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plotALL_Prepare_AngTrqPowEMG.m
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plotALL_Prepare_AngTrqPowEMG.m
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%% plotAll_MF_MeanBased
%
% Process all data, finding means
% ##################################
% SET 1 : ML SLOW
% SET 2 : ML FAST
% SET 3 : AP SLOW
% SET 4 : AP FAST
% ##################################
clear variables; close all; clc;
%% Set info
subjects = 1:10; % Dropped subject 3 in piece collection
g = 9.81;
col = jet(8); col(1:4,:) = col(4:-1:1,:); % Swap colors of first four
colb = [0.75 0.75 0.75];
lin1 = {'<','<','<','<','>','>','>','>'};
lin2 = {'v','v','v','v','^','^','^','^'};
linw = 0.5;
fnz = 10;
mrksiz1 = 3;
%% Pre alloc
% (only partially, as repetitions may vary per subject)
nsmpl = 50;
% Original time series
eventDatab = zeros(300,1,4,10); % data irep iset isubj (zeros, not NaN!!)
jAngDatab = NaN(300,9,3,1,4,10);
jAngDataDb = NaN(300,9,3,1,4,10);
jTrqDatab = NaN(300,9,3,1,4,10);
% comDataDb = NaN(300,10,3,1,4,10);
emgDatab = NaN(3000,12,1,4,10);
% fDatab = NaN(3000,12,1,4,10);
eventDatap = zeros(300,1,8,4,10); % data irep ipert iset isubj
jAngDatap = NaN(300,9,3,1,8,4,10);
jAngDataDp = NaN(300,9,3,1,8,4,10);
jTrqDatap = NaN(300,9,3,1,8,4,10);
% comDataDp = NaN(300,10,3,1,8,4,10);
emgDatap = NaN(3000,12,1,8,4,10);
% fDatap = NaN(3000,12,1,8,4,10);
% Data in resamples sequence
% NOTE : THE LAST NUMBER IS THE NUMBER OF SEQUENCES (5): TOR-HSR, HSR-TOL, TOL-HSL, HSL-TOR, TOR-TOR
nseq = 7;
jAngDatabt = NaN(nsmpl,9,3,1,4,10,nseq);
jAngDataDbt = NaN(nsmpl,9,3,1,4,10,nseq);
jTrqDatabt = NaN(nsmpl,9,3,1,4,10,nseq);
jPowDatabt = NaN(nsmpl,9,3,1,4,10,nseq);
% jEgyNegDatabt = NaN(nsmpl,9,3,1,4,10,nseq);
% jEgyPosDatabt = NaN(nsmpl,9,3,1,4,10,nseq);
% comDataDbt = NaN(nsmpl,10,3,1,4,10,nseq);
emgDatabt = NaN(nsmpl,12,1,4,10,nseq);
% fDatabt = NaN(nsmpl,12,1,4,10,nseq);
jAngDatapt = NaN(nsmpl,9,3,1,8,4,10,nseq);
jAngDataDpt = NaN(nsmpl,9,3,1,8,4,10,nseq);
jTrqDatapt = NaN(nsmpl,9,3,1,8,4,10,nseq);
jPowDatapt = NaN(nsmpl,9,3,1,8,4,10,nseq);
% jEgyNegDatapt = NaN(nsmpl,9,3,1,8,4,10,nseq);
% jEgyPosDatapt = NaN(nsmpl,9,3,1,8,4,10,nseq);
% comDataDpt = NaN(nsmpl,10,3,1,8,4,10,nseq);
emgDatapt = NaN(nsmpl,12,1,8,4,10,nseq);
% fDatapt = NaN(nsmpl,12,1,8,4,10,nseq);
% Data in events
nevt = 6;
tDatabe = NaN(nevt,1,4,10);
tDatape = NaN(nevt,1,8,4,10);
% Scaled constants
% w0 = NaN(4,10); % XCOM variable
%% Collecting data
% Collect data
for isubj = subjects
getInfo;
% Load Marker piece
load([subjroot '\pieceMarker.mat']);
% Load Event piece
load([subjroot '\pieceEvent.mat']);
% Load EMG piece
load([subjroot '\pieceEMG.mat']);
% Load force piece (Tycho)
% load([subjroot '\pieceForce.mat']);
% Sample freq
fs_mrk = pieceMarker.Set(1).Pert(1).Data.MarkerFrameRate;
fs_emg = pieceEMG.Set(1).Pert(1).Data.EMGFrameRate;
% Loop through the sets
missed = 0;
for iset = 1:4
% #####################################
% ## BASELINE ##
% #####################################
% Time series
eHSR = squeeze(pieceEvent.Set(iset).Base(1).Data.GaitPhaseM(:,2,:));
eTOL = squeeze(pieceEvent.Set(iset).Base(1).Data.GaitPhaseM(:,6,:));
eHSL = squeeze(pieceEvent.Set(iset).Base(1).Data.GaitPhaseM(:,3,:));
eTOR = squeeze(pieceEvent.Set(iset).Base(1).Data.GaitPhaseM(:,5,:));
event = eHSR + eTOL + eHSL + eTOR;
event(1:65,:) = 0; % Remove all before TOR, so we know order is correct (start with HSR)
event([50 65],:) = 1; % Insert start of sequence at TOR (and fictional end)
eventDatab(:,1:size(event,2),iset,isubj) = event;
dat = pieceMarker.Set(iset).Base(1).Data.JointAngData;
jAngDatab(:,:,:,1:size(dat,4),iset,isubj) = dat;
dat = pieceMarker.Set(iset).Base(1).Data.JointAngDataD;
jAngDataDb(:,:,:,1:size(dat,4),iset,isubj) = dat;
dat = pieceMarker.Set(iset).Base(1).Data.JointTrqData;
jTrqDatab(:,:,:,1:size(dat,4),iset,isubj) = dat;
% dat = pieceMarker.Set(iset).Base(1).Data.COMDataD;
% comDataDb(:,:,:,1:size(dat,4),iset,isubj) = dat;
dat = pieceEMG.Set(iset).Base(1).Data.EMGData;
emgDatab(:,:,1:size(dat,3),iset,isubj) = dat;
% dat = pieceForce.Set(iset).Base(1).Data.ForceData;
% fDatab(:,:,1:size(dat,3),iset,isubj) = dat;
% #####################################
% ## PERTURBATIONS ##
% #####################################
for ipert = 1:8
eHSR = squeeze(pieceEvent.Set(iset).Pert(ipert).Data.GaitPhaseM(:,2,:));
eTOL = squeeze(pieceEvent.Set(iset).Pert(ipert).Data.GaitPhaseM(:,6,:));
eHSL = squeeze(pieceEvent.Set(iset).Pert(ipert).Data.GaitPhaseM(:,3,:));
eTOR = squeeze(pieceEvent.Set(iset).Pert(ipert).Data.GaitPhaseM(:,5,:));
event = eHSR + eTOL + eHSL + eTOR;
event(1:65,:) = 0; % Remove all before TOR, so we know order is correct (start with HSR)
event([50 65],:) = 1; % Insert start and end of perturbation
eventDatap(:,1:size(event,2),ipert,iset,isubj) = event;
dat = pieceMarker.Set(iset).Pert(ipert).Data.JointAngData;
jAngDatap(:,:,:,1:size(dat,4),ipert,iset,isubj) = dat;
dat = pieceMarker.Set(iset).Pert(ipert).Data.JointAngDataD;
jAngDataDp(:,:,:,1:size(dat,4),ipert,iset,isubj) = dat;
dat = pieceMarker.Set(iset).Pert(ipert).Data.JointTrqData;
jTrqDatap(:,:,:,1:size(dat,4),ipert,iset,isubj) = dat;
% dat = pieceMarker.Set(iset).Pert(ipert).Data.COMDataD;
% comDataDp(:,:,:,1:size(dat,4),ipert,iset,isubj) = dat;
dat = pieceEMG.Set(iset).Pert(ipert).Data.EMGData;
emgDatap(:,:,1:size(dat,3),ipert,iset,isubj) = dat;
% dat = pieceForce.Set(iset).Pert(ipert).Data.ForceData;
% fDatap(:,:,1:size(dat,3),ipert,iset,isubj) = dat;
end
end
end
%% Free some memory
clear pieceMarker pieceForce pieceEvent foo dat
clear pieceForce
%% Make filler zeros equal to NaN
jAngDatab(jAngDatab == 0) = NaN;
jAngDataDb(jAngDataDb == 0) = NaN;
jTrqDatab(jTrqDatab == 0) = NaN;
% comDataDb(comDataDb == 0) = NaN;
emgDatab(emgDatab == 0) = NaN;
% fDatab(fDatab == 0) = NaN;
jAngDatap(jAngDatap == 0) = NaN;
jAngDataDp(jAngDataDp == 0) = NaN;
jTrqDatap(jTrqDatap == 0) = NaN;
% comDataDp(comDataDp == 0) = NaN;
emgDatap(emgDatap == 0) = NaN;
% fDatap(fDatap == 0) = NaN;
%% Downsample EMG data
% Not sure yet if I want to do this.
% But required if you use events based on markerdata
emgDatab = downsample(emgDatab,10);
emgDatap = downsample(emgDatap,10);
% fDatab = downsample(fDatab,10);
% fDatap = downsample(fDatap,10);
%% Get joint power
jPowDatab = jAngDataDb.*jTrqDatab;
jPowDatap = jAngDataDp.*jTrqDatap;
%% Remove outliers
%
% NOTE: THERE ARE SOME MAJOR ISSUES WITH SUBJECT 10 ANGLES & TORQUES IN SET 2
% (fast, ML)
% Joint Angles & velocities
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jAngDatab - repmat(nanmedian(jAngDatab,4) , [1 1 1 size(jAngDatab,4) 1 1])) > repmat( prctile( abs(jAngDatab - repmat(nanmedian(jAngDatab,4) , [1 1 1 size(jAngDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jAngDatab,4) 1 1]) ) > outSmpl;
outMaskB = sum(abs(jAngDatab)>0.5*pi,1) > 5;
outMaskC = sum( abs(jAngDataDb - repmat(nanmedian(jAngDataDb,4) , [1 1 1 size(jAngDataDb,4) 1 1])) > repmat( prctile( abs(jAngDataDb - repmat(nanmedian(jAngDataDb,4) , [1 1 1 size(jAngDataDb,4) 1 1])) , prct , 4 ), [1 1 1 size(jAngDataDb,4) 1 1]) ) > outSmpl;
outMaskD = sum(abs(jAngDataDb)>11,1) > 1;
outMask = outMaskA | outMaskB | outMaskC | outMaskD;
outMask = repmat(outMask, [size(jAngDatab,1) 1 1 1 1 1]);
% foo = jAngDataDb;
% foo(outMask) = NaN;
% return;
jAngDatab(outMask) = NaN;
jAngDataDb(outMask) = NaN;
prct = 99; % Repeat once more for large but short duration deviations
outSmpl = 10;
outMaskA = sum( abs(jAngDatab - repmat(nanmedian(jAngDatab,4) , [1 1 1 size(jAngDatab,4) 1 1])) > repmat( prctile( abs(jAngDatab - repmat(nanmedian(jAngDatab,4) , [1 1 1 size(jAngDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jAngDatab,4) 1 1]) ) > outSmpl;
outMaskC = sum( abs(jAngDataDb - repmat(nanmedian(jAngDataDb,4) , [1 1 1 size(jAngDataDb,4) 1 1])) > repmat( prctile( abs(jAngDataDb - repmat(nanmedian(jAngDataDb,4) , [1 1 1 size(jAngDataDb,4) 1 1])) , prct , 4 ), [1 1 1 size(jAngDataDb,4) 1 1]) ) > outSmpl;
outMask = outMaskA | outMaskC;
outMask = repmat(outMask, [size(jAngDatab,1) 1 1 1 1 1]);
jAngDatab(outMask) = NaN;
jAngDataDb(outMask) = NaN;
% Remove subject 10 in set 2
jAngDatab(:,:,:,:,2,10) = NaN;
jAngDataDb(:,:,:,:,2,10) = NaN;
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jAngDatap - repmat(nanmedian(jAngDatap,4) , [1 1 1 size(jAngDatap,4) 1 1 1])) > repmat( prctile( abs(jAngDatap - repmat(nanmedian(jAngDatap,4) , [1 1 1 size(jAngDatap,4) 1 1 1])) , prct , 4 ), [1 1 1 size(jAngDatap,4) 1 1 1]) ) > outSmpl;
outMaskB = sum(abs(jAngDatap)> 0.75*pi,1) > 5;
outMaskC = sum( abs(jAngDataDp - repmat(nanmedian(jAngDataDp,4) , [1 1 1 size(jAngDataDp,4) 1 1 1])) > repmat( prctile( abs(jAngDataDp - repmat(nanmedian(jAngDataDp,4) , [1 1 1 size(jAngDataDp,4) 1 1 1])) , prct , 4 ), [1 1 1 size(jAngDataDp,4) 1 1 1]) ) > outSmpl;
outMaskD = sum(abs(jAngDataDp)> 11,1) > 1;
outMask = outMaskA | outMaskB | outMaskC | outMaskD;
outMask = repmat(outMask, [size(jAngDatap,1) 1 1 1 1 1]);
% foo = jAngDatap;
% bar = jAngDataDp;
% foo(outMask) = NaN;
% bar(outMask) = NaN;
% return;
jAngDatap(outMask) = NaN;
jAngDataDp(outMask) = NaN;
% prct = 99; % Repeat once more for large but short duration deviations
% outSmpl = 10;
% outMaskA = sum( abs(jAngDatap - repmat(nanmedian(jAngDatap,4) , [1 1 1 size(jAngDatap,4) 1 1 1])) > repmat( prctile( abs(jAngDatap - repmat(nanmedian(jAngDatap,4) , [1 1 1 size(jAngDatap,4) 1 1 1])) , prct , 4 ), [1 1 1 size(jAngDatap,4) 1 1 1]) ) > outSmpl;
% outMaskC = sum( abs(jAngDataDp - repmat(nanmedian(jAngDataDp,4) , [1 1 1 size(jAngDataDp,4) 1 1 1])) > repmat( prctile( abs(jAngDataDp - repmat(nanmedian(jAngDataDp,4) , [1 1 1 size(jAngDataDp,4) 1 1 1])) , prct , 4 ), [1 1 1 size(jAngDataDp,4) 1 1 1]) ) > outSmpl;
% outMask = outMaskA | outMaskC;
% outMask = repmat(outMask, [size(jAngDatap,1) 1 1 1 1 1]);
% jAngDatap(outMask) = NaN;
% jAngDataDp(outMask) = NaN;
% Remove subject 10 in set 2
jAngDatap(:,:,:,:,:,2,10) = NaN;
jAngDataDp(:,:,:,:,:,2,10) = NaN;
% Joint Torques
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jTrqDatab - repmat(nanmedian(jTrqDatab,4) , [1 1 1 size(jTrqDatab,4) 1 1])) > repmat( prctile( abs(jTrqDatab - repmat(nanmedian(jTrqDatab,4) , [1 1 1 size(jTrqDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jTrqDatab,4) 1 1]) ) > outSmpl;
outMaskB = sum(abs(jTrqDatab)>170,1) > 5;
outMask = outMaskA | outMaskB;
outMask = repmat(outMask, [size(jTrqDatab,1) 1 1 1 1 1]);
% foo = jTrqDatab;
% foo(outMask) = NaN;
% return;
jTrqDatab(outMask) = NaN;
prct = 99; % Repeat once more for large but short duration deviations
outSmpl = 10;
outMaskA = sum( abs(jTrqDatab - repmat(nanmedian(jTrqDatab,4) , [1 1 1 size(jTrqDatab,4) 1 1])) > repmat( prctile( abs(jTrqDatab - repmat(nanmedian(jTrqDatab,4) , [1 1 1 size(jTrqDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jTrqDatab,4) 1 1]) ) > outSmpl;
outMask = repmat(outMaskA, [size(jTrqDatab,1) 1 1 1 1 1]);
jTrqDatab(outMask) = NaN;
% Remove subject 10 in set 2
jTrqDatab(:,:,:,:,2,10) = NaN;
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jTrqDatap - repmat(nanmedian(jTrqDatap,4) , [1 1 1 size(jTrqDatap,4) 1 1])) > repmat( prctile( abs(jTrqDatap - repmat(nanmedian(jTrqDatap,4) , [1 1 1 size(jTrqDatap,4) 1 1])) , prct , 4 ), [1 1 1 size(jTrqDatap,4) 1 1]) ) > outSmpl;
outMaskB = sum(abs(jTrqDatap)>170,1) > 5;
outMask = outMaskA | outMaskB;
outMask = repmat(outMask, [size(jTrqDatap,1) 1 1 1 1 1]);
% foo = jTrqDatap;
% foo(outMask) = NaN;
jTrqDatap(outMask) = NaN;
% return;
% prct = 99; % Repeat once more for large but short duration deviations
% outSmpl = 10;
% outMaskA = sum( abs(jTrqDatap - repmat(nanmedian(jTrqDatap,4) , [1 1 1 size(jTrqDatap,4) 1 1])) > repmat( prctile( abs(jTrqDatap - repmat(nanmedian(jTrqDatap,4) , [1 1 1 size(jTrqDatap,4) 1 1])) , prct , 4 ), [1 1 1 size(jTrqDatap,4) 1 1]) ) > outSmpl;
% outMask = repmat(outMaskA, [size(jTrqDatap,1) 1 1 1 1 1]);
% foo = jTrqDatap;
% foo(outMask) = NaN;
% % jTrqDatap(outMask) = NaN;
% Remove subject 10 in set 2
jTrqDatap(:,:,:,:,2,10) = NaN;
% Joint Power
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jPowDatab - repmat(nanmedian(jPowDatab,4) , [1 1 1 size(jPowDatab,4) 1 1])) > repmat( prctile( abs(jPowDatab - repmat(nanmedian(jPowDatab,4) , [1 1 1 size(jPowDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jPowDatab,4) 1 1]) ) > outSmpl;
outMaskB = sum(abs(jPowDatab)>170,1) > 5;
outMask = outMaskA | outMaskB;
outMask = repmat(outMask, [size(jPowDatab,1) 1 1 1 1 1]);
% foo = jPowDatab;
% foo(outMask) = NaN;
jPowDatab(outMask) = NaN;
prct = 99; % Repeat once more for large but short duration deviations
outSmpl = 10;
outMaskA = sum( abs(jPowDatab - repmat(nanmedian(jPowDatab,4) , [1 1 1 size(jPowDatab,4) 1 1])) > repmat( prctile( abs(jPowDatab - repmat(nanmedian(jPowDatab,4) , [1 1 1 size(jPowDatab,4) 1 1])) , prct , 4 ), [1 1 1 size(jPowDatab,4) 1 1]) ) > outSmpl;
outMask = repmat(outMaskA, [size(jPowDatab,1) 1 1 1 1 1]);
jPowDatab(outMask) = NaN;
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(jPowDatap - repmat(nanmedian(jPowDatap,4) , [1 1 1 size(jPowDatap,4) 1 1])) > repmat( prctile( abs(jPowDatap - repmat(nanmedian(jPowDatap,4) , [1 1 1 size(jPowDatap,4) 1 1])) , prct , 4 ), [1 1 1 size(jPowDatap,4) 1 1]) ) > outSmpl;
outMaskB = sum(abs(jPowDatap)>170,1) > 5;
outMask = outMaskA | outMaskB;
outMask = repmat(outMask, [size(jPowDatap,1) 1 1 1 1 1]);
% foo = jPowDatap;
% foo(outMask) = NaN;
jPowDatap(outMask) = NaN;
% EMG
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(emgDatab - repmat(nanmedian(emgDatab,3) , [1 1 size(emgDatab,3) 1 1])) > repmat( prctile( abs(emgDatab - repmat(nanmedian(emgDatab,3) , [1 1 size(emgDatab,3) 1 1])) , prct , 3 ), [1 1 size(emgDatab,3) 1 1]) ) > outSmpl;
outMask = outMaskA;
outMask = repmat(outMask, [size(emgDatab,1) 1 1 1 1 1]);
% foo = emgDatab;
% foo(outMask) = NaN;
% return;
emgDatab(outMask) = NaN;
prct = 90;
outSmpl = 100;
outMaskA = sum( abs(emgDatap - repmat(nanmedian(emgDatap,3) , [1 1 size(emgDatap,3) 1 1 1])) > repmat( prctile( abs(emgDatap - repmat(nanmedian(emgDatap,3) , [1 1 size(emgDatap,3) 1 1 1])) , prct , 3 ), [1 1 size(emgDatap,3) 1 1 1]) ) > outSmpl;
outMask = outMaskA;
outMask = repmat(outMask, [size(emgDatap,1) 1 1 1 1 1]);
% foo = emgDatab;
% foo(outMask) = NaN;
% return;
emgDatap(outMask) = NaN;
% Remove subject 10 adductor longi (Clipping Adductor Longi)
eDatab(:,[6 12],:,:,10) = NaN;
eDatap(:,[6 12],:,:,:,10) = NaN;
%% Get integrated joint power
% foo = jPowDatab; foo(foo>0) = 0;
% bar = jPowDatab; bar(bar<0) = 0;
% jEgyNegDatab = cumtrapz( foo , 1) ./ fs_mrk;
% jEgyPosDatab = cumtrapz( bar , 1) ./ fs_mrk;
%
% foo = jPowDatap; foo(foo>0) = 0;
% bar = jPowDatap; bar(bar<0) = 0;
% jEgyNegDatap = cumtrapz( foo , 1) ./ fs_mrk;
% jEgyPosDatap = cumtrapz( bar , 1) ./ fs_mrk;
%% Add belt velocity to global COM velocity
% for isubj = subjects
%
% getInfo;
%
% comDataDb(:,end,2,:,[1 3],isubj) = comDataDb(:,end,2,:,[1 3],isubj) + (2.25/3.6)*sqrt(subjleglen);
% comDataDp(:,end,2,:,:,[1 3],isubj) = comDataDp(:,end,2,:,:,[1 3],isubj) + (2.25/3.6).*sqrt(subjleglen);
%
% comDataDb(:,end,2,:,[2 4],isubj) = comDataDb(:,end,2,:,[2 4],isubj) + (4.5/3.6)*sqrt(subjleglen);
% comDataDp(:,end,2,:,:,[2 4],isubj) = comDataDp(:,end,2,:,:,[2 4],isubj) + (4.5/3.6).*sqrt(subjleglen);
%
% end
%% Get resampled time series
for isubj = subjects
for iset = 1:4
% Event based
foo = getEventData(eventDatab(:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,2,nevt) ./ fs_mrk;
tDatabe(:,1:size(foo,2),iset,isubj) = foo;
% Time sequence based
for iseq = 1:6
switch iseq
case 1
evts = [1 2]; % TOR-STOP
case 2
evts = [2 3]; % STOP-HSR
case 3
evts = [1 3]; % TOR-HSR
case 4
evts = [3 4]; % HSR-TOL
case 5
evts = [4 5]; % TOL-HSL
case 6
evts = [5 6]; % HSL-TOR
case 7
evts = [1 6]; % TOR-TOR
end
foo = getEventSequence(jAngDatab(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
jAngDatabt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
foo = getEventSequence(jAngDataDb(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
jAngDataDbt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
foo = getEventSequence(jTrqDatab(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
jTrqDatabt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
foo = getEventSequence(jPowDatab(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
jPowDatabt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
% foo = getEventSequence(jEgyNegDatab(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
% jEgyNegDatabt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
%
% foo = getEventSequence(jEgyPosDatab(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
% jEgyPosDatabt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
%
% foo = getEventSequence(comDataDb(:,:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,4,nsmpl,evts);
% comDataDbt(:,:,:,1:size(foo,4),iset,isubj,iseq) = foo;
foo = getEventSequence(emgDatab(:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,3,nsmpl,evts);
emgDatabt(:,:,1:size(foo,3),iset,isubj,iseq) = foo;
% foo = getEventSequence(fDatab(:,:,:,iset,isubj),eventDatab(:,:,iset,isubj),1,3,nsmpl,evts);
% fDatabt(:,:,1:size(foo,3),iset,isubj,iseq) = foo;
end
for ipert = 1:8
% Event based
foo = getEventData(eventDatap(:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,2,nevt) ./ fs_mrk;
tDatape(:,1:size(foo,2),ipert,iset,isubj) = foo;
% Time sequence based
for iseq = 1:6
switch iseq
case 1
evts = [1 2]; % Start(TOR)-STOP
case 2
evts = [2 3]; % STOP-HSR
case 3
evts = [1 3]; % Start-HSR
case 4
evts = [3 4]; % HSR-TOL
case 5
evts = [4 5]; % TOL-HSL
case 6
evts = [5 6]; % HSL-TOR
case 7
evts = [1 6]; % TOR-TOR
end
foo = getEventSequence(jAngDatap(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
jAngDatapt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
foo = getEventSequence(jAngDataDp(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
jAngDataDpt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
foo = getEventSequence(jTrqDatap(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
jTrqDatapt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
foo = getEventSequence(jPowDatap(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
jPowDatapt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
% foo = getEventSequence(jEgyNegDatap(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
% jEgyNegDatabt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
%
% foo = getEventSequence(jEgyPosDatap(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
% jEgyPosDatabt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
%
% foo = getEventSequence(comDataDp(:,:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,4,nsmpl,evts);
% comDataDpt(:,:,:,1:size(foo,4),ipert,iset,isubj,iseq) = foo;
%
foo = getEventSequence(emgDatap(:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,3,nsmpl,evts);
emgDatapt(:,:,1:size(foo,3),ipert,iset,isubj,iseq) = foo;
% foo = getEventSequence(fDatap(:,:,:,ipert,iset,isubj),eventDatap(:,:,ipert,iset,isubj),1,3,nsmpl,evts);
% fDatapt(:,:,1:size(foo,3),ipert,iset,iset,iseq) = foo;
end
end
end
end
% Clean up original storage matrices
clear eventDatab jAngDatab jAngDataDb jTrqDatab jPowDatab jEgyNegDatab jEgyPosDatab comDataDb emgDatab ...
eventDatap jAngDatap jAngDataDp jTrqDatap jPowDatap jEgyNegDatap jEgyPosDatap comDataDp emgDatap;
% clear fDatab fDatap
%% Make filler zeros equal to NaN, again
% Zero data can occur due "filling" of matrices
% (except for in eventData, as here the zero's are required
jAngDatabt(jAngDatabt == 0) = NaN;
jAngDataDbt(jAngDataDbt == 0) = NaN;
jTrqDatabt(jTrqDatabt == 0) = NaN;
jPowDatabt(jPowDatabt == 0) = NaN;
% comDataDbt(comDataDbt == 0) = NaN;
emgDatabt(emgDatabt == 0) = NaN;
% fDatabt(fDatabt == 0) = NaN;
jAngDatapt(jAngDatapt == 0) = NaN;
jAngDataDpt(jAngDataDpt == 0) = NaN;
jTrqDatapt(jTrqDatapt == 0) = NaN;
jPowDatapt(jPowDatapt == 0) = NaN;
% comDataDpt(comDatDpt == 0) = NaN;
emgDatapt(emgDatapt == 0) = NaN;
% fDatapt(fDatapt == 0) = NaN;
tDatabe(tDatabe == 0) = NaN;
tDatape(tDatape == 0) = NaN;
%% Do scaling
%
% Note: you don't have to scale angles, as these are already dimensionless
% Do scaling
for isubj = subjects
getInfo;
for iset = 1:4
% Scale to body weight and height
jTrqDatabt(:,:,:,:,iset,isubj,:) = jTrqDatabt(:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
jTrqDatapt(:,:,:,:,:,iset,isubj,:) = jTrqDatapt(:,:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
jPowDatabt(:,:,:,:,iset,isubj,:) = jPowDatabt(:,:,:,:,iset,isubj,:) ./ (subjmass*sqrt(g)*(subjheight.^1.5));
jPowDatapt(:,:,:,:,:,iset,isubj,:) = jPowDatapt(:,:,:,:,:,iset,isubj,:) ./ (subjmass*sqrt(g)*(subjheight.^1.5));
% jEgyNegDatabt(:,:,:,:,iset,isubj,:) = jEgyNegDatabt(:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
% jEgyPosDatabt(:,:,:,:,iset,isubj,:) = jEgyPosDatabt(:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
%
% jEgyNegDatapt(:,:,:,:,:,iset,isubj,:) = jEgyNegDatapt(:,:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
% jEgyPosDatapt(:,:,:,:,:,iset,isubj,:) = jEgyPosDatapt(:,:,:,:,:,iset,isubj,:) ./ (subjmass*g*subjheight);
% COM velocity (requires COM position and feet positions)
end
% fDatabt(:,:,:,:,isubj,:) = fDatabt(:,:,:,:,isubj,:) / subjmass;
% fDatapt(:,:,:,:,:,isubj,:) = fDatapt(:,:,:,:,:,isubj,:) / subjmass;
end
% EMG scaling to individual muscles, median of max values in the baseline.
% Scale all sequences of the same muscle the same
scalemask = nanmedian(max(max(emgDatabt,[],1),[],6),3);
emgDatabt = emgDatabt ./ repmat(scalemask,[size(emgDatabt,1) 1 size(emgDatabt,3) 1 1 nseq]);
emgDatapt = emgDatapt ./ permute( repmat(scalemask,[size(emgDatapt,1) 1 size(emgDatapt,3) 1 1 nseq 8]) , [1:3 7 4:6]);
%% Get repetition averages
% Averages
jAngDatabt_m1 = squeeze(nanmean(jAngDatabt,4));
jAngDataDbt_m1 = squeeze(nanmean(jAngDataDbt,4));
jTrqDatabt_m1 = squeeze(nanmean(jTrqDatabt,4));
jPowDatabt_m1 = squeeze(nanmean(jPowDatabt,4));
% jEgyNegDatabt_m1 = squeeze(nanmean(jEgyNegDatabt,4));
% jEgyPosDatabt_m1 = squeeze(nanmean(jEgyPosDatabt,4));
% comDataDbt_m1 = squeeze(nanmean(comDataDbt,4));
emgDatabt_m1 = squeeze(nanmean(emgDatabt,3));
% fDatabt_m1 = squeeze(nanmean(fDatabt,3));
jAngDatapt_m1 = squeeze(nanmean(jAngDatapt,4));
jAngDataDpt_m1 = squeeze(nanmean(jAngDataDpt,4));
jTrqDatapt_m1 = squeeze(nanmean(jTrqDatapt,4));
jPowDatapt_m1 = squeeze(nanmean(jPowDatapt,4));
% jEgyNegDatapt_m1 = squeeze(nanmean(jEgyNegDatapt,4));
% jEgyPosDatapt_m1 = squeeze(nanmean(jEgyPosDatapt,4));
% comDataDpt_m1 = squeeze(nanmean(comDataDpt,4));
emgDatapt_m1 = squeeze(nanmean(emgDatapt,3));
% fDatapt_m1 = squeeze(nanmean(fDatapt,3));
tDatabe_m1 = squeeze(nanmean(tDatabe,2));
tDatape_m1 = squeeze(nanmean(tDatape,2));
% Standard deviations
jAngDatabt_std1 = squeeze(nanstd(jAngDatabt,[],4));
jAngDataDbt_std1 = squeeze(nanstd(jAngDataDbt,[],4));
jTrqDatabt_std1 = squeeze(nanstd(jTrqDatabt,[],4));
jPowDatabt_std1 = squeeze(nanstd(jPowDatabt,[],4));
% comDataDbt_std1 = squeeze(nanstd(comDataDbt,[],4));
emgDatabt_std1 = squeeze(nanstd(emgDatabt,[],3));
%
jAngDatapt_std1 = squeeze(nanstd(jAngDatapt,[],4));
jAngDataDpt_std1 = squeeze(nanstd(jAngDataDpt,[],4));
jTrqDatapt_std1 = squeeze(nanstd(jTrqDatapt,[],4));
jPowDatapt_std1 = squeeze(nanstd(jPowDatapt,[],4));
% comDataDpt_std1 = squeeze(nanstd(comDataDpt,[],4));
emgDatapt_std1 = squeeze(nanstd(emgDatapt,[],3));
%% Get subject averages
% Averages
jAngDatabt_m2 = squeeze(nanmean(jAngDatabt_m1,5));
jAngDataDbt_m2 = squeeze(nanmean(jAngDataDbt_m1,5));
jTrqDatabt_m2 = squeeze(nanmean(jTrqDatabt_m1,5));
jPowDatabt_m2 = squeeze(nanmean(jPowDatabt_m1,5));
% jEgyNegDatabt_m2 = squeeze(nanmean(jEgyNegDatabt_m1,5));
% jEgyPosDatabt_m2 = squeeze(nanmean(jEgyPosDatabt_m1,5));
% comDataDbt_m2 = squeeze(nanmean(comDataDbt_m1,5));
emgDatabt_m2 = squeeze(nanmean(emgDatabt_m1,4));
% fDatabt_m2 = squeeze(nanmean(fDatabt_m1,4));
jAngDatapt_m2 = squeeze(nanmean(jAngDatapt_m1,6));
jAngDataDpt_m2 = squeeze(nanmean(jAngDataDpt_m1,6));
jTrqDatapt_m2 = squeeze(nanmean(jTrqDatapt_m1,6));
jPowDatapt_m2 = squeeze(nanmean(jPowDatapt_m1,6));
% jEgyNegDatapt_m2 = squeeze(nanmean(jEgyNegDatapt_m1,6));
% jEgyPosDatapt_m2 = squeeze(nanmean(jEgyPosDatapt_m1,6));
% comDataDpt_m2 = squeeze(nanmean(comDataDpt_m1,6));
emgDatapt_m2 = squeeze(nanmean(emgDatapt_m1,5));
% fDatapt_m2 = squeeze(nanmean(fDatapt_m1,5));
tDatabe_m2 = squeeze(nanmean(tDatabe_m1,3));
tDatape_m2 = squeeze(nanmean(tDatape_m1,4));
% Averages of within-subject standard deviations
jAngDatabt_std2b = squeeze(nanmean(jAngDatabt_std1,5));
jAngDataDbt_std2b = squeeze(nanmean(jAngDataDbt_std1,5));
jTrqDatabt_std2b = squeeze(nanmean(jTrqDatabt_std1,5));
jPowDatabt_std2b = squeeze(nanmean(jPowDatabt_std1,5));
% jEgyNegDatabt_std2b = squeeze(nanmean(jEgyNegDatabt_std1,5));
% jEgyPosDatabt_std2b = squeeze(nanmean(jEgyPosDatabt_sdt1,5));
% comDataDbt_std2b = squeeze(nanmean(comDataDbt_sdt1,5));
emgDatabt_std2b = squeeze(nanmean(emgDatabt_std1,4));
jAngDatapt_std2b = squeeze(nanmean(jAngDatapt_std1,6));
jAngDataDpt_std2b = squeeze(nanmean(jAngDataDpt_std1,6));
jTrqDatapt_std2b = squeeze(nanmean(jTrqDatapt_std1,6));
jPowDatapt_std2b = squeeze(nanmean(jPowDatapt_std1,6));
% jEgyNegDatapt_std2b = squeeze(nanmean(jEgyNegDatapt_std1,6));
% jEgyPosDatapt_std2b = squeeze(nanmean(jEgyPosDatapt_std1,6));
% comDataDpt_std2b = squeeze(nanmean(comDataDpt_std1,6));
emgDatapt_std2b = squeeze(nanmean(emgDatapt_std1,5));
% Standard deviations
jAngDatabt_std2 = squeeze(nanstd(jAngDatabt_m1,[],5));
jAngDataDbt_std2 = squeeze(nanstd(jAngDataDbt_m1,[],5));
jTrqDatabt_std2 = squeeze(nanstd(jTrqDatabt_m1,[],5));
jPowDatabt_std2 = squeeze(nanstd(jPowDatabt_m1,[],5));
% jEgyNegDatabt_std2 = squeeze(nanstd(jEgyNegDatabt_m1,[],5));
% jEgyPosDatabt_std2 = squeeze(nanstd(jEgyPosDatabt_m1,[],5));
% comDataDbt_std2 = squeeze(nanstd(comDataDbt_m1,[],5));
emgDatabt_std2 = squeeze(nanstd(emgDatabt_m1,[],4));
jAngDatapt_std2 = squeeze(nanstd(jAngDatapt_m1,[],6));
jAngDataDpt_std2 = squeeze(nanstd(jAngDataDpt_m1,[],6));
jTrqDatapt_std2 = squeeze(nanstd(jTrqDatapt_m1,[],6));
jPowDatapt_std2 = squeeze(nanstd(jPowDatapt_m1,[],6));
% jEgyNegDatapt_std2 = squeeze(nanmean(jEgyNegDatapt_m1,[],6));
% jEgyPosDatapt_std2 = squeeze(nanmean(jEgyPosDatapt_m1,[],6));
% comDataDpt_std2 = squeeze(nanstd(comDataDpt_m1,[],6));
emgDatapt_std2 = squeeze(nanstd(emgDatapt_m1,[],5));
tDatabe_std2 = squeeze(nanstd(tDatabe_m1,[],3));
tDatape_std2 = squeeze(nanstd(tDatape_m1,[],4));
%% Project average resmapled time-series back on time axis
% Using repetition average durations of the sequences
% This is non-cumulative, so the time axis resets at every phase
% (i.e. starts at 0)
% Convert event times to matching sequence durations
tDatabt_m2 = zeros(7,4);
tDatabt_m2(1,:) = 0.15; % TOR-PertEnd
tDatabt_m2(2,:) = tDatabe_m2(3,:) - 0.15; % PertEnd-HSR
tDatabt_m2(3:6,:) = tDatabe_m2(3:6,:); % Remaining sequence durations
tDatabt_m2(7,:) = sum(tDatabe_m2(3:6,:),1); % TOR-TOR2
tDatabt_m2 = repmat( [(0:nsmpl-1)/nsmpl].' , [1 4 7]) .* permute( repmat( tDatabt_m2 , [1 1 nsmpl]) , [3 2 1]);
tDatapt_m2 = zeros(7,8,4);
tDatapt_m2(1,:,:) = 0.15; % TOR-PertEnd
tDatapt_m2(2,:,:) = tDatape_m2(3,:,:) - 0.15; % PertEnd-HSR
tDatapt_m2(3:6,:,:) = tDatape_m2(3:6,:,:); % Remaining sequence durations
tDatapt_m2(7,:,:) = sum(tDatape_m2(3:6,:,:),1); % TOR-TOR2
tDatapt_m2 = repmat( [(0:nsmpl-1)/nsmpl].' , [1 8 4 7]) .* permute( repmat( tDatapt_m2, [1 1 1 nsmpl]) , [4 2 3 1]);