Merge pull request #174 from stanfordnmbl/dev

Speed up IK by removing patella constraints

main.py

@@ -590,7 +590,7 @@ def main(sessionName, trialName, trial_id, cameras_to_use=['all'],
                 # Run IK tool. 
                 logging.info('Running Inverse Kinematics')
                 try:
-                    pathOutputIK = runIKTool(
+                    pathOutputIK, pathModelIK = runIKTool(
                         pathGenericSetupFile4IK, pathScaledModel, 
                         pathTRCFile4IK, outputIKDir)
                 except Exception as e:
@@ -608,7 +608,7 @@ def main(sessionName, trialName, trial_id, cameras_to_use=['all'],
         os.makedirs(outputJsonVisDir,exist_ok=True)
         outputJsonVisPath = os.path.join(outputJsonVisDir,
                                          trialName + '.json')
-        generateVisualizerJson(pathScaledModel, pathOutputIK,
+        generateVisualizerJson(pathModelIK, pathOutputIK,
                                outputJsonVisPath, 
                                vertical_offset=vertical_offset)  
 

utilsOpenSim.py

@@ -163,11 +163,44 @@ def runIKTool(pathGenericSetupFile, pathScaledModel, pathTRCFile,
     pathOutputSetup =  os.path.join(
         pathOutputFolder, 'Setup_IK_' + IKFileName + '.xml')
 
-    # Setup IK tool.
+    # To make IK faster, we remove the patellas and their constraints from the
+    # model. Constraints make the IK problem more difficult, and the patellas
+    # are not used in the IK solution for this particular model. Since muscles
+    # are attached to the patellas, we also remove all muscles.
     opensim.Logger.setLevelString('error')
+    model = opensim.Model(pathScaledModel)
+    # Remove all actuators.                                         
+    forceSet = model.getForceSet()
+    forceSet.setSize(0)
+    # Remove patellofemoral constraints.
+    constraintSet = model.getConstraintSet()
+    patellofemoral_constraints = [
+        'patellofemoral_knee_angle_r_con', 'patellofemoral_knee_angle_l_con']
+    for patellofemoral_constraint in patellofemoral_constraints:
+        i = constraintSet.getIndex(patellofemoral_constraint, 0)
+        constraintSet.remove(i)       
+    # Remove patella bodies.
+    bodySet = model.getBodySet()
+    patella_bodies = ['patella_r', 'patella_l']
+    for patella in patella_bodies:
+        i = bodySet.getIndex(patella, 0)
+        bodySet.remove(i)
+    # Remove patellofemoral joints.
+    jointSet = model.getJointSet()
+    patellofemoral_joints = ['patellofemoral_r', 'patellofemoral_l']
+    for patellofemoral in patellofemoral_joints:
+        i = jointSet.getIndex(patellofemoral, 0)
+        jointSet.remove(i)
+    # Print the model to a new file.
+    model.finalizeConnections
+    model.initSystem()
+    pathScaledModelWithoutPatella = pathScaledModel.replace('.osim', '_no_patella.osim')
+    model.printToXML(pathScaledModelWithoutPatella)   
+
+    # Setup IK tool.    
     IKTool = opensim.InverseKinematicsTool(pathGenericSetupFile)            
     IKTool.setName(IKFileName)
-    IKTool.set_model_file(pathScaledModel)          
+    IKTool.set_model_file(pathScaledModelWithoutPatella)          
     IKTool.set_marker_file(pathTRCFile)
     if timeRange:
         IKTool.set_time_range(0, timeRange[0])
@@ -180,7 +213,7 @@ def runIKTool(pathGenericSetupFile, pathScaledModel, pathTRCFile,
     command = 'opensim-cmd -o error' + ' run-tool ' + pathOutputSetup
     os.system(command)
 
-    return pathOutputMotion
+    return pathOutputMotion, pathScaledModelWithoutPatella
 
 
 # %% This function will look for a time window, of a minimum duration specified