Processing Mocap Data

This documentation is WIP:

Nimble is focused on human motion and biomechanics analysis. We include many utilities that will be familiar to biomechanics practitioners: loading C3D files, loading multiple OpenSim formats, and the algorithms that power AddBiomechanics.

To load C3D files, check out:

class nimblephysics.biomechanics.C3DLoader

static debugToGUI(file: nimblephysics_libs._nimblephysics.biomechanics.C3D, server: nimblephysics_libs._nimblephysics.server.GUIWebsocketServer) → None

static fixupMarkerFlips(c3d: nimblephysics_libs._nimblephysics.biomechanics.C3D) → None

static loadC3D(uri: str) → nimblephysics_libs._nimblephysics.biomechanics.C3D

To run some heuristics to clean up the C3D data, you can use:

class nimblephysics.biomechanics.MarkerFixer

static generateDataErrorsReport(immutableMarkerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], dt: float) → nimblephysics_libs._nimblephysics.biomechanics.MarkersErrorReport

This will return you an object with a field markerObservationsAttemptedFixed

class nimblephysics.biomechanics.MarkersErrorReport

property info

property markerObservationsAttemptedFixed

property warnings

For OpenSim files, check out:

nimblephysics.biomechanics.OpenSimParser: alias of <module ‘nimblephysics_libs._nimblephysics.biomechanics.OpenSimParser’>

This class is the basis of the kinematic fit (just bone scaling, marker offsets, and IK, no dynamics) for AddBiomechanics.

class nimblephysics.biomechanics.MarkerFitter

addZeroConstraint(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, name: str, loss: Callable[[nimblephysics_libs._nimblephysics.biomechanics.MarkerFitterState], float]) → None

autorotateC3D(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, c3d: nimblephysics_libs._nimblephysics.biomechanics.C3D) → None

checkForEnoughMarkers(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]]) → bool

checkForFlippedMarkers(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], init: nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization, report: nimblephysics_libs._nimblephysics.biomechanics.MarkersErrorReport) → bool

debugTrajectoryAndMarkersToGUI(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, server: nimblephysics_libs._nimblephysics.server.GUIWebsocketServer, init: nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], forcePlates: List[nimblephysics_libs._nimblephysics.biomechanics.ForcePlate] = None, goldOsim: nimblephysics_libs._nimblephysics.biomechanics.OpenSimFile = None, goldPoses: numpy.ndarray[numpy.float64[m, n]] = array([], shape=(0, 0), dtype=float64)) → None

findJointCenters(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, initializations: nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization, newClip: List[bool], markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]]) → None

generateDataErrorsReport(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], dt: float) → nimblephysics_libs._nimblephysics.biomechanics.MarkersErrorReport

getInitialization(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], newClip: List[bool], params: nimblephysics_libs._nimblephysics.biomechanics.InitialMarkerFitParams = InitialMarkerFitParams(numBlocks=12)) → nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization

getMarkerIsTracking(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, marker: str) → bool

getNumMarkers(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter) → int

optimizeBilevel(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], initialization: nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization, numSamples: int, applyInnerProblemGradientConstraints: bool = True) → nimblephysics_libs._nimblephysics.biomechanics.BilevelFitResult

static pickSubset(markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], subsetSize: int) → List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]]

removeZeroConstraint(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, name: str) → None

runKinematicsPipeline(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], newClip: List[bool], params: nimblephysics_libs._nimblephysics.biomechanics.InitialMarkerFitParams, numSamples: int = 20, skipFinalIK: bool = False) → nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization

runMultiTrialKinematicsPipeline(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerTrials: List[List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]]], params: nimblephysics_libs._nimblephysics.biomechanics.InitialMarkerFitParams, numSamples: int = 50) → List[nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization]

runPrescaledPipeline(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], params: nimblephysics_libs._nimblephysics.biomechanics.InitialMarkerFitParams) → nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization

saveTrajectoryAndMarkersToGUI(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, path: str, init: nimblephysics_libs._nimblephysics.biomechanics.MarkerInitialization, markerObservations: List[Dict[str, numpy.ndarray[numpy.float64[3, 1]]]], frameRate: int, forcePlates: List[nimblephysics_libs._nimblephysics.biomechanics.ForcePlate] = None, goldOsim: nimblephysics_libs._nimblephysics.biomechanics.OpenSimFile = None, goldPoses: numpy.ndarray[numpy.float64[m, n]] = array([], shape=(0, 0), dtype=float64)) → None

setAnatomicalMarkerDefaultWeight(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setAnthropometricPrior(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, prior: nimblephysics_libs._nimblephysics.biomechanics.Anthropometrics, weight: float = 0.001) → None

setCustomLossAndGrad(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, loss: Callable[[nimblephysics_libs._nimblephysics.biomechanics.MarkerFitterState], float]) → None

setDebugJointVariability(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, debug: bool) → None

setDebugLoss(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, debug: bool) → None

setIgnoreJointLimits(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, ignore: bool) → None

setInitialIKMaxRestarts(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, starts: int) → None

setInitialIKSatisfactoryLoss(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, loss: float) → None

setIterationLimit(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, iters: int) → None

setMarkerIsTracking(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, marker: str, isTracking: bool = True) → None

setMaxAxisWeight(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setMaxJointWeight(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setMaxMarkerOffset(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, offset: float) → None

setMinAxisFitScore(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, score: float) → None

setMinJointVarianceCutoff(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, cutoff: float) → None

setMinSphereFitScore(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, score: float) → None

setRegularizeAllBodyScales(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setRegularizeAnatomicalMarkerOffsets(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setRegularizeIndividualBodyScales(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setRegularizeTrackingMarkerOffsets(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setTrackingMarkerDefaultWeight(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, weight: float) → None

setTrackingMarkers(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter, trackingMarkerNames: List[str]) → None

setTriadsToTracking(self: nimblephysics_libs._nimblephysics.biomechanics.MarkerFitter) → None