geomorph (version 3.0.2)

digit.fixed: Digitize 3D landmarks on mesh3d object

Description

An interactive function to digitize three-dimensional (3D) landmarks. Input for the function is either a matrix of vertex coordinates defining a 3D surface object or a mesh3d object as obtained from read.ply.

Usage

digit.fixed(spec, fixed, index = FALSE, ptsize = 1, center = TRUE)

Arguments

spec

An object of class shape3d/mesh3d, or matrix of 3D vertex coordinates

fixed

Numeric The number landmarks (fixed, and curve sliders if desired)

index

Logical Whether selected landmark addresses should be returned (internal use only)

ptsize

Numeric Size to plot the mesh points (vertices), e.g. 0.1 for dense meshes, 3 for sparse meshes

center

Logical Whether the object 'spec' should be centered prior to digitizing (default center=TRUE)

Value

Function writes to the working directory an NTS file with the name of the specimen and .nts suffix containing the landmark coordinates. If index=FALSE function returns to the console an n x 3 matrix containing the x,y,z coordinates of the digitized landmarks. If index=TRUE, function returns a list:

selected

a matrix containing the x,y,z coordinates of the digitized landmarks

fix

a matrix of addresses for landmarks that are "fixed" (for internal use)

Details

Function for digitizing "n" three-dimensional landmarks. The landmarks are "fixed" (traditional landmarks). They can be later designated as "curve sliders" (semilandmarks, that will "slide" along curves lacking known landmarks if required. A sliding semi-landmark ("sliders") will slide between two designated points, along a line tangent to the specified curvature, and must be defined as "sliders" using function define.sliders or with similar format matrix made outside R.

For 3D "surface sliders" (surface semilandmarks that slide over a surface) the function digitsurface should be used instead. NOTE: Function centers the mesh before digitizing by default (center=TRUE). If one chooses not to center, specimen may be difficult to manipulate in rgl window.

Digitizing Digitizing is interactive between landmark selection using a mouse (see below for instructions), and the R console. Once a point is selected, the user is asked if the system should keep or discard the selection #'(y/n). If "y", the user is asked to continue to select the next landmark. If "n" the removes the last chosen landmark, and the user is asked to select it again. This can be repeated until the user is comfortable with the landmark chosen.

To digitize with a standard 3-button (PC):

1. the RIGHT mouse button (primary) to select points to be digitized,
2. the LEFT mouse button (secondary) is used to rotate mesh,
3. the mouse SCROLLER (third/middle) is used to zoom in and out.

NOTE: Digitizing functions on MACINTOSH computers using a standard 3-button mice works as specified. Macs using platform specific single button mice, XQuartz must be configured: go to Preferences > Input > tick "Emulate three button mouse":

1. press button to rotate 3D mesh,
2. press button while pressing COMMAND key to select vertex to be used as a landmark,
3. press button while pressing OPTION key to adjust mesh perspective.
4. the mouse SCROLLER or trackpad two finger scroll is used to zoom in an out.

NOTE: there is no pan (translate) functionality in rgl library for all platforms at this time.

See Also

read.ply