diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33f0c789d9..24c7a589f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ request related to the change, then we may provide the commit.
This is not a comprehensive list of changes but rather a hand-curated collection of the more notable ones. For a comprehensive history, see the [OpenSim Core GitHub repo](https://github.com/opensim-org/opensim-core).
+v4.4.1
+======
+-
+
v4.4
====
- Updated ezc3d to version 1.4.6 which better manage the events defined in a c3d file.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f8bd4ef10b..a36a16b6d0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -29,7 +29,7 @@ include(FeatureSummary)
# ----------------
set(OPENSIM_MAJOR_VERSION 4)
set(OPENSIM_MINOR_VERSION 4)
-set(OPENSIM_PATCH_VERSION 0)
+set(OPENSIM_PATCH_VERSION 1)
# Don't include the patch version if it is 0.
set(PATCH_VERSION_STRING)
diff --git a/OpenSim/Simulation/Test/CMakeLists.txt b/OpenSim/Simulation/Test/CMakeLists.txt
index cb55a75a3b..6c07766115 100644
--- a/OpenSim/Simulation/Test/CMakeLists.txt
+++ b/OpenSim/Simulation/Test/CMakeLists.txt
@@ -1,5 +1,5 @@
file(GLOB TEST_PROGS "test*.cpp")
-file(GLOB TEST_FILES *.osim *.xml *.sto *.mot *.obj *.vtp *.stl)
+file(GLOB TEST_FILES *.osim *.xml *.sto *.mot *.obj *.vtp *.stl *.trc)
OpenSimAddTests(
TESTPROGRAMS ${TEST_PROGS}
diff --git a/OpenSim/Simulation/Test/simple_arm_model.osim b/OpenSim/Simulation/Test/simple_arm_model.osim
new file mode 100644
index 0000000000..78aa6666eb
--- /dev/null
+++ b/OpenSim/Simulation/Test/simple_arm_model.osim
@@ -0,0 +1,743 @@
+
+
+
+
+
+
+
+
+ ..
+
+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
+
+
+
+ 0 -9.8065999999999995 0
+
+ The OpenSim Development Team (Reinbolt, J; Seth, A; Habib, A; Hamner, S) adapted from a model originally created by Kate Holzbaur (11/22/04) License: Creative Commons (CCBY 3.0). You are free to distribute, remix, tweak, and build upon this work, even commercially, as long as you credit us for the original creation. http://creativecommons.org/licenses/by/3.0/
+
+ Holzbaur, K.R.S., Murray, W.M., Delp, S.L. A Model of the Upper Extremity for Simulating Musculoskeletal Surgery and Analyzing Neuromuscular Control. Annals of Biomedical Engineering, vol 33, pp 829–840, 2005
+
+ meters
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+ N
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+
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+ ..
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+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
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+
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+ ..
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+ 1 1 1
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+
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+ 1
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+ 1 1 1
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+ arm_r_humerus.vtp
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+
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+
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+ 1.8645719999999999
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+ 0 -0.18049599999999999 0
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+ 0.01481 0.0045510000000000004 0.013193 0 0 0
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+
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+ ..
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+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
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+
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+ ..
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+ 1 1 1
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+
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+ 1
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+ 1 1 1
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+ arm_r_ulna.vtp
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+
+
+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_radius.vtp
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+
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+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_lunate.vtp
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+
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+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_scaphoid.vtp
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+
+
+ ..
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+ 1 1 1
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+
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+ 1
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+ 1 1 1
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+
+ arm_r_pisiform.vtp
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+
+
+ ..
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+ 1 1 1
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+
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+ 1
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+ 1 1 1
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+ arm_r_triquetrum.vtp
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+
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+ 1 1 1
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+ arm_r_capitate.vtp
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+ arm_r_trapezium.vtp
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+ arm_r_trapezoid.vtp
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+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_hamate.vtp
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+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_1mc.vtp
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+ ..
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+ 1
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+ 1 1 1
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+ arm_r_2mc.vtp
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+ ..
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+ 1 1 1
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+ 1
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+ 1 1 1
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+ arm_r_3mc.vtp
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+
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+ ..
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+ 1 1 1
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+ 1
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+ arm_r_4mc.vtp
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+ 1 1 1
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+ 1
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+ arm_r_5mc.vtp
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+ arm_r_thumbprox.vtp
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+ arm_r_thumbdist.vtp
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+ 1
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+ arm_r_2proxph.vtp
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+ arm_r_2midph.vtp
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+ arm_r_3proxph.vtp
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+ arm_r_4proxph.vtp
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+ arm_r_4midph.vtp
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+ arm_r_5proxph.vtp
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+ 1.5343150000000001
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+ 0 -0.181479 0
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+ 0.019281 0.0015709999999999999 0.020062 0 0 0
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+ r_humerus_offset
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+ r_ulna_radius_hand_offset
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+ 0
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+ 0
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+ 0 2.2689280300000001
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+ ..
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+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
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+ /bodyset/r_humerus
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+ 0.0061000000000000004 -0.29039999999999999 -0.0123
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+ 0 0 0
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+ ..
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+ 0.20000000000000001 0.20000000000000001 0.20000000000000001
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+ /bodyset/r_ulna_radius_hand
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+ 0 0 0
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+
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+ r_elbow_flex
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+ 0.049400010000000001 0.036600010000000002 0.99810825000000003
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+ 0
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+ /ground
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+ /bodyset/r_humerus
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+ /bodyset/r_humerus
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+ /bodyset/r_humerus
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+ -0.0011000000238418578 -0.28346645828075678 -0.058446575204937373
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+ false
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+ /bodyset/r_humerus
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+ -0.0011000000238418578 0.0035589390606764085 -0.036418536000312231
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+ false
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+ /bodyset/r_ulna_radius_hand
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+ -0.0011000000238418578 -0.24114234002047005 0.026639625027417423
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+ false
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+ /bodyset/r_ulna_radius_hand
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+ -0.043896693289424138 0.0028173076876591096 -0.00023637803659903511
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+ false
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+
+ /bodyset/r_ulna_radius_hand
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+ -0.0011000000000000001 -0.23558999999999999 0.094299999999999995
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+ false
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diff --git a/OpenSim/Simulation/Test/simple_arm_trc.trc b/OpenSim/Simulation/Test/simple_arm_trc.trc
new file mode 100644
index 0000000000..21d4f838df
--- /dev/null
+++ b/OpenSim/Simulation/Test/simple_arm_trc.trc
@@ -0,0 +1,126 @@
+PathFileType 4 (X/Y/Z) simple_arm.trc
+DataRate CameraRate NumFrames NumMarkers Units OrigDataRate OrigDataStartFrame OrigNumFrames
+60 60 120 6 m 60 0 120
+Frame# Time r_humerus1 r_humerus2 r_humerus3 r_radius1 r_radius2 r_radius3
+ X1 Y1 Z1 X2 Y2 Z2 X3 Y3 Z3 X4 Y4 Z4 X5 Y5 Z5 X6 Y6 Z6
+
+1 0 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.004999999976158143 -0.5315423400204701 0.01433962502741742 -0.03779669328942414 -0.2875826923123409 -0.01253637803659904 0.005 -0.52599 0.08199999999999999
+2 0.01666666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.009607585998439389 -0.5315444154371833 0.01411165492968093 -0.03784251051569402 -0.2884182965015624 -0.01250346928835709 0.009549751621619987 -0.526056356676267 0.08177724949113424
+3 0.03333333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.01421463661529234 -0.531458587266501 0.01388048796111986 -0.03787239794991396 -0.2892547282442323 -0.01247131861763037 0.01410020005999056 -0.526035909548386 0.08155128145265253
+4 0.05 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.01881863379126121 -0.5312849024187773 0.01364625046864711 -0.03788633925676985 -0.2900915303791514 -0.01243994359673043 0.01864885821621473 -0.5259286697919648 0.08132221938993392
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+7 0.1 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.03259852757457464 -0.5302374317091968 0.01292582327135666 -0.03783248167984237 -0.2926016529253336 -0.01235056456850108 0.03227047664412565 -0.5250867172439718 0.08061716203946009
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+10 0.15 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.04629460852097185 -0.5284033540751165 0.01218069988873664 -0.03763529672197854 -0.295104849563627 -0.01226853330275091 0.04582030018319538 -0.5234668963078088 0.07988713412836926
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+12 0.1833333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.05535676570845757 -0.5267464610674447 0.01167142350881183 -0.03742450932912987 -0.2967657798054485 -0.0122180606569779 0.05479186564145694 -0.5219573531417272 0.07938774469007155
+13 0.2 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.05986207796965017 -0.5257886686211077 0.01141331755300003 -0.03729542935761132 -0.2975929325607991 -0.0121941181164433 0.05925400856757279 -0.5210745052734731 0.07913452351293156
+14 0.2166666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.06434857542512934 -0.5247449772341036 0.01115299294956457 -0.03715060247717795 -0.2984175766537058 -0.01217104693883791 0.06369877029060109 -0.5201065778738543 0.07887904278118675
+15 0.2333333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.06881380592912878 -0.5236159573477267 0.01089059198185243 -0.03699010784459407 -0.2992392613656426 -0.01214885973397397 0.06812372147591061 -0.5190540999745037 0.0786214421307114
+16 0.25 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.07325696355470646 -0.5224018127381411 0.01062616201046667 -0.03681397442744563 -0.3000578383911979 -0.0121275605064076 0.07252806346655091 -0.5179172615365656 0.07836176805570204
+17 0.2666666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.07767561984396869 -0.5211032070097721 0.01035984756258942 -0.03662229849343757 -0.3008728603278695 -0.01210716089747175 0.07690938901975121 -0.5166966839119049 0.07810016248395196
+18 0.2833333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.0820685763632477 -0.51972050495634 0.010091721329824 -0.03641513430890287 -0.3016841059919821 -0.01208766633199619 0.08126650965129199 -0.5153927105728457 0.07783669683278777
+19 0.3 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.08643463461214579 -0.5182540711532083 0.009821855999069441 -0.03619253609995909 -0.3024913541900552 -0.01206908223716063 0.08559823681410525 -0.5140056847751736 0.07757144251470623
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+108 1.783333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2233984140889848 -0.1825449617309 -0.009267224606908134 0.02327336258954957 -0.3308622425150206 -0.01397192312993764 0.2255239857184356 -0.1844368355872138 0.05856092279292333
+109 1.8 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2213088480585018 -0.1784323844306032 -0.009314610035808376 0.02403900017326729 -0.3305265414579738 -0.01402212726995647 0.2235179701589575 -0.1803468975844061 0.05851023231611006
+110 1.816666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2191413715138239 -0.1743602718061265 -0.009356655575252738 0.02479807559767538 -0.3301762850017017 -0.01407254036228252 0.221434457391458 -0.1762958271685117 0.05846480270846695
+111 1.833333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2168965633539583 -0.1703297371092854 -0.009393349054806972 0.02555038147811182 -0.3298115664243559 -0.01412314872224214 0.219274003531876 -0.1722847316481529 0.05842464705011207
+112 1.85 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2145756505041134 -0.1663429832742597 -0.009424670419236144 0.02629550663331594 -0.3294325850669867 -0.01417392468926561 0.217037789400626 -0.1683158033328087 0.05838978728857317
+113 1.866666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.212179274660467 -0.162401088617909 -0.00945061188720967 0.02703324938807919 -0.3290394459640412 -0.01422485443016488 0.2147264336100269 -0.164390115912646 0.05836023217802714
+114 1.883333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2097080773232562 -0.1585051315735709 -0.009471165663427992 0.0277634080480244 -0.3286322541132055 -0.01427592411215117 0.2123405545772908 -0.1605087431901079 0.05833599048642437
+115 1.9 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2071634091532467 -0.1546572415204922 -0.009486320513992981 0.02848558353670397 -0.3282112320697763 -0.014327105822514 0.2098814563315024 -0.1566738065732158 0.05831707546333476
+116 1.916666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2045457294361651 -0.1508581129621838 -0.009496073703614194 0.02919964550907021 -0.3277764558237856 -0.01437839032349527 0.2073495827139206 -0.1528859982275222 0.05830349052272015
+117 1.933333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.2018564688943733 -0.147109822355192 -0.009500419901575871 0.02990520368650156 -0.3273281630070924 -0.01442974958497276 0.2047463175486164 -0.1491473884223836 0.05829524308958303
+118 1.95 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.1990963687871181 -0.1434133821896746 -0.009499358668110398 0.03060206733696061 -0.326866477403205 -0.01448116962785934 0.2020723786796082 -0.145458987240022 0.05829233467429836
+119 1.966666666666667 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.1962661701897103 -0.1397698050904196 -0.009492889549409666 0.03129004570583456 -0.3263915227608571 -0.0145326364732257 0.1993284837674095 -0.141821804893027 0.05829476680110397
+120 1.983333333333333 -0.001100000023841858 0.00895180173079595 0.03814219573978216 -0.001100000023841858 -0.2834664582807568 -0.05844657520493737 -0.001100000023841858 0.003558939060676408 -0.03641853600031223 0.1933674199791017 -0.1361810824955693 -0.009481016081243439 0.03196876277078942 -0.3259035586718633 -0.01458412199128724 0.1965161325187198 -0.1382378293244169 0.05830253814069355
diff --git a/OpenSim/Simulation/Test/testInverseKinematicsSolver.cpp b/OpenSim/Simulation/Test/testInverseKinematicsSolver.cpp
index 7f4f306de7..4a135d7630 100644
--- a/OpenSim/Simulation/Test/testInverseKinematicsSolver.cpp
+++ b/OpenSim/Simulation/Test/testInverseKinematicsSolver.cpp
@@ -41,6 +41,9 @@ using namespace std;
// Verify that the marker weight are consistent with the initial Set
// of MarkerWeights used to construct the MarkersReference
void testMarkersReference();
+// Repeat test of MarkersReference when constructed from trc file, the more
+// conventional workflow
+void testMarkersReferenceFromFile();
// Verify that the orientations sensor weights are consistent with the initial
// Set of OrientationWeights used to construct the OrientationsReference
void testOrientationsReference();
@@ -98,6 +101,11 @@ int main()
cout << e.what() << endl;
failures.push_back("testMarkersReference");
}
+ try { testMarkersReferenceFromFile(); }
+ catch (const std::exception& e) {
+ cout << e.what() << endl;
+ failures.push_back("testMarkersReferenceFromFile");
+ }
try { testOrientationsReference(); }
catch (const std::exception& e) {
cout << e.what() << endl;
@@ -212,6 +220,38 @@ void testMarkersReference()
}
}
+void testMarkersReferenceFromFile()
+{
+
+ auto fileName = "simple_arm_trc.trc";
+ auto modelFileName = "simple_arm_model.osim";
+
+
+ Model model(modelFileName);
+ SimTK::State& state = model.initSystem();
+ std::vector markerNames = { "r_humerus1", "r_humerus2", "r_humerus3", "r_radius1",
+ "r_radius2", "r_radius3" };
+ Set markerWeightSet;
+ for (auto mn : markerNames)
+ markerWeightSet.cloneAndAppend(MarkerWeight(mn, 1.0));
+
+ MarkersReference markersReference(fileName, markerWeightSet); // 4.4 beta
+ // markersReference = MarkersReference(fileName); % 4.0
+ // markersReference.setMarkerWeightSet(markerWeightSet); % 4.0
+ SimTK::Array_ coordinateReferences;
+ InverseKinematicsSolver ikSolver(model, markersReference, coordinateReferences);
+
+ ikSolver.assemble(state);
+ int numMarkersInUse = ikSolver.getNumMarkersInUse();
+ auto error = new double[numMarkersInUse];
+ std::cout << "Errors:" << std::endl;
+ for (int i = 0; i < numMarkersInUse; i++) {
+ error[i] = ikSolver.computeCurrentMarkerError(i);
+ std::cout << error[i] << " ";
+ }
+ std::cout << std::endl;
+}
+
void testOrientationsReference() {
// column labels for orientation sensor data
vector labels{"A", "B", "C", "D", "E", "F"};
@@ -432,7 +472,8 @@ void testUpdateMarkerWeights()
InverseKinematicsSolver ikSolver(*pendulum, markersRef, coordRefs);
ikSolver.setAccuracy(1.0e-8);
ikSolver.assemble(state);
-
+ int nmm = ikSolver.getNumMarkersInUse();
+ cout << "tNumMarkersInUse:" << nmm << endl;
double coordValue = coord.getValue(state);
cout << "Assembled " << coord.getName() << " value = "
<< coordValue << endl;