def _load_virtual_markers():
markers = {}
marker_coords = {}
if opensim_version == 4.0:
_dummy_model = opensim.Model()
_osim_markerset = opensim.MarkerSet(_dummy_model, MARKERSET_PATH)
else:
_osim_markerset = opensim.MarkerSet(MARKERSET_PATH)
for mi in range(_osim_markerset.getSize()):
osim_marker = _osim_markerset.get(mi)
# create a copy because the markerset and its marers only exists
# in the function
_v = opensim.Vec3()
osim_marker.getOffset(_v)
offset = np.array([_v.get(i) for i in range(3)])
marker = Marker(
name=osim_marker.getName(),
bodyname=osim_marker.getBodyName(),
offset=offset,
)
markers[marker.name] = marker
marker_coords[marker.name] = marker.offset
return markers, marker_coords
def check_tasks(self):
"""Lists tasks that are <apply>'d for markers that either
don't exist in the model or are not in the TRC file.
Also lists tasks for which there is data, but that are either not in
the model or do not have an IK task.
"""
scale = osm.ScaleTool(self.setup_fpath)
tasks = scale.getMarkerPlacer().getIKTaskSet()
trc = util.TRCFile(self.marker_trajectories_fpath)
trc_names = trc.marker_names
model = osm.Model(self.generic_model_fpath)
markerset = osm.MarkerSet(self.prescale_markerset_fpath)
# Markers with IK tasks but without data.
# ---------------------------------------
markers_without_data = []
for i in range(tasks.getSize()):
task = tasks.get(i)
name = task.getName()
applied = task.getApply()
if applied:
if (not name in trc_names) or (not markerset.contains(name)):
if task.getConcreteClassName() != 'IKCoordinateTask':
markers_without_data.append(name)
if markers_without_data != [] and not self.ignore_nonexistant_data:
raise Exception('There are IK tasks for the following markers, '
'yet data does not exist for them: {}'.format(
markers_without_data))
del name
# Markers for which there is data but they're not specified elsewhere.
# --------------------------------------------------------------------
unused_markers = []
for name in trc.marker_names:
if (not markerset.contains(name)) or (not tasks.contains(name)):
unused_markers.append(name)
if unused_markers != []:
raise Exception("You have data for the following markers, but "
"you are not using them in Scale's IK: {}".format(
unused_markers))
# No data for these markers in the model or prescale markerset.
# -------------------------------------------------------------
excess_model_markers = []
for im in range(markerset.getSize()):
name = markerset.get(im).getName()
if not tasks.contains(name):
excess_model_markers.append(name)
if excess_model_markers != []:
raise Exception("The following model markers do not have tasks or "
"experimental data: {}".format(excess_model_markers))
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)
def scale():
import os
import opensim as osim
import shutil
import directories
# Global Directories
allDir = list(directories.main(directories))
parentDir = allDir[0]
paramsDir = allDir[1]
genericDir = allDir[2]
subID = allDir[4]
subResultsDir = allDir[5]
# Get generic Model
genericModel = "gait2354_LockedJoints.osim"
genericModelFile = genericDir + "/" + genericModel
if not os.path.exists(subResultsDir):
os.mkdir(subResultsDir)
# generic input XML files
scaleSetupFull = paramsDir + "/setupScale.xml"
markerSetFull = paramsDir + "/markerSet.xml"
# Make scale directory if non-existent
scaleResultsDir = subResultsDir + "/scale"
if os.path.exists(scaleResultsDir):
shutil.rmtree(scaleResultsDir, ignore_errors=True)
if not os.path.exists(scaleResultsDir):
os.mkdir(scaleResultsDir)
# Output XML Files
outputScaleFile = subID + "_scaleFactors.xml"
adjustedMarkerSet = subID + "_movedMarkers.xml"
# Output Model Files
outputModelFile = subID + ".osim"
# Input Data Files
dataFiles = parentDir + "/data/osDemo"
staticMarkerFile = "subject01_static.trc"
staticMarkerFull = dataFiles + "/" + staticMarkerFile
shutil.copy(staticMarkerFull, scaleResultsDir + "/" + staticMarkerFile)
# Output Data Files
staticCoordinates = subID + "_staticCoordinates.mot"
# Subject Measurements
subjectMass = 72.60000000
# Load Model
aModel = osim.Model(genericModelFile)
aModel.setName(subID)
# Initialize System
aModel.initSystem()
aState = aModel.initSystem()
# Add Marker Set
newMarkers = osim.MarkerSet(markerSetFull)
aModel.replaceMarkerSet(aState, newMarkers)
# Re-initialize State
aState = aModel.initSystem()
# Get Time Array for .trc file
markerData = osim.MarkerData(staticMarkerFull)
# Get Initial and Final Time
initial_time = markerData.getStartFrameTime()
final_time = markerData.getLastFrameTime()
# Create an array double and apply the time range
TimeArray = osim.ArrayDouble()
TimeArray.set(0, initial_time)
TimeArray.set(1, final_time)
# Scale Tool
scaleTool = osim.ScaleTool(scaleSetupFull)
scaleTool.setSubjectMass(subjectMass)
# GenericModelMaker-
# Tell scale tool to use the loaded model
scaleTool.getGenericModelMaker().setModelFileName(genericDir + "/" +
genericModel)
# # Set the Marker Set file (incase a markerset isnt attached to the model)
scaleTool.getGenericModelMaker().setMarkerSetFileName(markerSetFull)
# ModelScaler-
# Whether or not to use the model scaler during scale
scaleTool.getModelScaler().setApply(1)
# Set the marker file (.trc) to be used for scaling
scaleTool.getModelScaler().setMarkerFileName("/" + staticMarkerFile)
# set a time range
scaleTool.getModelScaler().setTimeRange(TimeArray)
# Indicating whether or not to preserve relative mass between segments
scaleTool.getModelScaler().setPreserveMassDist(1)
# Name of OpenSim model file (.osim) to write when done scaling.
scaleTool.getModelScaler().setOutputModelFileName("")
# Filename to write scale factors that were applied to the unscaled model (optional)
scaleTool.getModelScaler().setOutputScaleFileName(outputScaleFile)
# Run model scaler Tool
scaleTool.getModelScaler().processModel(aState, aModel, scaleResultsDir,
subjectMass)
# initialize
aState = aModel.initSystem()
# # Marker Placer
# # Whether or not to use the model scaler during scale
scaleTool.getMarkerPlacer().setApply(1)
# # Set the marker placer time range
scaleTool.getMarkerPlacer().setTimeRange(TimeArray)
# # Set the marker file (.trc) to be used for scaling
scaleTool.getMarkerPlacer().setStaticPoseFileName("/" + staticMarkerFile)
# # Return name to a variable for future use in functions
scaledAdjustedModel = scaleTool.getMarkerPlacer().setOutputModelFileName(
"/" + outputModelFile)
# # Set the output motion filename
scaleTool.getMarkerPlacer().setOutputMotionFileName("/" +
staticCoordinates)
# # Set the output xml of the marker adjustments
scaleTool.getMarkerPlacer().setOutputMarkerFileName("/" +
adjustedMarkerSet)
# # Maximum amount of movement allowed in marker data when averaging
scaleTool.getMarkerPlacer().setMaxMarkerMovement(-1)
# # Run Marker Placer
scaleTool.getMarkerPlacer().processModel(aState, aModel, scaleResultsDir)
scaleTool.printToXML(scaleResultsDir + "/" + subID + "_setupScale.xml")
# Clear Terminal
os.system('cls' if os.name == 'nt' else 'clear')
shutil.copy(scaleResultsDir + "/" + outputModelFile, subResultsDir)
return ()
['femur_l'], ['tibia_l'],
['patella_l'], ['talus_l'], ['calcn_l'], ['toes_l'],
['torso'], ['torso'],
['humerus_r'], ['ulna_r'], ['radius_r'], ['hand_r'],
['humerus_l'], ['ulna_l'], ['radius_l'], ['hand_l']])
nBody = bodyNames.shape[0]
# The first step is to create an XML file with all the information used to scale the model
# Load the generic musculoskeletal model
osimModel = osim.Model(generic_MM_Path)
state = osimModel.initSystem()
# Add a marker set to the model
markerSet = osim.MarkerSet(XML_markers_path)
osimModel.replaceMarkerSet(state, markerSet)
state = osimModel.initSystem()
# Get the marker data from a .trc file
markerData = osim.MarkerData(TRC_file)
initial_time = markerData.getStartFrameTime()
final_time = markerData.getLastFrameTime()
TimeArray = osim.ArrayDouble() # Time range
TimeArray.set(0,initial_time)
TimeArray.set(1,final_time)
# Scale Tool
scaleTool = osim.ScaleTool(XML_generic_ST_path)
scaleTool.setName('Subject') # Name of the subject
scaleTool.setSubjectMass(70) # Mass of the subject