Merge pull request #47 from aymanhab/treatment_optimization

Treatment optimization basic functionality works
aymanhab · Jan 3, 2025 · c65e35b · c65e35b
2 parents d72cbd7 + 20d9e70
commit c65e35b
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Showing 17 changed files with 548 additions and 342 deletions.
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties
@@ -181,12 +181,12 @@ TreatmentOptimizationJPanel.jRCNLTorqueControllerPanel.border.title=RCNL Torque
 TreatmentOptimizationJPanel.jLabel2.text=Surrogate model data directory
 TreatmentOptimizationJPanel.jCoordinatesListPanel3.border.title=Coordinate List
 TreatmentOptimizationJPanel.jSynergyControllerDetailsPanel1.border.title=RCNL Synergy Controller
-TreatmentOptimizationJPanel.jControllersPanel.TabConstraints.tabTitle=RCNL Controllers     
+TreatmentOptimizationJPanel.jControllersPanel.TabConstraints.tabTitle=RCNL Controllers
 TreatmentOptimizationJPanel.jLabel6.text=Tracked Quantities Dir:
 TreatmentOptimizationJPanel.jLabel8.text=Optimal Control Solver Settings File:
 TreatmentOptimizationJPanel.jLabel5.text=Results Dir:
 TreatmentOptimizationJPanel.outputPanel.border.title=Output
-TreatmentOptimizationJPanel.inputOutputPanel.TabConstraints.tabTitle=Settings     
+TreatmentOptimizationJPanel.inputOutputPanel.TabConstraints.tabTitle=Settings
 TreatmentOptimizationJPanel.jLabel4.text=Initial Guess Dir:
 TreatmentOptimizationJPanel.jLabel3.text=Osimx File:
 TreatmentOptimizationJPanel.currentModelFileTextField.toolTipText=Current Model in GUI
@@ -214,3 +214,5 @@ EditCostTermJPanel.jErrorCenterTextField.text=0.
 EditCosnstraintTermJPanel.jComponentTypeTextField.text=\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ 
 EditCosnstraintTermJPanel.jMaxErrorTextField.text=0
 EditCosnstraintTermJPanel.jMinErrorTextField.text=0
+SelectQuantitiesFromListJPanel.jSelectAllCheckBox.toolTipText=select all shown quantities
+SelectQuantitiesFromListJPanel.jSelectAllCheckBox.text=select all shown
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java
@@ -117,5 +117,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
 
     }
+
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+            selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
 
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java
@@ -116,5 +116,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
 
     }
+
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+            selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
 
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form
@@ -19,28 +19,23 @@
           <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Group type="102" attributes="0">
-                      <Group type="103" groupAlignment="1" attributes="0">
-                          <Component id="jComponentListPanel" alignment="0" pref="0" max="32767" attributes="0"/>
-                          <Group type="103" groupAlignment="0" attributes="0">
-                              <Component id="jEnabledCheckBox" min="-2" max="-2" attributes="0"/>
-                              <Group type="102" alignment="0" attributes="0">
-                                  <Component id="jLabel11" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jComponentTypeTextField" min="-2" pref="220" max="-2" attributes="0"/>
-                              </Group>
-                              <Group type="102" alignment="0" attributes="0">
-                                  <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jMaxErrorTextField" min="-2" pref="150" max="-2" attributes="0"/>
-                                  <EmptySpace min="-2" pref="131" max="-2" attributes="0"/>
-                                  <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jErrorCenterTextField" min="-2" pref="215" max="-2" attributes="0"/>
-                              </Group>
-                          </Group>
+                  <Component id="jComponentListPanel" alignment="0" pref="0" max="32767" attributes="0"/>
+                  <Group type="103" alignment="1" groupAlignment="0" attributes="0">
+                      <Component id="jEnabledCheckBox" min="-2" max="-2" attributes="0"/>
+                      <Group type="102" alignment="0" attributes="0">
+                          <Component id="jLabel11" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jComponentTypeTextField" min="-2" pref="220" max="-2" attributes="0"/>
+                      </Group>
+                      <Group type="102" alignment="0" attributes="0">
+                          <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jMaxErrorTextField" min="-2" pref="150" max="-2" attributes="0"/>
+                          <EmptySpace min="-2" pref="131" max="-2" attributes="0"/>
+                          <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jErrorCenterTextField" min="-2" pref="215" max="-2" attributes="0"/>
                       </Group>
-                      <EmptySpace max="-2" attributes="0"/>
                   </Group>
                   <Group type="102" attributes="0">
                       <Group type="103" groupAlignment="0" attributes="0">
@@ -55,9 +50,10 @@
                               <Component id="jCostTermNameTextField" min="-2" pref="460" max="-2" attributes="0"/>
                           </Group>
                       </Group>
-                      <EmptySpace max="32767" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
                   </Group>
               </Group>
+              <EmptySpace max="-2" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -130,9 +126,9 @@
         <DimensionLayout dim="0">
           <Group type="103" groupAlignment="0" attributes="0">
               <Group type="102" alignment="0" attributes="0">
-                  <Component id="jScrollPane2" min="-2" pref="780" max="-2" attributes="0"/>
+                  <Component id="jScrollPane2" min="-2" pref="559" max="-2" attributes="0"/>
                   <EmptySpace max="-2" attributes="0"/>
-                  <Component id="editComonentListButton" min="-2" max="-2" attributes="0"/>
+                  <Component id="editComonentListButton" min="-2" pref="89" max="-2" attributes="0"/>
                   <EmptySpace max="32767" attributes="0"/>
               </Group>
           </Group>

diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java
@@ -136,9 +136,9 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jComponentListPanelLayout.setHorizontalGroup(
             jComponentListPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jComponentListPanelLayout.createSequentialGroup()
-                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 780, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 559, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(editComonentListButton)
+                .addComponent(editComonentListButton, javax.swing.GroupLayout.PREFERRED_SIZE, 89, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         jComponentListPanelLayout.setVerticalGroup(
@@ -216,24 +216,21 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addGroup(layout.createSequentialGroup()
-                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
-                            .addComponent(jComponentListPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
-                            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                                .addComponent(jEnabledCheckBox)
-                                .addGroup(layout.createSequentialGroup()
-                                    .addComponent(jLabel11)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jComponentTypeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 220, javax.swing.GroupLayout.PREFERRED_SIZE))
-                                .addGroup(layout.createSequentialGroup()
-                                    .addComponent(jLabel2)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jMaxErrorTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                    .addGap(131, 131, 131)
-                                    .addComponent(jLabel3)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jErrorCenterTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE))))
-                        .addContainerGap())
+                    .addComponent(jComponentListPanel, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                    .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                        .addComponent(jEnabledCheckBox)
+                        .addGroup(layout.createSequentialGroup()
+                            .addComponent(jLabel11)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jComponentTypeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 220, javax.swing.GroupLayout.PREFERRED_SIZE))
+                        .addGroup(layout.createSequentialGroup()
+                            .addComponent(jLabel2)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jMaxErrorTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addGap(131, 131, 131)
+                            .addComponent(jLabel3)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jErrorCenterTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE)))
                     .addGroup(layout.createSequentialGroup()
                         .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                             .addGroup(layout.createSequentialGroup()
@@ -244,7 +241,8 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
                                 .addComponent(jLabel4)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                                 .addComponent(jCostTermNameTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 460, javax.swing.GroupLayout.PREFERRED_SIZE)))
-                        .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
+                        .addGap(0, 0, Short.MAX_VALUE)))
+                .addContainerGap())
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)

diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java
@@ -417,14 +417,9 @@ public void pressedCancel() {
         super.pressedCancel(); //To change body of generated methods, choose Tools | Templates.
     }
 
-    @Override
-    String getToolXML() {
-        return gcpPersonalizationToolModel.getToolAsObject().dump();
-    }
-
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        gcpPersonalizationToolModel = new GCPPersonalizationToolModel(model, fileName);
@@ -453,9 +448,8 @@ public void setSettingsFileDescription(String description) {
     }
 
     @Override
-    public void saveSettings(String fileName, String contents) {
+    public void saveSettings(String fileName) {
 
-        String adjustedContents = contents;
         // Before saving the settings, we need to make motion file and grf file relative to input_directory
         String inputDir = gcpPersonalizationToolModel.getDataDir();
         String saveInputMotion = gcpPersonalizationToolModel.getInputMotionFile();
@@ -469,10 +463,11 @@ public void saveSettings(String fileName, String contents) {
             String relativeGRFFile = FileUtils.makePathRelative(saveGRFfile, inputDir);
             if (relativeGRFFile != null)
                 gcpPersonalizationToolModel.setInputGRFFile(relativeGRFFile);
-            adjustedContents = getToolXML();
         }
         // Set proprties from relative path
-        super.saveSettings(fileName, adjustedContents); //To change body of generated methods, choose Tools | Templates.
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        gcpPersonalizationToolModel.getToolAsObject().print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
         // Restore from model
         gcpPersonalizationToolModel.setInputMotionFile(saveInputMotion);
         gcpPersonalizationToolModel.setInputGRFFile(saveGRFfile);

diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java
@@ -304,13 +304,17 @@ public void pressedCancel() {
     }
 
     @Override
-    public String getToolXML() {
-        return jointPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = jointPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
     }
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        jointPersonalizationToolModel = new JointPersonalizationToolModel(model, fileName);
@@ -331,6 +335,24 @@ public void setSettingsFileDescription(String description) {
         super.setSettingsFileDescription(description); //To change body of generated methods, choose Tools | Templates.
     }
 
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        // For each JMPTask in tasklist, force write of parent_frame_transformation, child_frame_transformation
+        // dObject is an instance of JointModelPersonalizationTool
+        AbstractProperty ap = dObject.getPropertyByName("JMPTaskList");
+        PropertyObjectList olist = PropertyObjectList.getAs(ap);
+        for (int i=0; i< olist.size(); i++){
+            OpenSimObject ithTask = olist.getValue(i);
+            AbstractProperty apJnts = ithTask.getPropertyByName("JMPJointSet");
+            PropertyObjectList poJointList = PropertyObjectList.updAs(apJnts);
+             for (int j=0; j<poJointList.size(); j++){
+                poJointList.getValue(j).updPropertyByName("parent_frame_transformation").setValueIsDefault(false);
+                poJointList.getValue(j).updPropertyByName("child_frame_transformation").setValueIsDefault(false);
+             }
+        }
+    }
+
 
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JButton addJointTaskButton;

diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java
@@ -112,9 +112,7 @@ public void setToolAsObject(OpenSimObject toolAsObject) {
     public PropertyObjectList getJointTaskListAsObjectList() {
         AbstractProperty ap = toolAsObject.getPropertyByName("JMPTaskList");
         PropertyObjectList olist = PropertyObjectList.getAs(ap);
-        for (int i=0; i< olist.size(); i++){
-            OpenSimObject ithTask = olist.getValue(i);
-        }
+
         return olist;
     }
 

diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java
@@ -633,7 +633,7 @@ public void pressedCancel() {
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        mtpPersonalizationToolModel = new MTPPersonalizationToolModel(model, fileName);
@@ -701,8 +701,20 @@ public void setSettingsFileDescription(String description) {
     // End of variables declaration//GEN-END:variables
 
     @Override
-    String getToolXML() {
-        return mtpPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = mtpPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
     }
 
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        dObject.updPropertyByName("MuscleTendonLengthInitialization").setValueIsDefault(false);
+        dObject.updPropertyByName("MTPSynergyExtrapolation").setValueIsDefault(false);
+    }
+
+
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java
@@ -115,4 +115,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
 
     }
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+           selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
+
+
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java
@@ -571,7 +571,7 @@ public void pressedCancel() {
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        ncpPersonalizationToolModel = new NCPPersonalizationToolModel(model, fileName);
@@ -633,8 +633,18 @@ public void setSettingsFileDescription(String description) {
     // End of variables declaration//GEN-END:variables
 
     @Override
-    String getToolXML() {
-        return ncpPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = ncpPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
+    }
+
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        dObject.updPropertyByName("MuscleTendonLengthInitialization").setValueIsDefault(false);
     }
 
 }