def construct_ik_task_set(model, marker_data, task_set):
"""Construct OpenSim Inverse Kinematics task set.
In older versions of OpenSim (e.g. 3.3) IK will not execute when there are
virtual markers that do not exist in the marker data.
"""
virtual_markers = model.getMarkerSet()
marker_names = marker_data.getMarkerNames()
for i in range(0, marker_names.getSize()):
marker_name = marker_names.get(i)
exists = False
for j in range(0, virtual_markers.getSize()):
if virtual_markers.get(j).getName() == marker_name:
task = opensim.IKMarkerTask()
task.setName(marker_name)
task.setApply(True)
task.setWeight(1)
task_set.adoptAndAppend(task)
exists = True
break
if not exists:
task = opensim.IKMarkerTask()
task.setName(marker_name)
task.setApply(False)
task.setWeight(1)
task_set.adoptAndAppend(task)
def test_markAdoptedSets():
# Set's.
fus = osim.FunctionSet()
fu1 = osim.Constant()
fus.adoptAndAppend(fu1)
del fus
del fu1
s = osim.ScaleSet()
o = osim.Scale()
s.adoptAndAppend(o)
del s
del o
s = osim.ControlSet()
o = osim.ControlLinear()
s.adoptAndAppend(o)
del s
del o
s = osim.BodyScaleSet()
o = osim.BodyScale()
s.adoptAndAppend(o)
del s
del o
s = osim.PathPointSet()
o = osim.PathPoint()
s.adoptAndAppend(o)
del s
del o
s = osim.IKTaskSet()
o = osim.IKMarkerTask()
s.adoptAndAppend(o)
del s
del o
s = osim.MarkerPairSet()
o = osim.MarkerPair()
s.adoptAndAppend(o)
del s
del o
s = osim.MeasurementSet()
o = osim.Measurement()
s.adoptAndAppend(o)
del s
del o
s = osim.FrameSet()
o = osim.Body()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.CoordinateLimitForce()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.SpringGeneralizedForce()
s.append(o)
s = osim.ProbeSet()
o = osim.Umberger2010MuscleMetabolicsProbe()
s.adoptAndAppend(o)
del s
del o
a = osim.Model()
body = osim.Body('body',
1.0,
osim.Vec3(0, 0, 0),
osim.Inertia(0, 0, 0)
)
loc_in_parent = osim.Vec3(0, -0, 0)
orient_in_parent = osim.Vec3(0, 0, 0)
loc_in_body = osim.Vec3(0, 0, 0)
orient_in_body = osim.Vec3(0, 0, 0)
joint = osim.WeldJoint("weld_joint",
a.getGround(),
loc_in_parent, orient_in_parent,
body,
loc_in_body, orient_in_parent)
a.addBody(body)
constr = osim.ConstantDistanceConstraint()
constr.setBody1ByName("ground")
constr.setBody1PointLocation(osim.Vec3(0, 0, 0))
constr.setBody2ByName("body")
constr.setBody2PointLocation(osim.Vec3(1, 0, 0))
constr.setConstantDistance(1)
a.addConstraint(constr)
def test_markAdoptedSets():
# Set's.
fus = osim.FunctionSet()
fu1 = osim.Constant()
fus.adoptAndAppend(fu1)
del fus
del fu1
gs = osim.GeometrySet()
dg = osim.DisplayGeometry()
gs.adoptAndAppend(dg)
del gs
del dg
s = osim.ScaleSet()
o = osim.Scale()
s.adoptAndAppend(o)
del s
del o
s = osim.ForceSet()
o = osim.BushingForce()
s.adoptAndAppend(o)
del s
del o
cs = osim.ControllerSet()
csc = osim.PrescribedController()
cs.adoptAndAppend(csc)
del cs
del csc
s = osim.ContactGeometrySet()
o = osim.ContactHalfSpace()
s.adoptAndAppend(o)
del s
del o
s = osim.AnalysisSet()
o = osim.MuscleAnalysis()
s.adoptAndAppend(o)
del s
del o
s = osim.ControlSet()
o = osim.ControlLinear()
s.adoptAndAppend(o)
del s
del o
s = osim.MarkerSet()
o = osim.Marker()
s.adoptAndAppend(o)
del s
del o
s = osim.BodySet()
o = osim.Body()
s.adoptAndAppend(o)
del s
del o
s = osim.BodyScaleSet()
o = osim.BodyScale()
s.adoptAndAppend(o)
del s
del o
s = osim.CoordinateSet()
o = osim.Coordinate()
s.adoptAndAppend(o)
del s
del o
s = osim.JointSet()
o = osim.BallJoint()
s.adoptAndAppend(o)
del s
del o
s = osim.PathPointSet()
o = osim.PathPoint()
s.adoptAndAppend(o)
del s
del o
s = osim.IKTaskSet()
o = osim.IKMarkerTask()
s.adoptAndAppend(o)
del s
del o
s = osim.MarkerPairSet()
o = osim.MarkerPair()
s.adoptAndAppend(o)
del s
del o
s = osim.MeasurementSet()
o = osim.Measurement()
s.adoptAndAppend(o)
del s
del o
# TODO
# s = osim.ProbeSet()
# o = osim.Umberger2010MuscleMetabolicsProbe()
# s.adoptAndAppend(o)
# del s
# del o
s = osim.ConstraintSet()
a = osim.Model()
body = osim.Body('body', 1.0, osim.Vec3(0, 0, 0), osim.Inertia(0, 0, 0))
loc_in_parent = osim.Vec3(0, -0, 0)
orient_in_parent = osim.Vec3(0, 0, 0)
loc_in_body = osim.Vec3(0, 0, 0)
orient_in_body = osim.Vec3(0, 0, 0)
joint = osim.WeldJoint("weld_joint", a.getGroundBody(), loc_in_parent,
orient_in_parent, body, loc_in_body,
orient_in_parent)
a.addBody(body)
constr = osim.ConstantDistanceConstraint()
constr.setBody1ByName("ground")
constr.setBody1PointLocation(osim.Vec3(0, 0, 0))
constr.setBody2ByName("body")
constr.setBody2PointLocation(osim.Vec3(1, 0, 0))
constr.setConstantDistance(1)
s.adoptAndAppend(constr)
TimeArray.set(1, final_time)
# The static pose weights will be used to adjust the markers position in
# the model from a static pose. The weights of the markers depend of the
# confidence you have on its position.In this example, all marker weight
# are fixed to one.
scaleTool.getMarkerPlacer().setApply(1) # Ajustement placement de marqueurs(true or false)
scaleTool.getMarkerPlacer().setStaticPoseFileName(TRC_file) # trc files for adjustements(usually the same as static)
scaleTool.getMarkerPlacer().setTimeRange(TimeArray) # Time range
scaleTool.getMarkerPlacer().setOutputModelFileName(scaled_MM_path2)
scaleTool.getMarkerPlacer().setOutputMarkerFileName(XML_markers_path_move)
scaleTool.getMarkerPlacer().setMaxMarkerMovement(-1.0)
measurementTemp = osim.Measurement()
ikMarkerTaskTemp = osim.IKMarkerTask()
for i in range(0, markerList.shape[0]):
ikMarkerTask = ikMarkerTaskTemp.clone()
ikMarkerTask.setName(markerList[i]) # Name of the markers
ikMarkerTask.setApply(1)
ikMarkerTask.setWeight(1)
scaleTool.getMarkerPlacer().getIKTaskSet().adoptAndAppend(ikMarkerTask)
# Create the subject Scale Tool XML file
scaleTool.printToXML(XML_ST_file)
print('XML files : ' + XML_ST_file + ' created')
path, filename = os.path.split(TRC_file)
filename, ext = os.path.splitext(filename)
MOT_file = 'MOT\\' + filename + '.mot' # Path to the output .MOT file that will be created and contain the IK results
XML_IK_file = 'XML\\' + filename + '_IK.xml' # Path to the IK XML file that will be created
# Marker Data
markerData = osim.MarkerData(TRC_file)
initial_time = markerData.getStartFrameTime()
final_time = markerData.getLastFrameTime()
# Set the IK tool
ikTool = osim.InverseKinematicsTool(XML_generic_IK_path)
ikTool.setModel(osimModel)
ikTool.setName(filename + ext)
ikTool.setMarkerDataFileName(TRC_file)
ikTool.setStartTime(initial_time)
ikTool.setEndTime(final_time)
ikTool.setOutputMotionFileName(MOT_file)
# Set the ikTool with the MarkerTask
for j in range(0, markerList.shape[0]):
ikMarkerTask = osim.IKMarkerTask()
ikMarkerTask.setName(markerList[j])
ikMarkerTask.setApply(1)
ikMarkerTask.setWeight(markerWeight[j])
ikTool.getIKTaskSet().adoptAndAppend(ikMarkerTask)
# Create the IK XML file
ikTool.printToXML(XML_IK_file)
ikTool.run()
def setup_IK_xml(trial: str, model: str, directory: str, time_range: list, marker_names: list):
'''
Rewrites the IK setup xml file for a new trial
Inputs: trial: trial name, e.g., "_12Mar_ss_12ms_01"
model: model name, e.g., "AB08"
directory: output directory name
time_range: start and end times
marker_names: list of the markers names which we are using
'''
# Create an instance of the inverse kinematics tool
IK_tool = osim.InverseKinematicsTool()
# Set the name of the tool
IK_tool.setName(model)
# Set the input and results directory
IK_tool.setInputsDir(directory + "\\" + model + "\\" + trial)
IK_tool.setResultsDir(directory + "\\" + model + "\\" + trial)
# Set the time range, NOTE: Must be a double (np.float64)
IK_tool.setStartTime(np.float64(time_range[0]))
IK_tool.setEndTime(np.float64(time_range[-1]))
# Set the marker file
marker_file_name = directory + "\\" + model + "\\" + trial + "\\" + trial + ".trc"
IK_tool.setMarkerDataFileName(marker_file_name)
# Set the coordinate file
coordinate_file_name = ''
IK_tool.setCoordinateFileName(coordinate_file_name)
# Set the output motion file
output_file_name = directory + "\\" + model + "\\" + trial + "\\" + trial + "IKResults.mot"
IK_tool.setOutputMotionFileName(output_file_name)
''' Add markers and set weighting '''
# List of bony anatomical landmarkers to give high weighting
bony_landmarks = ['LMMAL','RMMAL','LLMAL','RLMAL','LASI','RASI','LPSI','RPSI']
# Create IKTaskSet
IK_task_set = IK_tool.getIKTaskSet()
# Assign markers and weights
for marker in marker_names:
IK_marker_task = osim.IKMarkerTask()
IK_marker_task.setName(marker)
if marker in bony_landmarks:
IK_marker_task.setApply(True)
IK_marker_task.setWeight(10)
else:
IK_marker_task.setApply(True)
IK_marker_task.setWeight(1)
IK_task_set.cloneAndAppend(IK_marker_task)
''' Write changes to an XML setup file '''
xml_setup_path = directory + "\\" + model + "\\" + trial + "\\" + trial + "IKSetup.xml"
IK_tool.printToXML(xml_setup_path)
''' Temporary fix for setting model name using XML parsing '''
dom = minidom.parse(xml_setup_path)
dom.getElementsByTagName("model_file")[0].firstChild.nodeValue = directory + "\\" + model + "\\" + model + ".osim"
with open(xml_setup_path, 'w') as xml_file:
dom.writexml(xml_file, addindent='\t', newl='\n', encoding='UTF-8')
