{WIP} Major updates to Metabolic's Tutorial Package

CMakeLists.txt

@@ -25,13 +25,26 @@ install(FILES Models/BouncingBlock/run_forward_bouncingBlock.xml
 
 install(FILES Models/Gait10dof18musc/gait10dof18musc.osim
               Models/Gait10dof18musc/subject01.osim
+              Models/Gait10dof18musc/subject01_metabolics.osim
+              Pipelines/Gait10dof18musc/ExperimentalData/subject01_static.trc
+              Pipelines/Gait10dof18musc/ExperimentalData/subject01_walk.trc
+              Pipelines/Gait10dof18musc/ExperimentalData/subject01_walk_grf.xml
+              Pipelines/Gait10dof18musc/ExperimentalData/subject01_walk_grf.mot
+              Pipelines/Gait10dof18musc/RRA/Setup_RRA.xml
+              Pipelines/Gait10dof18musc/IK/Setup_IK.xml
+              Pipelines/Gait10dof18musc/ID/Setup_ID.xml
+              Pipelines/Gait10dof18musc/OutputReference/IK/subject01_walk_IK.mot
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/Controls_Constraints_43p_r.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/Gait10dof_Kinematics_Tracking_Tasks.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/Gait10dof_Reserve_Actuators.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/Setup_CMC_ActuatorConstraints.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/Setup_CMC.xml
+        DESTINATION Models/Gait10dof18musc)
+
+install(DIRECTORY Pipelines/Gait10dof18musc/OutputReference/ResultsRRA
+                  Tutorials/Design_to_Reduce_Metabolic_Cost/Scripts
+                  Tutorials/Design_to_Reduce_Metabolic_Cost/PlantarFlexorAssistCurves
         DESTINATION Models/Gait10dof18musc)
-# TODO subject01_metabolics* files?
-install(DIRECTORY Pipelines/Gait10dof18musc/
-        DESTINATION Models/Gait10dof18musc
-        PATTERN "CMC/ResultsCMC_*" EXCLUDE
-        PATTERN "CMC/controls_43p_r.xml" EXCLUDE
-        PATTERN "CMC/*.osim" EXCLUDE)
 
 install(FILES Models/Gait2354_Simbody/gait2354_simbody.osim
         DESTINATION Models/Gait2354_Simbody)

Pipelines/Gait10dof18musc/ExperimentalData/subject01_walk_grf.xml

@@ -42,9 +42,5 @@
 		<groups />
 		<!--Storage file (.sto) containing (3) components of force and/or torque and point of application.Note: this file overrides the data source specified by the individual external forces if specified.-->
 		<datafile>subject01_walk_grf.mot</datafile>
-		<!--Optional motion file (.mot) or storage file (.sto) containing the model kinematics used to transform a point expressed in ground to the body of force application.If the point is not expressed in ground, the point is not transformed-->
-		<external_loads_model_kinematics_file />
-		<!--Optional low-pass cut-off frequency for filtering the model kinematics corresponding used to transform the point of application. A negative value results in no filtering. The default value is -1.0, so no filtering.-->
-		<lowpass_cutoff_frequency_for_load_kinematics>-1</lowpass_cutoff_frequency_for_load_kinematics>
-	</ExternalLoads>
+		</ExternalLoads>
 </OpenSimDocument>

Pipelines/Gait10dof18musc/ID/walk_Setup_ID.xml → Pipelines/Gait10dof18musc/ID/Setup_ID.xml

@@ -2,17 +2,17 @@
 <OpenSimDocument Version="30000">
 	<InverseDynamicsTool name="walk_subject">
 			<!--Name of the .osim file used to construct a model.-->
-		<model_file>../subject01.osim</model_file>
+		<model_file>subject01.osim</model_file>
 		<!--Directory used for writing results.-->
 		<results_directory>Results</results_directory>
 		<!--Time range over which the inverse dynamics problem is solved.-->
 		<time_range> 0 2.5</time_range>
 		<!--List of forces by individual or grouping name (e.g. All, actuators, muscles, ...) to be excluded when computing model dynamics.-->
 		<forces_to_exclude> Muscles</forces_to_exclude>
 		<!--XML file (.xml) containing the external loads applied to the model as a set of ExternalForce(s).-->
-		<external_loads_file>../ExperimentalData/subject01_walk_grf.xml</external_loads_file>
+		<external_loads_file>subject01_walk_grf.xml</external_loads_file>
 		<!--The name of the file containing coordinate data. Can be a motion (.mot) or a states (.sto) file.-->
-		<coordinates_file>../IK/subject01_walk_IK.mot</coordinates_file>
+		<coordinates_file>subject01_walk_IK.mot</coordinates_file>
 		<!--Low-pass cut-off frequency for filtering the coordinates_file data (currently does not apply to states_file or speeds_file). A negative value results in no filtering. The default value is -1.0, so no filtering.-->
 		<lowpass_cutoff_frequency_for_coordinates>6</lowpass_cutoff_frequency_for_coordinates>
 		<!--Name of the storage file (.sto) to which the generalized forces are written.-->

Tutorials/Design_to_Reduce_Metabolic_Cost/IK/walk_Setup_IK.xml → Pipelines/Gait10dof18musc/IK/Setup_IK.xml

@@ -2,11 +2,11 @@
 <OpenSimDocument Version="30000">
 	<InverseKinematicsTool>
 		<!--Directory used for writing results.-->
-		<results_directory>./</results_directory>
+		<results_directory></results_directory>
 		<!--Directory for input files-->
 		<input_directory />
 		<!--Name of the .osim file used to construct a model.-->
-		<model_file />
+		<model_file> subject01.osim </model_file>
 		<!--A positive scalar that is used to weight the importance of satisfying constraints.A weighting of 'Infinity' or if it is unassigned results in the constraints being strictly enforced.-->
 		<constraint_weight>Inf</constraint_weight>
 		<!--The accuracy of the solution in absolute terms. I.e. the number of significantdigits to which the solution can be trusted.-->
@@ -252,7 +252,7 @@
 			<groups />
 		</IKTaskSet>
 		<!--TRC file (.trc) containing the time history of observations of marker positions.-->
-		<marker_file>../ExperimentalData/subject01_walk.trc</marker_file>
+		<marker_file>subject01_walk.trc</marker_file>
 		<!--The name of the storage (.sto or .mot) file containing coordinate observations.Coordinate values from this file are included if there is a corresponding coordinate task. -->
 		<coordinate_file>Unassigned</coordinate_file>
 		<!--Time range over which the inverse kinematics problem is solved.-->