R/matrix_retobj.R

In yinscapital/retina-analysis-reference: Tools for plotting and analyzing vertebrate retinas.

##' @title Extract a matrix from a retinal object
##' @description
##' You can decide how much to rotate the retina before returning the matrix. You can also pass arguments to the polar plotter.
##' @param retina_object A retina
##' @param rotation in degrees. By default 0; set to zero rotation.
##' @param n the number by which to divide the matrix by. Useful when generating partial averages.
##' @param reflect logical, by default it is TRUE, in order to view the retina from outside the eye (rather than from within.)
##' @param ... Other arguments passed from other functions
##' @return mat A square matrix of the evaluated retina fit.
##' @author Brian Cohn \email{brian.cohn@@usc.edu} and Lars Schmitz
##' @export
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE, 
    ...) {
    x2 <- retina_object$azimuthal_data.datapoints[[1]]$x
    y2 <- retina_object$azimuthal_data.datapoints[[1]]$y
    z2 <- retina_object$azimuthal_data.datapoints[[1]]$z
    
    # Rotation
    ori <- c(-90, 90, rotation)
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[, 
        1], projection = "azequidistant", orientation = ori)
    x2 <- az$x  #overwirte old value
    ifelse(reflect, x2 <- (-1 * x2), message(""))
    y2 <- az$y  #overwrite old value
    
    # Fitting models
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE, 
        outer.radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]], 
        ...)
    MAT <- map2fit[[2]]$z
    # reflect the eye
    return(MAT/n)
}