Apply a fitted Deformetrica diffeomorphism to 3D points (geodesic shooting)

Flows arbitrary points through the diffeomorphism defined by a fitted registration's control points and initial momenta, by writing a <model-type>Shooting model and calling deformetrica compute.

Usage

deformetrica_shoot(
  x,
  control_points,
  momenta = NULL,
  kernel_width = NULL,
  timepoints = 10L,
  object_type = "Landmark",
  device = c("auto", "cpu", "cuda"),
  deformetrica = NULL,
  workdir = tempfile("dfca_shoot_"),
  flow = FALSE,
  verbose = FALSE
)

Arguments

x: An N x 3 matrix of coordinates, or anything nat::xyzmatrix() accepts.
control_points, momenta: Path to the estimated Deformetrica ...ControlPoints.txt / ...Momenta.txt, or a numeric matrix. Passing the files Deformetrica itself wrote is strongly preferred: it writes momenta with a leading n_subjects n_cp dim header that its own reader expects, so a bare matrix is best-effort only. Alternatively pass a deformetricareg object (from deformetrica_register()) as control_points and leave momenta/kernel_width unset — they are taken from the registration.
kernel_width: Deformation kernel width, in the coordinate units. Larger = stiffer / more global; must match the width the registration was fit with.
timepoints: Number of geodesic integration steps; must match the fit.
object_type: Deformetrica deformable-object-type (default "Landmark").
device: kernel-device: "auto", "cpu" or "cuda".
deformetrica: Optional path to the executable (auto-detected otherwise).
workdir: Working directory for the run (a fresh tempdir by default).
flow: If TRUE, return the whole geodesic flow (every timepoint) as a list of deformed objects (one per timepoint, named tp_00..tp_NN) rather than just the final shape. Useful for animating a warp.
verbose: Show deformetrica output.

Value

By default an N x 3 matrix of deformed coordinates (or a warped object of the input class), in the input units and row order. With flow = TRUE, a list of such objects, one per geodesic timepoint.