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Branch for 4.4 release #1368

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fe14d24
Update java binding (#1367)
aymanhab Jun 10, 2022
7f928b6
Update continuous-integration.yml
aymanhab Jun 11, 2022
d6da1e6
Leave experimental data alone when cleaning up motion objects upon mo…
aymanhab Jul 10, 2022
30319b7
Fix addpathpt 44 (#1380)
aymanhab Jul 24, 2022
aea742b
Update about dialog splash.gif
aymanhab Jul 28, 2022
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7 changes: 5 additions & 2 deletions .github/workflows/continuous-integration.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ jobs:
with:
repository: opensim-org/opensim-core
path: 'opensim-core'
ref: 'branch_4.4'

- name: Cache opensim-core-dependencies
id: cache-dependencies
Expand Down Expand Up @@ -156,7 +157,8 @@ jobs:
with:
repository: opensim-org/opensim-core
path: 'opensim-core'

ref: 'branch_4.4'

- name: Install packages
run: |
brew install cmake pkgconfig autoconf libtool automake wget pcre doxygen
Expand Down Expand Up @@ -301,7 +303,8 @@ jobs:
with:
repository: opensim-org/opensim-core
path: 'opensim-core'

ref: 'branch_4.4'

- name: Install packages
run: sudo apt-get update && sudo apt-get install --yes liblapack-dev freeglut3-dev libxi-dev libxmu-dev doxygen python3 python3-dev python3-numpy python3-setuptools

Expand Down
4 changes: 2 additions & 2 deletions Gui/opensim/branding/modules/org-netbeans-core.jar/org/netbeans/core/ui/Bundle.properties
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@@ -1,4 +1,4 @@
LBL_ProductInformation=OpenSim 4.3
currentVersion=OpenSim 4.3
LBL_ProductInformation=OpenSim 4.4
currentVersion=OpenSim 4.4


Binary file modified Gui/opensim/helpUtils/src/org/opensim/helputils/helpmenu/images/splash.gif
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12 changes: 4 additions & 8 deletions Gui/opensim/modeling/src/org/opensim/modeling/MocoTrack.java
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Expand Up @@ -673,10 +673,8 @@ public void setMarkersReference(TableProcessor markers) {

/**
* Set the markers reference directly from a TRC file. By default, the<br>
* marker data is lowpass filtered with a 6 Hz cutoff frequency, but you<br>
* may set any frequency using the optional argument. If the markers data<br>
* is in millimeters (detected via the 'Units' metadata tag), then it is<br>
* converted to meters.<br>
* marker data is low-pass filtered with a 6 Hz cutoff frequency, but you<br>
* may set any frequency using the optional argument.<br>
* Note: Overrides any existing TableProcessor for 'markers_reference'.
*/
public void setMarkersReferenceFromTRC(String filename, double lowpassFilterFreq) {
Expand All @@ -685,10 +683,8 @@ public void setMarkersReferenceFromTRC(String filename, double lowpassFilterFreq

/**
* Set the markers reference directly from a TRC file. By default, the<br>
* marker data is lowpass filtered with a 6 Hz cutoff frequency, but you<br>
* may set any frequency using the optional argument. If the markers data<br>
* is in millimeters (detected via the 'Units' metadata tag), then it is<br>
* converted to meters.<br>
* marker data is low-pass filtered with a 6 Hz cutoff frequency, but you<br>
* may set any frequency using the optional argument.<br>
* Note: Overrides any existing TableProcessor for 'markers_reference'.
*/
public void setMarkersReferenceFromTRC(String filename) {
Expand Down
153 changes: 21 additions & 132 deletions Gui/opensim/modeling/src/org/opensim/modeling/opensimMoco.java
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Expand Up @@ -324,23 +324,16 @@ public static TimeSeriesTable createExternalLoadsTableForGait(Model model, MocoT

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* provided StatesTrajectory and controls table.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* We assume the StatesTrajectory and controls table contain the same time<br>
* points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
Expand All @@ -349,64 +342,27 @@ public static TimeSeriesTable createExternalLoadsTableForGait(Model model, MocoT
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
*
*/
public static TimeSeriesTable analyzeMocoTrajectory(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths, TimeSeriesTable discreteVariablesTable) {
return new TimeSeriesTable(opensimMocoJNI.analyzeMocoTrajectory__SWIG_1(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths, TimeSeriesTable.getCPtr(discreteVariablesTable), discreteVariablesTable), true);
}

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
* that already satisfies kinematic constraints. If your provided trajectory<br>
* does not satisfy kinematic constraints, many outputs will be incorrect.<br>
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
* Note: Parameters and Lagrange multipliers in the MocoTrajectory are **not**<br>
* applied to the model.<br>
*
*/
public static TimeSeriesTable analyzeMocoTrajectory(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths) {
return new TimeSeriesTable(opensimMocoJNI.analyzeMocoTrajectory__SWIG_2(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths), true);
public static TimeSeriesTable analyzeMocoTrajectory(Model model, MocoTrajectory trajectory, StdVectorString outputPaths) {
return new TimeSeriesTable(opensimMocoJNI.analyzeMocoTrajectory(Model.getCPtr(model), model, MocoTrajectory.getCPtr(trajectory), trajectory, StdVectorString.getCPtr(outputPaths), outputPaths), true);
}

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* provided StatesTrajectory and controls table.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* We assume the StatesTrajectory and controls table contain the same time<br>
* points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
Expand All @@ -415,64 +371,27 @@ public static TimeSeriesTable analyzeMocoTrajectory(Model model, TimeSeriesTable
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
*
*/
public static TimeSeriesTableVec3 analyzeMocoTrajectoryVec3(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths, TimeSeriesTable discreteVariablesTable) {
return new TimeSeriesTableVec3(opensimMocoJNI.analyzeMocoTrajectoryVec3__SWIG_0(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths, TimeSeriesTable.getCPtr(discreteVariablesTable), discreteVariablesTable), true);
}

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
* that already satisfies kinematic constraints. If your provided trajectory<br>
* does not satisfy kinematic constraints, many outputs will be incorrect.<br>
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
* Note: Parameters and Lagrange multipliers in the MocoTrajectory are **not**<br>
* applied to the model.<br>
*
*/
public static TimeSeriesTableVec3 analyzeMocoTrajectoryVec3(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths) {
return new TimeSeriesTableVec3(opensimMocoJNI.analyzeMocoTrajectoryVec3__SWIG_1(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths), true);
public static TimeSeriesTableVec3 analyzeMocoTrajectoryVec3(Model model, MocoTrajectory trajectory, StdVectorString outputPaths) {
return new TimeSeriesTableVec3(opensimMocoJNI.analyzeMocoTrajectoryVec3(Model.getCPtr(model), model, MocoTrajectory.getCPtr(trajectory), trajectory, StdVectorString.getCPtr(outputPaths), outputPaths), true);
}

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* provided StatesTrajectory and controls table.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* We assume the StatesTrajectory and controls table contain the same time<br>
* points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
Expand All @@ -481,43 +400,13 @@ public static TimeSeriesTableVec3 analyzeMocoTrajectoryVec3(Model model, TimeSer
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
*
*/
public static TimeSeriesTableSpatialVec analyzeMocoTrajectorySpatialVec(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths, TimeSeriesTable discreteVariablesTable) {
return new TimeSeriesTableSpatialVec(opensimMocoJNI.analyzeMocoTrajectorySpatialVec__SWIG_0(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths, TimeSeriesTable.getCPtr(discreteVariablesTable), discreteVariablesTable), true);
}

/**
* Calculate the requested outputs using the model in the problem and the<br>
* provided states and controls tables.<br>
* The controls table is used to set the model's controls vector.<br>
* We assume the states and controls tables contain the same time points.<br>
* The output paths can be regular expressions. For example,<br>
* ".*activation" gives the activation of all muscles.<br>
* <br>
* The output paths must correspond to outputs that match the type provided in<br>
* the template argument, otherwise they are not included in the report.<br>
* <br>
* Controls missing from the controls table are given a value of 0.<br>
* <br>
* If you analysis depends on the values of discrete variables in the state,<br>
* you may provide those values via the optional argument<br>
* "discreteVariablesTable". This table should contain column labels with the<br>
* following format: &lt;path_to_component&gt;/&lt;discrete_var_name&gt;. For example,<br>
* "/forceset/muscle/implicitderiv_normalized_tendon_force".<br>
* <br>
* Note: The provided trajectory is not modified to satisfy kinematic<br>
* constraints, but SimTK::Motions in the Model (e.g., PositionMotion) are<br>
* applied. Therefore, this function expects that you've provided a trajectory<br>
* that already satisfies kinematic constraints. If your provided trajectory<br>
* does not satisfy kinematic constraints, many outputs will be incorrect.<br>
* For example, in a model with a patella whose location is determined by a<br>
* CoordinateCouplerConstraint, the length of a muscle that crosses the patella<br>
* will be incorrect.<br>
* Note: Parameters and Lagrange multipliers in the MocoTrajectory are **not**<br>
* applied to the model.<br>
*
*/
public static TimeSeriesTableSpatialVec analyzeMocoTrajectorySpatialVec(Model model, TimeSeriesTable statesTable, TimeSeriesTable controlsTable, StdVectorString outputPaths) {
return new TimeSeriesTableSpatialVec(opensimMocoJNI.analyzeMocoTrajectorySpatialVec__SWIG_1(Model.getCPtr(model), model, TimeSeriesTable.getCPtr(statesTable), statesTable, TimeSeriesTable.getCPtr(controlsTable), controlsTable, StdVectorString.getCPtr(outputPaths), outputPaths), true);
public static TimeSeriesTableSpatialVec analyzeMocoTrajectorySpatialVec(Model model, MocoTrajectory trajectory, StdVectorString outputPaths) {
return new TimeSeriesTableSpatialVec(opensimMocoJNI.analyzeMocoTrajectorySpatialVec(Model.getCPtr(model), model, MocoTrajectory.getCPtr(trajectory), trajectory, StdVectorString.getCPtr(outputPaths), outputPaths), true);
}

}
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