey.interval.Aframe0: analog frame interval of events (starting at frame 1)
%
% C3Dkey.sequence.frames: force plate frame sequence
% C3Dkey.sequence.plates: force plate number sequence
% C3Dkey.sequence.eventIndex: force plate event boundaries
% C3Dkey.sequence.txt: force plate event text sequence
%
% C3Dkey.offset: offset in mm to put the model on the platform in OpenSim
% C3Dkey.averageSpeed: average trial speed (m/s)
% C3Dkey.FP_order: Force plate order (in terms of stepping #)
% C3Dkey.FP_order_inv: Force plate order inverse
% C3Dkey.trialType: trial type (either will be SIMPLE or GENERAL)
% C3Dkey.numPlatesTotal = total number of force plates in the trial
% C3Dkey.numPlatesUsed = number of force plates used for extraction
% C3Dkey.stanceFrames = (1,:) - Right leg, (2,:) - Left leg (event index)
%
% C3Dkey.allowed.markers: 1 if markers can be extracted from this c3dfile
% C3Dkey.allowed.kinetics: 1 if markers can be extracted from this c3dfile
% C3Dkey.allowed.EMG: 1 if EMG can be extracted from this c3dfile
%
%
% Time Vectors (of labelled event):
% ---------------------------------
% C3Dkey.timeVec.c3dAnalogFrame: actual analog frame number (from c3d)
% C3Dkey.timeVec.analogFrame: analog frame number (starting at 1)
% C3Dkey.timeVec.c3dVideoFrame: actual video frame number (from c3d)
% C3Dkey.timeVec.videoFrame: video frame number (starting at 1)
% C3Dkey.timeVec.Asec: analog time (sec) -> starting at 0 sec
% C3Dkey.timeVec.Vsec: video time (sec) -> starting at 0 sec
% C3Dkey.timeVec.Apercent: analog percentage of labeled event
% C3Dkey.timeVec.Vpercent: video percentage of labeled event
%
%
% Notes
% -----
%
% Events must be examined and labeled in Vicon before using this script.
%
% --------------------------------------------------------------------
%
% Copyright (c) 2008 Tim Dorn
% Use of the GaitExtract Toolbox is permitted provided that the following
% conditions are met:
% 1. The software is not distributed or redistributed. Software distribution is allowed
% only through https://simtk.org/home/c3dtoolbox.
% 2. Use of the GaitExtract Toolbox software must be acknowledged in all publications,
% presentations, or documents describing work in which the GaitExtract Toolbox was used.
% 3. Credits to developers may not be removed from source files
% 4. Modifications of source code must retain the above copyright notice, this list of
% conditions and the following disclaimer.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
% EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
% OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
% SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
% INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
% TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
% HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
% OR BUSINESS INTERRUPTION) OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
% WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
%
% --------------------------------------------------------------------
function C3Dkey = getEvents(c3dFile, direction, FP_order, FP_sequence)
C3Dkey.allowed.markers = 1;
C3Dkey.allowed.kinetics = 1;
C3Dkey.allowed.EMG = 1;
if nargin == 1,
direction = 0;
FP_order = [];
FP_sequence = [];
C3Dkey.allowed.markers = 0;
C3Dkey.allowed.kinetics = 0;
elseif nargin == 2,
FP_order = [];
FP_sequence = [];
C3Dkey.allowed.kinetics = 0;
elseif nargin == 3,
FP_sequence = [];
elseif nargin ~= 4,
fprintf('Usage: getEvents(c3dFile, direction*, FP_order*, FP_seqnence*)\n');
clear C3Dkey
return
end
if abs(direction > 2)
error('Invalid direction scalar: type help getEvents for allowable direction values');
end
isStaticTrial = 0;
autoNotStatic = 1;
if FP_order == -1
isStaticTrial = 1;
FP_order = [];
end
% Open C3D File
% -------------
loadLabels;
[c3dpathstr, c3dname] = fileparts(c3dFile);
C3Dkey.c3dFile = c3dname;
C3Dkey.c3dPath = c3dpathstr;
C3Dkey.c3dFileFULL = c3dFile;
itf = c3dserver();
openc3d(itf, 0, C3Dkey.c3dFileFULL);
fprintf('\nEXTRACTING EVENTS FOR: %s\n--------------------------------------------\n', c3dFile);
% Extract Misc Trial Information
% ------------------------------
try
aIndex = itf.GetParameterIndex('SUBJECTS', 'NAMES');
C3Dkey.name = itf.GetParameterValue(aIndex, 0);
if isempty(C3Dkey.name)
C3Dkey.name = input('No Subject Name Found. Enter Name Here: ', 's');
% C3Dkey.name = 'SubjectName';
end
Units_index = itf.GetParameterIndex('POINT', 'UNITS');
C3Dkey.units = itf.GetParameterValue(Units_index, 0);
if strcmp(C3Dkey.units, 'mm')
C3Dkey.divide_to_meters = 1000;
C3Dkey.divide_to_mm = 1;
else
C3Dkey.divide_to_meters = 1;
C3Dkey.divide_to_mm = 0.001;
end
aIndex = itf.GetParameterIndex('SUBJECTS', 'MARKER_SETS');
C3Dkey.markerSet = itf.GetParameterValue(aIndex, 0);
if isempty(C3Dkey.markerSet)
C3Dkey.markerSet = 'MarkerSet';
end
fprintf('Subject Name: %s\nMarkerset: %s\n', C3Dkey.name, C3Dkey.markerSet);
catch
fprintf('WARNING: Cameras have been disabled for this trial\n');
end
% Capture Frequencies
C3Dkey.r = double(itf.GetAnalogVideoRatio);
C3Dkey.vFreq = double(itf.GetVideoFrameRate);
C3Dkey.aFreq = C3Dkey.r * C3Dkey.vFreq;
C3Dkey.numFrames.uncroppedV = nframes(itf);
C3Dkey.numFrames.uncroppedA = C3Dkey.numFrames.uncroppedV * C3Dkey.r - C3Dkey.r + 1;
% Extract Coordinate & Force Plate Information
% --------------------------------------------
aIndex = itf.GetParameterIndex('FORCE_PLATFORM', 'USED');
C3Dkey.numPlatesTotal = double(itf.GetParameterValue(aIndex, 0));
C3Dkey.numPlatesUsed = length(FP_order);
C3Dkey.FP_order = FP_order;
C3Dkey.FP_order_inv = invFP(C3Dkey.FP_order);
C3Dkey.direction = direction;
ind = find([1 -1 2 -2 3 -3] == C3Dkey.direction);
if ~isempty(ind)
% Build Transform Matrices for each force plate used in extraction
% ------------------------------------------------------------------
C3Dkey.transform.VICMODEL = make3DTransform(glab.transform.VICMODEL(ind,:));
C3Dkey.transform.MODELVIC = inv(C3Dkey.transform.VICMODEL);
for i = 1:C3Dkey.numPlatesUsed
% use FP -> Vicon transform if FPVIC provided in loadLabels
% (assumes all FPs use same transform)
if isfield(glab.transform,'FPVIC')
C3Dkey.transform.FPVICON{i} = make3DTransform(glab.transform.FPVIC);
% otherwise calculate it
else
% Now we need to detect the transform from FP to VICON. We use the FP
% corners to do this.
% FP X = FROM corner 2 TO corner 1 (VICON)
% FP Y = FROM corner 3 TO corner 2 (VICON)
% FP Z = cross(FP X, FP Y)
% ------------------------------------------------------------
FP = calcFPData(itf, C3Dkey, 1);
fpx = FP.corners(1,:,i) - FP.corners(2,:,i);
fpx = fpx/norm(fpx);
fpy = FP.corners(2,:,i) - FP.corners(3,:,i);
fpy = fpy/norm(fpy);
fpz = cross(fpx, fpy);
C3Dkey.transform.FPVICON{i} = [fpx;fpy;fpz];
end
% VICON TO FP
C3Dkey.transform.VICONFP{i} = inv(C3Dkey.transform.FPVICON{i});
% MODEL TO FP
C3Dkey.transform.MODELFP{i} = C3Dkey.transform.VICONFP{i} * C3Dkey.transform.MODELVIC;
% FP TO MODEL
C3Dkey.transform.FPMODEL{i} = inv(C3Dkey.transform.MODELFP{i});
end
end
fprintf('\nDetected transforms for all coordinate systems sucsessfully.');
fprintf('\nVICON TO MODEL\n------------------------\n')
print3x3Matrix(C3Dkey.transform.VICMODEL)
for i = 1:C3Dkey.numPlatesUsed
fprintf('\nFP(#%d) TO MODEL\n------------------------\n', C3Dkey.FP_order(i))
print3x3Matrix(C3Dkey.transform.FPMODEL{i})
end
fprintf('\n\n');
% Extract Event Information
% -------------------------
noEvents = 0;
try
aIndex = itf.GetParameterIndex('EVENT', 'USED');
C3Dkey.event.nEvent = double(itf.GetParameterValue(aIndex, 0));
catch
noEvents = 1;
end
% Detected no events
if noEvents || C3Dkey.event.nEvent == 1
fprintf('WARNING: No events detected in the c3d file.\n')
%insertArtEvents = input('Do you want to insert artificial events at the start/end frame? [y/n]: ', 's');
insertArtEvents = 'y'; % override input for static trials
if insertArtEvents == 'y'
txtRaw = {'GEN', 'GEN'};
timeRaw = [itf.GetVideoFrame(0), itf.GetVideoFrame(1)]/C3Dkey.vFreq;
C3Dkey.event.nEvent = 2;
else
return
end
% Detected some events
else
fprintf('Detected %d events\n', C3Dkey.event.nEvent);
bIndex = itf.GetParameterIndex('EVENT', 'CONTEXTS');
cIndex = itf.GetParameterIndex('EVENT', 'LABELS');
dIndex = itf.GetParameterIndex('EVENT', 'TIMES');
for i = 1:C3Dkey.event.nEvent
txtRawtmp = [itf.GetParameterValue(bIndex, i-1),...
itf.GetParameterValue(cIndex, i-1)];
timeRaw(i) = double(itf.GetParameterValue(dIndex, 2*i-1));
if strmatch(upper(txtRawtmp),'RIGHTFOOT OFF') txtRawtmp= 'rFO';
elseif strmatch(upper(txtRawtmp),'LEFTFOOT OFF') txtRawtmp= 'lFO';
elseif strmatch(upper(txtRawtmp),'RIGHTFOOT STRIKE') txtRawtmp= 'rFS';
elseif strmatch(upper(txtRawtmp),'LEFTFOOT STRIKE') txtRawtmp= 'lFS';
elseif strmatch(upper(txtRawtmp),'RIGHTEVENT') txtRawtmp= 'rGEN';
elseif strmatch(upper(txtRawtmp),'LEFTEVENT') txtRawtmp= 'lGEN';
elseif strmatch(upper(txtRawtmp),'GENERALEVENT') txtRawtmp= 'GEN';
end
txtRaw{i} = txtRawtmp;
end
end
[timeNew, idNew] = sort(timeRaw); % sort the events in time order
for i = 1:C3Dkey.event.nEvent;
j = idNew(i);
C3Dkey.event.txt{i} = txtRaw{j};
time(i) = timeRaw(j);
end
% Create the list of event frame numbers
% --------------------------------------
% Note that a video frame V is equivalent to an analog frame A where
% A = (V-1)*r + 1, where r is the analog/video frame ratio. For example
% if r = 9 and we start at video frame 8, this is equivalent to analog
% frame (8-1)*9 + 1 = 64
% ----------------------------------------------------------------------
C3Dkey.event.times = time;
C3Dkey.event.times0 = C3Dkey.event.times - C3Dkey.event.times(1);
for i = 1:C3Dkey.event.nEvent,
C3Dkey.event.percent(i) = (time(i) - time(1)) / (time(end) - time(1)) * 100;
end
C3Dkey.event.Vframes = round(C3Dkey.vFreq * time(1:C3Dkey.event.nEvent) + 1)';
C3Dkey.event.Aframes = C3Dkey.event.Vframes * C3Dkey.r - C3Dkey.r + 1;
C3Dkey.event.Vframes0 = C3Dkey.event.Vframes - C3Dkey.event.Vframes(1) + 1;
C3Dkey.event.Aframes0 = C3Dkey.event.Aframes - C3Dkey.event.Aframes(1) + 1;
C3Dkey.numFrames.croppedV = C3Dkey.event.Vframes(end) - C3Dkey.event.Vframes(1) + 1;
C3Dkey.numFrames.croppedA = C3Dkey.event.Aframes(end) - C3Dkey.event.Aframes(1) + 1;
% Get trial intervals
% -------------------
C3Dkey.interval.numInterval = C3Dkey.event.nEvent-1;
for i = 1:C3Dkey.event.nEvent-1;
C3Dkey.interval.txt(i,:) = [C3Dkey.event.txt(i),C3Dkey.event.txt(i+1)];
C3Dkey.interval.time(i,:) = [C3Dkey.event.times(i), C3Dkey.event.times(i+1)];
C3Dkey.interval.Vframe(i,:) = [C3Dkey.event.Vframes(i), C3Dkey.event.Vframes(i+1)];
C3Dkey.interval.Aframe(i,:) = [C3Dkey.event.Aframes(i), C3Dkey.event.Aframes(i+1)];
C3Dkey.interval.time0(i,:) = [C3Dkey.event.times0(i), C3Dkey.event.times0(i+1)];
C3Dkey.interval.Vframe0(i,:) = [C3Dkey.event.Vframes0(i), C3Dkey.event.Vframes0(i+1)];
C3Dkey.interval.Aframe0(i,:) = [C3Dkey.event.Aframes0(i), C3Dkey.event.Aframes0(i+1)];
end
% Set up various time vectors
% ---------------------------
C3Dkey.timeVec.c3dAnalogFrame = C3Dkey.event.Aframes(1) : C3Dkey.event.Aframes(end);
C3Dkey.timeVec.analogFrame = C3Dkey.timeVec.c3dAnalogFrame - C3Dkey.event.Aframes(1) + 1;
C3Dkey.timeVec.c3dVideoFrame = C3Dkey.event.Vframes(1) : C3Dkey.event.Vframes(end);
C3Dkey.timeVec.videoFrame = C3Dkey.timeVec.c3dVideoFrame - C3Dkey.event.Vframes(1) + 1;
C3Dkey.timeVec.Asec = (C3Dkey.timeVec.analogFrame - 1) / C3Dkey.aFreq;
C3Dkey.timeVec.Vsec = (C3Dkey.timeVec.videoFrame - 1) / C3Dkey.vFreq;
C3Dkey.timeVec.Apercent = makepercent(C3Dkey.timeVec.analogFrame-1);
C3Dkey.timeVec.Vpercent = makepercent(C3Dkey.timeVec.videoFrame-1);
% Detect the offset to the platform in mm (OpenSim)
% and get the average trial speed (m/s)
% -------------------------------------------------
if strcmp(glab.offsetMarker, '');
fprintf('No marker offset provided. Offset set to [0 0 0]\n')
C3Dkey.offset = [0 0 0];
elseif C3Dkey.allowed.markers == 0
fprintf('Warning: No direction given. Unable to compute marker offset.\n')
fprintf('Marker offset set to [0 0 0]\n')
C3Dkey.offset = [0 0 0];
else
try
% Added by: Prasanna Sritharan, June 2017
% Constrict time window for speed calculation to avoid inclusion of
% data distortion due to C3Dserver trimming issues if possible,
% otherwise use Tim's original version. Calculate from 5th frame to
% 5th-last frame if data stream is long enough.
if (C3Dkey.event.Vframes(end)-C3Dkey.event.Vframes(1))>=10
tmp = -get3dtarget(itf, glab.offsetMarker, 0, C3Dkey.event.Vframes(1)+5, C3Dkey.event.Vframes(end)-4);
else
tmp = -get3dtarget(itf, glab.offsetMarker, 0, C3Dkey.event.Vframes(1), C3Dkey.event.Vframes(end));
end
C3Dkey.offset = coordChange(tmp(1,:)', C3Dkey.transform.VICMODEL)';
C3Dkey.offset(2) = 0;
fprintf('\n[%s Offset Calculation (%s)] --> [X=%.2f Y=%.2f Z=%.2f] mm\n', ...
c3dFile, glab.offsetMarker, C3Dkey.offset(1), C3Dkey.offset(2), C3Dkey.offset(3));
tmp2 = coordChange(tmp', C3Dkey.transform.VICMODEL)';
% Added by: Prasanna Sritharan, January 2016
% Before calculating speed, check for NaNs in selected marker data
% and adjust bounds as required. NaNs in data can occur in data if
% the marker is not visible while the trial is being recorded.
% Valid numerical data is only recorded if the marker is visible.
tstart = 1;
tend = size(tmp2,1);
while isnan(tmp2(tstart,1)), tstart = tstart + 1; end;
while isnan(tmp2(tend,1)), tend = tend - 1; end;
C3Dkey.averageSpeed = double(abs((tmp2(tend,1) - tmp2(tstart,1)) / 1000 / ...
(C3Dkey.timeVec.Vsec(tend) - (C3Dkey.timeVec.Vsec(tstart)))));
fprintf('Average Trial Speed: %.3f m/s\n', C3Dkey.averageSpeed)
tspeed = C3Dkey.averageSpeed;
save trialSpeed.data tspeed -ASCII % Write average speed to file
catch
C3Dkey.offset = [0 0 0];
fprintf('\nERROR: Marker %s does not exist. Offset has been ignored...\n', ...
glab.offsetMarker)
end
end
% ==================================================
% Detect feet on force plates during event intervals
% Used by getKinetics.m for kinetic extraction
% ==================================================
C3Dkey.sequence.frames = C3Dkey.interval.Aframe - C3Dkey.event.Aframes(1) + 1; %analog frames starting at 1
numSeq = length(C3Dkey.sequence.frames(:,1));
C3Dkey.sequence.plates = zeros(numSeq, 2);
C3Dkey.sequence.txt = C3Dkey.interval.txt;
if ~isempty(FP_sequence)
if sum(size(FP_sequence) == size(C3Dkey.sequence.plates)) ~= 2
[m n] = size(C3Dkey.sequence.plates);
error('FP_sequence must be a vector of %d rows and %d columns\n\n\n', m, n);
end
end
if ~isfield(glab, 'vertForceCutoff')
glab.vertForceCutoff = 10; % default value
fprintf('Setting glab.vertForceCutoff = 10\n')
end
if length(C3Dkey.event.txt) == 2
% TWO LABELLED EVENTS
% --------------------
% Only start and end events are labelled.
% This type of trial is used for static trials or trials where only
% EMG has been recorded. In cases like this, we would like to try to
% obtain the subject's mass from the force plate (if indeed it is a
% static trial.
% -----------------------------------------------------------------
C3Dkey.trialType = '2_EVENTS'; % Simple / Static Trial
if isStaticTrial == 0
if autoNotStatic == 0
isStatic = input('2 Events are detected. Is this a static trial? [y/n]: ', 's');
else
isStatic = 'N';
end
else
isStatic = 'Y';
end
if strcmpi(isStatic, 'Y')
fprintf('Defined as a STATIC TRIAL\n');
% Get static mass of subject (useful for static trials)
[C3Dkey.mass, plateNum] = getStaticMass(itf, C3Dkey);
C3Dkey.mass = double(C3Dkey.mass);
C3Dkey.sequence.plates = [plateNum 0];
fprintf('Subject Mass: %f kg\n', C3Dkey.mass);
tmass = C3Dkey.mass;
save tmass.data tmass -ASCII % Write mass to file
% Get leg length of subject (also useful for static trials)
if isfield(glab, 'legLengthMarkers')
if ~isempty(glab.legLengthMarkers)
fprintf('Calculating Average Leg Length...\n');
markersSta = getMarkers(C3Dkey, 'legLengthMarkers', 0);
ll = [];
if isempty(markersSta.FAILED)
for i = 1:floor(length(glab.legLengthMarkers)/2)
[a b c] = getDistance2Markers(markersSta, ...
glab.legLengthMarkers{2*(i-1)+1}, glab.legLengthMarkers{2*(i-1)+2});
ll = [ll c];
end
legLength = mean(ll)/1000;
fprintf('Average Leg Length: %.3f m\n', legLength);
save legLength.data legLength -ASCII % Write legLength to file
else
fprintf('Could not obtain leg length because marker extraction failed...\n')
end
end
end
% Save zero coordinates file (for static trial in OpenSim)
colnamesJoints = {'time'};
datarows = length(C3Dkey.timeVec.Vsec');
numJoints = length(glab.(glab.jointModel));
file = sprintf('%s_coordinates.mot', C3Dkey.c3dFile);
bigM = [C3Dkey.timeVec.Vsec', zeros(datarows, numJoints)];
for i = 1:numJoints
colnamesJoints(i+1) = glab.(glab.jointModel){i}(1);
end
generateMotFile(bigM, colnamesJoints, file);
else
fprintf('Defined as a NON-STATIC TRIAL\n');
if isempty(FP_sequence)
C3Dkey = detectSeq(C3Dkey, itf, numSeq, glab.vertForceCutoff);
else
C3Dkey.sequence.plates = FP_sequence;
end
end
else
% GENERAL TRIAL PATTERN WITH > 2 LABELLED EVENTS
% ----------------------------------------------
% This could be a trial where start, end and intermediate events are labelled.
% Alternativly, it could identify the boundaries of multiple gait cycles.
% Either way, we want to try and detect which foot lands on which plate.
% -----------------------------------------------------------------
C3Dkey.trialType = '>2_EVENTS'; % General / Dynamic Trial
if C3Dkey.numPlatesUsed > C3Dkey.numPlatesTotal,
error('Error in FP_order: number of plates in FP_order exceeds number of plates in the trial...')
end
if isempty(FP_order)
fprintf('Warning: No force plate order vector given (FP_order). Skipping FP detection.\n')
fprintf('Warning: Can''t use this event key to extract kinetics...\n')
else
% Algorithm to detect left and right foot plate force plate orders.
% To determine if a foot hits a plate, we check the vertical FP
% averages across the plates for each sequence, and check that they
% are above a cricical minimum value (vertForceCutoff).
% Alternatively, a manually overridden FP_sequence can be specified.
if isempty(FP_sequence)
C3Dkey = detectSeq(C3Dkey, itf, numSeq, glab.vertForceCutoff);
else
C3Dkey.sequence.plates = FP_sequence;
end
end
end
C3Dkey = detectStanceFrames(C3Dkey);
C3Dkey = detectEventBoundaries(C3Dkey);
fprintf('Trial %s detected as: %s\n', c3dFile, upper(C3Dkey.trialType));
tmpallowed = [C3Dkey.allowed.markers, C3Dkey.allowed.kinetics, C3Dkey.allowed.EMG];
tmpallowedTxt1 = {'MARKERS', 'KINETICS', 'EMG'};
tmpallowedTxt2 = {'NO', 'YES'};
fprintf('==============================================\n');
for i = 1:length(tmpallowed)
fprintf('Key compatible for extracting %s: %s\n', ...
tmpallowedTxt1{i}, tmpallowedTxt2{tmpallowed(i)+1});
end
fprintf('==============================================\n');
closec3d(itf);
% Save event information to file
% ------------------------------
if glab.storeInfo == 1,
if exist(glab.infoDirectory, 'dir') ~= 7,
mkdir(glab.infoDirectory);
end
f1 = sprintf('%sKey_%s.mat', glab.infoDirectory, C3Dkey.c3dFile);
save(f1, 'C3Dkey')
% save txt file of events...
filename = sprintf('%sEVENTS_%s.txt', glab.infoDirectory, C3Dkey.c3dFile);
fid = fopen(filename, 'w');
if fid < 0
fprintf('\nERROR: %s could not be opened for writing...\n\n', filename);
return
end
fprintf(fid, 'EVENT time time0 Percent Vframes Vframes0 Aframes Aframes0\n');
for i = 1:length(C3Dkey.event.txt)
fprintf(fid, '%s\t\t%9.3f\t\t%9.3f\t\t%9.3f\t\t%9.3f\t\t%9.3f\t\t%9.3f\t\t%9.3f\n', ...
C3Dkey.event.txt{i}, C3Dkey.event.times(i), C3Dkey.event.times0(i), ...
C3Dkey.event.percent(i), C3Dkey.event.Vframes(i), C3Dkey.event.Vframes0(i), ...
C3Dkey.event.Aframes(i), C3Dkey.event.Aframes0(i));
end
fclose(fid);
end
fclose all;
% ========================================================================
% SUBFUNCTION: C3Dkey = detectSeq(C3Dkey, itf, numSeq, vertForceCutoff)
% ========================================================================
% Detect foot sequence in C3Dkey. Adds the eventIndex and updates the
% plates field of the C3Dkey.sequence structure
%
% for each sequence in the trial,
% work out which plates have force on them (these are the active plates)
% assign the active plates to the forcePlateOrder
% if no plates are active, then we are airborne
% ========================================================================
function C3Dkey = detectSeq(C3Dkey, itf, numSeq, vertForceCutoff)
% vertForceCutoff = 10; % Cutoff to detect if foot is on/off a plate (N), this now
% appears in loadlabels as glab.vertForceCutoff (TD, 11 Mar 2010)
R=1; L=2;
try
for i = 1:numSeq
% determine active plate numbers in the sequence
for j = 1:C3Dkey.numPlatesUsed
avrF(j) = avrVertForceOnPlate(itf, abs(C3Dkey.FP_order(j)), ...
C3Dkey.interval.Vframe(i,1), C3Dkey.interval.Vframe(i,2));
end
activePlates = abs(C3Dkey.FP_order(find(avrF>vertForceCutoff)));
% zero support sequence (airborne)
if isempty(activePlates),
C3Dkey.sequence.plates(i,:) = [0 0];
% single support sequence
elseif length(activePlates) == 1,
if findstr(C3Dkey.sequence.txt{i,1}, 'FO')
footOnPlate = opp(C3Dkey.sequence.txt{i}(1));
elseif findstr(C3Dkey.sequence.txt{i,1}, 'FS')
footOnPlate = C3Dkey.sequence.txt{i,1}(1);
elseif findstr(C3Dkey.sequence.txt{i,1}, 'GEN')
footOnPlate = C3Dkey.sequence.txt{i,1}(1);
else
error('unable to detect single foot activePlate...')
end
switch footOnPlate
case 'r'
C3Dkey.sequence.plates(i,R) = activePlates;
case 'l'
C3Dkey.sequence.plates(i,L) = activePlates;
end
% double support sequence
else
% find foot-off foot
for k = 1:2
if findstr(C3Dkey.sequence.txt{i,k}, 'FO')
FOfoot = C3Dkey.sequence.txt{i,k}(1);
end
end
% sort activePlates into gait style order
if find(abs(C3Dkey.FP_order)==activePlates(1)) > ...
find(abs(C3Dkey.FP_order)==activePlates(2))
activePlatesOrdered = fliplr(activePlates);
else
activePlatesOrdered = activePlates;
end
% the foot representing FS is on the front force plate and
% the foot representing FO is on the back force plate
if strcmp(FOfoot, 'r')
% right foot at back
C3Dkey.sequence.plates(i,:) = activePlatesOrdered;
else
% left foot at back
C3Dkey.sequence.plates(i,:) = fliplr(activePlatesOrdered);
end
end
end
% disp(C3Dkey.sequence.plates) % DEBUG STEP
fprintf('Force plate sequence was automatically detected.\n');
catch
fprintf('Warning: Could not detect force plate sequence.\n');
end
% ========================================================================
% SUBFUNCTION: C3Dkey = detectEventBoundaries(C3Dkey)
% ========================================================================
% Use C3Dkey.sequence.plates to determine the event boundaries
% for each force plate used in the trial.
% Adds the eventIndex field to the C3Dkey.sequence structure
%
% Modified by Prasanna Sritharan, April 2018
% Ignores active force plates that have no bounding events
% ========================================================================
function C3Dkey = detectEventBoundaries(C3Dkey)
try
fpremove = [];
for i = 1:C3Dkey.numPlatesUsed
[ii,jj] = find(C3Dkey.sequence.plates == C3Dkey.FP_order(i));
if ~isempty(ii) % FP is active, and there are bounding events
C3Dkey.sequence.eventIndex(i,:) = [ii(1) ii(end)+1];
else % FP is active but there are no bounding events
fpremove(end+1) = i;
C3Dkey.sequence.eventIndex(i,:) = [-1 -1];
fprintf('Warning: FP%d is active but not bounded by events, and will be ignored.\n',C3Dkey.FP_order(i));
end
end
C3Dkey.FP_order(fpremove) = [];
C3Dkey.FP_order_inv = invFP(C3Dkey.FP_order);
C3Dkey.sequence.eventIndex(fpremove,:) = [];
C3Dkey.numPlatesUsed = C3Dkey.numPlatesUsed - length(fpremove);
catch
fprintf('Warning: Could not detect event boundaries.\n');
end
% ========================================================================
% SUBFUNCTION: C3Dkey = detectStanceFrames(C3Dkey)
% ========================================================================
% Detect foot sequence in C3Dkey. Adds the C3Dkey.stanceFrames and
% C3Dkey.strideLength fields
% ========================================================================
function C3Dkey = detectStanceFrames(C3Dkey)
try
[stanceRight, stanceRightIndex] = getTimes('rFS', 'rFO', C3Dkey.event.txt, C3Dkey.event.Vframes);
C3Dkey.stanceFrames.right = stanceRightIndex;
catch
fprintf('Warning: Could not detect right foot stance frames.\n');
end
try
[stanceLeft, stanceLeftIndex] = getTimes('lFS', 'lFO', C3Dkey.event.txt, C3Dkey.event.Vframes);
C3Dkey.stanceFrames.left = stanceLeftIndex;
catch
fprintf('Warning: Could not detect left foot stance frames.\n');
end
try
tmp = getTimes('lFS', 'rFS', C3Dkey.event.txt, C3Dkey.event.Vframes);
C3Dkey.strideLength = 2*C3Dkey.averageSpeed*(tmp(2)-tmp(1))/C3Dkey.vFreq;
sl = C3Dkey.strideLength;
save strideLength.data sl -ASCII % Write stride length to file
catch
try
tmp = getTimes('rFS', 'lFS', C3Dkey.event.txt, C3Dkey.event.Vframes);
C3Dkey.strideLength = 2*C3Dkey.averageSpeed*(tmp(2)-tmp(1))/C3Dkey.vFreq;
sl = C3Dkey.strideLength;
save strideLength.data sl -ASCII % Write stride length to file
catch
fprintf('Warning: Could not detect stride length.\n');
end
end
% ========================================================================
% SUBFUNCTION: avrF = avrVertForceOnPlate(itf, plateNum, startFrame, endFrame)
% ========================================================================
% Returns the average vertical force of a force plate over a specified
% time period.
function avrF = avrVertForceOnPlate(itf, plateNum, startVFrame, endVFrame)
loadLabels;
plateLabel = sprintf(glab.FP.string, glab.FP.prefix{glab.FP.verticalForceIndex}, ...
plateNum, glab.FP.suffix{glab.FP.verticalForceIndex});
try
warning off MATLAB:divideByZero
forceVec = getanalogchannel(itf, plateLabel, startVFrame, endVFrame);
% if ~isempty(forceVec),
avrF = mean(abs(forceVec));
% end
catch
fprintf('ERROR: Force Plate [%s] does not exist.\n', plateLabel);
return
end
% DEBUG STEP
% figure;
% plot(abs(forceVec));
% title(sprintf('plate %d frame %d:%d', plateNum, startVFrame, endVFrame));
% hline(avrF);
% ========================================================================
% SUBFUNCTION: m = toMatrix(transform)
% ========================================================================
% Turns the rigid body direction vector into a rigid body transformation
% matrix
function m = toMatrix(transform)
m = zeros(3,3);
for i = 1:3
m(i,abs(transform(i))) = sign(transform(i));
end
% ========================================================================
% SUBFUNCTION: invFP
% ========================================================================
% Returns the inverse of the given FP_order vector
% Input: FP_order (i.e position 1 = first vicon plate number stepped on)
% Output: FP_inv (i.e. position 1 = order of stepping of vicon plate 1)
function fpinv = invFP(fp)
if isempty(fp),
fpinv = [];
else
for i = 1:length(fp)
fpinv(abs(fp(i))) = i;
end
end
% ========================================================================
% SUBFUNCTION: mass = getStaticMass(itf, C3Dkey)
% ========================================================================
% Gets the mass of the subject. This should be only used during static
% trials for reasonable results. This function examines all channels of all
% force plates between the event periods and takes an average of the force
% on each channel. The maximum average would correspond to the subject's
% downward vertical force and hence divinging by 9.81 represents its mass
function [mass, plateNum] = getStaticMass(itf, C3Dkey)
g = 9.81;
for p = 1:C3Dkey.numPlatesTotal
try
avrF(p) = avrVertForceOnPlate(itf, p, ...
C3Dkey.event.Vframes(1), C3Dkey.event.Vframes(end));
catch
fprintf('ERROR: Force plate #%d does not exist on this trial\n', p)
mass = input('Enter subject mass in kg (press ENTER to ignore mass): ');
if ~isnumeric(mass),
mass = 0;
fprintf('Invalid Mass: Mass will be set to 0. You can edit this in C3Dkey.mass later\n')
end
plateNum = -1;
return
end
end
if C3Dkey.numPlatesTotal > 0
[force, plateNum] = max(avrF);
mass = force / g;
else
mass = 0;
plateNum = 0;
end
detectionMass = 10; % kg
if mass < detectionMass,
fprintf('Warning: Detected subject mass (%.3f kg) is < %d kg\n', mass, detectionMass)
newmass = input('Enter new subject mass in kg or press ENTER to accept the current mass: ');
if ~isnumeric(newmass),
mass = 0;
plateNum = -1;
fprintf('Invalid Mass: Mass will be set to 0. You can edit this in C3Dkey.mass later\n')
elseif isempty(newmass),
return
else mass = newmass;
end
end
% ========================================================================
% SUBFUNCTION: times = getTimes(from, to, events, frames)
% ========================================================================
% Gets the frame values from and to a particular event.
function [times, index] = getTimes(from, to, events, frames)
if length(frames) ~= length(events)
error('Event and frame vector must be the same length...')
end
% find the index of the first occuring 'from' event
[fromNum, fromIndex] = getFrame(from, events, frames);
fromIndex = fromIndex(1);
fromNum = fromNum(1);
% find the index of the first 'to' event that follows after the 'from' event
[toNum, toIndex] = getFrame(to, events, frames);
for i = 1:length(toNum)
if toIndex(i) > fromIndex,
toNum = toNum(i);
toIndex = toIndex(i);
times = [fromNum, toNum];
index = [fromIndex(1), toIndex(1)];
return
end
end
% if we get here, the 'to' event actually comes before the 'from' event
% in which case we need to wrap and have 2 parts to the frame values
toIndex = toIndex(1);
toNum = toNum(1);
times = [fromNum, frames(end) ; frames(1), toNum];
index = [fromIndex(1), toIndex(1)];
% ========================================================================
% SUBFUNCTION: [frameNum, frameIndex] = getFrame(event, eventList, frameList)
% ========================================================================
% Gets the frame number & index of a particular event from a frameList
function [frameNum, frameIndex] = getFrame(event, eventList, frameList)