diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022.osim b/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022.osim
new file mode 100644
index 0000000..613b694
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022.osim
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+ Rajagopal, A., Dembia, C.L., DeMers, M.S., Delp, D.D., Hicks, J.L., Delp, S.L. (2016)
+ Full-body musculoskeletal model for muscle-driven simulation of human gait. IEEE Transactions on Biomedical Engineering.
+ Lai, A.K.M., Arnold, A.S., Wakeling, J.M. (2017)
+ Why are antagonist muscles co-activated in my simulation? A musculoskeletal model for analysing human locomotor tasks. Annals of Biomedical Engineering
+ Uhlrich, S.D., Jackson, R.W., Seth, A., Kolesar, J.A., Delp, S.L. (2022)
+ Muscle coordination retraining inspired by musculoskeletal simulations reduces knee contact force. Scientific Reports
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+
+
+
+ 3
+
+
+
+ 0.029000000000000001
+
+ 0.14999999999999999
+
+
+
+
+
+ 3.7075
+
+ 0 -0.1867 0
+
+ 0.0504 0.0051000000000000004 0.0511 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ l_patella.vtp
+
+
+
+
+
+
+
+
+ 0.086199999999999999
+
+ 0.0018 0.0264 0
+
+ 2.8700000000000001e-06 1.311e-05 1.311e-05 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ l_talus.vtp
+
+
+
+
+
+
+
+
+ 0.10000000000000001
+
+ 0 0 0
+
+ 0.001 0.001 0.001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+
+ 3
+
+
+
+ l_foot.vtp
+
+
+
+
+
+
+
+
+ 1.25
+
+ 0.10000000000000001 0.029999999999999999 0
+
+ 0.0014 0.0038999999999999998 0.0041000000000000003 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ l_bofoot.vtp
+
+
+
+
+
+
+
+
+ 0.21659999999999999
+
+ 0.034599999999999999 0.0060000000000000001 0.017500000000000002
+
+ 0.0001 0.00020000000000000001 0.001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ hat_spine.vtp
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ hat_jaw.vtp
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ hat_skull.vtp
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ 1
+
+ 1 1 1
+
+
+ hat_ribs_scap.vtp
+
+
+
+
+
+
+
+
+ 26.826599999999999
+
+ -0.029999999999999999 0.32000000000000001 0
+
+ 1.4744999999999999 0.75549999999999995 1.4314 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+
+ 3
+
+
+
+ humerus_rv.vtp
+
+
+
+
+
+
+
+
+ 2.0325000000000002
+
+ 0 -0.16450200000000001 0
+
+ 0.011946 0.0041209999999999997 0.013409000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ulna_rv.vtp
+
+
+
+
+
+
+
+
+ 0.60750000000000004
+
+ 0 -0.12052499999999999 0
+
+ 0.0029619999999999998 0.00061799999999999995 0.0032130000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ radius_rv.vtp
+
+
+
+
+
+
+
+
+ 0.60750000000000004
+
+ 0 -0.12052499999999999 0
+
+ 0.0029619999999999998 0.00061799999999999995 0.0032130000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ pisiform_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ lunate_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ scaphoid_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ triquetrum_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ hamate_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ capitate_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ trapezoid_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ trapezium_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal2_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_proximal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_medial_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_distal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal3_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_proximal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_medial_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_distal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal4_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_proximal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_medial_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_distal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal5_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_proximal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_medial_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_distal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal1_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ thumb_proximal_rvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ thumb_distal_rvs.vtp
+
+
+
+
+
+
+
+
+ 0.45750000000000002
+
+ 0 -0.068095000000000003 0
+
+ 0.000892 0.00054699999999999996 0.00134 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ humerus_lv.vtp
+
+
+
+
+
+
+
+
+ 2.0325000000000002
+
+ 0 -0.16450200000000001 0
+
+ 0.011946 0.0041209999999999997 0.013409000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ulna_lv.vtp
+
+
+
+
+
+
+
+
+ 0.60750000000000004
+
+ 0 -0.12052499999999999 0
+
+ 0.0029619999999999998 0.00061799999999999995 0.0032130000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 1 1 1
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ radius_lv.vtp
+
+
+
+
+
+
+
+
+ 0.60750000000000004
+
+ 0 -0.12052499999999999 0
+
+ 0.0029619999999999998 0.00061799999999999995 0.0032130000000000001 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ pisiform_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ lunate_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ scaphoid_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ triquetrum_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ hamate_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ capitate_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ trapezoid_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ trapezium_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal2_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_proximal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_medial_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ index_distal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal3_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_proximal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_medial_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ middle_distal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal4_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_proximal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_medial_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ ring_distal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal5_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_proximal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_medial_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ little_distal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ metacarpal1_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ thumb_proximal_lvs.vtp
+
+
+
+ ..
+
+ 0.84999999999999998 0.84999999999999998 0.84999999999999998
+
+
+
+ true
+
+ 1
+
+ 1 1 1
+
+
+ thumb_distal_lvs.vtp
+
+
+
+
+
+
+
+
+ 0.45750000000000002
+
+ 0 -0.068095000000000003 0
+
+ 0.000892 0.00054699999999999996 0.00134 0 0 0
+
+
+
+
+
+
+
+
+
+ ground_offset
+
+ pelvis_offset
+
+
+
+
+ 0
+
+ 0
+
+ -1.5707963300000001 1.5707963300000001
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0
+
+ 0
+
+ -1.5707963300000001 1.5707963300000001
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0
+
+ 0
+
+ -6.283185307179586 6.283185307179586
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0
+
+ 0
+
+ -50 50
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0.92999999909764297
+
+ 0
+
+ -1 2
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0
+
+ 0
+
+ -3 3
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+ /ground
+
+ 0 0 0
+
+ 0 0 0
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+ /bodyset/pelvis
+
+ 0 0 0
+
+ 0 0 0
+
+
+
+
+
+
+
+ pelvis_tilt
+
+ 0 0 1
+
+
+ 1 0
+
+
+
+
+ pelvis_list
+
+ 1 0 0
+
+
+ 1 0
+
+
+
+
+ pelvis_rotation
+
+ 0 1 0
+
+
+ 1 0
+
+
+
+
+
+ pelvis_tx
+
+ 1 0 0
+
+
+ 1 0
+
+
+
+
+ pelvis_ty
+
+ 0 1 0
+
+
+ 1 0
+
+
+
+
+ pelvis_tz
+
+ 0 0 1
+
+
+ 1 0
+
+
+
+
+
+
+ pelvis_offset
+
+ femur_r_offset
+
+
+
+
+ 0
+
+ 0
+
+ -0.52359878000000004 2.0943950999999998
+
+ true
+
+ false
+
+
+
+ false
+
+
+
+ 0
+
+ 0
+
+ -0.87266463000000005 0.52359878000000004
+
+ true
+
+ false
+
+
+
+ false
+
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diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022_shoulder.osim b/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022_shoulder.osim
new file mode 100644
index 0000000..0c6a9bf
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/LaiUhlrich2022_shoulder.osim
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+ Full-body musculoskeletal model for muscle-driven simulation of human gait. IEEE Transactions on Biomedical Engineering.
+ Lai, A.K.M., Arnold, A.S., Wakeling, J.M. (2017)
+ Why are antagonist muscles co-activated in my simulation? A musculoskeletal model for analysing human locomotor tasks. Annals of Biomedical Engineering
+ Uhlrich, S.D., Jackson, R.W., Seth, A., Kolesar, J.A., Delp, S.L. (2022)
+ Muscle coordination retraining inspired by musculoskeletal simulations reduces knee contact force. Scientific Reports
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+
+ addbrev_r addlong_r glmin1_r grac_r iliacus_r psoas_r recfem_r sart_r tfl_r
+
+
+ addlong_r addmagDist_r addmagIsch_r addmagMid_r addmagProx_r bflh_r glmax1_r glmax2_r glmax3_r glmed1_r glmed2_r glmed3_r glmin3_r semimem_r semiten_r
+
+
+ glmed1_r glmed2_r glmed3_r glmin1_r iliacus_r psoas_r tfl_r
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+
+ glmin3_r piri_r
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+
+ bflh_r bfsh_r gaslat_r gasmed_r grac_r sart_r semimem_r semiten_r
+
+
+ recfem_r vasint_r vaslat_r vasmed_r
+
+
+ edl_r ehl_r tibant_r
+
+
+ fdl_r fhl_r gaslat_r gasmed_r perbrev_r perlong_r soleus_r tibpost_r
+
+
+ edl_r perbrev_r perlong_r
+
+
+ ehl_r fdl_r fhl_r tibant_r tibpost_r
+
+
+ addbrev_l addlong_l addmagDist_l addmagIsch_l addmagMid_l addmagProx_l bflh_l grac_l semimem_l semiten_l
+
+
+ glmax1_l glmed1_l glmed2_l glmed3_l glmin1_l glmin2_l glmin3_l piri_l sart_l tfl_l
+
+
+ addbrev_l addlong_l glmin1_l grac_l iliacus_l psoas_l recfem_l sart_l tfl_l
+
+
+ addlong_l addmagDist_l addmagIsch_l addmagMid_l addmagProx_l bflh_l glmax1_l glmax2_l glmax3_l glmed1_l glmed2_l glmed3_l glmin3_l semimem_l semiten_l
+
+
+ glmin3_l piri_l
+
+
+ glmed1_l glmed2_l glmed3_l glmin1_l iliacus_l psoas_l tfl_l
+
+
+ bflh_l bfsh_l gaslat_l gasmed_l grac_l sart_l semimem_l semiten_l
+
+
+ recfem_l vasint_l vaslat_l vasmed_l
+
+
+ edl_l ehl_l tibant_l
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+
+ fdl_l fhl_l gaslat_l gasmed_l perbrev_l perlong_l soleus_l tibpost_l
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+
+ edl_l perbrev_l perlong_l
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+ ehl_l fdl_l fhl_l tibant_l tibpost_l
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/Marker_add.xml b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Marker_add.xml
new file mode 100644
index 0000000..7493071
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Marker_add.xml
@@ -0,0 +1,352 @@
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diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK.xml b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK.xml
new file mode 100644
index 0000000..15434fd
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK.xml
@@ -0,0 +1,289 @@
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+
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+ Unassigned
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+ Unassigned
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+ -Inf Inf
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+ false
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diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK_shoulder.xml b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK_shoulder.xml
new file mode 100644
index 0000000..308d683
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_IK_shoulder.xml
@@ -0,0 +1,369 @@
+
+
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diff --git a/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_scaling_LSTM.xml b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_scaling_LSTM.xml
new file mode 100644
index 0000000..df14235
--- /dev/null
+++ b/Pose2Sim/Demo/OpenSim_Setup/LSTM/Setup_scaling_LSTM.xml
@@ -0,0 +1,749 @@
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+ 0.10000000000000001
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+ 0.10000000000000001
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+ manual_value
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+ 0
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+ 0.10000000000000001
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+ manual_value
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+ true
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+ 0.10000000000000001
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+ manual_value
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+ 0.087266462599716474
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+ true
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+ 0.10000000000000001
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+ 0
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+ true
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+ 0.10000000000000001
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+ manual_value
+
+ 0.087266462599716474
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+
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+ true
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+ 0.10000000000000001
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+ manual_value
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+ 0
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+
+
+ true
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+ 0.10000000000000001
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+ manual_value
+
+ 0
+
+
+
+ true
+
+ 0.10000000000000001
+
+ manual_value
+
+ 0
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+
+
+
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+ Unassigned
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+ Unassigned
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+ 3.41 3.66
+
+
+
+
+
+
+
+ -1
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+
+
diff --git a/Pose2Sim/Demo/S00_Demo_Session/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/Config.toml
index 29ca45a..e0cc8c0 100644
--- a/Pose2Sim/Demo/S00_Demo_Session/Config.toml
+++ b/Pose2Sim/Demo/S00_Demo_Session/Config.toml
@@ -27,7 +27,7 @@ frame_range = [] # For example [10,300], or [] for all frames
exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
+## Only taken into account if want to use marker augmentation
participant_height = 1.7 # m
participant_mass = 70 # kg
@@ -94,8 +94,7 @@ calibration_type = 'convert' # 'convert' or 'calculate'
[pose]
pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII
#With mediapipe: BLAZEPOSE.
#With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
#With deeplabcut: CUSTOM. See example at the end of the file.
diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml
index ef2d3d5..ce8eef7 100644
--- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml
+++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml
@@ -27,7 +27,7 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml
index 8aef4a7..ce8eef7 100644
--- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml
+++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml
@@ -9,8 +9,8 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
-# If you wish to overwrite a parameter for a specific trial or participant,
+#
+# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
# [filtering.butterworth] and set cut_off_frequency = 10, etc.
@@ -27,7 +27,7 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml
index eb23604..ce8eef7 100644
--- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml
+++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml
@@ -9,8 +9,8 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
-# If you wish to overwrite a parameter for a specific trial or participant,
+#
+# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
# [filtering.butterworth] and set cut_off_frequency = 10, etc.
@@ -27,7 +27,7 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -140,9 +139,9 @@
# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
-[filtering]
+# [filtering]
# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = true # true or false (lowercase)
+# display_figures = true # true or false (lowercase)
# [filtering.butterworth]
# order = 4
diff --git a/Pose2Sim/Demo/S01_Empty_Session/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/Config.toml
index 27a08e7..089a89c 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/Config.toml
@@ -27,7 +27,7 @@ frame_range = [] # For example [10,300], or [] for all frames
exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
+## Only taken into account if want to use marker augmentation
participant_height = 1.7 # m
participant_mass = 70 # kg
@@ -95,7 +95,6 @@ calibration_type = 'convert' # 'convert' or 'calculate'
[pose]
pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
#With mediapipe: BLAZEPOSE.
#With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
#With deeplabcut: CUSTOM. See example at the end of the file.
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml
index e99bc70..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml
@@ -9,7 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -27,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -163,7 +162,7 @@
# [opensim]
-# static_trial = ['S01_P00_Participant0/S01_P00_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml
index 96077d0..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml
@@ -9,6 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -26,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -94,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
-# BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -162,7 +162,7 @@
# [opensim]
-# static_trial = ['S01_P00_Participant0/S01_P00_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml
index d4ff549..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml
@@ -9,6 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -26,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -94,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -139,9 +139,9 @@
# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
-[filtering]
+# [filtering]
# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = true # true or false (lowercase)
+# display_figures = true # true or false (lowercase)
# [filtering.butterworth]
# order = 4
@@ -162,7 +162,7 @@ display_figures = true # true or false (lowercase)
# [opensim]
-# static_trial = ['S01_P00_Participant/0S01_P00_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml
index 3e255e4..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml
@@ -9,6 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -26,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -94,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -139,9 +139,9 @@
# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
-[filtering]
+# [filtering]
# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = true # true or false (lowercase)
+# display_figures = true # true or false (lowercase)
# [filtering.butterworth]
# order = 4
@@ -162,7 +162,7 @@ display_figures = true # true or false (lowercase)
# [opensim]
-# static_trial = ['S01_P00_Participant0/S01_P00_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml
index e60bd75..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml
@@ -9,7 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -27,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -163,7 +162,7 @@
# [opensim]
-# static_trial = ['S01_P01_Participant1/S01_P01_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml
index e60bd75..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml
@@ -9,7 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -27,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -163,7 +162,7 @@
# [opensim]
-# static_trial = ['S01_P01_Participant1/S01_P01_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml
index eded427..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml
@@ -9,7 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -27,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -140,9 +139,9 @@
# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
-[filtering]
+# [filtering]
# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = true # true or false (lowercase)
+# display_figures = true # true or false (lowercase)
# [filtering.butterworth]
# order = 4
@@ -163,7 +162,7 @@ display_figures = true # true or false (lowercase)
# [opensim]
-# static_trial = ['S01_P01_Participant1/S01_P01_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml
index eded427..ce8eef7 100644
--- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml
+++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml
@@ -9,7 +9,7 @@
# If a parameter is not found here, Pose2Sim will look for its value in the
# Config.toml file of the level above. This way, you can set global
# instructions for the Session and alter them for specific Participants or Trials.
-#
+#
# If you wish to overwrite a parameter for a specific trial or participant,
# edit its Config.toml file by uncommenting its key (e.g., [project])
# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment
@@ -27,9 +27,9 @@
# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
+## Only taken into account if want to use marker augmentation
# participant_height = 1.7 # m
# participant_mass = 70 # kg
-## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon!
## Take heart, calibration is not that complicated once you get the hang of it!
@@ -95,8 +95,7 @@
# [pose]
# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut'
-# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
- # BODY_25_AUGMENTED # Coming soon!
+# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII,
# #With mediapipe: BLAZEPOSE.
# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133.
# #With deeplabcut: CUSTOM. See example at the end of the file.
@@ -140,9 +139,9 @@
# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
-[filtering]
+# [filtering]
# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = true # true or false (lowercase)
+# display_figures = true # true or false (lowercase)
# [filtering.butterworth]
# order = 4
@@ -163,7 +162,7 @@ display_figures = true # true or false (lowercase)
# [opensim]
-# static_trial = ['S01_P01_Participant1/S01_P01_T00_StaticTrial']
+# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
# # If this Config.toml file is at the Trial level, set to true or false (lowercase);
# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/mean.npy b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/mean.npy
new file mode 100644
index 0000000..c945e2c
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/mean.npy differ
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/metadata.json b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/metadata.json
new file mode 100644
index 0000000..6d8aa2f
--- /dev/null
+++ b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/metadata.json
@@ -0,0 +1 @@
+{"reference_marker": "midHip"}
\ No newline at end of file
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/model.json b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/model.json
new file mode 100644
index 0000000..14d244b
--- /dev/null
+++ b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/model.json
@@ -0,0 +1 @@
+{"class_name": "Sequential", "config": {"name": "sequential_2", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": [null, null, 47], "dtype": "float32", "sparse": false, "ragged": false, "name": "lstm_8_input"}}, {"class_name": "LSTM", "config": {"name": "lstm_8", "trainable": true, "dtype": "float32", "batch_input_shape": [null, null, 47], "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_9", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_10", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_11", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "TimeDistributed", "config": {"name": "time_distributed_2", "trainable": true, "dtype": "float32", "layer": {"class_name": "Dense", "config": {"name": "dense_2", "trainable": true, "dtype": "float32", "units": 105, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}}}]}, "keras_version": "2.12.0", "backend": "tensorflow"}
\ No newline at end of file
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/std.npy b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/std.npy
new file mode 100644
index 0000000..c8ad375
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/std.npy differ
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/weights.h5 b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/weights.h5
new file mode 100644
index 0000000..9a974dc
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_lower/weights.h5 differ
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/mean.npy b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/mean.npy
new file mode 100644
index 0000000..a4ddcbe
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/mean.npy differ
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/metadata.json b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/metadata.json
new file mode 100644
index 0000000..6d8aa2f
--- /dev/null
+++ b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/metadata.json
@@ -0,0 +1 @@
+{"reference_marker": "midHip"}
\ No newline at end of file
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/model.json b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/model.json
new file mode 100644
index 0000000..dd30ad6
--- /dev/null
+++ b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/model.json
@@ -0,0 +1 @@
+{"class_name": "Sequential", "config": {"name": "sequential", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": [null, null, 23], "dtype": "float32", "sparse": false, "ragged": false, "name": "lstm_input"}}, {"class_name": "LSTM", "config": {"name": "lstm", "trainable": true, "dtype": "float32", "batch_input_shape": [null, null, 23], "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_1", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_2", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_3", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "LSTM", "config": {"name": "lstm_4", "trainable": true, "dtype": "float32", "return_sequences": true, "return_state": false, "go_backwards": false, "stateful": false, "unroll": false, "time_major": false, "units": 128, "activation": "tanh", "recurrent_activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "recurrent_initializer": {"class_name": "Orthogonal", "config": {"gain": 1.0, "seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "unit_forget_bias": true, "kernel_regularizer": null, "recurrent_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "recurrent_constraint": null, "bias_constraint": null, "dropout": 0.0, "recurrent_dropout": 0.0, "implementation": 2}}, {"class_name": "TimeDistributed", "config": {"name": "time_distributed", "trainable": true, "dtype": "float32", "layer": {"class_name": "Dense", "config": {"name": "dense", "trainable": true, "dtype": "float32", "units": 24, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}}}]}, "keras_version": "2.12.0", "backend": "tensorflow"}
\ No newline at end of file
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/std.npy b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/std.npy
new file mode 100644
index 0000000..39897c5
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/std.npy differ
diff --git a/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/weights.h5 b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/weights.h5
new file mode 100644
index 0000000..20d507f
Binary files /dev/null and b/Pose2Sim/MarkerAugmenter/LSTM/v0.3_upper/weights.h5 differ
diff --git a/Pose2Sim/Pose2Sim.py b/Pose2Sim/Pose2Sim.py
index 438677e..0581d41 100644
--- a/Pose2Sim/Pose2Sim.py
+++ b/Pose2Sim/Pose2Sim.py
@@ -371,12 +371,12 @@ def triangulation(config=None):
logging.info(f"Triangulation of 2D points for {seq_name}, for {frames}.")
logging.info("---------------------------------------------------------------------")
logging.info(f"\nProject directory: {project_dir}")
-
+
triangulate_all(config_dict)
end = time.time()
logging.info(f'Triangulation took {end-start:.2f} s.')
-
+
def filtering(config=None):
'''
@@ -420,6 +420,37 @@ def filtering(config=None):
filter_all(config_dict)
+def augmenter(config=None):
+ from Pose2Sim.augmenter import augmentTRC
+ level, config_dicts = read_config_files(config)
+
+ if type(config) == dict:
+ config_dict = config_dicts[0]
+ if config_dict.get('project').get('project_dir') is None:
+ raise ValueError('Please specify the project directory in config_dict:\n \
+ config_dict.get("project").update({"project_dir":""})')
+
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..', '..'))
+ setup_logging(session_dir)
+
+ for config_dict in config_dicts:
+ start = time.time()
+ project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
+ seq_name = os.path.basename(project_dir)
+ frame_range = config_dict.get('project').get('frame_range')
+ frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
+
+ logging.info("\n\n---------------------------------------------------------------------")
+ logging.info(f"Augmentation process for {seq_name}, for {frames}.")
+ logging.info("---------------------------------------------------------------------")
+ logging.info(f"\nProject directory: {project_dir}")
+
+ augmentTRC(config_dict)
+
+ end = time.time()
+ logging.info(f'Augmentation took {end - start:.2f} s.')
+
+
def opensimProcessing(config=None):
'''
@@ -469,4 +500,4 @@ def opensimProcessing(config=None):
# end = time.time()
# logging.info(f'Model scaling took {end-start:.2f} s.')
-
\ No newline at end of file
+
diff --git a/Pose2Sim/augmenter.py b/Pose2Sim/augmenter.py
new file mode 100644
index 0000000..7b83e8b
--- /dev/null
+++ b/Pose2Sim/augmenter.py
@@ -0,0 +1,213 @@
+import os
+import numpy as np
+from . import utilsDataman
+import copy
+import tensorflow as tf
+from .utils import TRC2numpy
+import json
+import os
+import glob
+
+
+# subject_height must be in meters
+def get_midhip_data(trc_file):
+ try:
+ # Find MidHip data
+ midhip_data = trc_file.marker("CHip")
+ if midhip_data is None or len(midhip_data) == 0:
+ raise ValueError("MidHip data is empty")
+ except (KeyError, ValueError):
+ # If MidHip data is not found, calculate it from RHip and LHip
+ rhip_data = trc_file.marker("RHip")
+ lhip_data = trc_file.marker("LHip")
+ midhip_data = (rhip_data + lhip_data) / 2
+
+ return midhip_data
+
+
+def augmentTRC(config_dict):
+
+ # get parameters from Config.toml
+ project_dir = config_dict.get('project').get('project_dir')
+ session_dir = os.path.realpath(os.path.join(project_dir, '..', '..'))
+ pathInputTRCFile = os.path.realpath(os.path.join(project_dir, 'pose-3d'))
+ pathOutputTRCFile = os.path.realpath(os.path.join(project_dir, 'pose-3d'))
+ subject_height = config_dict.get('project').get('participant_height')
+ if subject_height is None or subject_height == 0:
+ raise ValueError("Subject height is not set or invalid in the config file.")
+ subject_mass = config_dict.get('project').get('participant_mass')
+ augmenterDir = os.path.join(session_dir, '..', '..', 'MarkerAugmenter')
+ augmenterModelName = 'LSTM'
+ augmenter_model = 'v0.3'
+ offset = True
+
+ # Apply all trc files
+ trc_files = [f for f in glob.glob(os.path.join(pathInputTRCFile, '*.trc')) if '_LSTM' not in f]
+ for pathInputTRCFile in trc_files:
+ pathOutputTRCFile = os.path.splitext(pathInputTRCFile)[0] + "_LSTM.trc"
+
+ # This is by default - might need to be adjusted in the future.
+ featureHeight = True
+ featureWeight = True
+
+ # Augmenter types
+ if augmenter_model == 'v0.0':
+ from .utils import getOpenPoseMarkers_fullBody
+ feature_markers_full, response_markers_full = getOpenPoseMarkers_fullBody()
+ augmenterModelType_all = [augmenter_model]
+ feature_markers_all = [feature_markers_full]
+ response_markers_all = [response_markers_full]
+ elif augmenter_model == 'v0.1' or augmenter_model == 'v0.2':
+ # Lower body
+ augmenterModelType_lower = '{}_lower'.format(augmenter_model)
+ from .utils import getOpenPoseMarkers_lowerExtremity
+ feature_markers_lower, response_markers_lower = getOpenPoseMarkers_lowerExtremity()
+ # Upper body
+ augmenterModelType_upper = '{}_upper'.format(augmenter_model)
+ from .utils import getMarkers_upperExtremity_noPelvis
+ feature_markers_upper, response_markers_upper = getMarkers_upperExtremity_noPelvis()
+ augmenterModelType_all = [augmenterModelType_lower, augmenterModelType_upper]
+ feature_markers_all = [feature_markers_lower, feature_markers_upper]
+ response_markers_all = [response_markers_lower, response_markers_upper]
+ else:
+ # Lower body
+ augmenterModelType_lower = '{}_lower'.format(augmenter_model)
+ from .utils import getOpenPoseMarkers_lowerExtremity2
+ feature_markers_lower, response_markers_lower = getOpenPoseMarkers_lowerExtremity2()
+ # Upper body
+ augmenterModelType_upper = '{}_upper'.format(augmenter_model)
+ from .utils import getMarkers_upperExtremity_noPelvis2
+ feature_markers_upper, response_markers_upper = getMarkers_upperExtremity_noPelvis2()
+ augmenterModelType_all = [augmenterModelType_lower, augmenterModelType_upper]
+ feature_markers_all = [feature_markers_lower, feature_markers_upper]
+ response_markers_all = [response_markers_lower, response_markers_upper]
+ print('Using augmenter model: {}'.format(augmenter_model))
+
+ # %% Process data.
+ # Import TRC file
+ trc_file = utilsDataman.TRCFile(pathInputTRCFile)
+
+ # Loop over augmenter types to handle separate augmenters for lower and
+ # upper bodies.
+ outputs_all = {}
+ n_response_markers_all = 0
+ for idx_augm, augmenterModelType in enumerate(augmenterModelType_all):
+ outputs_all[idx_augm] = {}
+ feature_markers = feature_markers_all[idx_augm]
+ response_markers = response_markers_all[idx_augm]
+
+ augmenterModelDir = os.path.join(augmenterDir, augmenterModelName,
+ augmenterModelType)
+
+ # %% Pre-process inputs.
+ # Step 1: import .trc file with OpenPose marker trajectories.
+ trc_data = TRC2numpy(pathInputTRCFile, feature_markers)
+
+ # # Add these lines to get RHip and LHip data and calculate midHip
+ # rhip_data = trc_file.marker("RHip") # Replace "RHip" with the actual name in your trc file
+ # lhip_data = trc_file.marker("LHip") # Replace "LHip" with the actual name in your trc file
+
+ # Calculate the midHip marker as the average of RHip and LHip
+ midhip_data = get_midhip_data(trc_file)
+
+ trc_data_data = trc_data[:,1:]
+
+ # Step 2: Normalize with reference marker position.
+ with open(os.path.join(augmenterModelDir, "metadata.json"), 'r') as f:
+ metadata = json.load(f)
+
+ # Use midhip_data as the reference marker data
+ referenceMarker_data = midhip_data # instead of trc_file.marker(referenceMarker)
+
+ norm_trc_data_data = np.zeros((trc_data_data.shape[0],
+ trc_data_data.shape[1]))
+ for i in range(0,trc_data_data.shape[1],3):
+ norm_trc_data_data[:,i:i+3] = (trc_data_data[:,i:i+3] -
+ referenceMarker_data)
+
+
+ # Step 3: Normalize with subject's height.
+ norm2_trc_data_data = copy.deepcopy(norm_trc_data_data)
+ norm2_trc_data_data = norm2_trc_data_data / subject_height
+
+ # Step 4: Add remaining features.
+ inputs = copy.deepcopy(norm2_trc_data_data)
+ if featureHeight:
+ inputs = np.concatenate(
+ (inputs, subject_height*np.ones((inputs.shape[0],1))), axis=1)
+ if featureWeight:
+ inputs = np.concatenate(
+ (inputs, subject_mass*np.ones((inputs.shape[0],1))), axis=1)
+
+ # Step 5: Pre-process data
+ pathMean = os.path.join(augmenterModelDir, "mean.npy")
+ pathSTD = os.path.join(augmenterModelDir, "std.npy")
+ if os.path.isfile(pathMean):
+ trainFeatures_mean = np.load(pathMean, allow_pickle=True)
+ inputs -= trainFeatures_mean
+ if os.path.isfile(pathSTD):
+ trainFeatures_std = np.load(pathSTD, allow_pickle=True)
+ inputs /= trainFeatures_std
+
+ # Step 6: Reshape inputs if necessary (eg, LSTM)
+ if augmenterModelName == "LSTM":
+ inputs = np.reshape(inputs, (1, inputs.shape[0], inputs.shape[1]))
+
+ # %% Load model and weights, and predict outputs.
+ json_file = open(os.path.join(augmenterModelDir, "model.json"), 'r')
+ pretrainedModel_json = json_file.read()
+ json_file.close()
+ model = tf.keras.models.model_from_json(pretrainedModel_json)
+ model.load_weights(os.path.join(augmenterModelDir, "weights.h5"))
+ outputs = model.predict(inputs)
+
+ # %% Post-process outputs.
+ # Step 1: Reshape if necessary (eg, LSTM)
+ if augmenterModelName == "LSTM":
+ outputs = np.reshape(outputs, (outputs.shape[1], outputs.shape[2]))
+
+ # Step 2: Un-normalize with subject's height.
+ unnorm_outputs = outputs * subject_height
+
+ # Step 2: Un-normalize with reference marker position.
+ unnorm2_outputs = np.zeros((unnorm_outputs.shape[0],
+ unnorm_outputs.shape[1]))
+ for i in range(0,unnorm_outputs.shape[1],3):
+ unnorm2_outputs[:,i:i+3] = (unnorm_outputs[:,i:i+3] +
+ referenceMarker_data)
+
+ # %% Add markers to .trc file.
+ for c, marker in enumerate(response_markers):
+ x = unnorm2_outputs[:,c*3]
+ y = unnorm2_outputs[:,c*3+1]
+ z = unnorm2_outputs[:,c*3+2]
+ trc_file.add_marker(marker, x, y, z)
+
+ # %% Gather data for computing minimum y-position.
+ outputs_all[idx_augm]['response_markers'] = response_markers
+ outputs_all[idx_augm]['response_data'] = unnorm2_outputs
+ n_response_markers_all += len(response_markers)
+
+ # %% Extract minimum y-position across response markers. This is used
+ # to align feet and floor when visualizing.
+ responses_all_conc = np.zeros((unnorm2_outputs.shape[0],
+ n_response_markers_all*3))
+ idx_acc_res = 0
+ for idx_augm in outputs_all:
+ idx_acc_res_end = (idx_acc_res +
+ (len(outputs_all[idx_augm]['response_markers']))*3)
+ responses_all_conc[:,idx_acc_res:idx_acc_res_end] = (
+ outputs_all[idx_augm]['response_data'])
+ idx_acc_res = idx_acc_res_end
+ # Minimum y-position across response markers.
+ min_y_pos = np.min(responses_all_conc[:,1::3])
+
+ # %% If offset
+ if offset:
+ trc_file.offset('y', -(min_y_pos-0.01))
+
+ # %% Return augmented .trc file
+ trc_file.write(pathOutputTRCFile)
+
+ return min_y_pos
+
diff --git a/Pose2Sim/filtering.py b/Pose2Sim/filtering.py
index 1917e20..7dd6a2e 100644
--- a/Pose2Sim/filtering.py
+++ b/Pose2Sim/filtering.py
@@ -464,9 +464,17 @@ def filter_all(config):
# Trc paths
trc_f_in = f'{seq_name}_{f_range[0]}-{f_range[1]}.trc'
+ trc_f_in_LSTM = f'{seq_name}_{f_range[0]}-{f_range[1]}_LSTM.trc'
trc_f_out = f'{seq_name}_filt_{filter_type}_{f_range[0]}-{f_range[1]}.trc'
- trc_path_in = os.path.join(pose3d_dir, trc_f_in)
- trc_path_out = os.path.join(pose3d_dir, trc_f_out)
+ trc_f_out_LSTM = f'{seq_name}_filt_{filter_type}_{f_range[0]}-{f_range[1]}_LSTM.trc'
+ if os.path.exists(os.path.join(pose3d_dir, trc_f_in_LSTM)):
+ trc_path_in = os.path.join(pose3d_dir, trc_f_in_LSTM)
+ trc_path_out = os.path.join(pose3d_dir, trc_f_out_LSTM)
+ elif os.path.exists(os.path.join(pose3d_dir, trc_f_in)):
+ trc_path_in = os.path.join(pose3d_dir, trc_f_in)
+ trc_path_out = os.path.join(pose3d_dir, trc_f_out)
+ else:
+ raise FileNotFoundError("Not found .trc file.")
# Read trc header
with open(trc_path_in, 'r') as trc_file:
diff --git a/Pose2Sim/skeletons.py b/Pose2Sim/skeletons.py
index 6ec0244..233fa4f 100644
--- a/Pose2Sim/skeletons.py
+++ b/Pose2Sim/skeletons.py
@@ -116,7 +116,6 @@ BODY_25 = Node("CHip", id=8, children=[
]),
])
-
'''BODY_135 (full-body with hands and face, experimental, from OpenPose)
https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/blob/master/experimental_models/README.md)'''
BODY_135 = Node("CHip", id=None, children=[
diff --git a/Pose2Sim/utils.py b/Pose2Sim/utils.py
new file mode 100644
index 0000000..d91cbd0
--- /dev/null
+++ b/Pose2Sim/utils.py
@@ -0,0 +1,190 @@
+from . import utilsDataman
+import numpy as np
+
+def TRC2numpy(pathFile, markers,rotation=None):
+ # rotation is a dict, eg. {'y':90} with axis, angle for rotation
+
+ trc_file = utilsDataman.TRCFile(pathFile)
+ time = trc_file.time
+ num_frames = time.shape[0]
+ data = np.zeros((num_frames, len(markers)*3))
+
+ if rotation != None:
+ for axis,angle in rotation.items():
+ trc_file.rotate(axis,angle)
+ for count, marker in enumerate(markers):
+ data[:,3*count:3*count+3] = trc_file.marker(marker)
+ this_dat = np.empty((num_frames, 1))
+ this_dat[:, 0] = time
+ data_out = np.concatenate((this_dat, data), axis=1)
+
+ return data_out
+
+def numpy2TRC(f, data, headers, fc=50.0, t_start=0.0, units="m"):
+
+ header_mapping = {}
+ for count, header in enumerate(headers):
+ header_mapping[count+1] = header
+
+ # Line 1.
+ f.write('PathFileType 4\t(X/Y/Z) %s\n' % os.getcwd())
+
+ # Line 2.
+ f.write('DataRate\tCameraRate\tNumFrames\tNumMarkers\t'
+ 'Units\tOrigDataRate\tOrigDataStartFrame\tOrigNumFrames\n')
+
+ num_frames=data.shape[0]
+ num_markers=len(header_mapping.keys())
+
+ # Line 3.
+ f.write('%.1f\t%.1f\t%i\t%i\t%s\t%.1f\t%i\t%i\n' % (
+ fc, fc, num_frames,
+ num_markers, units, fc,
+ 1, num_frames))
+
+ # Line 4.
+ f.write("Frame#\tTime\t")
+ for key in sorted(header_mapping.keys()):
+ f.write("%s\t\t\t" % format(header_mapping[key]))
+
+ # Line 5.
+ f.write("\n\t\t")
+ for imark in np.arange(num_markers) + 1:
+ f.write('X%i\tY%s\tZ%s\t' % (imark, imark, imark))
+ f.write('\n')
+
+ # Line 6.
+ f.write('\n')
+
+ for frame in range(data.shape[0]):
+ f.write("{}\t{:.8f}\t".format(frame+1,(frame)/fc+t_start)) # opensim frame labeling is 1 indexed
+
+ for key in sorted(header_mapping.keys()):
+ f.write("{:.5f}\t{:.5f}\t{:.5f}\t".format(data[frame,0+(key-1)*3], data[frame,1+(key-1)*3], data[frame,2+(key-1)*3]))
+ f.write("\n")
+
+def getOpenPoseMarkerNames():
+
+ markerNames = ["Nose", "Neck", "RShoulder", "RElbow", "RWrist",
+ "LShoulder", "LElbow", "LWrist", "midHip", "RHip",
+ "RKnee", "RAnkle", "LHip", "LKnee", "LAnkle", "REye",
+ "LEye", "REar", "LEar", "LBigToe", "LSmallToe",
+ "LHeel", "RBigToe", "RSmallToe", "RHeel"]
+
+ return markerNames
+
+def getOpenPoseFaceMarkers():
+
+ faceMarkerNames = ['Nose', 'REye', 'LEye', 'REar', 'LEar']
+ markerNames = getOpenPoseMarkerNames()
+ idxFaceMarkers = [markerNames.index(i) for i in faceMarkerNames]
+
+ return faceMarkerNames, idxFaceMarkers
+
+def getOpenPoseMarkers_fullBody():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RHip", "LHip", "RKnee", "LKnee",
+ "RAnkle", "LAnkle", "RHeel", "LHeel", "RSmallToe", "LSmallToe",
+ "RBigToe", "LBigToe", "RElbow", "LElbow", "RWrist", "LWrist"]
+
+ response_markers = ["C7_study", "r_shoulder_study", "L_shoulder_study",
+ "r.ASIS_study", "L.ASIS_study", "r.PSIS_study",
+ "L.PSIS_study", "r_knee_study", "L_knee_study",
+ "r_mknee_study", "L_mknee_study", "r_ankle_study",
+ "L_ankle_study", "r_mankle_study", "L_mankle_study",
+ "r_calc_study", "L_calc_study", "r_toe_study",
+ "L_toe_study", "r_5meta_study", "L_5meta_study",
+ "r_lelbow_study", "L_lelbow_study", "r_melbow_study",
+ "L_melbow_study", "r_lwrist_study", "L_lwrist_study",
+ "r_mwrist_study", "L_mwrist_study",
+ "r_thigh1_study", "r_thigh2_study", "r_thigh3_study",
+ "L_thigh1_study", "L_thigh2_study", "L_thigh3_study",
+ "r_sh1_study", "r_sh2_study", "r_sh3_study",
+ "L_sh1_study", "L_sh2_study", "L_sh3_study",
+ "RHJC_study", "LHJC_study"]
+
+ return feature_markers, response_markers
+
+def getOpenPoseMarkers_lowerExtremity():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RHip", "LHip", "RKnee", "LKnee",
+ "RAnkle", "LAnkle", "RHeel", "LHeel", "RSmallToe", "LSmallToe",
+ "RBigToe", "LBigToe"]
+
+ response_markers = ["C7_study", "r_shoulder_study", "L_shoulder_study",
+ "r.ASIS_study", "L.ASIS_study", "r.PSIS_study",
+ "L.PSIS_study", "r_knee_study", "L_knee_study",
+ "r_mknee_study", "L_mknee_study", "r_ankle_study",
+ "L_ankle_study", "r_mankle_study", "L_mankle_study",
+ "r_calc_study", "L_calc_study", "r_toe_study",
+ "L_toe_study", "r_5meta_study", "L_5meta_study",
+ "r_thigh1_study", "r_thigh2_study", "r_thigh3_study",
+ "L_thigh1_study", "L_thigh2_study", "L_thigh3_study",
+ "r_sh1_study", "r_sh2_study", "r_sh3_study",
+ "L_sh1_study", "L_sh2_study", "L_sh3_study",
+ "RHJC_study", "LHJC_study"]
+
+ return feature_markers, response_markers
+
+# Different order of markers compared to getOpenPoseMarkers_lowerExtremity
+def getOpenPoseMarkers_lowerExtremity2():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RHip", "LHip", "RKnee", "LKnee",
+ "RAnkle", "LAnkle", "RHeel", "LHeel", "RSmallToe", "LSmallToe",
+ "RBigToe", "LBigToe"]
+
+ response_markers = [
+ 'r.ASIS_study', 'L.ASIS_study', 'r.PSIS_study',
+ 'L.PSIS_study', 'r_knee_study', 'r_mknee_study',
+ 'r_ankle_study', 'r_mankle_study', 'r_toe_study',
+ 'r_5meta_study', 'r_calc_study', 'L_knee_study',
+ 'L_mknee_study', 'L_ankle_study', 'L_mankle_study',
+ 'L_toe_study', 'L_calc_study', 'L_5meta_study',
+ 'r_shoulder_study', 'L_shoulder_study', 'C7_study',
+ 'r_thigh1_study', 'r_thigh2_study', 'r_thigh3_study',
+ 'L_thigh1_study', 'L_thigh2_study', 'L_thigh3_study',
+ 'r_sh1_study', 'r_sh2_study', 'r_sh3_study', 'L_sh1_study',
+ 'L_sh2_study', 'L_sh3_study', 'RHJC_study', 'LHJC_study']
+
+ return feature_markers, response_markers
+
+
+def getMarkers_upperExtremity_pelvis():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RHip", "LHip", "RElbow", "LElbow",
+ "RWrist", "LWrist"]
+
+ response_markers = ["r_lelbow_study", "L_lelbow_study", "r_melbow_study",
+ "L_melbow_study", "r_lwrist_study", "L_lwrist_study",
+ "r_mwrist_study", "L_mwrist_study"]
+
+ return feature_markers, response_markers
+
+def getMarkers_upperExtremity_noPelvis():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RElbow", "LElbow", "RWrist",
+ "LWrist"]
+
+ response_markers = ["r_lelbow_study", "L_lelbow_study", "r_melbow_study",
+ "L_melbow_study", "r_lwrist_study", "L_lwrist_study",
+ "r_mwrist_study", "L_mwrist_study"]
+
+ return feature_markers, response_markers
+
+# Different order of markers compared to getMarkers_upperExtremity_noPelvis.
+def getMarkers_upperExtremity_noPelvis2():
+
+ feature_markers = [
+ "Neck", "RShoulder", "LShoulder", "RElbow", "LElbow", "RWrist",
+ "LWrist"]
+
+ response_markers = ["r_lelbow_study", "r_melbow_study", "r_lwrist_study",
+ "r_mwrist_study", "L_lelbow_study", "L_melbow_study",
+ "L_lwrist_study", "L_mwrist_study"]
+
+ return feature_markers, response_markers
diff --git a/Pose2Sim/utilsDataman.py b/Pose2Sim/utilsDataman.py
new file mode 100644
index 0000000..6b5f0fe
--- /dev/null
+++ b/Pose2Sim/utilsDataman.py
@@ -0,0 +1,282 @@
+"""Manages the movement and use of data files."""
+
+import os
+import warnings
+from scipy.spatial.transform import Rotation as R
+
+import numpy as np
+from numpy.lib.recfunctions import append_fields
+
+class TRCFile(object):
+ """A plain-text file format for storing motion capture marker trajectories.
+ TRC stands for Track Row Column.
+
+ The metadata for the file is stored in attributes of this object.
+
+ See
+ http://simtk-confluence.stanford.edu:8080/display/OpenSim/Marker+(.trc)+Files
+ for more information.
+
+ """
+ def __init__(self, fpath=None, **kwargs):
+ #path=None,
+ #data_rate=None,
+ #camera_rate=None,
+ #num_frames=None,
+ #num_markers=None,
+ #units=None,
+ #orig_data_rate=None,
+ #orig_data_start_frame=None,
+ #orig_num_frames=None,
+ #marker_names=None,
+ #time=None,
+ #):
+ """
+ Parameters
+ ----------
+ fpath : str
+ Valid file path to a TRC (.trc) file.
+
+ """
+ self.marker_names = []
+ if fpath != None:
+ self.read_from_file(fpath)
+ else:
+ for k, v in kwargs.items():
+ setattr(self, k, v)
+
+ def read_from_file(self, fpath):
+ # Read the header lines / metadata.
+ # ---------------------------------
+ # Split by any whitespace.
+ # TODO may cause issues with paths that have spaces in them.
+ f = open(fpath)
+ # These are lists of each entry on the first few lines.
+ first_line = f.readline().split()
+ # Skip the 2nd line.
+ f.readline()
+ third_line = f.readline().split()
+ fourth_line = f.readline().split()
+ f.close()
+
+ # First line.
+ if len(first_line) > 3:
+ self.path = first_line[3]
+ else:
+ self.path = ''
+
+ # Third line.
+ self.data_rate = float(third_line[0])
+ self.camera_rate = float(third_line[1])
+ self.num_frames = int(third_line[2])
+ self.num_markers = int(third_line[3])
+ self.units = third_line[4]
+ self.orig_data_rate = float(third_line[5])
+ self.orig_data_start_frame = int(third_line[6])
+ self.orig_num_frames = int(third_line[7])
+
+ # Marker names.
+ # The first and second column names are 'Frame#' and 'Time'.
+ self.marker_names = fourth_line[2:]
+
+ len_marker_names = len(self.marker_names)
+ if len_marker_names != self.num_markers:
+ warnings.warn('Header entry NumMarkers, %i, does not '
+ 'match actual number of markers, %i. Changing '
+ 'NumMarkers to match actual number.' % (
+ self.num_markers, len_marker_names))
+ self.num_markers = len_marker_names
+
+ # Load the actual data.
+ # ---------------------
+ col_names = ['frame_num', 'time']
+ # This naming convention comes from OpenSim's Inverse Kinematics tool,
+ # when it writes model marker locations.
+ for mark in self.marker_names:
+ col_names += [mark + '_tx', mark + '_ty', mark + '_tz']
+ dtype = {'names': col_names,
+ 'formats': ['int'] + ['float64'] * (3 * self.num_markers + 1)}
+ usecols = [i for i in range(3 * self.num_markers + 1 + 1)]
+ self.data = np.loadtxt(fpath, delimiter='\t', skiprows=5, dtype=dtype,
+ usecols=usecols)
+ self.time = self.data['time']
+
+ # Check the number of rows.
+ n_rows = self.time.shape[0]
+ if n_rows != self.num_frames:
+ warnings.warn('%s: Header entry NumFrames, %i, does not '
+ 'match actual number of frames, %i, Changing '
+ 'NumFrames to match actual number.' % (fpath,
+ self.num_frames, n_rows))
+ self.num_frames = n_rows
+
+ def __getitem__(self, key):
+ """See `marker()`.
+
+ """
+ return self.marker(key)
+
+ def units(self):
+ return self.units
+
+ def time(self):
+ this_dat = np.empty((self.num_frames, 1))
+ this_dat[:, 0] = self.time
+ return this_dat
+
+ def marker(self, name):
+ """The trajectory of marker `name`, given as a `self.num_frames` x 3
+ array. The order of the columns is x, y, z.
+
+ """
+ this_dat = np.empty((self.num_frames, 3))
+ this_dat[:, 0] = self.data[name + '_tx']
+ this_dat[:, 1] = self.data[name + '_ty']
+ this_dat[:, 2] = self.data[name + '_tz']
+ return this_dat
+
+ def add_marker(self, name, x, y, z):
+ """Add a marker, with name `name` to the TRCFile.
+
+ Parameters
+ ----------
+ name : str
+ Name of the marker; e.g., 'R.Hip'.
+ x, y, z: array_like
+ Coordinates of the marker trajectory. All 3 must have the same
+ length.
+
+ """
+ if (len(x) != self.num_frames or len(y) != self.num_frames or len(z) !=
+ self.num_frames):
+ raise Exception('Length of data (%i, %i, %i) is not '
+ 'NumFrames (%i).', len(x), len(y), len(z), self.num_frames)
+ self.marker_names += [name]
+ self.num_markers += 1
+ if not hasattr(self, 'data'):
+ self.data = np.array(x, dtype=[('%s_tx' % name, 'float64')])
+ self.data = append_fields(self.data,
+ ['%s_t%s' % (name, s) for s in 'yz'],
+ [y, z], usemask=False)
+ else:
+ self.data = append_fields(self.data,
+ ['%s_t%s' % (name, s) for s in 'xyz'],
+ [x, y, z], usemask=False)
+
+ def marker_at(self, name, time):
+ x = np.interp(time, self.time, self.data[name + '_tx'])
+ y = np.interp(time, self.time, self.data[name + '_ty'])
+ z = np.interp(time, self.time, self.data[name + '_tz'])
+ return [x, y, z]
+
+ def marker_exists(self, name):
+ """
+ Returns
+ -------
+ exists : bool
+ Is the marker in the TRCFile?
+
+ """
+ return name in self.marker_names
+
+ def write(self, fpath):
+ """Write this TRCFile object to a TRC file.
+
+ Parameters
+ ----------
+ fpath : str
+ Valid file path to which this TRCFile is saved.
+
+ """
+ f = open(fpath, 'w')
+
+ # Line 1.
+ f.write('PathFileType 4\t(X/Y/Z) %s\n' % os.path.split(fpath)[0])
+
+ # Line 2.
+ f.write('DataRate\tCameraRate\tNumFrames\tNumMarkers\t'
+ 'Units\tOrigDataRate\tOrigDataStartFrame\tOrigNumFrames\n')
+
+ # Line 3.
+ f.write('%.1f\t%.1f\t%i\t%i\t%s\t%.1f\t%i\t%i\n' % (
+ self.data_rate, self.camera_rate, self.num_frames,
+ self.num_markers, self.units, self.orig_data_rate,
+ self.orig_data_start_frame, self.orig_num_frames))
+
+ # Line 4.
+ f.write('Frame#\tTime\t')
+ for imark in range(self.num_markers):
+ f.write('%s\t\t\t' % self.marker_names[imark])
+ f.write('\n')
+
+ # Line 5.
+ f.write('\t\t')
+ for imark in np.arange(self.num_markers) + 1:
+ f.write('X%i\tY%s\tZ%s\t' % (imark, imark, imark))
+ f.write('\n')
+
+ # Line 6.
+ f.write('\n')
+
+ # Data.
+ for iframe in range(self.num_frames):
+ f.write('%i' % (iframe + 1))
+ f.write('\t%.7f' % self.time[iframe])
+ for mark in self.marker_names:
+ idxs = [mark + '_tx', mark + '_ty', mark + '_tz']
+ f.write('\t%.7f\t%.7f\t%.7f' % tuple(
+ self.data[coln][iframe] for coln in idxs))
+ f.write('\n')
+
+ f.close()
+
+ def add_noise(self, noise_width):
+ """ add random noise to each component of the marker trajectory
+ The noise mean will be zero, with the noise_width being the
+ standard deviation.
+
+ noise_width : int
+ """
+ for imarker in range(self.num_markers):
+ components = ['_tx', '_ty', '_tz']
+ for iComponent in range(3):
+ # generate noise
+ noise = np.random.normal(0, noise_width, self.num_frames)
+ # add noise to each component of marker data.
+ self.data[self.marker_names[imarker] + components[iComponent]] += noise
+
+ def rotate(self, axis, value):
+ """ rotate the data.
+
+ axis : rotation axis
+ value : angle in degree
+ """
+ for imarker in range(self.num_markers):
+
+ temp = np.zeros((self.num_frames, 3))
+ temp[:,0] = self.data[self.marker_names[imarker] + '_tx']
+ temp[:,1] = self.data[self.marker_names[imarker] + '_ty']
+ temp[:,2] = self.data[self.marker_names[imarker] + '_tz']
+
+ r = R.from_euler(axis, value, degrees=True)
+ temp_rot = r.apply(temp)
+
+ self.data[self.marker_names[imarker] + '_tx'] = temp_rot[:,0]
+ self.data[self.marker_names[imarker] + '_ty'] = temp_rot[:,1]
+ self.data[self.marker_names[imarker] + '_tz'] = temp_rot[:,2]
+
+ def offset(self, axis, value):
+ """ offset the data.
+
+ axis : rotation axis
+ value : offset in m
+ """
+ for imarker in range(self.num_markers):
+ if axis.lower() == 'x':
+ self.data[self.marker_names[imarker] + '_tx'] += value
+ elif axis.lower() == 'y':
+ self.data[self.marker_names[imarker] + '_ty'] += value
+ elif axis.lower() == 'z':
+ self.data[self.marker_names[imarker] + '_tz'] += value
+ else:
+ raise ValueError("Axis not recognized")
diff --git a/README.md b/README.md
index 38ecb3a..dc691ff 100644
--- a/README.md
+++ b/README.md
@@ -415,6 +415,22 @@ Output:\
+### Marker Augmentation (Test)
+Set parameters(height, mass) in [project] of Config.toml
+
+Open a terminal, enter `pip show pose2sim`, report package location. \
+Copy this path and go to the Demo folder with `cd \pose2sim\Demo\S00_Demo_Session`. \
+Type `ipython`, If you want to triangulate and marker augment without filtering, test the following code:
+``` python
+from Pose2Sim import Pose2Sim
+Pose2Sim.augmenter()
+```
+Recommand you augment markers after filtering.\
+The .trc file should be located in pose-3d folder.\
+If you enter inexact height, model'll be unstable.\
+If there is a Nan value in the .trc file, it will not work properly.\
+Should input Marker_add.xml in OpenSim when you scale your model.
+
## OpenSim kinematics
> _**Obtain 3D joint angles.**_\
> Your OpenSim .osim scaled model and .mot inverse kinematic results will be found in the OpenSim folder of your `Participant` directory.