Usage
slider3d(dat.array, SMvector, outlines = NULL, surp = NULL,
sur.path = "sur", sur.name = NULL, meshlist = NULL, ignore = NULL,
sur.type = "ply", tol = 1e-05, deselect = FALSE, inc.check = TRUE,
recursive = TRUE, iterations = 0, initproc = TRUE, speed = TRUE,
pairedLM = 0, weights = NULL, mc.cores = parallel::detectCores(),
fixRepro = TRUE)
Arguments
dat.array
Input k x m x n real array, where k is the number of
points, m is the number of dimensions, and n is the sample size. Ideally the
dimnames[[3]] vector contains the names of the surface model (without file
extension) - e.g. if the model is named "surface.p
SMvector
A vector containing the landmarks on the curve(s) and
surfaces that are allowed to slide
outlines
A vector (or if threre are several curves) a list of vectors
(containing the rowindices) of the (Semi-)landmarks forming the curve(s) in
the successive position on the curve - including the beginning and end
points, that are not allowed to slide.
surp
A vector containing Semilandmarks positioned on surfaces.
sur.path
Path to the surface models (e.g. ply, obj, stl files)
sur.name
character vector: containing the filenames of the
corresponding surfaces - e.g. if the dat.array[,,i] belongs to
surface_i.ply, sur.name[i] would be surface_i.ply. Only necessary if
dat.array does not contain surface names.
meshlist
list containing triangular meshes of class 'mesh3d', for
example imported with mesh2ply or file2mesh in
the same order as the specimen in the array (see e ignore
vector containing indices of landmarks that are to be ignored.
Indices of outlines/surfaces etc will be updated automatically.
sur.type
character:if all surfaces are of the same file format and
the names stored in dat.array, the file format will be specified here.
tol
numeric: Threshold for convergence in the sliding process
deselect
Logical: if TRUE, the SMvector is interpreted as those
landmarks, that are not allowed to slide.
inc.check
Logical: if TRUE, the program stops when convergence
criterion starts increasing and reports result from last iteration.
recursive
Logical: if TRUE, during the iterations of the sliding
process, the outcome of the previous iteration will be used. Otherwise the
original configuration will be used in all iterations.
iterations
integer: select manually the max. number of iterations
that will be performed during the sliding process (usefull, when there is
very slow convergence). 0 means iteration until convergence.
initproc
requests initial Procrustes fit before sliding.
speed
Logical: if TRUE, only a partial procrustes fit will be
performed - this is faster and can be required, when large samples are
processed.
pairedLM
A X x 2 numeric matrix with the indices of the rows
containing paired Landmarks. E.g. the left column contains the lefthand
landmarks, while the right side contains the corresponding right hand
landmarks. - This will ideally create symmetric mean to get r
weights
vector: assign a weight to each landmark: the smaller the
value is, the less it will be affected by sliding. 0 = fix. This is highly
experimental!!!
mc.cores
integer: determines how many cores to use for the
computation. The default is autodetect. But in case, it doesn't work as
expected cores can be set manually. In Windows, parallel processing is
disabled.
fixRepro
logical: if TRUE, fix landmarks will also be
projected onto the surface. If you have landmarks not on the surface, select
fixRepro=FALSE