A function that produces a three-dimensional rendering of surface DNE. The DNE function will identify amount of change in mesh face normal orientation between adjacent faces, and associate these values (adjusted for face size) to each face on the surface. It must be performed prior to using the DNE3d function.
DNE3d(
DNE_File,
setRange = c(0, 0),
logColors = TRUE,
edgeMask = TRUE,
outlierMask = TRUE,
legend = TRUE,
legendScale = 1,
leftOffset = 1,
fieldofview = 0,
fileName = NA,
binary = FALSE
)An object that stores the output of the DNE function
User-defined range for plotting color scheme, see Details
Logical that log transforms the color scheme
Logical that colors edge faces black to indicate their lack of contribution to the total Dirichlet normal energy
Logical that colors outlier faces dark gray to indicate their lack of contribution to the Dirichlet normal energy
Logical indicating whether or not a legend should be displayed
numeric value setting the relative size of the legend, similar in function to cex
numeric value between -1 and 1 setting the degree of offset for the plotted surface to the left; larger values set further to left while 0 is centered
Passes an argument to par3d changing the field of view in degrees of the resulting surface plot
String indicating a name to save the plotted surface to as a *.ply file; default of 'NA' will not save a file
Logical indicating whether or not the saved surface plot should be binary, passed to vcgPlyWrite
This function creates a heat map on the mesh surface corresponding to the Dirichlet normal energy of each face calculated by the DNE function. Hottest colors represent highest normal energy values.
Dirichlet normal energies for the faces of a mesh surface tend to be positively skewed, with a small proportion of the faces contributing much of the total energy for the surface. When logColors is enabled the function colorizes based on the log-transformed Dirichlet normal energies, allowing for finer visual discriminiation between faces near the mode of the energy per face distribution. Disabling logColors will display the untransformed Dirichlet normal energies.
The legend reflects the other arguments chosen by the user, including log transformation, and whether or not an outlier or edge mask is enabled.
By default, the function sets the lowest Dirichlet normal energy calculated among all faces to a cool color and the highest normal energy calculated among all faces to red, and then colors the remaining faces on a continuous color spectrum between these two end points using either absolute or log-transformed Dirichlet normal energy values (depending on the value of logColors). Since the scale is relative to the energies of the input surface, visual comparisons cannot directly be made between multiple plots of different surfaces. The setRange argument allows users to define the minimum and maximum of the plotting color scheme and use it in multiple plots. This enables the direct comparison of different surfaces to one another with red equal to the user-defined maximum and a cool color equal to the user-defined minimum. The user should choose reasonable bounds for the maximum and minimum that are near the maximum and minimum Dirichlet normal energies calculated for their surfaces. setRange will not accept negative values.
The leftOffset value sets how far to the left the surface will appear, intended to help avoid overlap with the legend. A value of 0 for this argument will center the surface in the plotting window and negative values will shift it to the right.
legendScale sets the relative size of the legend, analogous to the cex argument of par graphics.
fieldofview is set to a default of 0, which is an isometric parallel projection. Raising it corresondingly increases the amount of obliquity used to render the surface in the plotting window, up to a maximum of 179 degrees.
The plotted, colorized surface can be saved as a *.ply to the working directory by changing the fileName argument from NA to a string (e.g., "DNEPlot"). The resultant ply file can be opened and manipulated in other 3D visualizing programs, such as MeshLab, but will NOT retain its legend (a background of the plotting window). To retain the legend, the user is encouraged to utilize the snapshot3d function. The binary argument saves a file in ascii format by default, which is supported by more 3D visualization software than is binary. However, binary files will be considerably smaller.
# NOT RUN {
DNE_output <- DNE(Tooth)
DNE3d(DNE_output)
# }
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