Following code shows that "log(imageData, base=2)" is broken. Could it be fixed? Thanks!!

> library(EBImage)

> image.data Image colorMode : Grayscale storage.mode : double dim : 28 380 frames.total : 1 frames.render: 1

imageData(object)[1:5,1:6] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 187 186 188 192 185 185 [2,] 184 181 183 190 186 190 [3,] 184 189 183 179 186 180 [4,] 186 186 185 187 187 186 [5,] 184 185 186 196 179 182

> log(image.data, base=2) Image colorMode : Grayscale storage.mode : double dim : 28 380 frames.total : 1 frames.render: 1

imageData(object)[1:5,1:6] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 5.2311 5.2257 5.2364 5.2575 5.2204 5.2204 [2,] 5.2149 5.1985 5.2095 5.2470 5.2257 5.2470 [3,] 5.2149 5.2417 5.2095 5.1874 5.2257 5.1930 [4,] 5.2257 5.2257 5.2204 5.2311 5.2311 5.2257 [5,] 5.2149 5.2204 5.2257 5.2781 5.1874 5.2040

> log2(image.data) Image colorMode : Grayscale storage.mode : double dim : 28 380 frames.total : 1 frames.render: 1

imageData(object)[1:5,1:6] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 7.5469 7.5392 7.5546 7.5850 7.5314 7.5314 [2,] 7.5236 7.4998 7.5157 7.5699 7.5392 7.5699 [3,] 7.5236 7.5622 7.5157 7.4838 7.5392 7.4919 [4,] 7.5392 7.5392 7.5314 7.5469 7.5469 7.5392 [5,] 7.5236 7.5314 7.5392 7.6147 7.4838 7.5078

> save(image.data, file="image.data.RData")

> log(187) [1] 5.2311 > log(187, base=2) [1] 7.5469 > log2(187) [1] 7.5469

> library(help=EBImage)

Information on package ‘EBImage’

Description:

Package: EBImage Version: 4.8.3 Title: Image processing and analysis toolbox for R Author: Andrzej Oles, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais Maintainer: Andrzej Oles <andrzej.oles@embl.de> Depends: Imports: BiocGenerics (>= 0.7.1), methods, graphics, grDevices, stats, abind, tiff, jpeg, png, locfit Suggests: BiocStyle Description: EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. License: LGPL LazyLoad: true biocViews: Visualization Packaged: 2015-03-24 00:38:44 UTC; biocbuild Built: R 3.1.1; i686-pc-linux-gnu; 2015-11-05 20:45:53 UTC; unix

Thank you for reporting the issue!

The observed behaviour was caused by a missing definition of the log method for Image objects.  Unlike the rest of Math group generics, log has an extra formal argument which makes such specific definition necessary in order to capture the base argument.

This is now fixed in release, EBImage version 4.12.1.

Cheers,

Andrzej