The optimization parameters file specifies additional options for the run. It is model dependent. The available options are:
optimization-method-type which can be GradientAscent, ScipyLBFGSor McmcSaem. The default is GradientAscent. The longitudinal atlas and the Bayesian atlas supports all types and the other models support only GradientAscent and ScipyLBFGS.
max-iterations: the maximum number of iterations to run. Default is 100.
max-line-search-iterations: number of line search iterations for the GradientAscent estimator.
convergence-tolerance: a tolerance threshold for premature stopping of the estimation. If the relative decrease of the loss function during an iteration of the estimation of the model is below this threshold, the computations stops.
use-cuda: if On, all computations with kernel type torch will be made on GPU.
number-of-threads: the number of threads to use. Multi-threading is only supported for the deterministic atlas model.
downsampling-factor: a factor by which to downsample internally the images, to speed-up image deformations.
save-every-n-iters: when to periodically save the output. Default is 100. Beware, for large meshes, saving the whole output of a model can be expensive.
use-sobolev-gradient: a smoothing operation on the gradient to update the template. We advise to use it on meshes since it provides a smoother estimated template. Default is On.
initial-step-size: the initial step size for the GradientAscent estimator. Default is 1e-3. If the line search fails, try lower values.
scale-initial-step-size: scales the steps sizes by the squared norm of the gradient for GradientAscent. Default is On.
freeze-template: On if the template is to be kept at its initial value, Off to estimate the template.
freeze-control-points: Off if the control points are to be optimized. Default is On.
memory-length: length of the memory for the ScipyLBFGS estimator. Large values can induce a high memory use. Default is 10.
state-file: if a state-file is specified and the file exists, Deformetrica will attempt to restart the computation from this state file. If it does not exist, Deformetrica will run normally and save the state in this file. If a state-file is not specified, the state will be saved in the output folder under the name pydef-state.p.
use-rk2: A Runge-Kutta 2 scheme is used for integration of the deformation if it is On. A simple Euler scheme is used otherwise. Default is Off.
momenta-proposal-std, onset-age-proposal-std, log-acceleration-proposal-std, sources-proposal-std: standard deviation of the proposal distributions for the McmcSaem algorithm. See Longitudinal Atlas.
freeze-v0, freeze-p0, freeze-modulation-matrix, freeze-time-shift-variance, freeze-log-acceleration-variance, freeze-reference-time, freeze-noise-variance: whether to freeze some of the variables in a longitudinal atlas.