Stippling and TSP art in R: emulating StippleGen

Stippling is the creation of a pattern simulating varying degrees of solidity or shading by using small dots (Wikipedia).StippleGen is a piece of software that renders images using stipple patterns, which I discovered on Xi’an’s blog a couple days ago.

Stippled version of a sketch by Paul Cézanne, rendered in R


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Superpixels in imager

Superpixels are used in image segmentation as a pre-processing step. Instead of segmenting pixels directly, we first group similar pixels into “super-pixels”, which can then be processed further (and more cheaply).


(image from Wikimedia)

The current version of imager doesn’t implement them, but it turns out that SLIC superpixels are particularly easy to implement. SLIC is essentially k-means applied to pixels, with some bells and whistles.

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New version of imager package for image processing

A new version of imager is now available on CRAN. This release brings a lot of new features, including a whole new set of functions dealing with pixel sets, better support for videos, new and faster reduction functions.

The most significant change is the introduction of a “pixset” class, which deals with sets of pixels (for instance, the set of all pixels with a certain brightness, the foreground, the left-hand side of an image, an ROI, etc.). The pixset class includes many tools for working with pixsets, described in a new vignette.

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vecpack: an R package for packing stuff into vectors

Here’s a problem I’ve had again and again: let’s say you’ve defined a statistical model with several parameters. One of them is a scalar. Another is a matrix. The third one is a vector, and so on. When fitting the model the natural thing to do is to write a likelihood function that takes as many arguments as you have parameters in your model: i.e., lik(x,y,z) where x is a scalar, y a matrix and z a vector. The problem is that, while it’s the natural way of writing that function, that’s not what optimisers like “optim” want: they want a function with a single argument, and that argument should be a vector. So you have to pack everything into a vector, and write a whole lot of boilerplate code to unpack all the parameters out of that vector.

vecpack saves you from having to write all that boilerplate:


devtools::install_github("dahtah/vecpack")

library(vecpack)

#A cost function in two arguments:
cost <- function(a,b)  (3*a-b+2)^2

#Call optim via vpoptim
res <- vpoptim(list(a=1,b=0),cost)
res$par

vecpack knows how to automatically pack and unpack scalars, vectors, matrices and images (from the imager package). It’s also very easy to extend.

The package is quite new, and not on CRAN yet. Feedback welcome, either here or on the issues page on github.

 

New features in imager 0.30

imager is an R package for image processing, based on CImg. This new release brings many new features, including:

  • Support for automatic parallel processing using OpenMP.
  • A new S3 class, imlist, which makes it easy to work with image lists
  • New functions for interactively selecting image regions (grabRect,grabPoint,grabLine)
  • Experimental support for CImg’s byte-compiled DSL via imeval, patch_summary.
  • Improved plotting, API consistency, and documentation

To get started with imager, see the tutorial. Some of the new features are detailed below the fold.

And now, for your viewing pleasure, the following piece of code downloads a random cat picture, and makes a video of a bouncing kitten:

library(rvest)
library(imager)
#Run a search query (returning html content)
search <- read_html("https://www.google.com/search?site=&tbm=isch&q=cat")
#Grab all <img> tags, get their "src" attribute, a URL to an image
urls <- search %>% html_nodes("img") %>% html_attr("src") #Get urls of parrot pictures

#Load the first image, and resize 
sprite <- load.image(urls[1]) %>% resize(150,150)

#We'll use 30 frames
t <- seq(0,1,l=30)

#Equations of motion
xt <- function(t) 250*t
yt <- function(t) 400- 1100*abs(t-.5)
alpha <- function(t) 1-1.8*abs(t-.5)

#An empty frame for our cat
im <- imfill(400,400,val=rep(0,3))

#Let's make our video
vid <- lapply(t,function(t) imdraw(im,sprite,x=xt(t),y=yt(t),opacity=alpha(t))) %>% imappend("z")

play(vid,loop=TRUE,normalise=FALSE)

output

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New features in imager 0.20

imager, an R package for image processing, has been updated to v0.20 on CRAN. It’s a major upgrade with a lot of new features, better documentation and a more consistent API.

imager now has 130 functions, and I myself keep forgetting all that’s in there. I’ve added a tutorial vignette that should help you get started. It goes through a few basic tasks like plotting and histogram equalisation and builds up to a multi-scale blob detector. It also covers plotting with ggplot2 and has a thematic list of functions.

blobs

New features added in the last months include new assignment functions, a utility for getting information on image files (iminfo), auto-thresholding based on k-means, much better array subset operators, updated docs and a reorganised codebase. Windows support should also have improved. Last but not least, you can now interrupt lengthy computations by hitting Ctrl+c or the stop button in RStudio.

imager now has some easy-to-use replacement functions, meaning you can now do set image channels or change frames using a convenient R-like syntax:

library(imager)
boats.cp = boats #Make a copy of the boats image
R(boats.cp) = 0 #Set red channel to 0
G(boats.cp) =  0 #Set blue channel to 0
plot(boats.cp,main="Just the blue channel")
R(boats.cp) = G(boats)
G(boats.cp) = R(boats)
plot(boats.cp,main="Swapping red and green channels")

ab
see ?imager.replace for more.

Auto-thresholding finds an optimal threshold for converting an image to binary values, based on k-means (it’s essentially a variant of Otsu’s method).
Here’s an illustration on a sketch by Thomas Gainsborough:

url = "https://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Study_of_willows_by_Thomas_Gainsborough.jpg/375px-Study_of_willows_by_Thomas_Gainsborough.jpg"
im <- load.image(url)
layout(t(1:2))
plot(im)
grayscale(im) %>% threshold %>% plot

unnamed-chunk-2-1

Point-wise reductions are useful for combining a list of images into a single output image. For example, enorm(list(A,B,C)) computes  \sqrt{A^2+B^2+C^2} , ie. the Euclidean norm. Here’s how you can use it to compute gradient magnitude:

imgradient(im,"xy") %>% enorm %>% plot("Gradient magnitude")

unnamed-chunk-3-1

See also parmax, parmin, add, etc .

A note on compiling imager: if for some reason R tries to install imager from source (Linux or Mac), you will need the fftw library. On a Mac the easiest way is to grab it via Homebrew (“brew install fftw”), in Ubuntu “sudo apt-get install libfftw3-dev” should do it.

New R package for Eyelink eye-trackers

Eyelink eye-trackers output an avalanche of disorganised crap. I’ve written an R package that will hopefully filter that crap for you. It’s called eyelinker and it’s on Github.

It outputs a set of dataframes containing raw traces, saccades, fixations and blinks, meaning it’s easy to produce plots like this one:

example_eyelinker

There’s a vignette explaining everything, just hit vignette(“basics”,package=”eyelinker”).

I’ve tested it on some of our local datasets but given the relatively free-form nature of Eyelink asc files, there’s no guarantee it will work everywhere.

Bug reports are welcome on the github issues page.