using ruud meulenbroek david rosenbaum, mary klein breteler, bert steenbergen 12 may 2005 in a...

Using

Ruud Meulenbroek David Rosenbaum, Mary Klein Breteler, Bert Steenbergen

12 May 2005

in a Prehension Study

Overview1. Sneak Preview

• Report of experimental results to colleagues2. Use of Matlab

• Principle• File I/O• Data preprocessing• Finding relevant time indices in behaviour• Plotting• Calculating critical performance variables• Time-normalizing functions• Creating a data matrix for statistical analyses• Write output file for SPSSX

Topic: “Hand shaping in grasping”

• Background– Maximum aperture is linearly scaled to object size

(Jeannerod 1981; Paulignan et al. 1991,1997; Smeets, 1999)

• Research questions– Also when being blindfolded?– What about the rotations of the joints in the hand?

Newell, K. M., Scully, D. M., McDonald, P. V., & Baillargeon, R.  (1989).  Task constraints and infant grip configurations.  Developmental Psychobiology, 22, 817-832.

Sneak preview- Report of experimental results to colleagues -

Theory

• Motion planning– Entails goal-posture selection– Tuned to multiple task constraints

Rosenbaum, D. A., Meulenbroek, R.G.J., Jansen, C., Vaughan, J. (2002).Posture-based motion planning: Applications to grasping.Psychological Review, 108, 708-734.

Meulenbroek, R.G.J., Kappers, A.L., & Mutsaarts, M. (2001). Does haptic space play a role in the planning and execution of grasping movements? Poster presented at the 'Neural control of space coding and action production' meeting in Lyon (France), March 22-24, 2001

Sneak preview

Simulation

Slow movementFast movement

The orientation of the‘opposition axis’

reflects the final arm-hand posture

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Experiment

• 10 Participants• 9 Objects (cylinders of appr. 20 cm height and a

diameter of 0.3, 1.3, 2.3, 3.3, 4.3, 5.3, 6.3, 7.3, 8.3 cm)

• 2 Modality Conditions: (Vision present versus absent; eyes open versus closed; ABBA counterbalancing)

• 10 Replications (resulting in 180 trials per subject)

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Experimental Task– The participant sat comfortably at a table...

– with the left and right hand on two pieces of sandpaper fixated on the table top, appr. 20 cm in front of left and right shoulder

– At the start of each trial the experimenter placed a cylinder in the non-dominant hand of the participant

– The participant held the bottom half of the cylinder with opposing thumb and fingers (of the non-dominant hand)

– An acoustic go-signal was presented

– The participant’s task was to grasp with the dominant hand the top half of the cylinder that he/she held in the non-dominant hand

– In half the trials the participant was asked to close his/her eyes before the cylinder was placed in his/her non-dominant hand

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Method

Optotrak 3020 (NDI, Canada)

Infrared cameras

Data acquisition

Infrared light emitting diodes

Trunk Hand Finger joints

ForearmUpper arm

Pen

“Rigid bodies”

Bouwhuisen, C.F., Meulenbroek, R.G.J., & Thomassen, A.J.W.M. (2002). A 3D motion-tracking method in graphonomic research: Possible applications in future handwriting recognition studies. International Journal of Pattern Recognition, 35(5), 1039-1047 .

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Data acquisition

– Optotrak 3020; two time-locked camera systems– 8 IREDs on the joints of the hand– Sampling rate of 200 Hz– Recording interval of 3 s– Preprocessing: low-pass filtering (<8 Hz)

+

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IRED configuration and aperture index

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2

3

4

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6

8

Aperture (‘opposition axis’ )

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Use of Matlab

KISS : Keep It Simple Stupid (David Rosenbaum)

Principle

Use of Matlab Constants, loop parameters, toggle switches

% segmentation.m%clear all;

% constantsFs=200; % Hzsec=1/Fs;filtfreq_low=8;filtfreq_high=0.0;

% number of subjects and data filesibsubject=1;iesubject=12;ibfile=1;iefile=180;

% toggle switchesiplot=1;filter=1;outputwanted=1;

Give your matlab programme a sensible name!

Clear entire memory!

Set constants

Set loop parameters

Exploit toggle switches (0=Off;1=On)

Use of Matlab Windows, name of file with design codes

% windows for plotting purposesif iplot==1 fig1=figure('position',[5 300 400 220]); fig2=figure('position',[400 300 400 220]);end;

% subject loopfor subject=ibsubject:iesubject, pp=subject % without semi-colon to provide feedback in command window! ppstr=int2str(pp);

% read the data from the design file design.txtprefix=['C:\Ruud\Projects\Objectsize\data\pp' ppstr '\'];fname=['design'];ext=['.txt'];filename=[prefix fname ext];eval(['load ' filename]);design=eval(fname);

% put design information in separate arraystrialnr=design(:,1);vision=design(:,2);cylinder_size=design(:,3);ntrials=length(trialnr);

% data file loop for jfile=1:ntrials,

% feedback on filenumber in command windowfile=trialnr(jfile) % again without semicolon!fstr=int2str(file);

% pick up IRED displacement dataext=['.otd'];if jfile<10 fname=['C#000' fstr]; end;if jfile>9 & jfile<100 fname=['C#00' fstr]; end;if jfile>99 fname=['C#0' fstr]; end;filename=[prefix fname ext];

Use of Matlab Design information, file loop, filename datafile

Use of MatlabRead data file

% read IRED displacement data from file[hdr,cdata] = fpfread(filename);

X1 Y1 Z1 X2 Y2 Z2

Tim

e (s

ampl

es)

fpread.m is separate m-file

Units: mm

Use of Matlab Preprocessing IRED displacement data

% interpolate missing data pointsndim=size(cdata);ns_ireds=ndim(1);for idim=1:ndim(2), h=cdata(:,idim); hi=interpolate_missing_data_points(h); cdata(:,idim)=hi;end;

% convert to cm for idim=1:ndim(2), cdata(:,idim)=cdata(:,idim)./10;end;

% Detect missing data value (-36973140302885665500000000000.0000)% and interpolate linearlyfunction [x]=interpolate_missing_data_points(s);mdv=-36973140302885665500000000000.0000;ns=length(s);

if s(1)==mdv i=1; while s(i)==mdv i=i+1; end; s(1:i)=s(i+1);end;

for i=2:ns-1, if s(i)==mdv ib=i-1; j=i; while ((s(j)==mdv) & (j<ns)) j=j+1; end; ie=j; if ie==ns if ib>1 for k=ib:ie, s(k)=s(ib-1); end; end end; ds=(s(ie)-s(ib))./(ie-ib+1); for k=ib:ie, s(k)=s(ib)+((k-ib+1).*ds); end; end;end;x=s;

Use of Matlab Preprocessing IRED displacement data: A. filtering % filter datafor idim=1:ndim(2), h=cdata(:,idim); hf=filteren(h,Fs,filtfreq_low); cdata(:,idim)=hf;end;

• Filter = 3rd-order Butterworth filter• Applied forward and backward to prevent phase shift

function[smooth]=filteren(data,Fs,Fc)

% FILTEREN.M% function file voor filteren met verwijdering van de inslinger-effecten % Fs is de sample frequentie% Fc is de afsnijfrequentie

[m,n]=size(data);Fs=Fs./2;

[B,A]=butter(3,Fc/Fs); % 3e orde filter.

% 6e orde low-pass filter, zero phase lag.for j=1:n smooth(:,j) = filtfilt(B,A,data(:,j));end

Use of Matlab Preprocessing IRED displacement data: B. filtering% filter datafor idim=1:ndim(2), h=cdata(:,idim); hf=filteren(h,Fs,filtfreq_low); cdata(:,idim)=hf;end;

Red = raw signalBlue = smoothed signal

• Filter = 3rd-order Butterworth filter• Applied forward and backward to prevent phase shift

Use of Matlab Additional arrays to prepare plotting

% number of samples, time axis, y=0 axisns=ndim(1);t=[1:ns].*sec;t=t';y0=zeros(1,ns);y0=y0';

Use of Matlab Prepare plotting of top view of hand IRED positions

% put IRED data in separate 3D matrix

for i=1:ndim(1),

for j=1:8,

j1=j;

k=(j1-1).*3+1;

handx(i,j)=cdata(i,k);

handy(i,j)=cdata(i,k+1);

handz(i,j)=cdata(i,k+2);

end;

end;

cdata 600x24 115200 double array

handx 600x8 38400 double array handy 600x8 38400 double array handz 600x8 38400 double array

Use of Matlab Plot top view of hand

% Plot XY plot

if iplot==1,

figure(fig1);

set(gcf,'Color','white');

title('Top View');

hold on;

axis equal;

view(2);

for i=1:4:600,

plot3(handx(i,:),handy(i,:),handz(i,:),'k');

end;

xlabel('X (cm)');

ylabel('Y (cm)');

end; % of if iplot==1

Start

End

Use of Matlab Determine wrist speed function

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% Determine wrist speedxw=handx(:,4);yw=handy(:,4);zw=handz(:,4);dxw=afgeleid(xw,Fs);dyw=afgeleid(yw,Fs);dzw=afgeleid(zw,Fs);vw=sqrt(dxw.^2+dyw.^2+dzw.^2);

function [afgeleide]=afgeleid(data,sf)

% AFGELEID.M% dit programma differentieert een willekeurige data set data die staat in een matrix% sf = samplefrequentie in Hz; Ron Jacobs, juli 1989

[m,n]=size(data);afgeleide=zeros(m,n);

for i=3:m-2, afgeleide(i,:)=(-data(i-2,:)*1.5-data(i-1,:)*4+data(i+1,:)*4+data(i+2,:)*1.5)*(sf/14);end

afgeleide(1,:) = afgeleide(3,:); afgeleide(2,:) = afgeleide(3,:);afgeleide(m,:) = afgeleide(m-2,:); afgeleide(m-1,:) = afgeleide(m-2,:);

Use of Matlab Check wrist speed function

% Check wrist speed function in command windowplot(vw);xlabel(‘samples’);ylabel(‘wrist speed (cm/s);

Use of Matlab Find critical time indices in wrist speed function

% Find start and end of movement and time index of maximum speed[vmax,tvmax]=max(vw);vthreshold=.05.*vmax;ib=tvmax;while vw(ib)>=vthreshold & ib>2 ib=ib-1; end;ie=tvmax;while vw(ie)>=vthreshold & ie<ns-1 ie=ie+1; end;

threshold

ibie

tvmax

Use of Matlab Determine aperture-time function

% Determine aperture-time functionfor i=1:ndim(1); dx=handx(i,1)-handx(i,8); dy=handy(i,1)-handy(i,8); dz=handy(i,1)-handy(i,8); aperture(i)=sqrt(dx.^2+dy.^2+dz.^2);end;

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Use of Matlab Check aperture-time function

% Check aperture function in command windowplot(aperture);xlabel(‘samples’);ylabel(‘aperture (cm);

Use of Matlab Find critical time indices in aperture-time function

% Find maximum aperture and moment of maximum aperture[maxapt,tmaxapt]=max(aperture);mommaxapt=100.*((tmaxapt-ib)./(ie-ib));

tvmaxapt

maxapt

Use of Matlab Calculate amplitude-scaled wrist speed function to plot

simultaneously with aperture-time function

% Calculate amplitude scaled wrist speed functionscalefactor=max(aperture)./max(vw);vws=vw.*scalefactor;

Define reference lines of critical time indices for plotting

% Data for reference line in plotting

tref(1)=tmaxapt;tref(2)=tmaxapt;

aptref(1)=0;aptref(2)=maxapt;

% Data for reference line in plotting

trefv(1)=tvmax;trefv(2)=tvmax;

vwref(1)=0;vwref(2)=max(vws);

Use of Matlab Plot aperture-time and normalized speed functions

if iplot==1,

figure(fig2);

set(gcf,'Color','white');

title('Normalized Speed & Aperture')';

hold on;

axis([t(ib) t(ie) 0 max(aperture)]);

plot(t(ib:ie),aperture(ib:ie),'r');

plot(t(tref),aptref,'k');

plot(t(ib:ie),vws(ib:ie),'k-');

plot(t(trefv),vwref,'k');

xlabel('Time (s)');

ylabel('Aperture (cm)');

end; % of if iplot==1

Example: Prehension kinematics

Time (s)

Aperture (cm)

Normalized speed (arbitrary units)

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IRED configuration and joint angles

1

2

3

4

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6

8

j1

j2j3

j4j5

j6

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Use of Matlab Determine joint angles in hand

% Constants

degtorad=pi./180;

radtodeg=1./degtorad;

% Determine enclosed angle of hand joints (n=6)

for ired=1:6,

for i=1:ns,

pos1(1)=handx(i,ired);

pos1(2)=handy(i,ired);

pos1(3)=handz(i,ired);

pos2(1)=handx(i,ired+1);

pos2(2)=handy(i,ired+1);

pos2(3)=handz(i,ired+1);

pos3(1)=handx(i,ired+2);

pos3(2)=handy(i,ired+2);

pos3(3)=handz(i,ired+2);

joint(i,ired)=angle2d_signed(pos1,pos2,pos3);

end;

end;

function[alfa]=angle2d_signed(pos1,pos2,pos3);

% calculates the 2D joint angle % Mary Klein Breteler, March 2002

% orientation of first segmentth=atan2(pos2(1)-pos1(1),pos2(2)-pos1(2));

% orientation of second segment relative to first segmentRz = [cos(th) -sin(th) 0; sin(th) cos(th) 0; 0 0 1]; vec = pos2(1:2) - pos3(1:2); vec = [vec/norm(vec) 0]; vecrot = (Rz*vec')'; % angle alfa=atan2(vecrot(1),vecrot(2));beta=unwrap(alfa);alfa=beta.*180/pi;

% only positive valuesif alfa < 0, alfa = alfa + 360;end

Example: Joint rotations

j1

j2

j3

j5

j6j4

Note that joint angles may exceed 180 degs, partially due to their placement,i.e. imperfect alignment, and partially due to overextension.

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Use of Matlab Calculating critical performance variables, e.g.

% Find start and end of movement

ib=fileib(jfile);

ie=fileie(jfile);

[vmax,tvmax]=max(vw(ib:ie));

tvmax=tvmax+ib;

momvmax=100.*((tvmax-ib)./(ie-ib));

% Determine maximum and moment of maximum joint angles

for j=1:6,

[jointmax,tjointmax]=max(joint(ib:ie,j));

maxjntang(j)=jointmax;

tmaxjntang(j)=100.*((tjointmax)./(ie-ib));

end;

Use of Matlab Time normalizing functions

% store time-normalized kinematic functions

n1=ie-ib+1;

n2=50;

vwtn=time_normalize(vw(ib:ie),n1,n2);

% function [tx]=time_normalize(x,n1,n2);%% x = 1-dimensionaal input array (check op rij of kolom array)% n1 = lengte van input array x% n2 = gewenste lengte van outputarray tx%function [tx]=time_normalize(x,n1,n2);

s=1:n1;step=(n1-1)./(n2-1);si=1:step:n1;tx=interp1(s,x,si,'spline');

1. Resample function to 50 data points2. Write resampled function to output file3. Process resampled functions in Excel/SPSSX

Use of Matlab Creating a data matrix for statistical analysis

% clear output arrays

output=zeros(15,1);

if outputwanted==1

output(1)=pp;

output(2)=file;

output(3)=vision(file); % vision

output(4)=objectsize(file); % size

output(5)=(ie-ib).*sec; % MT

output(6)=vmax; % peak speed

output(7)=momvmax; % moment peak speed (%MT)

output(8)=maxapt; % peak aperture (cm)

…Etc.

Use of Matlab - Write outputfile for SPSSX% Write outputfile of, say 8 variables (independent + dependent) per observation

if outputwanted==1

ext_out=['.dat'];

fnameout=['output_new'];

outname=[prefix fnameout ext_out];

fid=fopen(outname,'a');

f='%8.3f ';

f_last='%8.3f\n';

% Take care number of f's equals number of output variables minus 1

outputformat=([f f f f f f f f_last]);

fprintf(fid,outputformat,output);

fclose(fid);

end; % of outputwanted==1