inst/doc/finding-thresholds.R

In autothresholdr: An R Port of the 'ImageJ' Plugin 'Auto Threshold'

## ----setup, include = FALSE---------------------------------------------------
if (utils::packageVersion("knitr") >= "1.20.15") {
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.width = 7, fig.height = 6,
    tidy = "styler"
  )
} else {
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.width = 7, fig.height = 6
  )
}
set.seed(1)

## ----create-high-low----------------------------------------------------------
x <- c(sample.int(9, 2e5, replace = TRUE), sample(51:99, 8e5, replace = TRUE))

## ----plot-high-low, message=FALSE---------------------------------------------
library(ggplot2)
library(dplyr)
tibble(x = x) %>%
  ggplot() +
  aes(x) +
  stat_density(bw = 3)

## ----try-all------------------------------------------------------------------
library(autothresholdr)
thresh_methods <- c(
  "IJDefault", "Huang", "Huang2", "Intermodes", "IsoData",
  "Li", "Mean", "MinErrorI", "Minimum", "Moments", "Otsu",
  "Percentile", "RenyiEntropy", "Shanbhag", "Triangle"
)
thresholds <- purrr::map_chr(thresh_methods, ~ auto_thresh(x, .)) %>%
  tibble(method = thresh_methods, threshold = .)
print(thresholds)

## ----successes----------------------------------------------------------------
filter(thresholds, threshold >= 10, threshold <= 49)

## ----tri----------------------------------------------------------------------
auto_thresh(x, "huang")
auto_thresh(x, "tri")
auto_thresh(x, "otsu")

## ----freq1--------------------------------------------------------------------
x_freqtab <- x %>% 
  table() %>% 
  as.data.frame() %>% 
  magrittr::set_names(c("value", "n"))
head(x_freqtab)

## ----freq2--------------------------------------------------------------------
auto_thresh(x_freqtab, "huang")