Reading and Writing Images

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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Reading TIFF files

Check out the following video:

As you can see, it's a colour video of a banana dancing in front of the R logo. Hence, it has colour channel (red, green and blue) and frame (a video is comprised of several frames) information inside. I have this video saved in a TIFF file.

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

To read it in, you just need read_tif() and the path to the image.

pacman::p_load(ijtiff, magrittr)
img_dancing_banana <- read_tif(path_dancing_banana)

Let's take a peek inside of img_dancing_banana.

print(img_dancing_banana)

You can see it's a r length(dim(img_dancing_banana))-dimensional array. The last two dimensions are r dplyr::nth(dim(img_dancing_banana), -2) and r dplyr::nth(dim(img_dancing_banana), -1); this is because these are the channel and frame slots respectively: the image has r dplyr::nth(dim(img_dancing_banana), -2) channels (red, green and blue) and r dplyr::nth(dim(img_dancing_banana), -1) frames. The first two dimensions tell us that the images in the video are r dim(img_dancing_banana)[1] pixels tall and r dim(img_dancing_banana)[2] pixels wide. The image object is of class ijtiff_img. This guarantees that it is a 4-dimensional array with this structure. The attributes of the ijtiff_img give information on the various TIFF tags that were part of the TIFF image. You can read more about various TIFF tags at https://www.awaresystems.be/imaging/tiff/tifftags.html. To read just the tags and not the image, use the read_tags() function.

Let's visualize the constituent parts of that 8-frame, colour TIFF.

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)

There you go: 8 frames in 3 colours.

Reading only certain frames

It's possible to read only certain frames. This can be a massive time and memory saver when working with large images.

Suppose we only want frames 3, 5 and 7 from the image above.

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

Let's visualize again.

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)

Just in case you're wondering, it's not currently possible to read only certain channels.

More examples

If you read an image with only one frame, the frame slot (4) will still be there:

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)

You can also have an image with only 1 channel:

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)

Writing TIFF files

To write an image, you need an object in the style of an ijtiff_img object (see help("ijtiff_img", package = "ijtiff")). The basic idea is to have your image in a 4-dimensional array with the structure img[y, x, channel, frame]. Then, to write this image to the location path, you just type write_tif(img, path).

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

Reading text images

Note: if you don't know what text images are, see vignette("text-images", package = "ijtiff").

You may have a text image that you want to read (but realistically, you might never).

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

Writing text images

Writing a text image works as you'd expect.

write_txt_img(txt_img, path = tempfile(pattern = "txtimg", fileext = ".txt"))

ijtiff documentation built on June 22, 2024, 11:54 a.m.