Below is an overview of the steps one needs to take in order to
digitize fixed landmarks, and semilandmarks on surfaces, in
geomorph using a 3D surface object or a mesh3d object. In its
simplest version, this involves the following geomorph
functions:
1. Digitizing fixed landmarks
We will be using the scallop example ply file included in geomorph,
so let´s load this first:
## Loading required package: RRPP
## Loading required package: rgl
## Loading required package: Matrix
data("scallopPLY")
my.ply <- scallopPLY$ply
Let´s also make sure that our working directory is set to an adequate
location. This is particularly relevant for 3D digitizing, as throughout
the process, files with the digitized landmark coordinates, as well as
the template we will create for replicating 3D surface semilandmarks
across specimens, will be stored and automatically read in by functions.
For this example, we will work in the subdirectory
~/example3D/, so go ahead and make sure your working directory
is set to a folder with that name.
Once a ply file is imported (usually using read.ply),
one will first digitize the fixed landmarks using
digit.fixed(). Note that this is an interactive function,
so you will need to replicate these steps in your R console to be able
to see the full version of this example. We will digitize 5 fixed
landmarks.
fixed.lms1 <- digit.fixed(spec = my.ply, fixed = 5)
PRACTICAL ADVICE: Note that landmark selection on
the 3dmesh is done by choosing the point of the scan closest to where
you click with your mouse. This means that occasionally points may
appear to “go through to the other side of the structure”, especially if
your initial point cloud is not very dense. To solve this issue, try
rotating the structure to find a better view for digitizing, or zooming
in such that you can click close to one of the scan points (these are
visible as tiny grey points when you zoom in).
Once you have completed the digitizing of the specimen, your
digitizing device should look something like this:
Now have a look at your working directory. A new file has been
created, called my.ply.nts. This contains the coordinates of the
digitized 3D fixed landmarks for your specimen.
Now let´s add a second specimen. For the example, we will just
replicate the ply file of the first one, but with a different name. Go
ahead and digitize the same five landmarks on this second specimen. A
second nts file, called my.ply.2.nts is now created in your working
directory.
my.ply.2 <- scallopPLY$ply
fixed.lms2 <- digit.fixed(my.ply.2, 5)
NOTE: If one wishes to continue and sample also
surface semilandmarks, this step can be performed together with the
acquisition of surface sliders (see below).
2. Sampling surface semilandmarks
2A: Building the template
Now that the fixed landmarks have been digitized, we can continue and
sample surface sliding semilandmarks. We will use the first specimen as
the reference from which to build a template, which will then be used to
sample these semilandmarks across all specimens in our sample. This is
done using the function buildtemplate. We will sample 100
surface semilandmarks.
surf.pts1 <- buildtemplate(spec = my.ply, fixed = fixed.lms1, surface.sliders = 100)
NOTE: One may want to import fixed landmarks already
digitized and saved as an nts file. This can be easily done using
readland.nts, but remember that the input to the argument
fixed above is a matrix, so you will need to combine that to
two.d.array to obtain a 2d-matrix with the coordinates of the
fixed landmarks.
When running buildtemplate you will see the sampled
surface semilandmarks in an rgl device, which will look (3D rotations
notwithstanding) more or less like this:
Note that a txt file containing the coordinates of the sampled
surface semilandmarks has been created in your working directory, with
the name template.txt. Also, note that the file my.ply.nts has been
modified, and it now contains the coordinates of the fixed landmarks AND
surface semilandmarks. Finally, a csv file containing the index of
sliding semilandmarks has been created, and can be read for use with the
argument surfaces of gpagen.
NOTE: One may choose to perform steps 1. and 2.
above at once for the reference specimen. In that case, the argument
fixed of buildtemplate would indicate the number
of fixed landmarks to be digitized (i.e. 5 in our example).
2B: Sampling surface semilandmarks in subsequent specimens
Now that the template has been created, we will use it to sample
homologous surface semilandmarks in the second specimen in our sample.
This is done using the function digitsurface.
surf.pts2 <- digitsurface(spec = my.ply.2, fixed = fixed.lms2)
Once the surface semilandmarks have been sampled, you will see a
graph with their position in specimen 2.
As before, the file my.ply.2.nts has been modified, and it now
contains the coordinates of the fixed landmarks AND surface
semilandmarks for specimen 2.
NOTE: Same as for building the template, one may
choose to simultaneously digitize fixed landmarks and sample surface
semilandmarks using the template.