main_bjii4t <- function(path_to_diagram_retina){
LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.
RESOLUTION_var <- 500 #Plot width in pixels
#defining coordinates
IJ <-data.frame(maxX = 1210,
maxY = -46,
minX = 72,
minY = -928,
deltaX = (1210-72)/20,
deltaY = (928-46)/15)
#assembling the retina object
my_retina <- retina_object(
path = path_to_diagram_retina,
#Eye Measurements from dissection
ED = 8.5, #Eye diameter (mm)
AL = 8, #Eye axial length (mm)
LD = 5, #Eye lens diameter (mm)
#Stereology Parameters
height = 45 ,# height of the counting frame in microns
width = 45, # width of the counting frame in microns
#Plotting Parameters
lambda = LAMBDA_var, #see fields::Tps for more information
extrapolate = TRUE , #Predicts densities to the equator.
spatial_res = RESOLUTION_var,
rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.
plot_suppress=TRUE,
#ImageJ Datapoint Calibration Measurements
IJcoords = IJ)
#plot
retinaplot(my_retina)
findPeak <- function(my_retina){
coord <- my_retina$trimmed_data
peak_temp <- coord[which.max(coord$z),]
peak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])
return(peak)
}
message(findPeak(my_retina))
#optional arguments
#lambda=0.001
#polynomial_m=2
#rotation=30
#e.g. rotate map by 30 degrees: retinaplot(my_retina, rotation=30)
}
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