Reading TIFF files
Check out the following video:
As you can see, it’s a colour video of a banana dancing in front ofthe R logo. Hence, it has colour channel (red, green and blue) and frame(a video is comprised of severalframes) information inside. Ihave 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/m1/sq5nmr5x2cj0t6f8wscs1wqm0000gp/T/RtmpbRtjZw/Rinst12a954d37bf78/ijtiff/img/Rlogo-banana.tif"To read it in, you just needread_tif() and the path tothe image.
library(ijtiff)img_dancing_banana<-read_tif(path_dancing_banana)#> Reading image from /private/var/folders/m1/sq5nmr5x2cj0t6f8wscs1wqm0000gp/T/RtmpbRtjZw/Rinst12a954d37bf78/ijtiff/img/Rlogo-banana.tif#> Reading an 8-bit, float image with dimensions 78x100x3x8 (y,x,channel,frame) . . .Let’s take a peek inside ofimg_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 ───────────────────────────────────────────────────────────────────#> • ImageWidth: 100#> • ImageLength: 78#> • ImageDepth: 1#> • BitsPerSample: 8#> • SamplesPerPixel: 3#> • SampleFormat: unsigned integer data#> • PlanarConfiguration: contiguous#> • RowsPerStrip: 78#> • Compression: Deflate#> • Threshholding: 1#> • ResolutionUnit: inch#> • Orientation: top_left#> • Software: ijtiff package, R 4.0.0#> • PhotometricInterpretation: BlackIsZeroYou can see it’s a 4-dimensional array. The last two dimensions are 3and 8; this is because these are the channel and frame slotsrespectively: the image has 3 channels (red, green and blue) and 8frames. The first two dimensions tell us that the images in the videoare 78 pixels tall and 100 pixels wide. The image object is of classijtiff_img. This guarantees that it is a 4-dimensionalarray with this structure. The attributes of theijtiff_imggive information on the various TIFF tags that were part of the TIFFimage. You can read more about various TIFF tags athttps://www.loc.gov/preservation/digital/formats/content/tiff_tags.shtml.To read just the tags and not the image, use theread_tags() function.
Let’s visualize the constituent parts of that 8-frame, colourTIFF.
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 timeand 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 image from /private/var/folders/m1/sq5nmr5x2cj0t6f8wscs1wqm0000gp/T/RtmpbRtjZw/Rinst12a954d37bf78/ijtiff/img/Rlogo-banana.tif#> Reading an 8-bit, float image with dimensions 78x100x3x3 (y,x,channel,frame) . . .Let’s visualize again.
Just in case you’re wondering, it’s not currently possible to readonly certain channels.
More examples
If you read an image with only one frame, the frame slot (4) willstill be there:
path_rlogo<-system.file("img","Rlogo.tif",package ="ijtiff")img_rlogo<-read_tif(path_rlogo)#> Reading image from /private/var/folders/m1/sq5nmr5x2cj0t6f8wscs1wqm0000gp/T/RtmpbRtjZw/Rinst12a954d37bf78/ijtiff/img/Rlogo.tif#> Reading an 8-bit, float image with dimensions 76x100x4x1 (y,x,channel,frame) . . .dim(img_rlogo)# 4 channels, 1 frame#> [1] 76 100 4 1class(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 image from /private/var/folders/m1/sq5nmr5x2cj0t6f8wscs1wqm0000gp/T/RtmpbRtjZw/Rinst12a954d37bf78/ijtiff/img/Rlogo-grey.tif#> Reading a 32-bit, float image with dimensions 76x100x1x1 (y,x,channel,frame) . . .dim(img_rlogo_grey)# 1 channel, 1 frame#> [1] 76 100 1 1display(img_rlogo_grey)