Treatment Optimization Tutorial 1.5.0

RobSalati · RobSalati · commit 10213c7c5b34 · 2025-10-02T17:26:02.000-05:00
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV1.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueDOResultsV1</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV2.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueDOResultsV2</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV3.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV3.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueDOResultsV3</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV4.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV4.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueDOResultsV4</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV5.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueDOSettingsV5.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueDOResultsV5</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueTOSettingsV1.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueTOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueTOResultsV1</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueTOSettingsV2.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueTOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueTOResultsV2</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueVOSettingsV1.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueVOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueVOResultsV1</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueVOSettingsV2.xml b/Step-7-Torque-Driven-Treatment-Optimization/CompletedSettingsFiles/TorqueVOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>TorqueVOResultsV2</results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/DesignOptimizationXMLReference.xml b/Step-7-Torque-Driven-Treatment-Optimization/DesignOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/GpopsSettings.xml b/Step-7-Torque-Driven-Treatment-Optimization/GpopsSettings.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<OptimalControlSolverSettings name="default">
 		<!--Settings for the GPOPS optimal control solver. Current options: GpopsSettings-->
 		<GpopsSettings>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/TorqueDrivenTreatmentOptimizationTutorial.docx b/Step-7-Torque-Driven-Treatment-Optimization/TorqueDrivenTreatmentOptimizationTutorial.docx
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/TorqueDrivenTreatmentOptimizationTutorial.pdf b/Step-7-Torque-Driven-Treatment-Optimization/TorqueDrivenTreatmentOptimizationTutorial.pdf
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/TrackingOptimizationXMLReference.xml b/Step-7-Torque-Driven-Treatment-Optimization/TrackingOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/TreatmentOptimizationIPOPTinfo.txt b/Step-7-Torque-Driven-Treatment-Optimization/TreatmentOptimizationIPOPTinfo.txt
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/VerificationOptimizationXMLReference.xml b/Step-7-Torque-Driven-Treatment-Optimization/VerificationOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/runDOTool.m b/Step-7-Torque-Driven-Treatment-Optimization/runDOTool.m
@@ -1,34 +1,28 @@
 %% Run Torque DO V1
-close all
 DesignOptimizationTool("TorqueDOSettingsV1.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV1.xml")
 
 %% Run Torque DO V2
-close all
 DesignOptimizationTool("TorqueDOSettingsV2.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV2.xml")
 
 %% Run Torque DO V3
-close all
 DesignOptimizationTool("TorqueDOSettingsV3.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV3.xml")
 
 %% Run Torque DO V4
-close all
 DesignOptimizationTool("TorqueDOSettingsV4.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV4.xml")
 
 %% Run Torque DO V5
-close all
 DesignOptimizationTool("TorqueDOSettingsV5.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV5.xml")
 
 %% Compare Results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueDOSettingsV5.xml", ...
     ["TorqueDOResultsV3", "TorqueDOResultsV4", "TorqueDOResultsV5"])
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/runTOTool.m b/Step-7-Torque-Driven-Treatment-Optimization/runTOTool.m
@@ -1,10 +1,8 @@
 %% Run Torque TO V1
-
 TrackingOptimizationTool("TorqueTOSettingsV1.xml");
 
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueTOSettingsV1.xml")
 
-
 %% Run Torque TO V2
 TrackingOptimizationTool("TorqueTOSettingsV2.xml");
 
diff --git a/Step-7-Torque-Driven-Treatment-Optimization/runVOTool.m b/Step-7-Torque-Driven-Treatment-Optimization/runVOTool.m
@@ -1,20 +1,13 @@
 %% Run Torque Driven VO V1
-
-close all
-tic
 VerificationOptimizationTool("TorqueVOSettingsV1.xml");
-toc
+
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueVOSettingsV1.xml")
 
 %% Run Torque Driven VO V2
-
-close all
-tic
 VerificationOptimizationTool("TorqueVOSettingsV2.xml");
-toc
+
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueVOSettingsV2.xml")
 
 %% Compare Results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("TorqueVOSettingsV2.xml", ...
     ["TorqueVOResultsV1", "TorqueVOResultsV2"])
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyDOSettingsV1.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyDOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyDOResultsV1</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyDOSettingsV2.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyDOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyDOResultsV2</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV1.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyTOResultsV1</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV2.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyTOResultsV2</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV3.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV3.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyTOResultsV3</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV4.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV4.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyTOResultsV4</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV5.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyTOSettingsV5.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyTOResultsV5</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyVOSettingsV1.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyVOSettingsV1.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyVOResultsV1</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyVOSettingsV2.xml b/Step-8-Synergy-Driven-Treatment-Optimization/CompletedSettingsFiles/SynergyVOSettingsV2.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool name="default">
 		<!--Directory used for writing results.-->
 		<results_directory>SynergyVOResultsV2</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/DesignOptimizationXMLReference.xml b/Step-8-Synergy-Driven-Treatment-Optimization/DesignOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<DesignOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/NCPSettings.xml b/Step-8-Synergy-Driven-Treatment-Optimization/NCPSettings.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<NMSMPipelineDocument Version="1.4.1">
+<NMSMPipelineDocument Version="1.5.0">
     <NeuralControlPersonalizationTool>
         <!--Directory used for writing results.-->
         <results_directory>ncpResults</results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/SynergyDrivenTreatmentOptimizationTutorial.docx b/Step-8-Synergy-Driven-Treatment-Optimization/SynergyDrivenTreatmentOptimizationTutorial.docx
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/SynergyDrivenTreatmentOptimizationTutorial.pdf b/Step-8-Synergy-Driven-Treatment-Optimization/SynergyDrivenTreatmentOptimizationTutorial.pdf
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/TrackingOptimizationXMLReference.xml b/Step-8-Synergy-Driven-Treatment-Optimization/TrackingOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<TrackingOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/VerificationOptimizationXMLReference.xml b/Step-8-Synergy-Driven-Treatment-Optimization/VerificationOptimizationXMLReference.xml
@@ -1,4 +1,4 @@
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<VerificationOptimizationTool>
 		<!--Directory used for writing results.-->
 		<results_directory></results_directory>
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/gpopsSettings.xml b/Step-8-Synergy-Driven-Treatment-Optimization/gpopsSettings.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<NMSMPipelineDocument Version="1.4.0">
+<NMSMPipelineDocument Version="1.5.0">
 	<OptimalControlSolverSettings>
 		<GpopsSettings>
 			<!--type of derivative approximation. Possible values 'sparsFD' 'sparseBD' 'sparseCD' 'adigator'. Default 'sparseFD'-->
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/runDOTool.m b/Step-8-Synergy-Driven-Treatment-Optimization/runDOTool.m
@@ -1,19 +1,17 @@
 %% Run Synergy DO V1
-close all
 DesignOptimizationTool("SynergyDOSettingsV1.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyDOSettingsV1.xml")
 
 %% Run Synergy DO V2
-
 DesignOptimizationTool("SynergyDOSettingsV2.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyDOSettingsV2.xml")
 
 %% Compare Synergy Driven Results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyDOSettingsV1.xml", ...
     ["SynergyDOResultsV1", "SynergyDOResultsV2"])
 
 %% Compare to Torque Driven Results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyDOSettingsV1.xml", ...
     ["SynergyDOResultsV2", "TorqueDOResultsV4"])
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/runTOTool.m b/Step-8-Synergy-Driven-Treatment-Optimization/runTOTool.m
@@ -1,29 +1,28 @@
 %% Run Synergy TO V1
-close all
 TrackingOptimizationTool("SynergyTOSettingsV1.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV1.xml")
 
 %% Run Synergy TO V2
-close all
 TrackingOptimizationTool("SynergyTOSettingsV2.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV2.xml")
 
 %% Run Synergy TO V3
-close all
 TrackingOptimizationTool("SynergyTOSettingsV3.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV3.xml")
 
 %% Run Synergy TO V4
-close all
 TrackingOptimizationTool("SynergyTOSettingsV4.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV4.xml")
 
 %% Run Synergy TO V5
-close all
 TrackingOptimizationTool("SynergyTOSettingsV5.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV5.xml")
 
 %% Compare results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyTOSettingsV5.xml", ...
     ["SynergyTOResultsV1", "SynergyTOResultsV4", "SynergyTOResultsV5"])
diff --git a/Step-8-Synergy-Driven-Treatment-Optimization/runVOTool.m b/Step-8-Synergy-Driven-Treatment-Optimization/runVOTool.m
@@ -1,14 +1,13 @@
 %% Run Synergy Driven VO V1
-close all
 VerificationOptimizationTool("SynergyVOSettingsV1.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyVOSettingsV1.xml")
 
 %% Run Synergy Driven VO V2
-close all
 VerificationOptimizationTool("SynergyVOSettingsV2.xml");
+
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyVOSettingsV2.xml")
 
 %% Compare Results
-close all
 plotTreatmentOptimizationResultsFromSettingsFile("SynergyVOSettingsV2.xml", ...
     ["SynergyVOResultsV1", "SynergyVOResultsV2"])

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<NMSMPipelineDocument Version="1.4.0">`
	`1`	`+<NMSMPipelineDocument Version="1.5.0">`
`2`	`2`	`<DesignOptimizationTool name="default">`
`3`	`3`	`<!--Directory used for writing results.-->`
`4`	`4`	`<results_directory>TorqueDOResultsV1</results_directory>`