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)
#> [1] "/private/var/folders/l_/2mwm03p55zg7zjykv084hhvr0000gn/T/RtmpcrTmou/Rinstf6c02b9dcbb8/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, 155x200 pixel image of
#> unsigned integer type. Reading 3 channels and 8 frames . . .
#> Done.Let’s take a peek inside of img_dancing_banana.
str(img_dancing_banana)
#> 'ijtiff_img' num [1:155, 1:200, 1:3, 1:8] 255 255 255 255 255 255 255 255 255 255 ...
#> - attr(*, "width")= int 200
#> - attr(*, "length")= int 155
#> - attr(*, "bits_per_sample")= int 8
#> - attr(*, "samples_per_pixel")= int 3
#> - attr(*, "sample_format")= chr "uint"
#> - attr(*, "planar_config")= chr "contiguous"
#> - attr(*, "rows_per_strip")= int 155
#> - attr(*, "compression")= chr "LZW"
#> - attr(*, "software")= chr "tiff package, R 3.5.0"
#> - attr(*, "color_space")= chr "RGB"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 155 pixels tall and 200 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.
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))
#> Reading Rlogo-banana.tif: an 8-bit, 155x200 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. This would be more difficult to implement, but if you need this, ask me and I’ll see what I can do.
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)
#> 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)