imager v0.41.2

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Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Readme

Linux Build Status CRAN Version

Imager is an image/video processing package for R, based on CImg, a C++ library by David Tschumperlé. CImg provides an easy-to-use and consistent API for image processing, which imager largely replicates. CImg supports images in up to four dimensions, which makes it suitable for applications like video processing/hyperspectral imaging/MRI.

Installing the package

Imager is on CRAN, so

install.packages("imager")

should do the trick. You may also want to install ImageMagick and ffmpeg, see "External Dependencies" below.

The version of CRAN will often lag the one on github. If you'd like to install the latest version, you'll have to build the package from source.

Install the devtools package if you haven't already. Run:

devtools::install_github("dahtah/imager")

If that doesn't work then you're probably missing a build environment or a library, see below.

OS X

Install XQuartz if you haven't already (it's required for the interactive functions). You'll need Xcode (OS X's development environment) to compile source packages. The FFTW library is needed, and the easiest way to install it is via Homebrew. Install Homebrew, then run: brew install fftw

Optionally, install libtiff for better support of TIFF files.

Windows

Building R packages on Windows is a bit of a pain so you're probably better off with the binary package (which may not be up-to-date). If you need the latest version of imager, you'll have to:

  • Install Rtools
  • Install additional libraries for Rtools. You want the package that's called "local tree". Put those libraries somewhere gcc can find them.

Linux

To build under Linux make sure you have the headers for libX11 and libfftw3 (optionally, libtiff as well). On my Ubuntu system this seems to be enough:

sudo apt-get install libfftw3-dev libX11-dev libtiff-dev

External dependencies

OS X users need XQuartz. On its own imager supports JPEG, PNG, TIFF and BMP formats. If you need support for other file types install ImageMagick. To load and save videos you'll need ffmpeg, no file formats are supported natively.

Getting started

Here's a small demo that actually demonstrates an interesting property of colour perception:

library(imager)
library(purrr)
parrots <- load.example("parrots")
plot(parrots)
#Define a function that converts to YUV, blurs a specific channel, and converts back
bchan <- function(im,ind,sigma=5) { 
    im <- RGBtoYUV(im)
    channel(im,ind) <- isoblur(channel(im,ind),sigma); 
    YUVtoRGB(im)
}
#Run the function on all three channels and collect the results as a list
blurred <- map_il(1:3,~ bchan(parrots,.))
names(blurred) <- c("Luminance blur (Y)","Chrominance blur (U)","Chrominance blur (V)")
plot(blurred)

We're much more sensitive to luminance edges than we are to colour edges.

Documentation is available here. To get a list of all package functions, run: ls(pos = "package:imager")

Important warning on memory usage

All images are stored as standard R numeric vectors (i.e., double-precision), meaning that they take up a lot of memory. It's easy to underestimate how much storage you need for videos, because they take up so little space in a compressed format. Before you can work on it in R a video has to be fully decompressed and stored as double-precision floats. To get a sense of the size, consider a low-resolution (400x300), colour video lasting 120 sec. The video might take up a few MBs when compressed. To store it in memory, you'll need: (400x300) x (25x120) x 3 values, corresponding to (space)x(time)x(colour). In addition, each value costs 8 bytes of storage, for a grand total of 8GB of memory.

For out-of-memory processing of videos, see the experimental package imagerstreams.

Current status

Imager is fully functional but still young, so the API might change. Open an issue on Github or email me if you've found a bug or would like to suggest a feature.

Contributing to imager

If you want to add features or fix a bug, just fork this repository and send me a pull request (they're welcome). Consider contributing documentation too: imager has got quite large over time, and it's in need of more how-to's and tutorials!

Contributors

The package's author is Simon Barthelmé (Gipsa-lab, CNRS). The following people have gracefully contributed code, bug fixes or testing:

  • Stefan Roediger
  • Aaron Robotham
  • Martin Roth
  • Jan Wijffels
  • Hong Ooi

Let me know if you're missing from the list!

Test pictures

Imager ships with four test pictures and a video. Two (parrots and boats) come from the Kodak set. Another is a sketch of birds by Leonardo, from Wikimedia. Also from Wikimedia: the Hubble Deep field. The test video comes from xiph.org's collection.

Functions in imager

Name Description
FFT Compute the Discrete Fourier Transform of an image
autocrop Autocrop image region
add.colour Add colour channels to a grayscale image or pixel set
as.cimg Convert to cimg object
display Display object using CImg library
as.data.frame.pixset Methods to convert pixsets to various objects
as.igraph.cimg Form a graph from an image
capture.plot Capture the current R plot device as a cimg image
display.cimg Display image using CImg library
center.stencil Center stencil at a location
cimg.extract Various shortcuts for extracting colour channels, frames, etc
cimg.use.openmp Control CImg's parallelisation
draw_circle Draw circle on image
bbox Compute the bounding box of a pixset
draw_rect Draw rectangle on image
blur_anisotropic Blur image anisotropically, in an edge-preserving way.
boxblur Blur image with a box filter (square window)
get.stencil Return pixel values in a neighbourhood defined by a stencil
boxblur_xy Blur image with a box filter.
cimg2im Convert cimg to spatstat im object
get_gradient Compute image gradient.
circles Add circles to plot
coord.index Coordinates from pixel index
correlate Correlation/convolution of image by filter
grow Grow/shrink a pixel set
gsdim Grayscale dimensions of image
idply Split an image along axis, apply function, return a data.frame
iiply Split an image, apply function, recombine the results as an image
hough_circle Circle detection using Hough transform
hough_line Hough transform for lines
%inr% Check that value is in a range
grayscale Convert an RGB image to grayscale
RGBtoHSL Colour space conversions in imager
imager.combine Combining images
imhessian Compute image hessian.
imlap Compute image Laplacian
iminfo Return information on image file
imlist Image list
interp Interpolate image values
is.cimg Checks that an object is a cimg object
is.imlist Check that an object is an imlist object
imager.replace Replace part of an image with another
load.example Load example image
imager.subset Array subset operator for cimg objects
load.image Load image from file or URL
imappend Combine a list of images into a single image
is.pixset Check that an object is a pixset object
load.video Load a video using ffmpeg
play Play a video
imchange Modify parts of an image
magick Convert a magick image to a cimg image or image list
plot.cimg Display an image using base graphics
periodic.part Compute the periodic part of an image, using the periodic/smooth decomposition of Moisan (2011)
imrotate Rotate an image along the XY plane.
imrep Replicate images
as.cimg.array Turn an numeric array into a cimg object
permute_axes Permute image axes
rm.alpha Remove alpha channel and store as attribute
save.image Save image
as.cimg.data.frame Create an image from a data.frame
isoblur Blur image isotropically.
split_connected Split pixset into connected components
medianblur Blur image with the median filter. In a window of size n x n centered at pixel (x,y), compute median pixel value over the window. Optionally, ignore values that are too far from the value at current pixel.
label Label connected components.
mirror Mirror image content along specified axis
as.igraph.pixset Form an adjacency graph from a pixset
patch_summary_cimg Extract a numerical summary from image patches, using CImg's mini-language Experimental feature.
squeeze Remove empty dimensions from an array
patchstat Return image patch summary
px.na A pixset for NA values
rotate_xy Rotate image by an arbitrary angle, around a center point.
as.imlist.list Convert various objects to image lists
renorm Renormalise image
stencil.cross A cross-shaped stencil
threshold Threshold grayscale image
boats Photograph of sailing boats from Kodak set
boundary Find the boundary of a shape in a pixel set
cimg Create a cimg object
vanvliet Young-Van Vliet recursive Gaussian filter.
cimg.dimensions Image dimensions
distance_transform Compute Euclidean distance function to a specified value.
display.list Display image list using CImg library
frames Split a video into separate frames
get.locations Return coordinates of subset of pixels
as.data.frame.cimg Convert a pixel image to a data.frame
as.data.frame.imlist Convert image list to data.frame
bucketfill Bucket fill
cannyEdges Canny edge detector
get_hessian Return image hessian.
grab Select image regions interactively
ilply Split an image along axis, apply function, return a list
common_pixsets Various useful pixsets
im2cimg Convert an image in spatstat format to an image in cimg format
contours Return contours of image/pixset
imfill Create an image of custom size by filling in repeated values
crop.borders Crop the outer margins of an image
imgradient Compute image gradient
deriche Apply recursive Deriche filter.
imnoise Generate (Gaussian) white-noise image
implot Plot objects on image using base graphics
draw_text Draw text on an image
erode Erode/dilate image by a structuring element.
liply Apply function to each element of a list, then combine the result as an image by appending along specified axis
as.cimg.function Create an image by sampling a function
haar Compute Haar multiscale wavelet transform.
load.dir Load all images in a directory
highlight Highlight pixel set on image
as.cimg.raster Convert a raster object to a cimg object
as.pixset Methods to convert various objects to pixsets
imcoord Coordinates as images
as.raster.cimg Convert a cimg object to a raster object for plotting
channels Split a colour image into a list of separate channels
imdirac Generates a "dirac" image, i.e. with all values set to 0 except one.
imsharpen Sharpen image.
ci Concatenation for image lists
nfline Plot a line, Hesse normal form parameterisation
pad Pad image with n pixels along specified axis
imshift Shift image content.
clean Clean up and fill in pixel sets (morphological opening and closing)
imwarp Image warping
plot.imlist Plot an image list
index.coord Linear index in internal vector from pixel coordinates
make.video Make/save a video using ffmpeg
colorise Fill in a colour in an area given by a pixset
diffusion_tensors Compute field of diffusion tensors for edge-preserving smoothing.
map_il Type-stable map for use with the purrr package
displacement Estimate displacement field between two images.
px.flood Select a region of homogeneous colour
where Return locations in pixel set
extract_patches Extract image patches and return a list
flatten.alpha Flatten alpha channel
pixel.grid Return the pixel grid for an image
im_split Split an image along a certain axis (producing a list)
pixset Pixel sets (pixsets)
imager imager: an R library for image processing, based on CImg
imdraw Draw image on another image
resize Resize image
imeval Evaluation in an image context
resize_doubleXY Resize image uniformly
warp Warp image
watershed Compute watershed transform.
imsplit Split an image along a certain axis (producing a list)
imsub Select part of an image
inpaint Fill-in NA values in an image
interact Build simple interactive interfaces using imager
at Return or set pixel value at coordinates
RasterPackage Convert a RasterLayer/RasterBrick to a cimg image/image list
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gettingstarted.Rmd
pixsets.Rmd
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Details

Type Package
Date 2018-05-30
License LGPL
URL http://dahtah.github.io/imager, https://github.com/dahtah/imager
BugReports https://github.com/dahtah/imager/issues
SystemRequirements fftw3,libtiff,C++11
LinkingTo Rcpp
LazyData true
RoxygenNote 6.0.1
VignetteBuilder knitr
NeedsCompilation yes
Packaged 2019-01-21 11:13:57 UTC; ripley
Repository CRAN
Date/Publication 2019-01-23 10:43:50 UTC
X-CRAN-Original-Maintainer Simon Barthelme
X-CRAN-Comment Orphaned on 2019-01-23 as no response to request to fix check issues.

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