read.age: read.age

In buddekai/AgeReader: Determining the age of fish by reading otoliths

Description

Main function for determining the age of a fish

Usage

read.age(input.dir = NULL, input.file = NULL, user.file.en = NULL,
  user.file.de = NULL, distance = 20, parameter.for.end = NULL,
  parameter.distance.deviation = 2, par.hyaline = 1.1,
  points.to.jump = 10, points.for.reconnecting = 20,
  remove.points.at.end = 25, remove.points.at.beginning = 0, t = 2,
  difference.in.percent = 0.25, outer.zone.pixel = 50,
  show.all.possible.rings = FALSE)

Arguments

input.dir	A character
input.file	A character
user.file.en	A character
user.file.de	A character
distance	A number (Lines for finding the outline of the otolith are this many pixels apart on the x- and y-axes.)
parameter.for.end	A number (The edge is being found by calculating a floating mean. The function marks an edge, if the next point differs more than floating mean divided by parameter.for.end.)
parameter.distance.deviation	A number (Outliers get detected by multiplying the parameter with the mean distance between points.)
par.hyaline	A number (This parameter is multiplied by the mean of the brightness of the image to give a lower limit for ring detection.)
points.to.jump	A number (It indicates how many points can be missed while finding a large ring.)
points.for.reconnecting	A number (It indicates how far rings should be away from each other. Otherwise they are being merged.)
remove.points.at.end	A number (It indicates how many points should be disregarded at the end of the line.)
remove.points.at.beginning	A number (It indicates how far the first ring should be away from the starting (midpoint).)
t	A number (This parameter is being multiplied by the standard deviation in order to delete outliers in the line values.)
difference.in.percent	A number (Rings that are smaller than this parameter in comparison to the previous and next ring are being deleted.)
outer.zone.pixel	A number (It defines how many pixels at the end of the line belong to the outer zone.)
show.all.possible.rings	A boolean (If it is true, than all possible rings are being maked blue.)

Details

Input should be tif-format. The output will be written in the current directory. Please be aware that the coordinate system is turned by 90<c2><b0> to the right. The origin of the x- and y-axes is in the upper-left corner of the image. (The x-axis points downwards and the y-axis to the right.)

Author(s)

Kai Budde

Examples

## Not run: 
read.age(input.file = "example.tif")

## End(Not run)

buddekai/AgeReader documentation built on May 22, 2019, 5:33 p.m.