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
