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1. WA PETRI TOIVIAINEN BIRGITTA BURGER 2015 a H W RSION 1 5 A 4 MoCap Toolbox Manual Copyright Petri Toiviainen Birgitta Burger 2008 2015 University of Jyv skyl Finland vers 07 Oct 2015 MoCap Toolbox Manual Table of Contents MoCap Toolbox Manual Foreword 5 Acknowledgments Geseent 5 Release Notes 7 Version NEE 7 New funchons 0 cececessesesessesseeeecececcececeeceeeeeecesecesaeaeaeaeaeaseaeaeesseseseseseseseeeeeeeeeeeeeeseeaesesaeaaaaaeaaaes 7 Introduction 9 General 12 FUMCHONS EE 13 D ta UCI ES aseene eg ECKER PAN EANAN NERAN EANNA SENEE IDENA ERRANS 17 Parameter structures scosnssscuscctvenn dsceneassedienhavereidnswsevawesioicuvasetere denawedesanvauslsdecsenneesdesscaseannens 18 Add ons and extensions vcsvsarssnesesecenccecdtenssdssiesdectaarenesiianaediacisessonisvaansectaneannievasiandetead 19 Periodic quantity Of MOtION 0 eee ee eetee ee eeetcne cette eae eee aE Eiana A EANTA EEEO SNARARE AEEA 19 Realtime streaming Of mocap data 19 Examples 21 Reading Editing and Visualizing MoCap Data mccdemo 22 Transforming MoCap data MCU MO2 ccccccceeeeeeeeeeeeeeeeeeeeeeneeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 32 Pipeline 36 Time series analysis MCASMOA o sccssscsssscssssseesssasssssssssesssssessssesssssssssssssdesesesssasaeeseesesenes 42 Kinetic analysis mcdemob Ennn nnmnnn 45 Creating animations mcedemo6 mccdemog 51 Basica Ee Jorand iranran xn aain REESEN TEE
2. Thanks to Erwin Schoonderwaldt for providing the function to read in mat files exported from QTM Thanks to Federico Visi for providing the mcpqom mcplotpgom and mcrepovizz functions and contributing to the mcsort function MoCap Toolbox Manual Thanks to Dominique de Beul Michiel Demey Frank Desmet Tommi Himberg Herbert Jager Alexander Refsum Jensenius Luiz Naveda Kristian Nymoen and Erwin Schoonderwaldt for re porting bugs in the toolbox and suggesting improvements MoCap Toolbox Manual Release Notes For new features and bug fixes done in previous versions please refer to the releasenotes_v1 5 txt included in the toolbox release Version 1 5 New functions mceaddframes duplicates frames mcecomplexity calculates the complexity of movement based on entropy of the first principal com ponent mcefluidity calculates the fluidity circularity of mocap data mcrepovizz exports MoCap structure as repoVizz files mcreverse reverses dimensions of motion capture data mcrotationrange calculates the rotation range between two markers mesetlength sets mocap data to the length given mcsort sorts mocap data according to marker names Bug fixes mcanimate mcplotframe mcinitanimpar direct video file making changing use of projection pa rameters returning from function with setting video parameters but without creating video mcdemodata updated animpar variables to fit new animation parameter structure mc
3. synopsis Parameters for creating frame plots and animations structure type structure type animpar scrsize two component vector containing the size of frames in pixels width height limits four component vector containing the limits of x and z coordinates for plotting xmin xmax zmin zmax az azimuth angle in degrees of viewing point el elevation angle in degrees of viewing point msize size of markers colors five character string or RGB triple 5x3 containing the colors of background mark ers connections traces and marker numbers respectively markercolors string or RGB triple nx3 containing the individual colors for the markers conncolors string or RGB triple containing the individual colors for the connector lines tracecolors string or RGB triple containing the individual colors for the trace lines numbercolors string or RGB triple containing the individual colors for numbers cwidth width of connection lines twidth width of trace lines conn matrix nMarkers x 2 indicating the connections between markers each row represents one connection with the numbers indicating the markers to be connected conn2 matrix nMarkers x 4 indicating the connections between midpoints of two marker pairs each row represents one connection with the first two numbers and the last two numbers indicating the markers whose midpoints are to be connected trm vector indicating the markers with a trace trl length of trace in seconds
4. velocity 2 accelera tion 3 jerk jolt surge lurch 4 jounce snap 5 crackle 6 pop 7 you name it markerName marker names cell structure data motion capture data nFrames x 3nMarkers matrix analogdata analog data nFrames x nAnalog matrix other other data read from the file depends on equipment and file format used for mocap data read from a tsv file the fields are other descr some description string other timeStamp some time stamp string other dataIncluded 3D comments see also mcread 64 MoCap Toolbox Manual norm data structure synopsis Data structure for vector norms Created by mcnorm structure type structure type norm data filename name of the file from where the data were read nFrames number of frames nCameras number of cameras nMarkers number of markers freq sampling frequency frame rate of motion data nAnalog number of analog devices anaFreq sampling frequency of analog data timederOrder order of time differentiation of data 0 location 1 velocity 2 accelera tion 3 jerk jolt surge lurch 4 jounce snap 5 crackle 6 pop 7 you name it markerName marker names cell structure data motion capture data nFrames x nMarkers matrix analogdata analog data nFrames x nAnalog matrix other other data read from the file depends on equipment and file format used comments The data structure is identical to MoCap data structure except that the data field
5. MoCap norm or segm data structure the only output in case of small to large Sethares transform in case of m best Sethares transform also per best periods for each degree of freedom pow powers of respective periods examples comments Dependent on the given input parameter either the m best or the small to large Sethares transform is chosen See syntax above about in and output argument structure Uses the Periodicity Toolbox downloadable at http eceserv0 ece wisc edu sethares down loadper html see also mcpcaproj mcicaproj 129 MoCap Toolbox Manual mcsetlength synopsis Sets mocap data to the length given syntax d2 mcsetLlength d n d2 mcsetlength d n timetype sec d2 mcsetlength d n position Location input parameters d MoCap or norm data structure n new length of mocap data timetype length given in frames frame or seconds sec default sec location position where to add or trim frames beginning or end default end output d2 MoCap or norm data structure examples d2 mcsetlength d 1200 d2 mcsetlength d n timetype sec d2 mcsetlength d 1200 location beginning comments If the given length is less than the number of frames in the mocap data the data will be trimmed to the given length from either beginning or end If the given length is more than the number of frames in the mocap data data will be added by replicating with firs
6. MoCap Toolbox Manual MoCap data 25 Walking tsv 401 8 20 60 H H H 1x20 cell 401x6 double C 1x1 struct The parameters for the visualization of the joint representation are in the variable japar japar japar type scrsize Limits az el msize colors markercolors conncolors tracecolors numbercolLors cwidth twidth conn conn2 trm trl animpar 400 300 C H H 6 kwwww C C C C 1 1 19x2 double C C H 47 MoCap Toolbox Manual showmnum numbers showfnum 9 animate fps 30 output tmp videoformat createframes Q getparams perspective pers 1x1 struct Let us visualize a frame from the new variable walk2j with marker numbers visible japar colors wkkkk japar scrsize 800 600 japar showmnum 1 japar msize 6 japar az 90 mcpLlotframeC walk2j 160 japar Se The next step is to make a joint to segment transformation The parameters needed for the trans formation are in the variable j2spar j2spar type j2spar rootMarker 1 48 MoCap Toolbox Manual frontalPlane 6 2 10 parent 01234167 81 10 11 11 13 14 15 11 17 18 19 segmentName 1x19 cell The transformation can be accomplished using the function mcj2s walk2s mcj2sCwalk2j j2spar The parameters for each body segment can be obtained using the function mcgetsegmpar segmindex 00876087 6 13 12 10
7. R amp Toiviainen P 2012 Emotions Move Us Basic Emotions in Music Influence People s Movement to Music In Proceedings of the 12th International Conference on Music Perception and Cognition ICMPC 8th Triennial Conference of the European Society for the Cognitive Sciences of Music ES COM Thessaloniki Greece 111 MoCap Toolbox Manual mcperiod synopsis Estimates the period of movement for each marker and each dimension syntax per ac eac lag mcperiod d per ac eac lag mcperiod d maxper per ac eac lag mcperiod d method per ac eac lag mcperiod d maxper method input parameters d MoCap or norm data structure maxper maximal period in seconds optional default 2 secs method sets if first or highest maximal value of the autocorrelation function is taken as pe riodicity estimation optional default first output per row vector containing period estimates for each column ac matrix containing autocorrelation functions for each column eac matrix containing enhanced autocorrelation functions for each column lag vector containing lag values for the normal and enhanced autocorrelation functions examples per ac eac Lag mcperiod Cd 3 per mcperiod d highest comments In ac and eac each column corresponds to a dimension of a marker or in case of norm data to a marker and each row corresponds to a time lag see also references Eerola
8. T Luck G amp Toiviainen P 2006 An investigation of pre schoolers corporeal synchronization with music Paper presented at the 9th International Conference on Music Perception and Cognition Bologna Italy 112 MoCap Toolbox Manual mcplotframe synopsis Plots frames of motion capture data COMPATIBILITY NOTES v 1 5 Please use the function without the projection input ar gument but specify it in the animation structure instead syntax par mcplotframe d n par mcplotframeCd n par input parameters d MoCap data structure n vector containing the numbers of the frames to be plotted par animpar structure optional output par animpar structure used for plotting the frames if color strings were used they will con verted to RGB triplets examples par mcplotframe d 1 mcplotframeCd 500 10 600 par comments If the animpar structure is not given as input argument the function creates it by calling the function mcinitanimpar and setting the limits field of the animpar structure auto matically so that all the markers fit into all frames see also mcanimate mcinitanimpar 113 MoCap Toolbox Manual mcplotphaseplane synopsis Plots motion capture data on a phase plane syntax mcpLotphaseplane d1 d2 marker dim for MoCap data structure mcpLlotphaseplane n1 n2 marker for norm data structure mcpLotphaseplane s1 s2 segm var for segm data structure input paramet
9. c mccomplexity d mnum input parameters d MoCap data structure mnum marker numbers optional if no value given all markers are used output c complexity value between 0 and 1 examples c mccomplexity d c mccomplexity d 4 7 comments Data will be filled in case of missing frames see also mcpcaproj references Burger B Saarikallio S Luck G Thompson M R amp Toiviainen P 2013 Relationships between perceived emotions in music and music induced movement Music Perception 30 5 519 535 79 MoCap Toolbox Manual mcconcatenate synopsis Concatenates markers from different MoCap or norm data structure syntax d2 mcconcatenateC d1 mnum1 d2 mnum2 d3 mnum3 input parameters d1 d2 d3 MoCap or norm data structure mnum1l mnum2 mnum3 vector containing the numbers of markers to be extracted from the preceding MoCap structure output d2 MoCap or norm data structure examples d2 mcconcatenate d1 1 3 5 d2 2 4 6 d2 mcconcatenate d1 1 d2 2 d1 3 d3 4 d2 5 comments Each mocap structure must have a corresponding marker number or number array All mocap structures must have identical frame rates If the numbers of frames are not equal the output MoCap structure will be as long as the shortest input MoCap structure see also mcgetmarker mcmerge 80 MoCap Toolbox Manual mccreateconnmatrix synopsis Creates a connection matrix for th
10. d2 mctrim d t1 t2 timetype input parameters d MoCap data norm or segm data structure tl start of extracted section t2 end of extracted section timetype either sec default or frame output d2 MoCap norm or segm data structure containing frames from tl to t2 if timetype frame or frames between tl and t2 seconds if timetype sec of MoCap data structure d examples d2 mctrim Cd 305 1506 frame d2 mctrimCd 3 5 sec comments see also 143 MoCap Toolbox Manual mcvar synopsis Calculates the variance of data ignoring missing values syntax m mcvar d input parameters d MoCap data structure norm data structure or data matrix output m row vector containing the variance of each data column examples comments see also mcmean mcstd mcskewness mckurtosis 144 MoCap Toolbox Manual mcevect2grid synopsis Converts a MoCap structure vector to a MoCap structure with three orthogonal views for each component syntax Lg gpar mcvect2grid c par dx dy input parameters c MoCap structure vector par animpar structure dx horizontal offset between components default 2000 dy vertical offset between orthogonal views default 2000 output g MoCap structure gpar animpar structure examples Lg gpar mcvect2grid c par 1000 2000 comments see also 145 MoCap Toolbox Manual mcwindow synopsis Performs a windowed time seri
11. see also 92 MoCap Toolbox Manual mchilberthuang synopsis Performs a Hilbert Huang transform of order N on MoCap norm or segm data syntax hh mchilberthuang d N input parameters d MoCap norm or segm data structure N order of the H H transform output hh vector of MoCap norm or segm data structures containing H H transforms examples comments See help hilberthuang see also 93 MoCap Toolbox Manual mcicaproj synopsis Performs an Independent Components analysis on MoCap norm or segm data using the FastICA algorithm and projects the data onto selected components syntax di p mcicaproj d pc ic input parameters d MoCap norm or segm data structure pc number of PCs entered into ICA ic number of ICs estimated output di vector of MoCap norm or segm data structures p structure containing the following fields icasig independent components A mixing matrix W separation matrix meanx mean vector of variables examples Ldi p mcicaprojCd 6 3 comments Uses the fastICA algorithm implemented in the FastICA Package which is available at http www cis hut fi projects ica fastica see also mcpcaproj mcsethares 94 MoCap Toolbox Manual mcinitanimpar synopsis Initializes an animation parameter animpar structure syntax ap mcinitanimpar input parameters none output ap animation parameter animpar structure examples comments See also description
12. the norm data structure and the segm data structure An instance of a MoCap data structure is created by the func tion mcread when motion capture data is read from a file to the workspace The MoCap data structure contains the recorded locations of the markers as well as some basic information such as the name of the file from which the data were read the number of frames in the data the number of cameras used in the capture session the number of markers in the data the sampling frequency or frame rate of the data the names of the markers The dorto field of the MoCap data structure is a matrix containing the locations of the markers It has three columns for each marker corresponding to the two horizontal dimensions 1st and 2nd column and the vertical dimension 3rd column For instance column contains the x coordinates of marker 1 column 2 contains the y coordinates of marker 1 column 3 contains the z vertical coordinates of marker 1 column 4 contains the x coor dinates of marker 2 etc Each row in the matrix corresponds to a frame Additionally the MoCap data structure contains a field that indicates the order of time differentiation of the data with zero corresponding to location one to velocity two to acceleration etc The value of this field is changed by the functions mctimeder and mctimeintegr that perform temporal derivation and integration respectively Finally the MoCap data structure contains fields that can hold data
13. tmp 95 MoCap Toolbox Manual videoformat specifies video file format either avi or mpeg4 avi createframes create png frames instead of video file 1 frames 0 video file 0 getparams return animation parameters without plotting or animating frames 1 yes 0 no 0 perspective perform perspective projection 0 orthographic default 1 perspective 0 pers perspective projection parameters pers c 3D position of the camera 0 4000 0 pers th orientation of the camera 0 0 0 pers e viewer s position relative to the display surface 0 2000 0 Colors can be given as strings if only the MATLAB string color options are used However any color can be specified by using RGB triplets for example plotting the first two mark ers in gray par markercolors 5 5 5 5 5 SI see also mccreateconnmatrix mcplotframe mcanimate 96 MoCap Toolbox Manual mcinitj2spar synopsis Initialises the parameter structure for joint to segment mapping syntax par mcinitj2spar input parameters none output par j2spar structure examples comments See explanation about the j2spar structure The initialized values are as follows type j2spar rootMarker 0 frontalPlane 1 2 3 parent segmentName The fields par parent and par segmentName have to be entered manually see also mcj2s 97 MoCap Toolbox Manual mcinitm2jpar synopsis Initialises the parameter structure for marker
14. 5 sec per optional period in seconds default 0 5 sec output e vector of MoCap or segm data structures examples e mceigenmovement d e mceigenmovement d 1 3 e mceigenmovement d 1 4 2 e mceigenmovement d 1 2 1 2 0 6 comments The sinusoidal projections are scaled to match the RMS amplitudes of the PC projections of respective degrees of freedom see also mcpcaproj 85 MoCap Toolbox Manual mcfillgaps synopsis Fills gaps in motion capture data syntax d2 mcfillgaps d d2 mcfillgaps Cd maxfill d2 mcfillgapsCd method d2 mcfillgapsCd maxfill method input parameters d MoCap norm or segm data structure maxfill maximal length of gap to be filled in frames optional default 1000000 method three different options for filling missing frames in the beginning and or end of a recording default parameter empty missing frames in the beginning and or in the end are set to 0 fillall fills missing frames in the beginning and end of the data with the first actual recorded value or the last actual recorded value respectively nobefill fills all the gap in the data but not missing frames in the beginning or end of the data but sets them to NaN instead output d2 MoCap norm or segment data structure examples d2 mcfillgaps d d2 mcfillgaps d 120 d2 mcfillgaps d nobefill d2 mcfillgaps d 60 fillall comments Uses linear interpolation Mo
15. Cd comments see also 109 MoCap Toolbox Manual mcnorm synopsis Calculates the norms of kinematic vectors syntax n mcnormCd n mcnormCd comps input parameters d MoCap data structure comps components included in the calculation optional default 1 3 output n norm data structure examples n mcnorm Cd n mcnorm d 1 2 calculates norm of horizontal projection comments see also 110 MoCap Toolbox Manual mcpcaproj synopsis Performs a Principal Components analysis on MoCap norm or segm data and projects the data onto selected components syntax dp p mcpcaproj d Ldp p mcpcaproj d pc Ldp p mcpcaproj d pc proj input parameters d MoCap norm or segm data structure pe optional selected Principal Components if not given projections onto the first PCs that contain a total of 90 of the variance are returned proj optional projection function if not given the PC projections of the data in d are used output dp vector of MoCap norm or segm data structures p structure containing the following fields l proportion of variance contained in each PC q PC vectors columns c PC projections rows meanx mean vector of variables examples dp p mcpcaproj d dp p mcpcaproj d 1 3 dp p mcpcaproj d 1 3 sin 2 pi 0 60 60 comments see also mcicaproj mcsethares references Burger B Saarikallio S Luck G Thompson M
16. ENEN ROTAN RAE ENRE tents 51 Merging data for animations mccemo cae eeeeeeeeeseeeeeaaeaaeceeeeeeeeseeseceeeneeeeeeeess 52 Colored animations medemo8 eee aeeeeeeeeeeaaesedeaeeseaeeesaaaeseneeeesaeeeeeneeeeaas 53 Perspective Projection medemo9 cccceseeecceeeeseeeeeeeeseceneeeesaeeneeeeeaeeeeessaaeeeeseeeeeeseeeeeseeneees 55 Principal Components Analysis medemo10 ccccccccceceeeeeeeeeeseeeeeeeeneeeeneeeeeeeeeeeeeeees 58 Analyzing Wii data medemo11 2 0 0 2 eee eee eeeeeeee eter rete aeee eee eeeeceaaaeeeeeeeeeeeeeeeeeeeenaas 59 Data and Parameter Structure Reference 63 MoCap data struchure ENEE 64 norm data structure E 65 Ee Eder 66 m2jpar ET 67 j2spar parameter structure WE 68 animpar DESEM EE 69 Function Reference 71 gen EE 72 ue ie 73 PUIG Lal nare E aceeeresschecrcntaencaand tan eanesetanar A E necteueasirieratiuaristectdubusturnivanciae 74 MoCap Toolbox Manual Wiesn 75 Weeer e EE 76 tee eA CeL EN E E E 77 ae E 78 MECOMPIEX Y so sessine cececioeenanetcaccnsupnnialvcsadenssthausnteanutnauhauseauatensladtaaededeviuuntnustiusweidacesecnianie 79 WT 80 Wee e RE E 81 MECUMAIS E 82 Eeer 83 iere COMPOSE E 84 Wee ne Ou 85 eise 86 weie En e E 87 wiele a ES E E E E N EEE E E 88 Wies sadtacidanccaccrhn csverseccennetacnannveiencnied can cam vanauunsustedtasesanisduasstmaienmiicniocsnieusdetecumurs 89 PACTS TITIARK ET 90 MICGSISCONID AM E 91 BS we E 92 eil tu EE 93 VAG HAO EE NEE NEA E E E E td olerlonera
17. MoCap or norm data structure examples d2 mcaddframes d 60 d2 mcaddframes d 60 Location middle 100 comments timetype location and position are optional Default values are used if not specified see also 73 MoCap Toolbox Manual mcanimate synopsis Creates animation of mocap data and saves it to file avi or mpeg 4 or as consecutive frames png Matlab s VideoWriter function is used to create the video file COMPATIBILITY NOTES v 1 5 The folder field animpar structure v 1 4 has been changed to output and is used as file name for the animation and stored to the current di rectory or as folder name in case frames are to be plotted Please use the function without the projection input argument but specify it in the animation structure instead syntax par mcanimate Cd par mcanimate d par input parameters d MoCap data structure par animpar structure optional output par animpar structure used for plotting the frames examples mcanimate d par comments If the animpar structure is not given as input argument the function creates it by calling the function mcinitanimpar and setting the limits field of the animpar structure auto matically so that all the markers fit into all frames Ifthe par pers field perspective projection is not given it is created internally for back wards compatibility For explanation of the par pers field see help mcinitanimpar
18. containing the names of the segments comments The number of each segment is identical to the number of the marker representing the distal joint of the segment in the MoCap data structure from which the segm data structure was derived That means the first segment is empty see also mcj2s 66 MoCap Toolbox Manual m2jpar parameter structure synopsis Parameters for conversion from markers to joints structure type structure type m2jpar nMarkers number of joints markerNum cell structure containing for each joint the numbers of the markers whose cen troid defines the location of that joint for instance if markerNum k m1 m2 m3 m4 the location of joint k is calculated as the centroid of markers m1 m2 m3 and m4 markerName cell structure containing the names of the joints comments see also mcinitm2jpar 67 MoCap Toolbox Manual 2spar parameter structure synopsis Parameters for conversion from joints to segments structure type structure type j2spar rootMarker number of the root joint frontalPlane numbers of three joints that define the frontal plane parent vector containing the number of the parent joint proximal joint in kinematic chain of each joint zero means no parent joint segmentName cell structure containing the names of each segment comments The parent number of the root joint is zero see also mcinitj2spar 68 MoCap Toolbox Manual animpar parameter structure
19. contains only one column per marker see also mcnorm 65 MoCap Toolbox Manual segm data structure synopsis Data structure for body segment data Created by mcj2s structure type structure type segm data filename name of the file from where the data were read nFrames number of frames nCameras number of cameras nMarkers number of markers freq sampling frequency frame rate of motion data nAnalog number of analog devices anaFreq sampling frequency of analog data timederOrder order of time differentiation of data 0 location 1 velocity 2 accelera tion 3 jerk jolt surge lurch 4 jounce snap 5 crackle 6 pop 7 you name it analogdata other 1x1 struct parent vector containing the number of the parent joint proximal joint in kinematic chain of each joint zero means no parent joint roottrans matrix nFrames x 3 containing the coordinates of body root rootrot 1x1 struct rootrot az azimuth angle of the normal vector of the frontal plane see the j2spar structure rootrot el elevation angle of the normal vector of the frontal plane see the j2spar structure segm 1 x nMarkers struct segm k eucl euclidean vector pointing from proximal to distal joint of the segment segm k r length of the segment averaged over time segm k quat quaternion representing rotation from 0 1 0 to segm k eucl segm k angle angle between segments k and k 1 segmentName cell structure
20. of the animpar structure default values given in parentheses scrsize frame size in pixels 800 600 limits plot limits xmin xmax zmin zmax az azimuth vector in degrees 0 el elevation vector in degrees 0 msize marker size 12 colors background marker connection trace markernumber kwwww or RGB triplet 5x3 markercolors String holding marker colors or RGB triplet conncolors String holding connector line colors or RGB triplet tracecolors String holding trace colors only animations or RGB triplet numbercolors String holding number colors indicated in the numbers array or RGB triplet cwidth width of connectors either single value or vector with entries for different widths 1 twidth width of traces either single value or vector with entries for different widths 1 conn marker to marker connectivity matrix M x 2 mccreateconnmatrix can be used for creating the connection matrix conn2 midpoint to midpoint connectivity matrix M x 4 trm vector indicating markers for which traces are added trl length of traces in seconds 0 showmnum show marker numbers 1 yes 0 no 0 numbers array indicating the markers for which number is to be shown showfnum show frame numbers 1 yes 0 no 0 animation create animation 1 yes 0 no 0 fps frames per second for animation 30 output either file name for video file of folder for pgn frames
21. parameters d MoCap data structure norm data structure or data matrix output m row vector containing the kurtosis values of each data column examples comments see also mcmean mcstd mcvar mcskewness 103 MoCap Toolbox Manual MoCap Toolbox Manual mcem2j synopsis Performs a marker to joint mapping syntax d2 mcm2j d par input parameters d MoCap data structure par m2jpar structure output d2 MoCap data structure examples comments The fields the fields par nMarkers par markerNum and par markerName have to be en tered manually See the explanation of the m2jpar structure see also mcinitm2jpar 104 mcmarkerdist synopsis Calculates the frame by frame distance of a marker pair syntax dist mcmarkerdist d m1 m2 input parameters d MoCap data structure m1 m2 marker numbers output dist column vector examples dist mcmarkerdist d 1 5 comments see also 105 MoCap Toolbox Manual MoCap Toolbox Manual mcemean synopsis Calculates the temporal mean of data ignoring missing values syntax m mcmean d input parameters d MoCap data structure norm data structure or data matrix output m row vector containing the means of each data column examples comments see also mcstd mcvar mcskewness mckurtosis 106 MoCap Toolbox Manual mcmerge synopsis Merges two MoCap data structures and optionally the corresponding animation paramet
22. periodic motion Animation of pcjCk shows that the first three PCs correspond to translation of the body periodic anti phase movement of arms and periodic rotation of torso Analyzing Wii data mcdemoi1 The Nintendo Wiimote provides an inexpensive means for simple motion capture This example shows how movement data collected with the Nintendo Wii controller can be analyzed using the MoCap Toolbox The MoCap Toolbox supports the file format used by the WiiDataCapture software available at www jyu fi music coe materials In the file mcdemodata the variable wiidata contains acceleration data captured using the Nin tendo Wii controller and the WiiDataCapture software load mcdemodata 59 MoCap Toolbox Manual wiidata wiidata type MoCap data filename data wii nFrames 1826 nCameras nMarkers 1 freq 100 nAnalog anaFreq timederOrder 2 markerName data 1826x3 double analogdata other As the field timederOrder indicates this variable holds acceleration data Let us plot the third vertical component of the acceleration data mcpLottimeseries wiidata 1 dim 3 Marker 1 s 3 The data is somewhat noisy so we smoothen it a bit wd2 mcsmoothenC wiidata 25 mcpLottimeseries wd2 1 dim 3 60 MoCap Toolbox Manual Marker 1 s 3 Let us do a windowed analysis of the period of this acceleration component using a window length of two s
23. synopsis Reads emg files in tsv format recorded with the Mega EMG system using QTM syntax d mcreademg fn input parameters fn File name tsv format norm data structure output d norm data structure examples d mcreademg filename tsv comments see also mcfilteremg 119 mcreorderdims synopsis Reorders the Euclidean dimensions in motion capture data syntax d2 mcreorderdims d dims input parameters d MoCap data structure dims vector containing the new order of dimensions output d2 MoCap data structure examples d2 mcreorderdims d 1 3 2 comments see also 120 MoCap Toolbox Manual MoCap Toolbox Manual mcrepovizz synopsis Exports MoCap structure as valid repoVizz csv files xml repoVizz struct and optional bones file syntax mcrepovizz d path p input parameters d MoCap data structure path path to save the csv files optional If no path is given files are saved in the current directory If the chosen directory does not exist it will be created p animpar parameter structure optional output csv files and repoVizz struct xml file saved in the current or in the specified directory Optional bones file saved as well if animpar structure specified in the third argument examples mcrepovizzCd mcrepovizz d folder mcrepovizz d path folder Conly Mac mcrepovizz d folder p mcrepovizz Cd p comments For info about repoVizz
24. to joint mapping syntax par mcinintm2jpar input parameters none output par m2jpar structure examples comments See the explanation of the m2jpar structure The initialized values are as follows type m2jpar nMarkers 0 markerNum markerName The fields par nMarkers par markerNum and par markerName have to be entered man ually see also mcm2j 98 MoCap Toolbox Manual meinitstruct synopsis Initializes MoCap or norm data structure syntax d1 d1 d1 d1 d1 d1 d1 d1 d1 mcinitstruct mcinitstruct type mcinitstruct type data mcinitstruct type data freq mcinitstruct type data freq markerName mcinitstruct type data freq markerName fn mcinitstruct data freq mcinitstructCdata freq markerName mcinitstructCdata freq markerName fn input parameters type MoCap data or nom data default MoCap data data data to be used in the data field of the mocap structure default freq frequency capture rate of recording default NaN markerName cell array with marker names default fn filename default output d1 mocap or norm data structure with default parameters or parameter adjustment according to the parameter input examples dl mcinitstruct dl mcinitstruct norm data data dl mcinitstruct data 120 markernames mydata 1 tsv comments default parameters for MoCap data type MoCap data filename nF
25. values mean default rotates data in all frames with the same angle to have a frontal view with respect to the mean locations of markers m1 and m2 frame rotates each frame separately to have a frontal view with respect to the instanta neous locations of markers m1 and m2 with this method each individual frame is cen tered as well output d2 MoCap data structure or data matrix examples d2 mc2frontal d 3 7 d2 mc2frontalCd 3 7 frame comments a naa The frontal plane is defined by the temporal mean of markers m1 and m2 right side 7 mc2frontal d 1 2 would rotate to that view EE f bet vache see also mcrotate nv 72 MoCap Toolbox Manual mcaddframes synopsis Duplicates frames in a given mocap structure either last frame in the end first frames in the beginning or at a given position in the middle syntax d2 mcaddframes d add d2 mcaddframes d add timetype frame location beginning d2 mcaddframes d add Location middle position n input parameters d MoCap or norm data structure add total amount of frames to be added timetype amount of frames given in frames frame or seconds sec default sec location location where frames are added beginning middle or end default end position position where frames are added only needed when using middle as location The timetype parameter applies to both add and position output d2
26. xv v d X j se V ve te Finally let us rotate the data in dance1 by 90 degrees counterclockwise around the y axis dirot3 mcrotateCdance1 90 Do 1 Q mcplotframeCdirot3 50 mapar 33 MoCap Toolbox Manual K we mes A H _ d WK j d m ec WI w R gt A E a H E mm To add data from several MoCap data structures to one visualization the functions mctranslate and mcmerge are useful all doncel translate dirot1 2000 mm to the right and merge with all merge also the parameter structures Lall allparams mcmerge all mctranslate d1rot1 2000 mapar mapar Same with d1rot2 and dirot3 but with different translations Lall allparams mcmerge Call mctranslateCdirot2 0 2000 allparams mapar Lall allparams mcmergeCall mctranslateCdirot3 2000 o 2000 allparams mapar Next let us plot one frame from the merged data allparams msize 6 mcplotframeCall 50 allparams 34 MoCap Toolbox Manual Let us now take excerpts from the variables dance1 and dance2 and merge them for visualization d1 mctrim dance1 2 d2 mctrim dance2 0 2 d2 mctranslate d2 2000 d par mcplotframeCd 60 par mcmerge d1 d2 N U p te Ag Several frames can be plotted with one 0 0 mapar mapar command by using a vector as the second parameter mcplotframe d 1 10 71 par 35 MoCap Toolbox Manual e
27. 11321 1132 1 spar mcgetsegmparC Dempster segmindex The second argument in the function call segmindex associates each joint in walk1j and walkis with a segment type The numbers refer to the distal joint of the respective segment Joints that are not distal to any segment have zero values Segment number values for model Dempster are as follows no parameter 0 hand 1 forearm 2 upper arm 3 forearm and hand 4 upper ex tremity 5 foot 6 leg 7 thigh 8 lower extremity 9 head 10 shoulder 11 thorax 12 ab domen 13 pelvis 14 thorax and abdomen 15 abdomen and pelvis 16 trunk 17 head arms and trunk to glenohumeral joint 18 head arms and trunk to mid rib 19 For instance the third component 8 tells that the body segment whose distal joint is joint number 3 is a thigh Now that we have a body segment representation of the movement we can estimate various kinetic variables The potential energy for each body segment can now be calculated as follows pot mcpotenergy walk2j walk2s spar The resulting variable pot is a matrix where each column corresponds to one of the body seg ments Let us plot the total potential energy as a function of time time 1 walk2 nFrames walk2 freq plotCtime sum Cpot 2 xlabeLC Time si ylabelC Potential energy W 49 MoCap Toolbox Manual We can see a relatively regularly oscillating pattern with the exception of the region between 3 0 and 4 5 seconds whe
28. 30 output tmp videoformat avi createframes Q getparams perspective pers 1x1 struct Let us change the frames per second value to 15 mapar fps 15 The animation will be stored into the current directory with the filename tmp avi If needed the current directory should be changed before creating the animation The animation is produced as follows newpar mcanimate walk2 mapar If you wish to plot consecutive frames png files instead of creating a video file set the animation parameter createframes to 1 mapar createframes 1 You will then find the png files in a folder called tmp in the current directory Merging data for animations mcdemo7 The next example shows how MoCap data from different sessions can be combined into the same animation It also shows how the viewing angle can be changed dynamically Let us create a 10 second animation with two dancers and a dynamically moving viewing angle The variable dance1 has some missing frames so we shall fill them first dance1 mcfillgapsCdance1 Next we extract the first ten seconds from the variables dance1 and dance2 d1 mctrim dance1 0 10 d2 mctrimCdance2 D 10 We make the viewing azimuth change dynamically from zero to 180 degrees and the elevation an gle from 45 to 45 degrees during the animation mapar az 0 180 mapar el 45 45 52 MoCap Toolbox Manual We set the movie to have 15 frames per secon
29. 4 Thus if the default window length of 7 is used the window length for the second order derivative will be 11 and the window length for the third order derivative will be 15 For information about the Savitzky Golay filter see help sgolayfilt The function updates the d timederorder field as follows d2 timederorder d timederorder order see also mcsmoothen mctimeintegr 140 MoCap Toolbox Manual mctimeintegr synopsis Estimates time integrals of motion capture data using the rectangle rule syntax d2 mctimeder d d2 mctimeintegr d order input parameters d MoCap data structure or segm data structure order order of time integral optional default 1 output d2 MoCap data structure or segm data structure examples d2 mctimeintegr d 2 second order time integral comments The function updates the d timederorder field as follows d2 timederorder d timederorder order see also mctimeder 141 mctranslate synopsis Translates motion capture data by a vector syntax d2 mctranslate d transvect input parameters d MoCap data structure or data matrix transvect translation vector output d2 MoCap data structure or data matrix examples d2 mctranslateCd 0 1000 Q comments see also 142 MoCap Toolbox Manual MoCap Toolbox Manual mctrim synopsis Extracts a temporal section from a MoCap norm or segm data structure syntax d2 mctrim d t1 t2
30. 51 secs More accurate periodicity analysis can be done using windowed autocorrelation per ac eac lags wtime mcwindow mcperiod d2m1 2 25 Let us plot the periodicity estimates for the vertical dimension for each of the windows plotCwtime per C 3 xLabelC Time secs ylabelC Period secs 40 MoCap Toolbox Manual After displaying some initial transients the period settles at the vicinity of 0 5 secs The enhanced autocorrelation matrix can be plotted as an image to allow visual inspection of the time development of periodicity The colors provide an indication of the regularity of periodic movement with warm colors corresponding to regions of highly regular periodic movement imagesc eac 3 axis xy set gca XTick 4 46 set gca XTickLabel 5 0 4 46 set gca YTick 30 60 90 120 set gca YTickLabel 0 5 11 5 2 0 xLabelC Time secs ylabelC Period secs 41 MoCap Toolbox Manual Time series analysis mcdemo4 This example shows how you can perform various statistical analyses on time series data using the functions provided in the MoCap toolbox The first statistical moments mean standard deviation skewness and kurtosis can be calculated using the functions mcmean mcstd mcskewness and mckurtosis respectively These func tions ignore eventual missing frames The function mcstatmoments can be used to calculate these statistical moments with one f
31. MON dossiere srine nena ie a aa darentadh Eee eege eege 141 PCT EE ebe eelere ee 142 edu BEE 143 MEVA eerren EEEE E EEEE EET EE EE EEEE 144 ALe te E 145 ren ele EE 146 er 147 MoCap Toolbox Manual Foreword This manual provides an introduction and a reference to the MoCap Toolbox a Matlab toolbox for the analysis and visualization of Motion Capture data The toolbox is mainly aimed for the analysis of music related movement but might be useful in other areas of study as well I wrote most of the toolbox and this manual during my sabbatical at the Center for Advanced Study in the Behavioral Sciences at Stanford University in 2007 8 This manual requires that the user be familiar with the basic features of the Matlab software Novices in this programming platform are advised to consult the cornucopia of Matlab tutorials available on the Internet The reader should also be familiar with the basics of mechanics and calcu lus I would like to thank the Academy of Finland and the Center for Advanced Study in the Behavioral Sciences at Stanford University for their support Stanford June 1 2008 Petri Toiviainen Acknowledgments Thanks to Dominique de Beul for the providing the bvh parser Thanks to JJ Loh for providing a faster version for reading in c3d files Thanks to Kristian Nymoen for providing the function mcmocapgram and the real time streaming Thanks to Roberto Rovegno for contributing to the mewritetsv function
32. Matlab as well as how you can edit and visualize the data Motion capture data can be imported into Matlab and stored as a MoCap data structure using the function mcread Currently the function supports the generic c3d format the tsv format produced by the Qualisys motion capture system the mat format produced by the Qualisys motion capture system and the wii file format produced by the WiiDataCapture software available at www jyu fi music coe materials mocaptoolbox The MoCap toolbox folder includes the mat file mcdemodata mat that contains motion capture data and associated parameter structures as Matlab variables These data are used in the examples of this manual The commands used in the demo files are marked in dark green load mcdemodata whos Name Size Bytes Class Attributes dance1 1x1 1013572 struct dance2 1x1 1013572 struct j2spar 1x1 2168 struct japar 1x1 2530 struct m2jpar 1x1 3464 struct mapar 1x1 2914 struct walk1 1x1 241862 struct walk2 1x1 275474 struct wiidata 1x1 45560 struct Variable walk1 is a MoCap data structure walk1 22 walk1 type filename nFrames nCameras nMarkers freq nAnalog anaFreq timederOrder markerName data analogdata other MoCap Toolbox Manual MoCap data 28 Karolien WaLking tsv 351 8 28 60 H H H 28x1 cell 351x84 double C 1x1 struct Let us look if there are any missing data in the variable walk1 mt mm mgrid mcmissi
33. al mcpLotphasepLane mctrimCd2v 5 7 mctrimCd2a 5 7 1 19 25 3 This figure is below on the right The cumulative distance tavelled by a marker can be calculated with the function mccumdist d2dist mccumdist Cdance2 Let us have a look at the distance travelled by markers 1 19 and 25 left front head left hand and left foot mcpLottimeseries d2dist 1 19 25 38 MoCap Toolbox Manual J x Marte 19 Mart e 25 As we can see the head has travelled ca 13 meters the hand ca 33 meters and the foot ca 11 me ters Periodicity of movement can be estimated using the function mcperiod Let us estimate the period icity of the movement of marker 1 left front head in the three dimensions d2m1 mcgetmarker Cdance2 1 per ac eac lag mcperiodCd2m1 2 maximal period 2 sec per per NaN NaN 0 5167 There is thus no periodic movement along the horizontal dimensions dimensions 1 and 2 but a period of 0 51 seconds in the vertical direction The autocorrelation function for the vertical location of marker 1 looks like this plot Clag ac 3 xlabel Period secs 39 MoCap Toolbox Manual Ponoi pees The first maximum at non zero lag can be found at 0 51 secs corresponding to the previous result The enhanced autocorrelation function for the same data looks like this plotClag eacC 3 xlabelC Period secs Again there is a clear maximum at the period of 0
34. arameter is given a file open dia log opens output d MoCap data structure containing parameter values and data examples d mcread filename tsv d mcread filename c3d d mcread filename bvh d mcread filename mat d mcread filename wii d mcread comments Currently the c3d tsv as exported by QTM bvh mat as exported by QTM and wii WiiDataCapture software formats are supported The file names must have postfixes Led tsv bvh mat or wii respectively For reading c3d files the function provid ed at http www c3d org download_apps html is used For exporting in tsv format from Qualisys QTM recommended export parameter are 3D data and Include TSV header ticked Export time data for every frame and write column headers will be ignored by mcread if ticked The c3d format does not support more than 65535 frames per file see www c3d org HTML default htm The C3D file format gt Limitations Therefore if you happen to have longer recordings export them either in tsv or mat or in more than one c3d file If further problems occur when reading in c3d files try to adapt the machinetype parame ters as indicated in the readc3d m in the folder private Reading in bvh files requires additional toolboxes available here http staffwww dcs she f ac uk people N Lawrence mocap mocap and ndlutil see also 118 MoCap Toolbox Manual mcreademg
35. b and most platforms The latest implementations and developments have been made on Matlab version 8 4 R2014b running on Macintosh OS X v10 10 To use all the functions in the MoCap Toolbox the following toolboxes must be included in Mat lab s path e Signal Processing Toolbox e FastICA Package available at http www cis hut fi projects ica fastica for mcicaproj e Periodicity Toolbox available at http eceserv0 ece wisc edu sethares downloadper html for mcsethares e For reading in bvh files http staffwww dcs shef ac uk people N Lawrence mocap mocap and ndlutil toolboxes also the github versions work Register to the MoCap Toolbox mailing list www jyu fi music coe materials mocaptoolbox to stay informed about new releases bug reports and bug fixes It also serves as a general discus sion board for users so feel free to post anything motion capture and toolbox related that might be of interest to other users and developers The email address to send messages to the list is mocap toolbox freelists org requires registration to send The MoCap Toolbox comes with no warranty It is free software and you are welcome to redistrib ute it under certain conditions See the file License txt provided with the toolbox for details of GNU General Public License 11 MoCap Toolbox Manual MoCap Toolbox Manual Functions The MoCap Toolbox contains 64 functions for the analysis and visualization of m
36. bi label mm y axis label mm mcpLottimeseries d 5 dim 1 3 timetype frame label no x axis Cand no y axis label mcpLlottimeseries d 5 names 1 marker names instead of numbers plotted in title and legend mcpLottimeseries s 3 6 20 var angle for segm data structure mcplottimeseries s 5 10 var eucl timetype frame frames as x axis unit J mcpLottimeseries s 12 14 var quat dim 2 plotopt comb all in one plot component 2 comments see also 116 MoCap Toolbox Manual mcpotenergy synopsis Estimates the instantaneous potential energy of each body segment syntax pe mcpotenergy d segd segmpar input parameters d MoCap data structure segd segm data structure calculated from d segmpar segmpar structure see mcgetsegmpar output pe matrix containing potential energy values for each body segment examples segd mcj2s d j2spar spar mcgetsegmpar Dempster segmnum pe mckinenergy d segd spar comments The energy for a given segment is in the column corresponding to the number of the distal joint of the respective segment see also mcj2s mcgetsegmpar mckinenergy 117 MoCap Toolbox Manual mcread synopsis Reads a motion capture data file and returns a MoCap data structure syntax d mcread fn d mcread input parameters fn file name tsv c3d bvh mat or wii format If no input p
37. captured from ana log devices such as EEG GSR etc An instance of a MoCap data structure is also created when the function mcm2j is called This function performs a transformation from a marker representation to a joint While these two repre sentations use the same data structure they are conceptually different in the sense that the marker representation is related to actual marker locations whereas the joint representation is related to lo cations derived from marker locations This representation is helpful when we wish to calculate the location of a body part where it is impossible to attach a marker For instance the midpoint of a joint can be derived as the centroid of four markers located around the joint The norm data structure created by the function mcnorm is similar to the MoCap data structure except that its data field contains only one column per marker This column holds the Euclidean norm of the vector data from which it was derived If for instance the function mcnorm is applied to velocity data the resulting norm data structure holds the magnitudes of velocities or speeds of each marker MoCap Toolbox Manual While the MoCap and norm data structures are related to points in space markers or joints the segm data structure contains data about segments of the body The function mcj2s which carries out a transformation from a joint representation to a segment representation produces as output an instance of th
38. containing marker numbers or cell array containing marker names for MoCap or norm data structure segm body segment numbers or cell array containing segment names for segm data struc ture dim dimensions to be plotted for MoCap data structure default 1 var variable to be plotted for segment segm for segm data structure default 1 timetype time type used in the plot sec seconds default or frame plotopt plotting option for MoCap or norm data structure sep default or comb sep all time series are plotted in separate subplots comb all time series will be plotted into the same plot using different colors label y axis label default no y axis label X axis label is always set according to timetype however for plotting neither x axis nor y axis labels label 0 names if marker names instead of numbers are plotted in title and legend 0 numbers de fault 1 names output Figure examples mcplottimeseries d 2 MoCap or norm data structure marker 2 dim 1 mcplottimeseries d Head_FL Finger_L marker names instead of num bers works for segments as well 1 mcplottimeseries d 1 3 dim 1 3 markers 1 to 3 dimensions 1 to 3 mcplottimeseries d 1 3 dim 3 timetype frame frames as x axis unit 115 MoCap Toolbox Manual mcplottimeseries d 5 dm 1 3 plotopt comb all in one plot different colors per dim mcplottimeseries d 5 dim 1 3 plotopt com
39. d and give a name for the file mapar fps 15 mapar output twodancers The next step is to translate the data in d2 by two meters to the right and merge this with the data in d1 d par mcmergeCd1 mctranslateCd2 2000 o mapar mapar Next if needed we change the current directory Now we are ready to create the animation frames newpar mcanimate d par There should be now a file called twodancers avi in the current directory Colored animations mcdemo8 This example shows how to color plots and animations We will create a colored animation from the variable dance2 The animpar structure mapar looks like this load mcdemodata mapar mapar type animpar scrsize 400 300 Limits az 0 el 0 msize 6 colors kwwww markercolors conncolors tracecolors numbercolors cwidth 1 twidth 1 conn 43x2 double conn2 trm 53 trl showmnum numbers showfnum animate fps 30 output tmp videoformat avi createframes 9 getparams 0 perspective H pers Let us change the frames per second value to 15 mapar fps 15 1x1 struct MoCap Toolbox Manual Let us set individual colors for six markers head front left head back right shoulder left hip left back finger right knee left knee right heel left mapar markercoLlors bwwgwrwwwwwywwwwwwmwcbwg and let us have a look at the new colors mcpLotfram
40. d in the Chapter Data and Parameter Structure Reference Add ons and extensions Periodic quantity of motion Functions that estimate and plot the periodic quantity of motion have been implemented by Federi co Visi and Rodrigo Schramm These functions can be downloaded from the mocap toolbox down load page section Extensions To use the function download the zip folder and extract it either to the toolbox folder or to another folder that your Matlab distribution can access A demo explaining the use of the functions is included in the package For more information and support please contact Federico or Rodrigo and have a look at the following publication Visi Federico Schramm Rodrigo and Miranda Eduardo Gesture in Performance with Traditional Musical Instruments and Electronics Use of Embodied Music Cognition and Multimodal Motion Capture to Design Gestural Mapping Strategies Proceedings of the International Workshop on Movement and Computing MOCO 14 p 100 105 ACM Paris 2014 Realtime streaming of mocap data A solution for realtime streaming of mocap data from the mocap toolbox has been implemented by Kristian Nymoen It allows playback of synchronized sound and motion capture data as well as looping scrubbing etc You can visualise the data in 3D while interacting with the visualisation The visualisation and GUI is implemented in Max 6 and a standalone application for Mac is also included meaning that it is
41. demo6 mcdemo 9 fit new animation parameter structure mcgetmarkername now for norm data as well mchilbert keep data structure same as input file added flag for indicating phase wrap mcinitstruct fixed inconsistency in naming in the manual memerge fixing animation parameter structure merging MoCap Toolbox Manual mecmocapgram norm data included mcplotframe move axes definition outside the main plotting loop for efficiancy mcread added bvh support added potential troubleshoot for c3d data mcereadc3d check for matching frame no and data size Optitrack issue mcs2j runtime efficiency mctimeintegr for norm data as well readc3d changed machinetype parameter change back as indicated in script if you run into issues reading in c3d files MoCap Toolbox Manual Introduction MoCap Toolbox Manual The MoCap Toolbox is a Matlab toolbox that contains functions for the analysis and visualization of motion capture data It supports the generic c3d file format the tsv data format produced by the Qualisys motion capture system the mat file format produced by the Qualisys motion capture sys tem and the wii format produced by the WiiDataCapture software available at www jyu fi music coe materials mocaptoolbox To use the toolbox you need the Matlab software www mathworks com Before using it the tool box has to be added in the Matlab path variable The toolbox should be compatible with most ver sions of Matla
42. e syntax mcewritetsvCd path input parameters d MoCap data structure path path to save the tsv file optional If no path is given file is saved to current directory output tsv file saved in the current or in the specified directory examples mcewritetsvCd mcewritetsv d folder mewritetsvCd path folder CMac comments see also mcread 147 MoCap Toolbox Manual Never confuse motion with action Benjamin Franklin 148
43. e animation parameters conn field by using the bones connections saved as a label list of the Qualisys track manager software QTM syntax par mccreateconnmatrixCfn par input parameters fn text file ending txt that contains the bones connections made in QTM par animpar structure output par animpar structure with connection matrix examples par mccreateconnmatrix labellist txt par comments This function works only with label list files created by Qualisys Track Manager This function works for marker representations before any marker reduction or joint trans formation has been applied The markers in the MoCap structure must resemble the struc ture of the marker connections in the label list file see also mcinitanimpar 81 MoCap Toolbox Manual mccumdist synopsis Calculates the cumulative distance traveled by each marker syntax d2 mccumdist d input parameters d MoCap data or norm data structure output d2 norm data structure examples comments If the input consists of one dimensional data i e norm data the cumulative distance to the origin of the reference space coordination system is calculated which is not necessarily the cumulated distance traveled by the marker see also 82 MoCap Toolbox Manual mccut synopsis Cuts two MoCap structures to the length of the shorter one syntax d11 d22 mccut d1 d2 input parameters d1 d2 MoCap or nor
44. e segm data structure The segm data structure contains most of the fields of the Mo Cap data structure The data field of the MoCap data structure is however replaced by a few other fields The parent field contains information about the kinematic chains of the body in other words how the joints are connected to each others to form segments and how these segments are connected to each other The location and orientation of the center of the body the root is con tained in the fields roottrans and rootrot The segm field contains several subfields that store the orientation of the body segments in various forms The eucl subfield contains for each segment the euclidean vector pointing from proximal to distal joint of the segment The r sub field contains the length of each segment The quat subfield contains the rotation of each seg ment as a quaternion representation to learn about the use of quaternions to represent 3D rotations see for instance http en wikipedia org wiki Quaternion Finally the angle subfield holds the angle between each segment and its proximal segment A more detailed description of the data structures used in the MoCap Toolbox can be found in the Chapter Data and Parameter Structure Reference Parameter structures To facilitate the converting between different representations marker joint and segment and the producing of certain visualizations the MoCap Toolbox uses three different parameter struct
45. eCdance2 150 mapar Now let us set the markers that we want to trace and the trace length in seconds mapar trm 1 6 12 19 21 24 MoCap Toolbox Manual mapar trl 3 And let us set individual colors for the traces mapar tracecolors grymcb We rotate the figure to be frontal on average dance2 mc2frontalCdance2 9 10 Now we make the animation newpar mcanimateCdance2 mapar For plotting a figure with traces just select one frame that was calculated during the animation for instance frame number 100 of dance2 Perspective Projection mcdemo9 Next the possibility of creating an animation with a perspective three dimensional effect will be explained We will create a couple of animations of the walk2 data with and without the perspec tive projection to see the differences Let us load the mcdemodata and change a couple of parame ters of the animpar structure mapar load mcdemodata mapar scrsize 600 400 mapar msize 8 mapar fps 15 mapar colors wkkkk 55 MoCap Toolbox Manual And we also set the azimuth parameter in the animpar structure mapar so that the walker will walk towards us mapar az 270 We do not want to create a video this time but have a look at the separate frames to better see the differences in the projection we set the createframes parameter accordingly and re name the de fault file name which will serve as the folder name now into which the frames Ge png file
46. econds and a hop factor of 0 25 per ac eac lags wstart mcwindow mcperiod wd2 2 25 Next let us plot the estimated period of the third component as a function of the starting point of the window plotCwstart perC 3 set gcf Position 4 200 560 420 xlabelC Time si ylabelC Period si We observe a periodic motion that starts with a period of ca 0 2 seconds slows down to a period of ca 1 second and speeds again up to a period of ca 0 2 seconds 61 i MoCap Toolbox Manual A similar representation can be obtained by plotting the enhanced autocorrelation image imagesc eac 3 axis xy set gcf Position 4 200 560 420 set gca XTick 2 32 set gca XTickLabel 5 2 32 set gca YTick 1 51 101 151 201 set gca YTickLabel 0 5 11 5 2 0 xLabelC Time secs ylabelC Period secs 62 MoCap Toolbox Manual Data and Parameter Structure Reference MoCap Toolbox Manual MoCap data structure synopsis Data structure for motion capture data Created by the function mcread structure type structure type MoCap data filename name of the file from where the data were read nFrames number of frames nCameras number of cameras nMarkers number of markers freq sampling frequency frame rate of motion data nAnalog number of analog devices anaFreq sampling frequency of analog data timederOrder order of time differentiation of data 0 location 1
47. er files syntax d3 mcmerge d1 d2 d3 p3 mcmerge d1 d2 p1 p2 input parameters d1 d2 MoCap or norm data structures pl p2 animpar structures for d1 and d2 output d3 MoCap or norm data structure p3 animpar structure examples comments dl and d2 must have identical frame rates If the numbers of frames are not equal the MoCap data structure with the higher number of frames will be cut before merging All animation parameters will be taken from the first animpar file apart from any color marker trace definition and connection matrices see also mcconcatenate 107 MoCap Toolbox Manual mcmissing synopsis Reports missing data per marker and frame syntax mf mm mgrid mcmissing d input parameters d MoCap or norm data structure output mf number of missing frames per marker mm number of missing markers per frame megrid matrix showing missing data per marker and frame rows correspond to frames and columns to markers examples comments see also 108 MoCap Toolbox Manual mcmocapgram synopsis Plots mocapgram shows positions of a large number of markers as projection onto a color space syntax h mcmocapgram Cd mcmocapgram d mcmocapgram d timetype input parameters d MoCap or norm data structure timetype time type used in the plot sec default or frame output h figure handle examples mcmocapgram d frame h mcmocapgram
48. er d order method d2 mctimeder d order window method input parameters d MoCap structure norm structure or segm structure order order of time derivative optional default 1 filterparams order and cutoff frequency for Butterworth smoothing filter optional default 2 0 2 method fast or accurate version fast version is default use acc for accurate version if no window length is given the default lengths are used see comment window window length for Savitzky Golay FIR smoothing filter optional default 7 for first order derivative output d2 MoCap data structure or segm data structure examples d2 mctimeder d first order time derivative using the fast method Butterworth filter with default parameters d2 mctimeder Cd 2 1 first order time derivative using fast version Csecond order Butterworth filter with 0 1 Hz cutoff frequency d2 mctimeder d acc first order time derivative using the accurate version CSavitzky Golay filter d2 mctimeder d 2 9 acc Second order time derivative with 9 frame window using the accurate version Savitzky Golay filter 139 MoCap Toolbox Manual comments The default parameters for the Butterworth smoothing filter create a second order zero phase digital Butterworth filter with a cutoff frequency of 0 2 Hz The window length is dependent on the order of the time derivative and the given window length It is calculated by 4 n w
49. erceived emotions in music and music induced movement Music Perception 30 5 519 535 88 mcgetmarker synopsis Extracts a subset of markers syntax d2 mcgetmarker d mnum input parameters d MoCap or norm data structure mnum vector containing the numbers of markers to be extracted output d2 MoCap or norm data structure examples d2 mcgetmarker d 1 3 5 comments see also mcesetmarker mcconcatenate 89 MoCap Toolbox Manual mcgetmarkername synopsis Returns the names of markers syntax mn mcgetmarkernames d input parameters d MoCap data or norm structure output mn cell structure containing marker names examples comments see also 90 MoCap Toolbox Manual MoCap Toolbox Manual mcgetsegmpar synopsis Get parameters for body segments syntax spar mcgetsegmpar model segmnum input parameters model string indicating the body segment model used possible value Dempster more to be added in the future segmnum vector indicating numbers for each segment output spar segmpar structure examples segmnum 00876087 6 13 12 10 113 21 11 3 2 1 spar mcgetsegmpar Dempster segmnum comments Returns the mass relative to total body mass spar m relative distance of center of mass from proximal joint spar comprox and distal joint spar comdist and radius of gyra tion relative to center of gravity spar rogcg proximal joint spar rogprox and dis
50. ers d1 d2 nl n2 sl s2 MoCap data structure norm data structure or segm data structure marker vector containing marker numbers to be plotted for MoCap and norm data structure dim vector containing dimensions to be plotted for MoCap data structure segm body segment number for segm data structure var variable to be plotted for segment segm for segm data structure output Figure examples mcplotphaseplane d1 d2 1 3 3 for MoCap data structure mcpLotphaseplane n1 n2 5 for norm data structure mcplotphaseplane s1 s2 3 5 7 angle for segm data structure mcplotphaseplane s1 s2 5 10 eucl for segm data structure mcplotphaseplane si1 s2 12 14 quat for segm data structure comments see also 114 MoCap Toolbox Manual mcplottimeseries synopsis Plots motion capture data as time series NEW SYNTAX IN VERSION 1 3 1 syntax mcpLottimeseries d marker for MoCap or norm data structure U mcplottimeseries d marker dim dim specifying dimensions mcpLottimeseries d marker timetype timetype axis unit mcplottimeseries d marker plotopt plotopt combined or separate plots mcplottimeseries d marker Label label y axis label mcpLottimeseries d marker names names marker names T mcpLottimeseries s segm var var for segm data structure input parameters d s MoCap data structure norm data structure or segm data structure marker vector
51. es analysis with a given function syntax varargout mcwindow Cfunctionhandle d varargout mcwindowCfunctionhandle d wlen hop varargout mcwindow functionhandle d wlen hop timetype input parameters functionhandle handle to function with which the windowed analysis is performed d MoCap data structure or norm data structure wlen length of window optional default 2 sec hop hop factor optional default 0 5 timetype time type sec frame optional default sech output When used with the functions mcmean mcstd mcvar mcskewness and mckurtosis the output is a two dimensional matrix where the first index corresponds to window num ber and the second index to marker dimension When used with mcperiod the function returns four output parameters per ac eac lag where per is a two dimensional matrix with the first index corresponding to win dow number and the second to marker dimension Output parameters ac and eac are three dimensional matrices with the first index corresponding to window number the sec ond to lag and the third to marker dimension The output parameter lag is a vector con taining the lag values for the autocorrelations examples stds mcwindow mcstd d 3 5 per ac eac lags mcwindow mcperiod d comments see also mcmean mcstd mcvar mcskewness mckurtosis mcperiod 146 MoCap Toolbox Manual mcewritetsv synopsis Saves mocap structure as a tsv fil
52. ess synopsis Calculates the skewness of data ignoring missing values syntax m mcskewness d input parameters d MoCap data structure norm data structure or data matrix output m row vector containing the skewness values of each data column examples comments see also mcmean mcstd mcvar mckurtosis 133 MoCap Toolbox Manual MoCap Toolbox Manual mcsmoothen synopsis Smoothens motion capture data using a Butterworth fast or a Savitzky Golay FIR accurate smoothing filter syntax d2 mcsmoothen Cd d2 mcsmoothen d filterparams d2 mcsmoothen d method d2 mcsmoothen d window input parameters d MoCap data structure or segm data structure filterparams order and cutoff frequency for Butterworth filter optional default 2 0 2 method Butterworth filtering is default if Savitzky Golay filtering is to be used use acc as method argument window window length optional default 7 for Savitzky Golay FIR smoothing filter if input is scalar or a string Savitzky Golay filter is chosen if input is vector it is consid ered as parameters for Butterworth filter output d2 MoCap data structure or segm data structure examples d2 mcsmoothen d Butterworth filter smoothing with default parameters d2 mcsmoothen d 2 1 second order Butterworth filter with 1 Hz cutoff frequency d2 mcsmoothen d acc S G filter smoothing with default frame Length d2 mc
53. http repovizz upf edu see also mcread mcwritetsv 121 MoCap Toolbox Manual mcresample synopsis Resamples motion capture data using interpolation syntax d2 mcresampleCd newfreq method input parameters d MoCap data structure newfreq new frame rate method interpolation method optional default linear for other options see help interp1 output d2 MoCap data structure examples d2 mcresampleCd 240 d2 mcresampleCd 360 spline comments see also 122 mcreverse synopsis Reverses dimensions of motion capture data syntax d2 mcreverse d x input parameters d MoCap structure or data matrix x reverse vector set 1 for each dimension to be reversed otherwise 0 output d2 MoCap structure or data matrix examples d2 mcreverse d 0 0 1 comments see also 123 MoCap Toolbox Manual MoCap Toolbox Manual mcrotate synopsis Rotates motion capture data syntax d2 mcrotate d theta d2 mcrotate d theta axis d2 mcrotate d theta point d2 mcrotate d theta axis point input parameters d MoCap data structure or data matrix theta rotation angle in degrees axis rotation axis optional default 0 0 1 point point through which the rotation axis goes optional default is the centroid of markers over time output d2 MoCap data structure or data matrix examples d2 mcrotate d 130 rotate 130 degrees counterclockwise arou
54. ipal components analysis can be used to decompose Motion Capture data into components that are orthogonal to each other Let us extract the first four seconds from the structure dance2 load mcdemodata d mctrimCdance2 Q 4 and convert it into a joint representation j mcm2jCd m2jpar Next we calculate the first three principal component projections of the structure j Lpc p mcpcaproj j 1 3 and plot the amount of variance contained in these principal components bar p 1 1 3 We see that the first PC contains ca 85 of the variance while the next two components contain only 9 and 2 The PC projections can be investigated for instance by creating animations mcanimate pc 1 japar The animations show that the principal component distort the body segment relations in particular the lengths of certain body segments vary Often better results can be obtained by performing the PCA on the segment representation s mcj2s j j2spar convert to segment structure 58 MoCap Toolbox Manual pcs ps mcpcaproj s 1 3 perform PCA for k 1 3 convert PC projections back to joint structures pcjCk mcs2j pcsCk j2spar end Next let us plot the first three PC projections plotC ps c 1 3 Legendc PC1 PC2 PC3 to i e m t PCI 409 200 4 10 j 40 A rn TM a 100 a D 30 The plot reveals that the first PC correspond to non periodic motion while PCs 2 and 3 correspond to almost
55. lors wbgcr mcplotframeCwalk1 160 mapar Changing individual marker connector and number colors is explained in section Colored anima tions 30 MoCap Toolbox Manual CG Zo d e n o LP F b D Li The connector widths and marker sizes can be adjusted by changing the values of the fields cwidth and msize respectively mapar cwidth 3 mapar msize 6 mcplotframeCwalk1 160 mapar The viewing azimuth and elevation can be changed by changing the values of the fields az and el respectively mapar az 45 mapar el d mcpLotframeC walk1 160 mapar 31 MoCap Toolbox Manual Transforming MoCap data mcdemo2 This example shows how you can do various coordinate transformations to MoCap data and merge data collected at different motion capture sessions Let us plot a motion capture frame load mcdemodata mapar scrsize 800 600 mapar colors wkkkk mcpLotframeCdance1 50 mapar Let us next rotate the data contained in the variable dance1 by 90 degrees counterclockwise around the z vertical axis and plot the same frame 32 MoCap Toolbox Manual diroti mcrotateCdance1 90 0 1 mcplotframeCdirot1 50 mapar Next let us rotate the data in dance1 by 90 degrees counterclockwise around the x axis dirot2 mcrotateCdance1 90 1 Q mcpLotframeCdirot2 50 mapar e 1 amot gt D ty f lt y A f e L
56. m M 8 dm 3 M Lion mcpLottimeseries waLk1 4 8 12 dim 3 label mm names 1 markers 4 8 amp 12 dimensions 1 3 label on y axis set marker names in stead of numbers 25 VN AWA YS VM VV mcpLottimeseries walk1 Head_BR Sternum Hip_BR dim 1 3 using marker names instead of numbers in function call dimensions 1 3 A a A WD E Mu NIR E Marker locations in single frames can be plotted using the function mcplotframe This function plots the x z projection of the markers mcplotframe walk1 160 26 MoCap Toolbox Manual Because the parameter structure was not given in the previous call the function used the default set tings for the animation parameters mcinitanimpar ans type animpar scrsize 800 600 Limits az el 0 msize 12 colors kwwww markercolors conncolors tracecolors numbercolors cwidth 1 twidth 1 conn conn2 trm trl showmnum numbers 27 showfnum animate fps output videoformat createframes getparams perspective pers 1x1 struct MoCap Toolbox Manual To obtain a visualisation that is easier to understand the markers should be connected The variable mapar contains among other things the connection matrix mapar mapar type scrsize Limits az el msize colors markercolors conncolo
57. m structures output d11 d22 MoCap or norm structures one shortened and one original both with same number of frames examples comments see also 83 MoCap Toolbox Manual mcdecompose synopsis Decomposes a kinematic variable into tangential and normal components syntax Ldt dn mcdecomposeCd order input parameters d MoCap data structure containing either location or velocity data timederorder 0 or 1 order time derivative order of the variable must be at least 2 2 acceleration 3 jerk etc output dt norm data structure containing the tangential components dn norm data structure containing the normal components examples Ldt dn mcdecompose d 2 acceleration Ldt dn mcdecompose d 3 jerk Ldt dn mcdecompose d 4 jounce snap Ldt dn mcdecompose d 5 crackle Ldt dn mcdecompose d 6 pop Ldt dn mcdecompose d 7 you name it comments see also 84 MoCap Toolbox Manual mceigenmovement synopsis Constructs eigenmovements using PCA and a scaled sinusoidal projection syntax e mceigenmovement d e mceigenmovement d eigind e mceigenmovement d eigind len e mceigenmovement d eigind len per input parameters d MoCap or segm data structure eigind optional selected eigenmovements if not given projections onto the first PCs that contain a total of 90 of the variance are returned len optional length in seconds default 0
58. nd the vertical axis d2 mcrotate d 90 1 rotate around the x axis d2 mcrotate d 45 0 1 0 0 500 rotate around the axis parallel to y axis going through point 0 500 d2 mcrotate d 20 CO 1000 0 rotate around the z vertical axis going through point 1000 ol comments If theta is a vector its values are used as evenly spaced break points in interpolation This al lows the creation of dynamic rotation of the data Rotation is performed according to the right hand rule For instance if the rotation axis is pointing vertically upwards positive rotation angle means counterclockwise rotation when viewed from up see also mc2frontal 124 MoCap Toolbox Manual mcrotationrange synopsis Calculates the rotation range between two markers syntax f mcrotationrange d m1 m2 input parameters d MoCap data structure m1 marker one m2 marker two output r rotation range the higher the value the more rotation examples r mcrotation d 13 17 comments see also references Burger B Saarikallio S Luck G Thompson M R amp Toiviainen P 2013 Relationships between perceived emotions in music and music induced movement Music Perception 30 5 519 535 125 mcs2j synopsis Performs a segment to joint mapping syntax d2 mcj2s d par input parameters d segm data structure par j2spar structure output d2 MoCap data structure examples c
59. neeS cls a E iSueckelneeaintils 94 Wien Un TEE 95 BIGHT 2S EE 97 PACA ZOE EE 98 Wie ld suspeaterrnnscneananencersusesnennmarnmeseenansesusibuoncunimamaieneusiuateasaussaubusisenounisbseusseeatmenneteucs 99 unter E 101 nie Wlan E 102 wei Din SIS nsnsi aaae EEE RAEE S Taena KEA EAEE tedden 103 MEMZ ea E E E EE E EE A E A a 104 lei E e E 105 wei EE 106 Aana HIG EEE EEE 107 FUG TAS SN DE 108 MIC MOCAD ONAN E 109 BUCA E 110 BCBG AIO E 111 ICD tee E 112 mue ie td EE 113 Mmeplotphaseplane ssccceceeeeseeeeeeeeeeeeeeeeeee renee reese ae aeesaaaaaeaaeeeeeaeeeeeeeeeeeeeeeeeeeeensenees 114 We PIO TIMMS SSS sciane ea Eaa a EE e A EE E EAA EEEN ERRA EAE AEE 115 MIGDOTSNIENOY A T E A E ET 117 UC AM D 118 mereaddemMg E 119 MoCap Toolbox Manual D eege Si INS i estore ch oecncnniedstcvenesdvoetentdiaciedurcdevastisibatsiuudesedelisvseuscudaecdeptsbeceusdeeetadsivisnsteteasnegts 120 wei ele EE 121 NAGFES ln ihc reccsvescsnmnspicanovnesavessaxvesudosasumsceeatevanasieenauchevanepusdeusmenneteusversatussaesmennnesweeaten 122 EE 123 leen 124 Wuiei te Meel 125 Ge E 126 PPS le EE 127 MICS CQNIANG EE 128 REENEN EEERESEN ERREECHEN 129 PACS ST SIN OUIN syisa aaa a aa a a DA 130 Maele 131 DT SINAN E 132 PON EN 133 MESMOOME M EE 134 MESON EE 135 MACS e1101 1g n p NE E E EEE 136 mcestatmoments cccc ccc ececeeceeeceeeceeceeeeaeeceecsaeeaeeseeecaeeaeeesuecseseueeaeeseesseeaeeseeeseeeaeeeaeees 137 ADIE EE 138 Dein EE 139 CPUS ENON
60. ng walk1 figure setCgcf Position 4 200 560 420 subplot 3 1 1 bar mf xlabel Marker ylabel Num of Missing frames subplot 3 1 2 bar mm xlabel Frame ylabel Num of Missing markers subplot 3 1 3 imagesc mgrid colormap gray xlabel Frame ylabel Marker 3 H Ze 5 HI H bi H Mee i T H f Ze se KI 150 me bi 3 se an Tree 3 H 5 EI E KI ie 15 w ase a DI Freee Markers 2 and 6 have missing frames The missing data can be filled using the function mcfill gaps 23 MoCap Toolbox Manual walk1 mcfillgapsCwalk1 100 mf mm mgrid mcmissingCwalk1 subplot 3 1 1 bar mf xlabelC Marker ylabelC Num of Missing frames subplot 3 1 2 bar mm xlabelC Frame ylabelC Num of Missing markers subplot 3 1 3 imagesc mgrid colormap gray xlabelC Frame ylabelC Marker Mim of Mereg mates Ham of Miring huner The variable walk1 has no more missing frames Marker location data can be plotted as a function of time using the function mcplottimeseries mcplottimeseries walk1 3 dim 3 marker 3 dimension 3 Marker 3 dm 3 1630 24 mcpLlottimeseries walk1 4 8 12 dim 3 timetype frame markers 4 8 amp 12 dimension 3 frames on x axis AAO PS WM RV VA mcpLlottimeseries walk1 4 8 12 dim 3 plotopt combi markers 4 8 amp 12 dimension 3 combined into one plot WYN A AAA ch do
61. nitm2jpar mcj2s perform a joint to segment mapping mcs2j perform a segment to joint mapping mcs2posture create a posture representation form segm data mcnorm calculate the norms of Euclidean MoCap data mctimeder estimate time derivatives of MoCap data mctimeintegr estimate time integrals of MoCap data calculate the cumulative distance traveled by each marker mcmarkerdist calculate the distance of a marker pair mcboundrect calculate the bounding rectangle KINEMATIC lexi e ANALYSIS mccompLexity calculate the complexity of movement mcfluidity calculate the fluidity circularity of MoCap data calculates rotation range between two markers calculate the angles between two markers estimate period of MoCap data decompose kinematic variable into tangential and normal components calculate amplitude spectrum of MoCap data mcgetsegmpar return segment parameters of a body model estimate instantaneous kinetic energy of the body mccumdist mcdecompose KINETIC mckinenergy ANALYSIS TIME SERIES ANALYSIS VISUALIZATION PROJECTION OTHER MoCap Toolbox Manual gatimate instantaneous potential energy of the am perform a PCA on MoCap data perform an ICA on MoCap data perform either an m best or a small to large Sethares transform mceigenmovement generate eigenmovements from PCA mcsethares MoCap Toolbox Manual Data Structures The MoCap Toolbox uses three kinds of data structures the MoCap data structure
62. not necessary to have Max installed The files can be downloaded from http www fourms uio no software mcrtanimate If somebody wants to have this running on Windows it should work in theory but you will have to have Max installed and download the necessary dependencies listed in the readme file MoCap Toolbox Manual The implementation requires the Instrument Control Toolbox for Matlab http www mathworks se products instrument A workaround without this Toolbox is under development and will be pro vided soon This is still a prototype implementation so please provide feedback suggestions new features to Kristian 20 MoCap Toolbox Manual 21 MoCap Toolbox Manual This chapter contains a number of examples that are intended to serve as an introduction to the use of the MoCap Toolbox The examples illustrate how MoCap data can be read into Matlab edited visualized and transformed They also explain how kinematic kinetic as well as time series analy sis can be performed and how animations can be created Finally the chapter contains an example of the analysis and visualization of data captured using the Nintendo Wii remote controller The examples presented in this chapter can also be found in the function mcdemo Just type mcdemo in the Matlab Command Window and follow the instructions Reading Editing and Visualizing MoCap Data mcdemo1 This example shows how you can read MoCap files into
63. omments See the description of the j2spar structure see also mcinitj2spar mcj2s 126 MoCap Toolbox Manual MoCap Toolbox Manual mcs2posture synopsis Creates a posture representation from segm data by setting root transition and root rotation to zero values syntax p mcs2posture d input parameters d segm data structure output p segm data structure examples comments see also mcj2s 127 mcsegmangle synopsis Calculates the angles between two markers syntax dn mcsegmangle d m1 m2 input parameters d MoCap data structure m1 marker one m2 marker two output dn norm data structure containing the three angles examples dn mcsegmangle d 1 2 comments see also 128 MoCap Toolbox Manual MoCap Toolbox Manual mcsethares synopsis Performs either an m best or a small to large Sethares transform on MoCap norm or segm data Returns the basis functions for each DOF for given periods and with the m best transform also the powers for the respective periods syntax ds mcsethares d per small to Large Sethares transform ds pers pows mcsethares d per nbasis m best Sethares transform input parameters d MoCap norm or segm data structure per period in frames in case of small to large Sethares transform maximum period in frames in case of m best Sethares transform nbasis number of basis functions estimated only for m best Sethares transform output ds
64. otion capture data The functions can be divided into nine categories e Data input and edit functions e Coordinate transformation functions e Coordinate system conversion functions e Kinematic analysis functions e Kinetic analysis functions e Time series analysis functions e Visualization functions e Projection functions e Other functions The following table provides an overview of the functions available in the MoCap Toolbox De tailed descriptions of each function are provided in the Chapter Function Reference MoCap Toolbox Manual Function Synopsis read MoCap data files read emg files in tsv format mcmissing report missing frames and markers extract a temporal segment from MoCap data cut two MoCap structures to the length of the shorter one concatenate markers from different MoCap or norm data structure get names of markers from MoCap data mcfillgaps fill missing data initialize MoCap or norm data structure reorder the Euclidean dimensions in the MoCap data TRANSFORMATIO mcconcatenate mcreorderdims MoCap Toolbox Manual rotate MoCap data to have a frontal view with mc2frontal respect to a pair of markers convert a MoCap structure vector to a MoCap mcvect2grid e s structure with three orthogonal views initialize parameters for marker to joint mapping mcm2j perform a marker to joint mapping COORDINATE ee initialize parameters for joint to segment SYSTEM mapping CONVERSION mci
65. r the frequency channels in the spectra examples comments see also 136 MoCap Toolbox Manual mcstatmoments synopsis Calculates the first four statistical moments mean standard deviation skewness and kurto sis of data ignoring missing values syntax mom mcstatmoments d input parameters d MoCap data structure norm data structure or data matrix output mom structure containing the fields mean std skewness and kurtosis examples comments Calls the functions mcmean mcstd mcskewness and mckurtosis see also mcmean mcstd mcskewness mckurtosis 137 MoCap Toolbox Manual mcstd synopsis Calculates the temporal standard deviation of data ignoring missing values syntax m mcstd d input parameters d MoCap data structure norm data structure or data matrix output m row vector containing the standard deviations of each data column examples comments see also mcmean mcvar mcskewness mckurtosis 138 MoCap Toolbox Manual mctimeder synopsis Estimates time derivatives of motion capture data Two options are available the fast version uses differences between two successive frames and a Butterworth smoothing filter whereas the accurate version uses derivation with a Savitzky Golay FIR smoothing filter syntax d2 mctimeder d d2 mctimeder d order d2 mctimeder d filterparams d2 mctimeder d method d2 mctimederCd order filterparams d2 mctimed
66. rames 0 nCameras NaN nMarkers 0 freq NaN nAnalog 0 anaFreq 0 timederOrder 0 99 MoCap Toolbox Manual markerName data analogdata other other descr DESCRIPTION other timeStamp TIME_STAMP other dataIncluded 3D see also 100 mcj2s synopsis Performs a joint to segment mapping syntax d2 mcj2s Cd par input parameters d MoCap data structure par j2spar structure output d2 segm data structure examples comments See explanation of the j2spar structure see also mcinitj2spar mcs2j 101 MoCap Toolbox Manual MoCap Toolbox Manual mckinenergy synopsis Estimates the instantaneous kinetic energy of each body segment syntax te re mckinenergyCd segd spar input parameters d MoCap data structure segd segm data structure calculated from d spar segmpar structure see mcgetsegmpar output te matrix containing translational energy values for each body segment re matrix containing rotational energy values for each body segment examples segd mcj2s d j2spar spar mcgetsegmpar Dempster segmnum te re mckinenergyCd segd spar comments The energy for a given segment is in the column corresponding to the number of the distal joint of the respective segment see also mcj2s mcgetsegmpar mcpotenergy 102 mckurtosis synopsis Calculates the kurtosis of data ignoring missing values syntax m mckurtosis d input
67. re sophisticated algorithms will be implemented in the future see also 86 MoCap Toolbox Manual mcfilteremg synopsis Filters EMG data syntax out mcfilteremgCemgdata out mcfilteremgCemgdata filterfreqs input parameters emgdata norm data structure containing EMG data filterfreqs cutoff frequencies in Hz for the Butterworth filters first value for high pass fil ter second value for low pass filter default 20 24 output out norm data structure containing filtered data examples out mcfilteremgCemgdata out mcfilteremgCemgdata 18 21 comments Filters the data using a 4th order Butterworth high pass filter default cutoff frequency 20 Hz then full wave rectifies it then filters it using a 4th order Butterworth low pass filter default cutoff frequency 24 Hz see also mcreademg 87 MoCap Toolbox Manual mcfluidity synopsis Calculates the fluidity circularity of mocap data defined as the ratio between velocity and ac celeration of the normed and averaged mocap data syntax f mcfluidity d mnum input parameters d MoCap data structure mnum marker numbers optional if no value given all markers are used output f fluidity value the higher the value the higher the smoothness fluidity examples f mcfluidity d 4 6 comments see also references Burger B Saarikallio S Luck G Thompson M R amp Toiviainen P 2013 Relationships between p
68. re the walker turns around The translational and rotational energy for each body segment can be calculated as follows trans rot mckinenergy walk2j walk2s spar Let us plot the total translational energy plotCtime sum Ctrans 2 xLabelC Time si ylabelC Translational energy W We can observe a region of low translational energy in the region between 3 0 and 4 5 seconds where the walker is turning 50 MoCap Toolbox Manual Creating animations mcdemo6 mcdemo9 Basics mcdemo6 This example shows how you can create animations with the MoCap toolbox You can either produce an animation video avi or mp4 format or animation frames single png files with the MoCap toolbox The frames would have to be compiled into a movie using some other software On a Macintosh you can use for instance the QuickTime Pro software Should you happen to use the Windows operating system you can use for instance the Movie Maker software Let us create an animation from the variable walk2 The animpar structure mapar contains the connector information for this variable load mcdemodata mapar mapar type animpar scrsize 400 300 limits az 0 el 0 msize 6 colors kwwww markercolors conncolors tracecolors numbercolors cwidth 1 twidth 1 conn 43x2 double conn2 trm trl showmnum 9 numbers showfnum 9 51 MoCap Toolbox Manual animate Q fps
69. rs tracecolors numbercolLors cwidth twidth conn conn2 trm trl animpar 400 300 C H H 6 kwwww C C C C 1 1 43x2 double C C H showmnum numbers showfnum C 28 animate fps output videoformat createframes getparams perspective pers The connection matrix is in the field conn mapar conn ans 1x1 struct Columns 1 through 10 1 2 2 4 3 4 Columns 11 through 20 8 8 10 5 Columns 21 through 30 7 5 6 13 8 5 5 6 9 11 13 13 16 15 16 19 Columns 31 through 40 18 9 20 21 11 21 10 12 22 22 Columns 41 through 43 24 27 27 28 It also has a smaller screen size than the default mapar scrsize ans 400 300 28 24 10 10 15 19 21 23 10 12 12 14 23 25 11 12 11 14 17 25 26 11 12 14 18 26 23 MoCap Toolbox Manual 17 20 22 24 For the purpose of making the frame plots look nicer on this manual let us increase the screen size mapar scrsize 800 600 Using the parameter structure mapar we get the following visualization 29 MoCap Toolbox Manual mcplotframeCwalk1 160 mapar We can add marker numbers to the plot by setting the field showmnum to have the value 1 mapar showmnum 1 mcplotframeCwalk1 160 mapar Different colors can be used by changing the value of the field colors mapar co
70. s are saved mapar createframes 1 mapar output persQ Now we create an animation out of that mcanimateCwalk2 mapar If we have a look at the animation frames the figure appears to walk on the spot although she is actually walking forwards As an example have a look at the 10th 20th and 40th frame a 22 E a TH fest bi bh ed e d ry t f fa A A A The idea of the perspective projection is to visualize that the figure is actually walking forward To activate the perspective projection we set the perspective parameter in the animpar structure to 1 and call the mcanimate function again mapar perspective 1 mapar output pers1 mcanimateCwalk2 mapar This animation looks far more natural regarding the movement direction of the walker 56 MoCap Toolbox Manual The parameters for the perspective projection are set in the pers part of the animpar structure ma par mapar pers mapar pers c 0 4000 0 th 0 0 0 e 0 2000 0 The field c sets the 3D position of the camera th is the orientation of the camera and e stores the viewer s position relative to the display surface We can now change for example the camera position and create another animation to see what happens mapar pers c 1000 4000 1000 mapar output pers2 mcanimate walk2 mapar 1 10 20 57 MoCap Toolbox Manual Principal Components Analysis mcdemo10 Princ
71. see also mcpLotframe mcinitanimpar 74 MoCap Toolbox Manual mcbandpass synopsis Band pass filters data in a MoCap or norm structure using an FFT filter syntax d2 mcbandpass d f1 f2 d2 mcbandpass d f1 f2 method input parameters d MoCap or norm data structure fl lower frequency in Hz of passband f2 higher frequency in Hz of passband method filtering window rect default or gauss output d2 MoCap or norm data structure containing band bass filtered data examples d2 mcbandpass d 0 5 3 comments see also 75 MoCap Toolbox Manual mcboundrect synopsis Calculates the bounding rectangle the smallest rectangular area that contains the projection of the trajectory of each marker on the horizontal plane 1 e floor syntax br mcboundrect d br mcboundrect d mnum br mcboundrect d mnum w hop input parameters d MoCap data structure mnum marker numbers optional if no value given all markers are used w length of analysis window optional default 4 sec hop overlap of analysis windows optional default 2 sec output br data matrix windows x nMarkers examples br mcboundrect d br mcboundrect d 1 3 5 br mcboundrect d 1 d nMarkers 3 1 comments If the function is called with the mocap data structure as the only input parameter the calcula tion is performed for all markers with the default parameters If the window and o
72. set gca XTickLabel mn marker titleC dance1 axis L Inf Inf 2 3 subplot 2 2 2 bar d2skew 3 3 end set gca XTickLabel mn marker titleC dance2 axisC Inf Inf 2 3 subplot 2 2 3 bar wiskew 3 3 end setCgca XTickLabel mn marker titleC walk1 axisC Inf Inf 2 3 subpLot 2 2 4 43 MoCap Toolbox Manual bar w2skew 3 3 end setCgca XTickLabel mn marker titleC walk2 axisC Inf Inf 2 3 dorcel Geer 2 2 H H 1 tread Firip Fl Fees ime besse In HES Fi Feger_Ltnes_i Price L i w b wae 2 2 i 1 o D 4 Je D H Fees Lines bie 1 Jet HE P Fees tee Prime There are some differences between dancing and walking with respect to the skewness values The interpretation of these differences will be left to the user Windowed analysis of the statistical time series descriptors can be carried out using the mcwindow command Let us compute the windowed standard deviation of markers 1 19 and 25 left front head left hand and left foot in the variable dance1 marker 1 19 25 distd mcwindow mcstd mcgetmarkerCdance1 marker 2 0 25 for k 1 9 subplot 3 3 k plotCdistdC k titleC Marker num2strCmarker 1 floorCCk 1 3 dim num2str 1it remCk 1 3 end 44 MoCap Toolbox Manual High values in these graph correspond to temporal regions where the particular marker shows wide movements for the respective dimension Kinetic anal
73. showmnum flag indicating whether marker numbers are shown 1 yes 0 no numbers array indicating the markers for which number is to be shown showfnum flag indicating whether frame numbers are shown 1 yes 0 no animation flag indicating whether animation is created 1 yes 0 no this is set by the mcan imate function before it calls the mcplotframe function fps frames per second used in animation output either file name for video file of folder for pgn frames tmp videoformat specifies video file format either avi or mpeg4 av createframes create png frames instead of video file 1 frames 0 video file 0 getparams return animation parameters without plotting or animating frames 1 yes 0 no 0 perspective perform perspective projection 0 orthographic default 1 perspective 0 pers perspective projection parameters pers c 3D position of the camera 0 4000 0 pers th orientation of the camera 0 0 0 pers e viewer s position relative to the display surface 0 2000 0 69 see also mcinitanimpar 70 MoCap Toolbox Manual Function Refer ence 71 MoCap Toolbox Manual mc2frontal synopsis Rotates MoCap data to have a frontal view with respect to a pair of markers syntax d2 mc2frontalCd m1 m2 d2 mc2frontalCd m1 m2 method input parameters d MoCap data structure or data matrix m1 m2 numbers of the markers that define the frontal plane method rotation method possible
74. smoothen d 9 S G filter smoothing using a 9 frame window comments The default parameters for the Butterworth filter create a second order zero phase digital But terworth filter with a cutoff frequency of 0 2 Hz For information about the Savitzky Golay filter see help sgolayfilt see also mctimeder 134 MoCap Toolbox Manual mcsort synopsis sorts mocap data according to marker names alphanumerical or according to given numeric or cell array indicating marker numbers or markers names as to how the output data is to be sorted syntax d2 mcsort d d2 mcsort d srt input parameters d MoCap data structure srt numeric or cell array containing markers numbers or marker names optional output d2 reordered mocap data structure examples d2 mcsort d d2 mcsort d 1 5 7 6 9 8 10 20 d2 mcsort d di markerName comments If the sort variable is not given the data will be sorted alphanumerical according to the mark er names The number of items in the sort array has to match the number of markers in the input mocap data structure see also 135 MoCap Toolbox Manual mcspecirum synopsis Calculates the amplitude spectrum of mocap time series syntax s mcspectrum d s f mcspectrum d input parameters d MoCap structure norm structure or segm structure output s MoCap structure norm structure or segm structure containing amplitude spectra in the data field f frequencies in Hz fo
75. t or last frame see also mcaddframes mctrim 130 MoCap Toolbox Manual mcsetmarker synopsis Replaces a subset of markers in an existing mocap or norm structure syntax d2 mcsetmarker d_orig d_repl mnum input parameters d orig MoCap or norm data structure the one to be changed d rent MoCap or norm data structure the one that contains the replacement data The data set must have the same amount of markers as indicated in mnum mnum vector containing the marker numbers to be replaced in the original data set order as in replacement mocap structure output d2 MoCap structure examples d2 mcsetmarker Cd d1 1 3 5 comments Use mcgetmarker to shorten the replacing data set to fit the mnum vector If the resulting mocap structure shall contain more markers than the original the data will be appended at the specified marker number Possible in between markers will be set to NaN Empty marker names will be set to EMPTY and can be adapted manually if desired see also mccombine mcgetmarker 131 mcsimmat synopsis Calculates self similarity matrix from MoCap or segm data syntax sm mcsimmatCd sm mcsimmatCd metric input parameters d MoCap or segm data structure metric distance metric used see help pdist default cityblock output sm self similarity matrix examples sm mcsimmatCd sm mcsimmatCd corr comments see also 132 MoCap Toolbox Manual mcskewn
76. tal joint spar rogdist of for body segments indicated in segmnum according to given body segment model Segment number values for model Dempster no parameter 0 hand 1 forearm 2 upper arm 3 forearm and hand 4 upper extremity 5 foot 6 leg 7 thigh 8 lower extremity 9 head 10 shoulder 11 thorax 12 abdomen 13 pelvis 14 thorax and ab domen 15 abdomen and pelvis 16 trunk 17 head arms and trunk to glenohumeral joint 18 head arms and trunk to mid rib 19 Note that the root needs its own segment being 0 so segmnum is of size segments 1 The first zero in the segmnum vector above See the description of the segmpar structure see also references Robertson D G E Caldwell G E Hamill J Kamen G amp Whittlesley S N 2004 Re search methods in biomechanics Champaign IL Human Kinetics 91 MoCap Toolbox Manual mchilbert synopsis Calculates the Hilbert transform of data in a MoCap or norm structure syntax Lamp phase h mchilbert Cd wrap input parameters d MoCap or norm data structure wrap flag to indicate if phase is returned as wrapped or unwrap default unwrapped 0 or empty unwrap 1 wrap output amp amplitude of analytic function derived from zero mean signal phase unwrapped or wrapped phase of analytic function derived from zero mean signal h analytic function examples amp mchilbert d amp phase h mchilbert d 1 comments See help hilbert
77. unction call Standard deviations provides a measure for the extent of movement Let us calculate the standard deviations for the markers 1 19 and 25 left front head left hand and left foot in the MoCap data structures dance1 and dance2 load mcdemodata std1 mcstdCmcgetmarkerCdance1 1 19 25 std2 mcstdCmcgetmarkerCdance2 1 19 25 figure setCgcf Position 4 200 560 420 subpLot 2 1 1 barCreshape std1 3 3 xLabelC Dimension Legend Head Hand Foot axisC Inf Inf o 400 titleC dance1 subpLot 2 1 2 barCreshape std2 3 3 xLabelC Dimension LegendC Head Hand Foot axisC Inf Inf 400 titleC dance2 42 MoCap Toolbox Manual derce The standard deviations for the dimensions 1 and 2 are larger for dance1 than for dance2 sug gesting that dancer 1 occupies a larger area horizontally The standard deviation for dimension 3 for the hand marker is larger for dance1 suggesting that dancer 1 uses larger vertical hand movements than dancer 2 Let us calculate and plot the skewness values for the vertical dimension of selected markers in vari ables dance1 dance2 walk1 and walk2 marker 1 9 19 21 25 diskew mcskewness mcgetmarker dance1 marker wiskew mcskewness mcgetmarker walk1 marker d2skew mcskewness mcgetmarker dance2 marker w2skew mcskewness mcgetmarker walk2 marker mn mcgetmarkername dance1 subplot 2 2 1 bar d1skew 3 3 end
78. ures the m2jpar j2spar and animpar structures The m2jpar structure is used by the function mcm2j and contains information needed to carry out a transformation from a marker representation to a joint representation Among other things it con tains a field that holds for each joint the numbers of the markers whose centroid defines the loca tion of that joint The j2spar structure is used by the function mcj2s and contains information needed to carry out a transformation from a joint representation to a segment representation Among other things it con tains the number of the joint that is the center root of the body It also contains the numbers of three joints that define the frontal plane of the body Finally it contains a vector that indicates the MoCap Toolbox Manual parent segment the segment proximal in the kinematic chain for each segment and a cell array with the segment names The animpar structure is used by the functions mcplotframe and mcanimate and holds informa tion needed to create frame plots and animations These include for both frame plots and anima tion the limits of the plotted area screen size viewing angle plotting colors marker size line widths and connections between markers Additionally the structure holds the possibility to plot traces and the frames per second used when creating animations A more detailed description of the parameter structures used in the MoCap Toolbox can be foun
79. verlap length are to be changed the markers have to be always specified e g all markers by 1 d nMarkers see also references Burger B Saarikallio S Luck G Thompson M R amp Toiviainen P 2013 Relationships between perceived emotions in music and music induced movement Music Perception 30 5 519 535 76 MoCap Toolbox Manual mec3d2tsv synopsis Converts a c3d file into a tsv file syntax mcc3d2tsvCfn path input parameters fn name of c3d file path path to save the tsv file optional If no path is given file is saved to current directory output tsv file saved in the current or in the specified directory examples mcc3d2tsvC file c3d mcc3d2tsvC file c3d folder mcc3d2tsvC file c3d path folder Mac comments see also mcread 77 MoCap Toolbox Manual mccenter synopsis Translates motion capture data to have a centroid of 0 0 0 across markers and over time syntax d2 mccenter d input parameters d MoCap data structure or data matrix output d2 MoCap data structure or data matrix examples comments Missing data NaN s is ignored when calculating the centroid see also 78 MoCap Toolbox Manual mccomplexity synopsis Calculates the complexity of movement based on entropy of the proportion of variance con tained in the principal components A high value indicates a high complexity whereas a low value indicated low complexity syntax
80. ys s s Sid i t4 4s ph 2 t s a oe tld ab e ST ef et D Ce SZ ve ez En f oy R t f a D gt Dk A e wf ta 4 In Matlab the frames will be plotted as separate figures Chapter Creating Animations explains how these frames can be used to create an animation Kinematic analysis mcdemo3 This example shows how you can estimate kinematic variables from MoCap data and visualize them Time derivatives of motion capture data can be estimated using the function mctimeder load mcdemodata d2v mctimederCdance2 1 velocity d2a mctimederCdance2 2 acceleration Let us have a look at the vertical velocity component of markers 1 19 and 25 left front head left hand and left foot mcpLottimeseries Cd2v 1 19 25 dim 3 36 MoCap Toolbox Manual The subplots display the vertical velocities of markers 1 19 and 25 from top to bottom Next let us plot the vertical acceleration components of the same markers mcpLottimeseries d2a 1 19 25 dim 3 The phase plane plots for velocity and acceleration can be produced as follows figure set gcf Position 4 40 200 800 change the shape of the figure to make the subplots rectangular mcpLotphaseplaneCd2v d2a 1 19 25 3 This figure is below on the left The same phase plane plot but for the interval between 5 and 7 seconds can be produced as fol lows 37 MoCap Toolbox Manu
81. ysis mcdemo5 This example shows how the toolbox can be used to calculate kinetic variables from MoCap data using Dempster s body segment model Let us estimate various forms of mechanical energy in walking movement variable walk1 To start with we plot a MoCap frame with marker numbers load mcdemodata mapar colors wkkkk mapar showmnum 1 mapar msize 6 mapar az 90 mcpLotframeCwalk2 16 mapar 45 MoCap Toolbox Manual E a j D iy SA j SE r i d vd A b The first thing to do is to reduce the set of markers to make the data compatible with Dempster s model This can be accomplished using the marker to joint transformation implemented in function mcm2j The parameters needed for this conversion are in the variable m2jpar m2jpar m2jpar type m2jpar nMarkers 20 markerNum 1x20 cell markerName 1x20 cell The information concerning which markers correspond to each joint is contained in the field m2j par markerNum The names of the new joints are in m2jpar markerName For instance m2jpar markerName 1 ans root m2jpar markerNum 1 ans 9 10 11 12 the joint root is obtained by calculating the centroid of markers 9 10 11 and 12 The marker to joint conversion is carried out as follows waLlk2j mcm2jCwalk2 m2jpar 46 walk2j type filename nFrames nCameras nMarkers freq nAnalog anaFreq timederOrder markerName data analogdata other

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