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)
#> [1] "/tmp/RtmpkYw0MX/Rinst10e75a8717dd/ijtiff/img/Rlogo-banana.tif"
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)
#> Reading Rlogo-banana.tif: an 8-bit, 78x100 pixel image of
#> unsigned integer type. Reading 3 channels and 8 frames . . .
#> Done.
Let’s take a peek inside of img_dancing_banana
.
print(img_dancing_banana)
#> 78x100 pixel ijtiff_img with 3 channels and 8 frames.
#> Preview (top left of first channel of first frame):
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] 255 255 255 255 255 255
#> [2,] 255 255 255 255 255 255
#> [3,] 255 255 255 255 255 255
#> [4,] 255 255 255 255 255 255
#> [5,] 255 255 255 255 255 255
#> [6,] 255 255 255 255 255 255
#> ── TIFF tags ───────────────────────────────────────────────────────────────────
#> • bits_per_sample: 8
#> • samples_per_pixel: 3
#> • sample_format: uint
#> • planar_config: contiguous
#> • rows_per_strip: 78
#> • compression: deflate
#> • software: ijtiff package, R 4.0.0
#> • color_space: black is zero
You can see it’s a 4-dimensional array. The last two dimensions are 3
and 8; this is because these are the channel and frame slots
respectively: the image has 3 channels (red, green and blue) and 8
frames. The first two dimensions tell us that the images in the video
are 78 pixels tall and 100 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.
There you go: 8 frames in 3 colours.
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))
#> Reading Rlogo-banana.tif: an 8-bit, 78x100 pixel image of
#> unsigned integer type. Reading 3 channels and 3 frames . . .
#> Done.
Let’s visualize again.
Just in case you’re wondering, it’s not currently possible to read only certain channels.
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)
#> Reading Rlogo.tif: an 8-bit, 76x100 pixel image of unsigned
#> integer type. Reading 4 channels and 1 frame . . .
#> Done.
dim(img_rlogo) # 4 channels, 1 frame
#> [1] 76 100 4 1
class(img_rlogo)
#> [1] "ijtiff_img" "array"
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)
#> Reading Rlogo-grey.tif: a 32-bit, 76x100 pixel image of
#> floating point type. Reading 1 channel and 1 frame . . .
#> Done.
dim(img_rlogo_grey) # 1 channel, 1 frame
#> [1] 76 100 1 1
display(img_rlogo_grey)
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)
#> [1] "/tmp/Rtmpp9QUvk/dancing-banana13133b8f1130.tif"
write_tif(img_dancing_banana, path)
#> Writing dancing-banana13133b8f1130.tif: an 8-bit, 78x100 pixel
#> image of unsigned integer type with 3 channels and 8 frames .
#> . .
#> Done.
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).