make.colormesh.dataset: Combine metadata with calibrated colormesh data for analysis

In J0vid/Colormesh: Functions for Processing Image Color Data for Statistical Analysis

Description

Combine metadata with calibrated colormesh data for analysis

Usage

make.colormesh.dataset(
  df,
  specimen.factors,
  use.perimeter.data = F,
  write2csv = NULL
)

Arguments

df	A calibrated.mesh.colors object (generated from rgb.calibrate) or mesh.colors object (generated from rgb.measure)
specimen.factors	The covariate data that you want to combine with the calibrated data
use.perimeter.data	If TRUE, we will return the color values for the perimeter landmarks as well as the interior landmarks.
write2csv	A directory is to write a csv to, if desired

Value

The function will return a dataframe of specimen data (inherits the original column names) and landmark x & y values along with calibrated RGB values.

Examples

#covariate data and consensus lms
specimen.factors <- read.csv(system.file("extdata", "specimen_factors.csv", package = "Colormesh"), header = F)
consensus <- tps2array(system.file("extdata", "consensus_LM_coords.TPS", package = "Colormesh"))
test.image <- image_reader(paste0(path.package("Colormesh"),"/extdata/unwarped_images/"), "GPLP_unw_001.jpg")
delaunay.map <- tri.surf(consensus, point.map = c(1,8:17,2, 18:19,3,20:27,4, 28:42,5,43:52,6,53:54,7,55:62), 3, test.image)

rgb.test <- rgb.measure(imagedir = paste0(path.package("Colormesh"),"/extdata/unwarped_images/"), image.names = specimen.factors[,2], delaunay.map = delaunay.map, linearize.color.space = F)
cm.dataset <- make.colormesh.dataset(rgb.test, specimen.factors)

J0vid/Colormesh documentation built on Feb. 4, 2022, 1:33 a.m.