Python version of the tool

Example_deform_distal_femur_Rajagopal.py

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+# import libraries
+import numpy as np
+import opensim as osim
+import os
+import utils.getJointCentresForBone
+import utils.createTorsionProfile
+import utils.applyTorsionToJoints
+import utils.applyTorsionToVTPBoneGeom
+import utils.applyTorsionToMuscleAttachments
+import utils.applyTorsionToMarkers
+import utils.saveDeformedModel
+
+#---------------  MAIN SETTINGS ---------------
+# Model to deform
+modelFileName = './examples_Rajagopal2015/Rajagopal2015.osim'
+
+# where the bone geometries are stored
+OpenSim_Geometry_folder = './examples_Rajagopal2015/Geometry'
+
+# body to deform
+bone_to_deform = 'femur_r'
+
+# axis of deformation
+torsionAxis = 'y'
+
+# define the rotational profile at the joint centres of the bone of
+# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
+TorsionProfilePointsDeg = (40, 0)
+
+# decide if you want to apply torsion to joint as well as other objects.
+# E.g. choose no for investigating the effect of femoral anteversion in a
+# leg with straight alignment.
+# Choose yes for modelling a CP child with deformation of bone resulting in
+# joint rotation, meaning the kinematic model is altered.
+apply_torsion_to_joints = 'yes'
+
+# where the deformed models will be saved
+altered_models_folder = './examples_Rajagopal2015'
+#----------------------------------------------
+
+# import model
+osimModel = osim.Model(modelFileName)
+
+# compute bone length
+Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
+
+# define length corresponding to torsion points
+LengthProfilePoints = np.vstack((Pprox,Pdist))
+
+# compute torsion profile
+torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
+
+# suffix used for saving geometries
+bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
+deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
+
+# if you want you can apply torsion to joints
+if apply_torsion_to_joints == 'yes':
+    osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deforming muscle attachments
+osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# if there are markers rotate them
+osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deform the bone geometries of the generic model
+osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis, 
+                                            torsion_angle_func_rad, torsion_doc_string,
+                                            OpenSim_Geometry_folder)
+
+# save output model
+if not os.path.exists(altered_models_folder):
+    os.mkdir(altered_models_folder)
+
+_, name_ext = os.path.split(modelFileName)
+name, ext = os.path.splitext(name_ext)
+deformed_model_name = name + deformed_model_suffix + ext
+output_model_path = os.path.join(altered_models_folder, deformed_model_name)
+osimModel.setName(osimModel.getName()+deformed_model_suffix)
+
+# save model
+utils.saveDeformedModel(osimModel, output_model_path)

Example_deform_distal_femur_gait2392.py

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+# import libraries
+import numpy as np
+import opensim as osim
+import os
+import utils.getJointCentresForBone
+import utils.createTorsionProfile
+import utils.applyTorsionToJoints
+import utils.applyTorsionToVTPBoneGeom
+import utils.applyTorsionToMuscleAttachments
+import utils.applyTorsionToMarkers
+import utils.saveDeformedModel
+
+#---------------  MAIN SETTINGS ---------------
+# Model to deform
+modelFileName = './examples_gait2392/gait2392_simbody.osim'
+
+# where the bone geometries are stored
+OpenSim_Geometry_folder = 'C:/OpenSim 4.5/Geometry'
+
+# body to deform
+bone_to_deform = 'femur_r'
+
+# axis of deformation
+torsionAxis = 'y'
+
+# define the rotational profile at the joint centres of the bone of
+# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
+TorsionProfilePointsDeg = (40, 0)
+
+# decide if you want to apply torsion to joint as well as other objects.
+# E.g. choose no for investigating the effect of femoral anteversion in a
+# leg with straight alignment.
+# Choose yes for modelling a CP child with deformation of bone resulting in
+# joint rotation, meaning the kinematic model is altered.
+apply_torsion_to_joints = 'yes'
+
+# where the deformed models will be saved
+altered_models_folder = './examples_gait2392'
+#----------------------------------------------
+
+# import model
+osimModel = osim.Model(modelFileName)
+
+# compute bone length
+Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
+
+# define length corresponding to torsion points
+LengthProfilePoints = np.vstack((Pprox,Pdist))
+
+# compute torsion profile
+torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
+
+# suffix used for saving geometries
+bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
+deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
+
+# if you want you can apply torsion to joints
+if apply_torsion_to_joints == 'yes':
+    osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deforming muscle attachments
+osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# if there are markers rotate them
+osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deform the bone geometries of the generic model
+osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis, 
+                                            torsion_angle_func_rad, torsion_doc_string,
+                                            OpenSim_Geometry_folder)
+
+# save output model
+if not os.path.exists(altered_models_folder):
+    os.mkdir(altered_models_folder)
+
+_, name_ext = os.path.split(modelFileName)
+name, ext = os.path.splitext(name_ext)
+deformed_model_name = name + deformed_model_suffix + ext
+output_model_path = os.path.join(altered_models_folder, deformed_model_name)
+osimModel.setName(osimModel.getName()+deformed_model_suffix)
+
+# save model
+utils.saveDeformedModel(osimModel, output_model_path)

Example_deform_distal_tibia_Rajagopal.py

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+# import libraries
+import numpy as np
+import opensim as osim
+import os
+import utils.getJointCentresForBone
+import utils.createTorsionProfile
+import utils.applyTorsionToJoints
+import utils.applyTorsionToVTPBoneGeom
+import utils.applyTorsionToMuscleAttachments
+import utils.applyTorsionToMarkers
+import utils.saveDeformedModel
+
+#---------------  MAIN SETTINGS ---------------
+# Model to deform
+modelFileName = './examples_Rajagopal2015/Rajagopal2015.osim'
+
+# where the bone geometries are stored
+OpenSim_Geometry_folder = './examples_Rajagopal2015/Geometry'
+
+# body to deform
+bone_to_deform = 'tibia_l'
+
+# axis of deformation
+torsionAxis = 'y'
+
+# define the rotational profile at the joint centres of the bone of
+# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
+TorsionProfilePointsDeg = (0, -30)
+
+# decide if you want to apply torsion to joint as well as other objects.
+# E.g. choose no for investigating the effect of femoral anteversion in a
+# leg with straight alignment.
+# Choose yes for modelling a CP child with deformation of bone resulting in
+# joint rotation, meaning the kinematic model is altered.
+apply_torsion_to_joints = 'yes'
+
+# where the deformed models will be saved
+altered_models_folder = './examples_Rajagopal2015'
+#----------------------------------------------
+
+# import model
+osimModel = osim.Model(modelFileName)
+
+# compute bone length
+Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
+
+# define length corresponding to torsion points
+LengthProfilePoints = np.vstack((Pprox,Pdist))
+
+# compute torsion profile
+torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
+
+# suffix used for saving geometries
+bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
+deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
+
+# if you want you can apply torsion to joints
+if apply_torsion_to_joints == 'yes':
+    osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deforming muscle attachments
+osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# if there are markers rotate them
+osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deform the bone geometries of the generic model
+osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis, 
+                                            torsion_angle_func_rad, torsion_doc_string,
+                                            OpenSim_Geometry_folder)
+
+# save output model
+if not os.path.exists(altered_models_folder):
+    os.mkdir(altered_models_folder)
+
+_, name_ext = os.path.split(modelFileName)
+name, ext = os.path.splitext(name_ext)
+deformed_model_name = name + deformed_model_suffix + ext
+output_model_path = os.path.join(altered_models_folder, deformed_model_name)
+osimModel.setName(osimModel.getName()+deformed_model_suffix)
+
+# save model
+utils.saveDeformedModel(osimModel, output_model_path)

Example_deform_distal_tibia_gait2392.py

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+# import libraries
+import numpy as np
+import opensim as osim
+import os
+import utils.getJointCentresForBone
+import utils.createTorsionProfile
+import utils.applyTorsionToJoints
+import utils.applyTorsionToVTPBoneGeom
+import utils.applyTorsionToMuscleAttachments
+import utils.applyTorsionToMarkers
+import utils.saveDeformedModel
+
+#---------------  MAIN SETTINGS ---------------
+# Model to deform
+modelFileName = './examples_gait2392/gait2392_simbody.osim'
+
+# where the bone geometries are stored
+OpenSim_Geometry_folder = 'C:/OpenSim 4.5/Geometry'
+
+# body to deform
+bone_to_deform = 'tibia_l'
+
+# axis of deformation
+torsionAxis = 'y'
+
+# define the rotational profile at the joint centres of the bone of
+# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
+TorsionProfilePointsDeg = (0, -30)
+
+# decide if you want to apply torsion to joint as well as other objects.
+# E.g. choose no for investigating the effect of femoral anteversion in a
+# leg with straight alignment.
+# Choose yes for modelling a CP child with deformation of bone resulting in
+# joint rotation, meaning the kinematic model is altered.
+apply_torsion_to_joints = 'yes'
+
+# where the deformed models will be saved
+altered_models_folder = './examples_gait2392'
+#----------------------------------------------
+
+# import model
+osimModel = osim.Model(modelFileName)
+
+# compute bone length
+Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
+
+# define length corresponding to torsion points
+LengthProfilePoints = np.vstack((Pprox,Pdist))
+
+# compute torsion profile
+torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
+
+# suffix used for saving geometries
+bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
+deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
+
+# if you want you can apply torsion to joints
+if apply_torsion_to_joints == 'yes':
+    osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deforming muscle attachments
+osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# if there are markers rotate them
+osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
+
+# deform the bone geometries of the generic model
+osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis, 
+                                            torsion_angle_func_rad, torsion_doc_string,
+                                            OpenSim_Geometry_folder)
+
+# save output model
+if not os.path.exists(altered_models_folder):
+    os.mkdir(altered_models_folder)
+
+_, name_ext = os.path.split(modelFileName)
+name, ext = os.path.splitext(name_ext)
+deformed_model_name = name + deformed_model_suffix + ext
+output_model_path = os.path.join(altered_models_folder, deformed_model_name)
+osimModel.setName(osimModel.getName()+deformed_model_suffix)
+
+# save model
+utils.saveDeformedModel(osimModel, output_model_path)