read.gif & write.gif {caTools}

Read and Write Images in GIF format

Description

Read and write files in GIF format. Files can contain single images or multiple frames. Multi-frame images are saved as animated GIF's.

Usage

read.gif(filename, frame=0, flip=FALSE, verbose=FALSE) 
write.gif(image, filename, col="gray", scale=c("smart", "never", "always"), 
    transparent=NULL, comment=NULL, delay=0, flip=FALSE, interlace=FALSE)

Arguments

filename

Character string with name of the file. In case of read.gif URL's are also allowed.

image

Data to be saved as GIF file. Can be a 2D matrix or 3D array. Allowed formats in order of preference:

• array of integers in [0:255] range - this is format required by GIF file, and unless scale='always', numbers will not be rescaled. Each pixel i will have associated color col[image[i]+1]. This is the only format that can be safely used with non-continuous color maps.

• array of doubles in [0:1] range - Unless scale='never' the array will be multiplied by 255 and rounded.

• array of numbers in any range - will be scaled or clipped depending on scale option.

frame

Request specific frame from multiframe (i.e., animated) GIF file. By default all frames are read from the file (frame=0). Setting frame=1 will ensure that output is always a 2D matrix containing the first frame. Some files have to be read frame by frame, for example: files with subimages of different sizes and files with both global and local color-maps (palettes).

col

Color palette definition. Several formats are allowed:

• array (list) of colors in the same format as output of palette functions. Preferred format for precise color control.

• palette function itself (ex. 'col=rainbow'). Preferred format if not sure how many colors are needed.

• character string with name of internally defined palette. At the moment only "gray" and "jet" (Matlab's jet palette) are defined.

• character string with name of palette function (ex. 'col="rainbow"')

Usually palette will consist of 256 colors, which is the maximum allowed by GIF format. By default, grayscale will be used.

scale

There are three approaches to rescaling the data to required [0, 255] integer range:

• "smart" - Data is fitted to [0:255] range, only if it falls outside of it. Also, if image is an array of doubles in range [0, 1] than data is multiplied by 255.

• "never" - Pixels with intensities outside of the allowed range are clipped to either 0 or 255. Warning is given.

• "always" - Data is always rescaled. If image is a array of doubles in range [0, 1] than data is multiplied by 255; otherwise it is scaled to fit to [0:255] range.

delay

In case of 3D arrays the data will be stored as animated GIF, and delay controls speed of the animation. It is number of hundredths (1/100) of a second of delay between frames.

comment

Comments in text format are allowed in GIF files. Few file viewers can access them.

flip

By default data is stored in the same orientation as data displayed by print function: row 1 is on top, image x-axis corresponds to columns and y-axis corresponds to rows. However function image adopted different standard: column 1 is on the bottom, image x-axis corresponds to rows and y-axis corresponds to columns. Set flip to TRUE to get the orientation used by image.

transparent

Optional color number to be shown as transparent. Has to be an integer in [0:255] range. NA's in the image will be set to transparent.

interlace

GIF files allow image rows to be interlaced, or reordered in such a way as to allow viewer to display image using 4 passes, making image sharper with each pass. Irrelevant feature on fast computers.

verbose

Display details sections encountered while reading GIF file.

Details

Palettes often contain continuous colors, such that swapping palettes or rescaling of the image date does not affect image apperance in a drastic way. However, when working with non-continuous color-maps one should always provide image in [0:255] integer range (and set scale="never"), in order to prevent scaling.

If NA or other infinite numbers are found in the image by write.gif, they will be converted to numbers given by transparent. If transparent color is not provided than it will be created, possibly after reshretching.

There are some GIF files not fully supported by read.gif function:

• "Plain Text Extension" is not supported, and will be ignored.

• Multi-frame files with unique settings for each frame have to be read frame by frame. Possible settings include: frames with different sizes, frames using local color maps and frames using individual transparency colors.

Value

Function write.gif does not return anything. Function read.gif returns a list with following fields:

image

matrix or 3D array of integers in [0:255] range.

col

color palette definitions with number of colors ranging from 1 to 256. In case when frame=0 only the first (usually global) color-map (palette) is returned.

comment

Comments imbedded in GIF File

transparent

color number corresponding to transparent color. If none was stated than NULL, otherwise an integer in [0:255] range. In order for graphics:image to display transparent colors correctly one should use y$col[y$transparent+1] = NA.

Author(s)

Jarek Tuszynski (SAIC) [e-mail]. Encoding Algorithm adapted from code by Christoph Hohmann, which was adapted from code by Michael Mayer. Parts of decoding algorithm adapted from code by David Koblas.

References

Ziv, J., Lempel, A. (1977) An Universal Algorithm for Sequential Data Compression, IEEE Transactions on Information Theory, May 1977.

See Also

Displaying of images can be done through functions: graphics:image (part of R), fields::image.plot and fields::add.image or spatstat:plot.im, and possibly many other functions.

Displayed image can be saved in GIF, JPEG or PNG format using several different functions, like R2HTML:HTMLplot.

Functions for directly reading and writing image files:

• read.pnm and pixmap::write.pnm can process PBM, PGM and PPM images (file types supported by ImageMagic software)

• read.ENVI and write.ENVI from this package can process files in ENVI format. ENVI files can store 2D images and 3D data (multi-frame images), and are supported by most GIS (Geographic Information System) software including free "freelook".

There are many functions for creating and managing color palettes:

• fields::tim.colors contains a palette similar to Matlab's jet palette (see examples for simpler implementation)

• gplots::rich.colors contains two palettes of continuous colors.

• Functions RColorBrewer::brewer.pal and epitools::colorbrewer.palette contain tools for generating palettes.

• grDevices::rgb and grDevices::hsv create palette from RGB or HSV 3-vectors.

• grDevices::col2rgb translates palette colors to RGB 3-vectors.

Examples

# visual comparison between image and plot
write.gif( volcano, "volcano.gif", col=terrain.colors, flip=TRUE, 
           scale="always", comment="Maunga Whau Volcano")
y = read.gif("volcano.gif", verbose=TRUE, flip=TRUE)
image(y$image, col=y$col, main=y$comment, asp=1)
# browseURL("file://volcano.gif")  # inspect GIF file on your hard disk

# test reading & writing
col = heat.colors(256) # choose colormap
trn = 222              # set transparent color
com = "Hello World"    # imbed comment in the file
write.gif( volcano, "volcano.gif", col=col, transparent=trn, comment=com)
y = read.gif("volcano.gif")
# This tested col==y$col, but colours may or may not have an alpha channel
# and for col this changed in R 4.0
stopifnot(volcano==y$image, trn==y$transparent, com==y$comment)
# browseURL("file://volcano.gif") # inspect GIF file on your hard disk

# create simple animated GIF (using image function in a loop is very rough,
# but only way I know of displaying 'animation" in R)
x <- y <- seq(-4*pi, 4*pi, len=200)
r <- sqrt(outer(x^2, y^2, "+"))
image = array(0, c(200, 200, 10))
for(i in 1:10) image[,,i] = cos(r-(2*pi*i/10))/(r^.25)
write.gif(image, "wave.gif", col="rainbow")
y = read.gif("wave.gif")
for(i in 1:10) image(y$image[,,i], col=y$col, breaks=(0:256)-0.5, asp=1)
# browseURL("file://wave.gif") # inspect GIF file on your hard disk

# Another neat animation of Mandelbrot Set
jet.colors = colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F",
             "yellow", "#FF7F00", "red", "#7F0000")) # define "jet" palette
m = 400
C = complex( real=rep(seq(-1.8,0.6, length.out=m), each=m ), 
             imag=rep(seq(-1.2,1.2, length.out=m),      m ) )
C = matrix(C,m,m)
Z = 0
X = array(0, c(m,m,20))
for (k in 1:20) {
  Z = Z^2+C
  X[,,k] = exp(-abs(Z))
}
image(X[,,k], col=jet.colors(256))
write.gif(X, "Mandelbrot.gif", col=jet.colors, delay=100)
# browseURL("file://Mandelbrot.gif") # inspect GIF file on your hard disk
file.remove("wave.gif", "volcano.gif", "Mandelbrot.gif")

# Display interesting images from the web
## Not run: 
url = "http://www.ngdc.noaa.gov/seg/cdroms/ged_iib/datasets/b12/gifs/eccnv.gif"
y = read.gif(url, verbose=TRUE, flip=TRUE)
image(y$image, col=y$col, breaks=(0:length(y$col))-0.5, asp=1,
           main="January Potential Evapotranspiration mm/mo")
url = "http://www.ngdc.noaa.gov/seg/cdroms/ged_iib/datasets/b01/gifs/fvvcode.gif"
y = read.gif(url, flip=TRUE)
y$col[y$transparent+1] = NA # mark transparent color in R way
image(y$image, col=y$col[1:87], breaks=(0:87)-0.5, asp=1,
           main="Vegetation Types")
url = "http://talc.geo.umn.edu/people/grads/hasba002/erosion_vids/run2/r2_dems_5fps(8color).gif"
y = read.gif(url, verbose=TRUE, flip=TRUE)
for(i in 2:dim(y$image)[3]) 
  image(y$image[,,i], col=y$col, breaks=(0:length(y$col))-0.5,
            asp=1, main="Erosion in Drainage Basins")

## End(Not run)