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=detectCores(),
fixRepro=TRUE, ignore.stdout = FALSE)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
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.
speed
Logical: if TRUE, only a partial procrustes fit will be performed - this is faster and can be required, when large samples are processed.
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.
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
ignore.stdout
logical: supress console messages from system
calls.