New script to scale the muscles (Fmax and MaxControl) using matlab's …

…optimizer (fmincon) for now
AbdnBiomechEng · Dec 9, 2021 · d4aa8a0 · d4aa8a0
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diff --git a/...Testings_to_opensim_model/1.ScaleBones.py → ...pensim_model/1.ScaleBones/1.ScaleBones.py b/...Testings_to_opensim_model/1.ScaleBones.py → ...pensim_model/1.ScaleBones/1.ScaleBones.py
diff --git a/...estings_to_opensim_model/Geometry/1mc.vtp → ...ensim_model/1.ScaleBones/Geometry/1mc.vtp b/...estings_to_opensim_model/Geometry/1mc.vtp → ...ensim_model/1.ScaleBones/Geometry/1mc.vtp
diff --git a/...ngs_to_opensim_model/Geometry/2distph.vtp → ...m_model/1.ScaleBones/Geometry/2distph.vtp b/...ngs_to_opensim_model/Geometry/2distph.vtp → ...m_model/1.ScaleBones/Geometry/2distph.vtp
diff --git a/...ings_to_opensim_model/Geometry/2midph.vtp → ...im_model/1.ScaleBones/Geometry/2midph.vtp b/...ings_to_opensim_model/Geometry/2midph.vtp → ...im_model/1.ScaleBones/Geometry/2midph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/2proxph.vtp → ...m_model/1.ScaleBones/Geometry/2proxph.vtp b/...ngs_to_opensim_model/Geometry/2proxph.vtp → ...m_model/1.ScaleBones/Geometry/2proxph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/3distph.vtp → ...m_model/1.ScaleBones/Geometry/3distph.vtp b/...ngs_to_opensim_model/Geometry/3distph.vtp → ...m_model/1.ScaleBones/Geometry/3distph.vtp
diff --git a/...ings_to_opensim_model/Geometry/3midph.vtp → ...im_model/1.ScaleBones/Geometry/3midph.vtp b/...ings_to_opensim_model/Geometry/3midph.vtp → ...im_model/1.ScaleBones/Geometry/3midph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/3proxph.vtp → ...m_model/1.ScaleBones/Geometry/3proxph.vtp b/...ngs_to_opensim_model/Geometry/3proxph.vtp → ...m_model/1.ScaleBones/Geometry/3proxph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/4distph.vtp → ...m_model/1.ScaleBones/Geometry/4distph.vtp b/...ngs_to_opensim_model/Geometry/4distph.vtp → ...m_model/1.ScaleBones/Geometry/4distph.vtp
diff --git a/...ings_to_opensim_model/Geometry/4midph.vtp → ...im_model/1.ScaleBones/Geometry/4midph.vtp b/...ings_to_opensim_model/Geometry/4midph.vtp → ...im_model/1.ScaleBones/Geometry/4midph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/4proxph.vtp → ...m_model/1.ScaleBones/Geometry/4proxph.vtp b/...ngs_to_opensim_model/Geometry/4proxph.vtp → ...m_model/1.ScaleBones/Geometry/4proxph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/5distph.vtp → ...m_model/1.ScaleBones/Geometry/5distph.vtp b/...ngs_to_opensim_model/Geometry/5distph.vtp → ...m_model/1.ScaleBones/Geometry/5distph.vtp
diff --git a/...ings_to_opensim_model/Geometry/5midph.vtp → ...im_model/1.ScaleBones/Geometry/5midph.vtp b/...ings_to_opensim_model/Geometry/5midph.vtp → ...im_model/1.ScaleBones/Geometry/5midph.vtp
diff --git a/...ngs_to_opensim_model/Geometry/5proxph.vtp → ...m_model/1.ScaleBones/Geometry/5proxph.vtp b/...ngs_to_opensim_model/Geometry/5proxph.vtp → ...m_model/1.ScaleBones/Geometry/5proxph.vtp
diff --git a/...gs_to_opensim_model/Geometry/capitate.vtp → ..._model/1.ScaleBones/Geometry/capitate.vtp b/...gs_to_opensim_model/Geometry/capitate.vtp → ..._model/1.ScaleBones/Geometry/capitate.vtp
diff --git a/...gs_to_opensim_model/Geometry/clavicle.vtp → ..._model/1.ScaleBones/Geometry/clavicle.vtp b/...gs_to_opensim_model/Geometry/clavicle.vtp → ..._model/1.ScaleBones/Geometry/clavicle.vtp
diff --git a/...del/Geometry/das3_ground_ribs_rotated.vtp → ...nes/Geometry/das3_ground_ribs_rotated.vtp b/...del/Geometry/das3_ground_ribs_rotated.vtp → ...nes/Geometry/das3_ground_ribs_rotated.vtp
diff --git a/...pensim_model/Geometry/das_jaw_rotated.stl → ...1.ScaleBones/Geometry/das_jaw_rotated.stl b/...pensim_model/Geometry/das_jaw_rotated.stl → ...1.ScaleBones/Geometry/das_jaw_rotated.stl
diff --git a/...ensim_model/Geometry/das_ribs_rotated.stl → ....ScaleBones/Geometry/das_ribs_rotated.stl b/...ensim_model/Geometry/das_ribs_rotated.stl → ....ScaleBones/Geometry/das_ribs_rotated.stl
diff --git a/...nsim_model/Geometry/das_skull_rotated.stl → ...ScaleBones/Geometry/das_skull_rotated.stl b/...nsim_model/Geometry/das_skull_rotated.stl → ...ScaleBones/Geometry/das_skull_rotated.stl
diff --git a/...nsim_model/Geometry/das_spine_rotated.stl → ...ScaleBones/Geometry/das_spine_rotated.stl b/...nsim_model/Geometry/das_spine_rotated.stl → ...ScaleBones/Geometry/das_spine_rotated.stl
diff --git a/..._to_opensim_model/Geometry/ground_jaw.vtp → ...odel/1.ScaleBones/Geometry/ground_jaw.vtp b/..._to_opensim_model/Geometry/ground_jaw.vtp → ...odel/1.ScaleBones/Geometry/ground_jaw.vtp
diff --git a/...to_opensim_model/Geometry/ground_ribs.vtp → ...del/1.ScaleBones/Geometry/ground_ribs.vtp b/...to_opensim_model/Geometry/ground_ribs.vtp → ...del/1.ScaleBones/Geometry/ground_ribs.vtp
diff --git a/...o_opensim_model/Geometry/ground_skull.vtp → ...el/1.ScaleBones/Geometry/ground_skull.vtp b/...o_opensim_model/Geometry/ground_skull.vtp → ...el/1.ScaleBones/Geometry/ground_skull.vtp
diff --git a/...o_opensim_model/Geometry/ground_spine.vtp → ...el/1.ScaleBones/Geometry/ground_spine.vtp b/...o_opensim_model/Geometry/ground_spine.vtp → ...el/1.ScaleBones/Geometry/ground_spine.vtp
diff --git a/...to_opensim_model/Geometry/groundspine.vtp → ...del/1.ScaleBones/Geometry/groundspine.vtp b/...to_opensim_model/Geometry/groundspine.vtp → ...del/1.ScaleBones/Geometry/groundspine.vtp
diff --git a/...ngs_to_opensim_model/Geometry/humerus.vtp → ...m_model/1.ScaleBones/Geometry/humerus.vtp b/...ngs_to_opensim_model/Geometry/humerus.vtp → ...m_model/1.ScaleBones/Geometry/humerus.vtp
diff --git a/...ings_to_opensim_model/Geometry/lunate.vtp → ...im_model/1.ScaleBones/Geometry/lunate.vtp b/...ings_to_opensim_model/Geometry/lunate.vtp → ...im_model/1.ScaleBones/Geometry/lunate.vtp
diff --git a/...ings_to_opensim_model/Geometry/r_hand.vtp → ...im_model/1.ScaleBones/Geometry/r_hand.vtp b/...ings_to_opensim_model/Geometry/r_hand.vtp → ...im_model/1.ScaleBones/Geometry/r_hand.vtp
diff --git a/...ings_to_opensim_model/Geometry/radius.vtp → ...im_model/1.ScaleBones/Geometry/radius.vtp b/...ings_to_opensim_model/Geometry/radius.vtp → ...im_model/1.ScaleBones/Geometry/radius.vtp
diff --git a/...s_to_opensim_model/Geometry/rclavicle.vtp → ...model/1.ScaleBones/Geometry/rclavicle.vtp b/...s_to_opensim_model/Geometry/rclavicle.vtp → ...model/1.ScaleBones/Geometry/rclavicle.vtp
diff --git a/...gs_to_opensim_model/Geometry/rhumerus.vtp → ..._model/1.ScaleBones/Geometry/rhumerus.vtp b/...gs_to_opensim_model/Geometry/rhumerus.vtp → ..._model/1.ScaleBones/Geometry/rhumerus.vtp
diff --git a/...ngs_to_opensim_model/Geometry/rradius.vtp → ...m_model/1.ScaleBones/Geometry/rradius.vtp b/...ngs_to_opensim_model/Geometry/rradius.vtp → ...m_model/1.ScaleBones/Geometry/rradius.vtp
diff --git a/...gs_to_opensim_model/Geometry/rscapula.vtp → ..._model/1.ScaleBones/Geometry/rscapula.vtp b/...gs_to_opensim_model/Geometry/rscapula.vtp → ..._model/1.ScaleBones/Geometry/rscapula.vtp
diff --git a/...tings_to_opensim_model/Geometry/rulna.vtp → ...sim_model/1.ScaleBones/Geometry/rulna.vtp b/...tings_to_opensim_model/Geometry/rulna.vtp → ...sim_model/1.ScaleBones/Geometry/rulna.vtp
diff --git a/...ngs_to_opensim_model/Geometry/scapula.vtp → ...m_model/1.ScaleBones/Geometry/scapula.vtp b/...ngs_to_opensim_model/Geometry/scapula.vtp → ...m_model/1.ScaleBones/Geometry/scapula.vtp
diff --git a/...pensim_model/Geometry/sdfastPISIFORMw.vtp → ...1.ScaleBones/Geometry/sdfastPISIFORMw.vtp b/...pensim_model/Geometry/sdfastPISIFORMw.vtp → ...1.ScaleBones/Geometry/sdfastPISIFORMw.vtp
diff --git a/...pensim_model/Geometry/sdfastSCAPHOIDw.vtp → ...1.ScaleBones/Geometry/sdfastSCAPHOIDw.vtp b/...pensim_model/Geometry/sdfastSCAPHOIDw.vtp → ...1.ScaleBones/Geometry/sdfastSCAPHOIDw.vtp
diff --git a/...nsim_model/Geometry/sdfastTRIQUETRALw.vtp → ...ScaleBones/Geometry/sdfastTRIQUETRALw.vtp b/...nsim_model/Geometry/sdfastTRIQUETRALw.vtp → ...ScaleBones/Geometry/sdfastTRIQUETRALw.vtp
diff --git a/...el/Geometry/sdfast_1seg_hand_fr_c_2mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_2mc.vtp b/...el/Geometry/sdfast_1seg_hand_fr_c_2mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_2mc.vtp
diff --git a/...el/Geometry/sdfast_1seg_hand_fr_c_3mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_3mc.vtp b/...el/Geometry/sdfast_1seg_hand_fr_c_3mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_3mc.vtp
diff --git a/...el/Geometry/sdfast_1seg_hand_fr_c_4mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_4mc.vtp b/...el/Geometry/sdfast_1seg_hand_fr_c_4mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_4mc.vtp
diff --git a/...el/Geometry/sdfast_1seg_hand_fr_c_5mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_5mc.vtp b/...el/Geometry/sdfast_1seg_hand_fr_c_5mc.vtp → ...es/Geometry/sdfast_1seg_hand_fr_c_5mc.vtp
diff --git a/...Geometry/sdfast_1seg_hand_fr_c_hamate.vtp → ...Geometry/sdfast_1seg_hand_fr_c_hamate.vtp b/...Geometry/sdfast_1seg_hand_fr_c_hamate.vtp → ...Geometry/sdfast_1seg_hand_fr_c_hamate.vtp
diff --git a/...metry/sdfast_1seg_hand_fr_c_trapezium.vtp → ...metry/sdfast_1seg_hand_fr_c_trapezium.vtp b/...metry/sdfast_1seg_hand_fr_c_trapezium.vtp → ...metry/sdfast_1seg_hand_fr_c_trapezium.vtp
diff --git a/...metry/sdfast_1seg_hand_fr_c_trapezoid.vtp → ...metry/sdfast_1seg_hand_fr_c_trapezoid.vtp b/...metry/sdfast_1seg_hand_fr_c_trapezoid.vtp → ...metry/sdfast_1seg_hand_fr_c_trapezoid.vtp
diff --git a/...ings_to_opensim_model/Geometry/thorax.vtp → ...im_model/1.ScaleBones/Geometry/thorax.vtp b/...ings_to_opensim_model/Geometry/thorax.vtp → ...im_model/1.ScaleBones/Geometry/thorax.vtp
diff --git a/...s_to_opensim_model/Geometry/thumbdist.vtp → ...model/1.ScaleBones/Geometry/thumbdist.vtp b/...s_to_opensim_model/Geometry/thumbdist.vtp → ...model/1.ScaleBones/Geometry/thumbdist.vtp
diff --git a/...s_to_opensim_model/Geometry/thumbprox.vtp → ...model/1.ScaleBones/Geometry/thumbprox.vtp b/...s_to_opensim_model/Geometry/thumbprox.vtp → ...model/1.ScaleBones/Geometry/thumbprox.vtp
diff --git a/...stings_to_opensim_model/Geometry/ulna.vtp → ...nsim_model/1.ScaleBones/Geometry/ulna.vtp b/...stings_to_opensim_model/Geometry/ulna.vtp → ...nsim_model/1.ScaleBones/Geometry/ulna.vtp
diff --git a/...nts/Testings_to_opensim_model/markers.xml → ...to_opensim_model/1.ScaleBones/markers.xml b/...nts/Testings_to_opensim_model/markers.xml → ...to_opensim_model/1.ScaleBones/markers.xml
diff --git a/...l/model-das3-MOD2_withMarkersScaling.osim → ...s/model-das3-MOD2_withMarkersScaling.osim b/...l/model-das3-MOD2_withMarkersScaling.osim → ...s/model-das3-MOD2_withMarkersScaling.osim
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles.py b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles.py
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/2.ScaleMuscles_all_steps.py b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/2.ScaleMuscles_all_steps.py
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/1.model_scaled_bones.osim b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/1.model_scaled_bones.osim
diff --git a/...Patients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/2.model_scaled_muscles.osim b/...Patients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/2.model_scaled_muscles.osim
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/1mc.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/1mc.vtp
diff --git a/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/1mc_right.vtp b/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/1mc_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2distph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2distph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2distph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2distph_right.vtp
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2mc.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2mc.vtp
diff --git a/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2mc_right.vtp b/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2mc_right.vtp
diff --git a/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2midph.vtp b/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2midph.vtp
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2midph_right.vtp b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2midph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2proxph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2proxph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2proxph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/2proxph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3distph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3distph.vtp
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3mc.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3mc.vtp
diff --git a/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3mc_right.vtp b/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3mc_right.vtp
diff --git a/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3midph.vtp b/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3midph.vtp
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3midph_right.vtp b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3midph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3proxph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3proxph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3proxph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/3proxph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4distph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4distph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4distph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4distph_right.vtp
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4mc.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4mc.vtp
diff --git a/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4mc_right.vtp b/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4mc_right.vtp
diff --git a/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4midph.vtp b/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4midph.vtp
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4midph_right.vtp b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4midph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4proxph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4proxph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4proxph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/4proxph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5distph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5distph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5distph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5distph_right.vtp
diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5mc.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5mc.vtp
diff --git a/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5mc_right.vtp b/...rtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5mc_right.vtp
diff --git a/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5midph.vtp b/.../VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5midph.vtp
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5midph_right.vtp b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5midph_right.vtp
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5proxph.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5proxph.vtp
diff --git a/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5proxph_right.vtp b/...lPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/5proxph_right.vtp
diff --git a/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/ConePendulum.vtp b/...alPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/ConePendulum.vtp
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+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1e+299" RangeMax="-1e+299">
+        </DataArray>
+      </Verts>
+      <Lines>
+        <DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="1e+299" RangeMax="-1e+299">
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1e+299" RangeMax="-1e+299">
+        </DataArray>
+      </Lines>
+      <Strips>
+        <DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="1e+299" RangeMax="-1e+299">
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1e+299" RangeMax="-1e+299">
+        </DataArray>
+      </Strips>
+      <Polys>
+        <DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="0" RangeMax="62">
+          0 1 3 2 2 3
+          5 4 4 5 1 0
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+          58 59 12 59 60 12
+          60 61 12 61 62 12
+          62 13
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+        <DataArray type="Int64" Name="offsets" format="ascii" RangeMin="4" RangeMax="218">
+          4 8 12 15 18 68
+          71 74 77 80 83 86
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+          107 110 113 116 119 122
+          125 128 131 134 137 140
+          143 146 149 152 155 158
+          161 164 167 170 173 176
+          179 182 185 188 191 194
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+      </Polys>
+    </Piece>
+  </PolyData>
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diff --git a/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/Cube.vtp b/Code/VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/Cube.vtp
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
+  <PolyData>
+    <Piece NumberOfPoints="24" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="6">
+      <PointData Normals="Normals">
+        <DataArray type="Float32" Name="Normals" NumberOfComponents="3" format="ascii">
+          -1 0 0 -1 0 0
+          -1 0 0 -1 0 0
+          1 0 0 1 0 0
+          1 0 0 1 0 0
+          0 -1 0 0 -1 0
+          0 -1 0 0 -1 0
+          0 1 0 0 1 0
+          0 1 0 0 1 0
+          0 0 -1 0 0 -1
+          0 0 -1 0 0 -1
+          0 0 1 0 0 1
+          0 0 1 0 0 1
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" NumberOfComponents="3" format="ascii">
+          -.5 -.05 -1.1 -.5 -.05 0.2
+          -.5 0.00 -1.1 -.5 0.00 0.2
+          2.2 -.05 -1.1 2.2 -.05 0.2
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+          -.5 -.05 0.2 2.2 -.05 0.2
+          -.5 0.00 0.2 2.2 0.00 0.2
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+      </Points>
+      <Verts>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Verts>
+      <Lines>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Lines>
+      <Strips>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Strips>
+      <Polys>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+          0 1 3 2 4 6
+          7 5 8 10 11 9
+          12 13 15 14 16 18
+          19 17 20 21 23 22
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+          4 8 12 16 20 24
+        </DataArray>
+      </Polys>
+    </Piece>
+  </PolyData>
+</VTKFile>
diff --git a/...tings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/OpenSimLogoSmall.PNG b/...tings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/OpenSimLogoSmall.PNG
diff --git a/...atients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/README.md b/...atients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/README.md
@@ -0,0 +1,16 @@
+# Fixing missing polygons
+
+(1) Download Paraview and open .vtp file.
+
+(3) Use hotkey (S) to switch on polygon selection, select incorrect polygons.
+
+(4) Open Paraview Selection Display Inspector, select the Point Labels and ID. The selected Polygons will now show their coordinates.
+
+(5) Open the .vtp file in a text editor and search for the three numbers seen in Paraview. Switch the 1st and 3rd numbers.
+
+36 120 210 -> 210 10 210
+
+There may be one or two sets of with these three numbers, change all.
+
+36 120 210 -> 210 120 210
+210 36 120 -> 120 36 210
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/anchor1.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/anchor1.vtp
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
+  <PolyData>
+    <Piece NumberOfPoints="24" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="6">
+      <PointData Normals="Normals">
+        <DataArray type="Float32" Name="Normals" NumberOfComponents="3" format="ascii">
+          -1 0 0 
+          -1 0 0
+          -1 0 0 
+          -1 0 0
+           1 0 0 
+           1 0 0
+           1 0 0 
+           1 0 0
+           0 -1 0 
+           0 -1 0
+           0 -1 0 
+           0 -1 0
+           0 1 0 
+           0 1 0
+           0 1 0 
+           0 1 0
+           0 0 -1 
+           0 0 -1
+           0 0 -1 
+           0 0 -1
+           0 0 1 
+           0 0 1
+           0 0 1 
+           0 0 1
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" NumberOfComponents="3" format="ascii">
+   -0.2500         0    0.3000
+   -0.2500         0    0.4000
+   -0.2500    0.1000    0.3000
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+    0.2500         0    0.3000
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+    0.2500    0.1000    0.3000
+    0.2500    0.1000    0.4000
+   -0.2500         0    0.3000
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+   -0.2500    0.1000    0.4000
+    0.2500    0.1000    0.4000
+        </DataArray>
+      </Points>
+      <Verts>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Verts>
+      <Lines>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Lines>
+      <Strips>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Strips>
+      <Polys>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+          0 1 3 2 4 6
+          7 5 8 10 11 9
+          12 13 15 14 16 18
+          19 17 20 21 23 22
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+          4 8 12 16 20 24
+        </DataArray>
+      </Polys>
+    </Piece>
+  </PolyData>
+</VTKFile>
diff --git a/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/anchor2.vtp b/...VirtualPatients/Testings_to_opensim_model/2.ScaleMuscles/Data/Models/Geometry/anchor2.vtp
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
+  <PolyData>
+    <Piece NumberOfPoints="24" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="6">
+      <PointData Normals="Normals">
+        <DataArray type="Float32" Name="Normals" NumberOfComponents="3" format="ascii">
+          -1 0 0 
+          -1 0 0
+          -1 0 0 
+          -1 0 0
+           1 0 0 
+           1 0 0
+           1 0 0 
+           1 0 0
+           0 -1 0 
+           0 -1 0
+           0 -1 0 
+           0 -1 0
+           0 1 0 
+           0 1 0
+           0 1 0 
+           0 1 0
+           0 0 -1 
+           0 0 -1
+           0 0 -1 
+           0 0 -1
+           0 0 1 
+           0 0 1
+           0 0 1 
+           0 0 1
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" NumberOfComponents="3" format="ascii">
+   -0.2500         0   -0.4000
+   -0.2500         0   -0.3000
+   -0.2500    0.1000   -0.4000
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+   -0.2500    0.1000   -0.3000
+    0.2500    0.1000   -0.3000
+        </DataArray>
+      </Points>
+      <Verts>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Verts>
+      <Lines>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Lines>
+      <Strips>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+        </DataArray>
+      </Strips>
+      <Polys>
+        <DataArray type="Int32" Name="connectivity" format="ascii">
+          0 1 3 2 4 6
+          7 5 8 10 11 9
+          12 13 15 14 16 18
+          19 17 20 21 23 22
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" format="ascii">
+          4 8 12 16 20 24
+        </DataArray>
+      </Polys>
+    </Piece>
+  </PolyData>
+</VTKFile>