inst/doc/reading-and-writing-images.R

In ijtiff: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----dancing-banana-path------------------------------------------------------
path_dancing_banana <- system.file("img", "Rlogo-banana.tif",
                                   package = "ijtiff")
print(path_dancing_banana)

## ----read-dancing-banana------------------------------------------------------
pacman::p_load(ijtiff, magrittr)
img_dancing_banana <- read_tif(path_dancing_banana)

## ----peek---------------------------------------------------------------------
print(img_dancing_banana)

## ----red-blue-green-banana, echo=FALSE, message=FALSE, out.width='100%', dpi=300, fig.height=0.9----
d <- dim(img_dancing_banana)
reds <- purrr::map(seq_len(d[4]), ~ img_dancing_banana[, , 1, .]) %>% 
  purrr::reduce(cbind)
greens <- purrr::map(seq_len(d[4]), ~ img_dancing_banana[, , 2, .]) %>% 
  purrr::reduce(cbind)
blues <- purrr::map(seq_len(d[4]), ~ img_dancing_banana[, , 3, .]) %>% 
  purrr::reduce(cbind)
to_display <- array(0, dim = c(3 * nrow(reds), ncol(reds), 3, 1))
to_display[seq_len(nrow(reds)), , 1, ] <- reds
to_display[seq_len(nrow(reds)) + nrow(reds), , 2, ] <- greens
to_display[seq_len(nrow(reds)) + 2 * nrow(reds), , 3, ] <- blues
display(to_display)

## ----threefiveseven-----------------------------------------------------------
img_dancing_banana357 <- read_tif(path_dancing_banana, frames = c(3, 5, 7))

## ----red-bblue-green-banana357, echo=FALSE, message=FALSE, out.width='100%', dpi=300, fig.height=0.9----
d <- dim(img_dancing_banana357)
reds <- purrr::map(seq_len(d[4]), ~ img_dancing_banana357[, , 1, .]) %>% 
  purrr::reduce(cbind)
greens <- purrr::map(seq_len(d[4]), ~ img_dancing_banana357[, , 2, .]) %>% 
  purrr::reduce(cbind)
blues <- purrr::map(seq_len(d[4]), ~ img_dancing_banana357[, , 3, .]) %>% 
  purrr::reduce(cbind)
to_display <- array(0, dim = c(3 * nrow(reds), ncol(reds), 3, 1))
to_display[seq_len(nrow(reds)), , 1, ] <- reds
to_display[seq_len(nrow(reds)) + nrow(reds), , 2, ] <- greens
to_display[seq_len(nrow(reds)) + 2 * nrow(reds), , 3, ] <- blues
display(to_display)

## ----one-frame, dpi=300, fig.height=0.5, fig.width=0.5------------------------
path_rlogo <- system.file("img", "Rlogo.tif", package = "ijtiff")
img_rlogo <- read_tif(path_rlogo) 
dim(img_rlogo)  # 4 channels, 1 frame
class(img_rlogo)
display(img_rlogo)

## ----one-channel, dpi=300, fig.height=0.5, fig.width=0.5----------------------
path_rlogo_grey <- system.file("img", "Rlogo-grey.tif", package = "ijtiff")
img_rlogo_grey <- read_tif(path_rlogo_grey)
dim(img_rlogo_grey)  # 1 channel, 1 frame
display(img_rlogo_grey)

## ----write-tif----------------------------------------------------------------
path <- tempfile(pattern = "dancing-banana", fileext = ".tif")
print(path)
write_tif(img_dancing_banana, path)

## ----read-txt-img-------------------------------------------------------------
path_txt_img <- system.file("img", "Rlogo-grey.txt", package = "ijtiff")
txt_img <- read_txt_img(path_txt_img)

## ---- write-txt-img-----------------------------------------------------------
write_txt_img(txt_img, path = tempfile(pattern = "txtimg", fileext = ".txt"))