Bug Report for R Package "EBImage": log(image, base=2) is same as log(*) (natural log) instead of log2 (base 2).
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Entering edit mode
feimingc ▴ 20
@feimingc-9124
Last seen 5.7 years ago
United States

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

bug ebimage • 628 views
ADD COMMENT
0
Entering edit mode
Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 8 months ago
Heidelberg, Germany

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

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