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loadLabels.m
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loadLabels.m
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% This file contains parameters used to
% 1) Configure the scripts to the lab
% 2) Prepare labels for plotting
% ----------------------------------------
% LAB: SET UP FOR YOUR OWN LAB!
% ----------------------------------------
% =================================
% SECTION 1: LAB CONFIGURATION
% =================================
% 1a) Force Plate Naming Convention
% ---------------------------------------------------------------------
% Force plate numbers MUST be set up within the lab.
% The names of the channels of these force plates are defined here.
% EXAMPLE
% glab.FP.string = '%s%d%s';
% glab.FP.prefix = {'FP','FP','FP','FP','FP','FP'};
% glab.FP.suffix = {'Fx','Fy','Fz','Mx','My','Mz'};
%
% Moment about FP #3 in the X direction analog channel = 'FP3Mx'
% Please note that the glab.FP.string IS CASE SENSITIVE
%
% verticalForceIndex is the index of the vertical GRF
% (independant of direction) IN FORCE PLATE COORDINATES
%
% glab.vertForceCutoff defines the vertical cutoff force (N),
% above which a plate is deemed "active". Active plates together
% with events are used to determine the foot-plate sequence.
% ---------------------------------------------------------------------
glab.FP.string = '%s%d%s'; % Prefix, PlateNum, Suffix
glab.FP.prefix = {'FP','FP','FP','FP','FP','FP'};
glab.FP.suffix = {'Fx','Fy','Fz','Mx','My','Mz'};
glab.FP.verticalForceIndex = 3;
glab.FP.filterOrder = 4;
glab.vertForceCutoff = 10;
% 1b) Coordinate Vector Setup
% ---------------------------------------------------------------------
% This section sets transformation vectors that are crucial to the
% rigid body transformations needed between the Force Plate, Vicon,
% and the Model coordinate systems.
%
% Example: FP coord system -> Model coord system
% glab.dirVec.FPMODEL(3,:) = [2 -3 -1];
%
% MODEL X = FP Y
% MODEL Y = FP -Z
% MODEL Z = FP -X
% ---------------------------------------------------------------------
% X direction (Vicon) Gait -> transformation vectors
glab.transform.VICMODEL(1,:) = [1 3 -2]; % Vicon coord system -> Model coord system
% -X direction (Vicon) Gait -> transformation vectors
glab.transform.VICMODEL(2,:) = [-1 3 2]; % Vicon coord system -> Model coord system
% Y direction (Vicon) Gait -> transformation vectors
glab.transform.VICMODEL(3,:) = [2 3 1]; % Vicon coord system -> Model coord system
% -Y direction (Vicon) Gait -> transformation vectors
glab.transform.VICMODEL(4,:) = [-2 3 -1]; % Vicon coord system -> Model coord system
% 1c) Special Markers
% ---------------------------------------------------------------------
% offsetMarker: marker to be used as the offset point to line up the
% model to the walking platform in OpenSim. It is also
% used to get the average speed in getEvents.
%
% legLengthMarkers: a set of marker pairs that define the start and
% end of the leg to define leg length.
% ---------------------------------------------------------------------
glab.offsetMarker = 'SACR';
glab.legLengthMarkers = {'RASI', 'RLMAL', 'LASI', 'LLMAL'};
% 1d) Joint names used in OpenSim
% ---------------------------------------------------------------------
% Set this corresponding to the joint names in the OpenSim model
% Currently the joint label is only used to get create the coordinates
% file in getKinetics.m
% ---------------------------------------------------------------------
glab.jointModel = 'jointArms37'; % Joint convension
glab.muscleModel = 'musc92'; % Muscle convension
% 1e) Directory to store toolbox outputs
% ---------------------------------------------------------------------
% Output images, mat files, and text files from toolbox function calls
% can be stored in this directory for future reference. Must have
% a backslash at the end. i.e. '.\MyDir\'. This functionality is
% toggled by glab.storeInfo (1 = on, 0 = off)
% ---------------------------------------------------------------------
glab.storeInfo = 1;
glab.infoDirectory = '.\GaitExtract\';
% =================================
% SECTION 2: DATA EXTRACTION
% =================================
% 2a) Title Labels
% ---------------------------------------------------------------------
glab.name{1} = 'GRF';
glab.name{2} = 'CoP';
glab.name{3} = 'GRMo';
glab.name{4} = 'GRMx';
glab.name{5} = 'Joint Angles';
glab.name{6} = 'Joint Torques';
glab.name{7} = 'Muscle Forces';
glab.name{8} = 'EMG';
% GRF Direction Labels
% (x dir+-, y dir+-, z dir+-)
% ---------------------------------------------------------------------
glab.dir{1} = {'Fore', 'Aft'};
glab.dir{2} = {'Vertical', ''};
glab.dir{3} = {'Lateral', 'Medial'};
% GRF Labels
% (label, units, directionSign+, directionSign-)
% ---------------------------------------------------------------------
glab.S{1} = [{'GRF X (right)', 'N'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.S{2} = [{'GRF Y (right)', 'N'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.S{3} = [{'GRF Z (right)', 'N'}, glab.dir{3}(1), glab.dir{3}(2)];
glab.S{4} = [{'GRF X (left)', 'N'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.S{5} = [{'GRF Y (left)', 'N'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.S{6} = [{'GRF Z (left)', 'N'}, glab.dir{3}(1), glab.dir{3}(2)];
% CoP Labels
% (label, units, directionSign+, directionSign-)
% ---------------------------------------------------------------------
glab.X{1} = [{'CoP X (right)', 'm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.X{2} = [{'CoP Y (right)', 'm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.X{3} = [{'CoP Z (right)', 'm'}, glab.dir{3}(1), glab.dir{3}(2)];
glab.X{4} = [{'CoP X (left)', 'm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.X{5} = [{'CoP Y (left)', 'm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.X{6} = [{'CoP Z (left)', 'm'}, glab.dir{3}(1), glab.dir{3}(2)];
% GRM Labels (Origin)
% (label, units, directionSign+, directionSign-)
% ---------------------------------------------------------------------
glab.Mo{1} = [{'GRMo X (right)', 'Nm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.Mo{2} = [{'GRMo Y (right)', 'Nm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.Mo{3} = [{'GRMo Z (right)', 'Nm'}, glab.dir{3}(1), glab.dir{3}(2)];
glab.Mo{4} = [{'GRMo X (left)', 'Nm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.Mo{5} = [{'GRMo Y (left)', 'Nm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.Mo{6} = [{'GRMo Z (left)', 'Nm'}, glab.dir{3}(1), glab.dir{3}(2)];
% GRM Labels (CoP)
% (label, units, directionSign+, directionSign-)
% ---------------------------------------------------------------------
glab.Mx{1} = [{'GRMx X (right)', 'Nm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.Mx{2} = [{'GRMx Y (right)', 'Nm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.Mx{3} = [{'GRMx Z (right)', 'Nm'}, glab.dir{3}(1), glab.dir{3}(2)];
glab.Mx{4} = [{'GRMx X (left)', 'Nm'}, glab.dir{1}(1), glab.dir{1}(2)];
glab.Mx{5} = [{'GRMx Y (left)', 'Nm'}, glab.dir{2}(1), glab.dir{2}(2)];
glab.Mx{6} = [{'GRMx Z (left)', 'Nm'}, glab.dir{3}(1), glab.dir{3}(2)];
% Joint Labels
% (label, unitsAngle, unitsTorque)
% ---------------------------------------------------------------------
glab.jointArms37 = {{'pelvis_tx', 'm', 'N'}; ...
{'pelvis_ty', 'm', 'N'}; ...
{'pelvis_tz', 'm', 'N'}; ...
{'pelvis_list', 'deg', 'Nm'}; ...
{'pelvis_rotation', 'deg', 'Nm'}; ...
{'pelvis_tilt', 'deg', 'Nm'}; ...
{'hip_flexion_r', 'deg', 'Nm'}; ...
{'hip_adduction_r', 'deg', 'Nm'}; ...
{'hip_rotation_r', 'deg', 'Nm'}; ...
{'knee_angle_r', 'deg', 'Nm'}; ...
{'ankle_angle_r', 'deg', 'Nm'}; ...
{'subtalar_angle_r', 'deg', 'Nm'}; ...
{'mtp_angle_r', 'deg', 'Nm'}; ...
{'hip_flexion_l', 'deg', 'Nm'}; ...
{'hip_adduction_l', 'deg', 'Nm'}; ...
{'hip_rotation_l', 'deg', 'Nm'}; ...
{'knee_angle_l', 'deg', 'Nm'}; ...
{'ankle_angle_l', 'deg', 'Nm'}; ...
{'subtalar_angle_l', 'deg', 'Nm'}; ...
{'mtp_angle_l', 'deg', 'Nm'}; ...
{'lumbar_extension', 'deg', 'Nm'}; ...
{'lumbar_bending', 'deg', 'Nm'}; ...
{'lumbar_rotation', 'deg', 'Nm'}; ...
{'arm_flex_r', 'deg', 'Nm'}; ...
{'arm_add_r', 'deg', 'Nm'}; ...
{'arm_rot_r', 'deg', 'Nm'}; ...
{'elbow_flex_r', 'deg', 'Nm'}; ...
{'pro_sup_r', 'deg', 'Nm'}; ...
{'wrist_flex_r', 'deg', 'Nm'}; ...
{'wrist_dev_r', 'deg', 'Nm'}; ...
{'arm_flex_l', 'deg', 'Nm'}; ...
{'arm_add_l', 'deg', 'Nm'}; ...
{'arm_rot_l', 'deg', 'Nm'}; ...
{'elbow_flex_l', 'deg', 'Nm'}; ...
{'pro_sup_r', 'deg', 'Nm'}; ...
{'wrist_flex_r', 'deg', 'Nm'}; ...
{'wrist_dev_r', 'deg', 'Nm'}};
% Muscle Labels
% (muscle_name, spanning_joints)
% ---------------------------------------------------------------------
glab.musc92 = { {'glut_med1_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_med2_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_med3_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_min1_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_min2_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_min3_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'semimem_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'semiten_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'bifemlh_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'bifemsh_r', 'knee_angle_r'} ; ...
{'sar_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'add_long_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'add_brev_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'add_mag1_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'add_mag2_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'add_mag3_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'tfl_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'pect_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'grac_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'glut_max1_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_max2_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'glut_max3_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'iliacus_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'psoas_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'quad_fem_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'gem_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'peri_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r'} ; ...
{'rect_fem_r', 'hip_flexion_r', 'hip_adduction_r', 'hip_rotation_r', 'knee_angle_r'} ; ...
{'vas_med_r', 'knee_angle_r'} ; ...
{'vas_int_r', 'knee_angle_r'} ; ...
{'vas_lat_r', 'knee_angle_r'} ; ...
{'med_gas_r', 'knee_angle_r', 'ankle_angle_r'} ; ...
{'lat_gas_r', 'knee_angle_r', 'ankle_angle_r'} ; ...
{'soleus_r', 'ankle_angle_r'} ; ...
{'tib_post_r', 'ankle_angle_r'} ; ...
{'flex_dig_r', 'ankle_angle_r'} ; ...
{'flex_hal_r', 'ankle_angle_r'} ; ...
{'tib_ant_r', 'ankle_angle_r'} ; ...
{'per_brev_r', 'ankle_angle_r'} ; ...
{'per_long_r', 'ankle_angle_r'} ; ...
{'per_tert_r', 'ankle_angle_r'} ; ...
{'ext_dig_r', 'ankle_angle_r'} ; ...
{'ext_hal_r', 'ankle_angle_r'} ; ...
{'glut_med1_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_med2_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_med3_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_min1_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_min2_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_min3_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'semimem_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'semiten_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'bifemlh_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'bifemsh_l', 'knee_angle_l'} ; ...
{'sar_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'add_long_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'add_brev_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'add_mag1_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'add_mag2_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'add_mag3_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'tfl_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'pect_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'grac_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'glut_max1_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_max2_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'glut_max3_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'iliacus_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'psoas_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'quad_fem_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'gem_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'peri_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l'} ; ...
{'rect_fem_l', 'hip_flexion_l', 'hip_adduction_l', 'hip_rotation_l', 'knee_angle_l'} ; ...
{'vas_med_l', 'knee_angle_l'} ; ...
{'vas_int_l', 'knee_angle_l'} ; ...
{'vas_lat_l', 'knee_angle_l'} ; ...
{'med_gas_l', 'knee_angle_l', 'ankle_angle_l'} ; ...
{'lat_gas_l', 'knee_angle_l', 'ankle_angle_l'} ; ...
{'soleus_l', 'ankle_angle_l'} ; ...
{'tib_post_l', 'ankle_angle_l'} ; ...
{'flex_dig_l', 'ankle_angle_l'} ; ...
{'flex_hal_l', 'ankle_angle_l'} ; ...
{'tib_ant_l', 'ankle_angle_l'} ; ...
{'per_brev_l', 'ankle_angle_l'} ; ...
{'per_long_l', 'ankle_angle_l'} ; ...
{'per_tert_l', 'ankle_angle_l'} ; ...
{'ext_dig_l', 'ankle_angle_l'} ; ...
{'ext_hal_l', 'ankle_angle_l'} ; ...
{'ercspn_r', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'} ; ...
{'intobl_r', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'} ; ...
{'extobl_r', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'}
{'ercspn_l', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'} ; ...
{'intobl_l', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'} ; ...
{'extobl_l', 'lumbar_extension', 'lumbar_bending', 'lumbar_rotation'}};
% EMG Labels
% {label, name, associated muscles}
% note: associated muscle can take up any number of string cells
% Used by batchEMGprocess.m to know which EMG analog channels to
% extract from the C3D file
% ---------------------------------------------------------------------
% EMG set
% -------------------
glab.testEMG{1} = {'VASMED' ,'Vastus Medialis'};
glab.testEMG{2} = {'GAS' ,'Medial Gastrocnemius'};
glab.testEMG{3} = {'SOL' ,'Soleus'};
glab.testEMG{4} = {'HAMLAT' ,'Lateral Hamstring'};
% EMG Processing Tasks
% {ProcessTask1, Value1, ProcessTask2, Value2, ...}
% notes: refer to processEMG.m for more information or type help processEMG
% the operations are executed in order of appearance.
% ---------------------------------------------------------------------
glab.EMGprocessTKE1 = { 'tke', [], ... % TKE filter
'rect', [], ... % Rectification
'plot', 0 }; % Plot
glab.EMGprocessTKE2 = { 'tke', [], ... % TKE filter
'rect', [], ... % Rectification
'save', 1, ... % Save plots
'hide', [], ... % Hide raw/tke [1 2]
'plot', 1, ... % Plot
'vertlines', 'C3Dkey'}; % Plot event lines
glab.EMGprocessFILTERS = { 'remdc', [], ... % Remove DC Offset
'hpf', [4, 40], ... % High Pass Filter
'rect', [], ... % Rectification
'lpf', [4, 25], ... % Low Pass Filter
'abovezero', [], ... % Force EMG > 0
'plot', 1, ... % Plot transformations
'vertlines', 'C3Dkey' }; % Plot event lines
% Kinematic Marker Set
% Used by getMarkers.m to know which markers to extract
% from the C3D file
% ---------------------------------------------------------------------
glab.markersStatic = {'RSHO', 'LSHO', 'C7', ...
'RASI', 'LASI', 'SACR', ...
'RTHAP', 'RTHAD', 'RTHLD', 'RLEPI', 'RMEPI', ...
'RTIAP', 'RTIAD', 'RMMAL', 'RLMAL', ...
'RHEEL', 'RP1MT', 'RP5MT', 'RTOE', ...
'LTHAP', 'LTHAD', 'LTHLD', 'LLEPI', 'LMEPI', ...
'LTIAP', 'LTIAD', 'LMMAL', 'LLMAL', ...
'LHEEL', 'LP1MT', 'LP5MT', 'LTOE'};
glab.markersDynamic = {'RSHO', 'LSHO', 'C7', ...
'RASI', 'LASI', 'SACR', ...
'RTHAP', 'RTHAD', 'RTHLD', 'RLEPI', ...
'RTIAP', 'RTIAD', 'RLMAL', ...
'RHEEL', 'RP1MT', 'RP5MT', 'RTOE', ...
'LTHAP', 'LTHAD', 'LTHLD', 'LLEPI', ...
'LTIAP', 'LTIAD', 'LLMAL', ...
'LHEEL', 'LP1MT', 'LP5MT', 'LTOE'};