EBImage: Negative pixel intensities?!?
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@henrik-bengtsson-4333
Last seen 5 weeks ago
United States
[Package maintainer cc:ed] Hi, in EBImage (3.11.2), an Image object can take intensities outside [0,1] including negative ones. What are they/how are they mapped when rendered? Here are some examples adopted from example("Image") and example("readImage"): # (a) Image object with intensities in [0,1] > x <- readImage(system.file("images", "lena-color.png", package="EBImage")); > range(x) [1] 0.01176471 1.00000000 # (b) Image object with intensities in [0,1] > y <- readImage(system.file('images', 'nuclei.tif', package='EBImage')) > range(y) [1] 0 1 # (c) Image object with large negative and positive intensities > z <- Image(rnorm(300*300*3),dim=c(300,300,3), colormode='Color') > range(z) [1] -4.661843 4.353772 All three Image:s can be displayed using display(). I assume the colors in 'z' are rescaled/renormalized to (R,G,B) \in [0,1]x[0,1]x[0,1], but how? BTW, I went through the EBImage docs, but I cannot find any information on what range the intensities should have. I only inferred from the examples that [0,1] seems to be the scale, but the above 'z' puzzles me. Thanks, Henrik > library(EBImage) Loading required package: abind Warning message: package 'EBImage' was built under R version 2.15.0 > sessionInfo() R version 2.14.2 Patched (2012-02-29 r58590) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EBImage_3.11.2 abind_1.4-0
EBImage EBImage • 992 views
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@wolfgang-huber-3550
Last seen 12 hours ago
EMBL European Molecular Biology Laborat…
Hi Henrik you are right; the software (and documentation) is intentionally non-prescriptive about the range of the values in the images, to allow for flexibility. Restrictions may be imposed on the level of specific functions, e.g. by 'display'. The behaviour of EBImage's display depends on the behaviour of the external library function that it calls, and this can either be from GTK+ or ImageMagick. The GTK+ code seems to do something like function(x) ifelse(x<0, 0, ifelse(x>1, 1, x)), see the below code example. Best wishes Wolfgang library("EBImage") x = seq(0, 2*pi, length=300) y = seq(-1, 2, length=length(x)) img = Image(outer(x, y, function(x, y) sin(x)*y)) display(img) display(abs(img)) display(img-10) display(img*10) sessionInfo() R Under development (unstable) (2012-03-06 r58616) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EBImage_3.11.2 abind_1.4-0 fortunes_1.4-2 loaded via a namespace (and not attached): [1] tools_2.16.0 Mar/6/12 5:42 PM, Henrik Bengtsson scripsit:: > [Package maintainer cc:ed] > > Hi, > > in EBImage (3.11.2), an Image object can take intensities outside > [0,1] including negative ones. What are they/how are they mapped when > rendered? Here are some examples adopted from example("Image") and > example("readImage"): > > # (a) Image object with intensities in [0,1] >> x<- readImage(system.file("images", "lena-color.png", package="EBImage")); >> range(x) > [1] 0.01176471 1.00000000 > > # (b) Image object with intensities in [0,1] >> y<- readImage(system.file('images', 'nuclei.tif', package='EBImage')) >> range(y) > [1] 0 1 > > # (c) Image object with large negative and positive intensities >> z<- Image(rnorm(300*300*3),dim=c(300,300,3), colormode='Color') >> range(z) > [1] -4.661843 4.353772 > > All three Image:s can be displayed using display(). > > I assume the colors in 'z' are rescaled/renormalized to (R,G,B) \in > [0,1]x[0,1]x[0,1], but how? > > BTW, I went through the EBImage docs, but I cannot find any > information on what range the intensities should have. I only > inferred from the examples that [0,1] seems to be the scale, but the > above 'z' puzzles me. > > Thanks, > > Henrik > >> library(EBImage) > Loading required package: abind > Warning message: > package 'EBImage' was built under R version 2.15.0 >> sessionInfo() > R version 2.14.2 Patched (2012-02-29 r58590) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] EBImage_3.11.2 abind_1.4-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Thanks for the clarification Wolfgang. /Henrik On Tue, Mar 6, 2012 at 1:06 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Hi Henrik > > you are right; the software (and documentation) is intentionally > non-prescriptive about the range of the values in the images, to allow for > flexibility. Restrictions may be imposed on the level of specific functions, > e.g. by 'display'. > > The behaviour of EBImage's display depends on the behaviour of the external > library function that it calls, and this can either be from GTK+ or > ImageMagick. The GTK+ code seems to do something like function(x) > ifelse(x<0, 0, ifelse(x>1, 1, x)), see the below code example. > > ? ? ? ?Best wishes > ? ? ? ?Wolfgang > > library("EBImage") > > x = seq(0, 2*pi, length=300) > y = seq(-1, 2, length=length(x)) > img = Image(outer(x, y, function(x, y) sin(x)*y)) > display(img) > display(abs(img)) > display(img-10) > display(img*10) > > > sessionInfo() > R Under development (unstable) (2012-03-06 r58616) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] EBImage_3.11.2 abind_1.4-0 ? ?fortunes_1.4-2 > > loaded via a namespace (and not attached): > [1] tools_2.16.0 > > > > Mar/6/12 5:42 PM, Henrik Bengtsson scripsit:: >> >> [Package maintainer cc:ed] >> >> Hi, >> >> in EBImage (3.11.2), an Image object can take intensities outside >> [0,1] including negative ones. ?What are they/how are they mapped when >> rendered? ?Here are some examples adopted from example("Image") and >> example("readImage"): >> >> # (a) Image object with intensities in [0,1] >>> >>> x<- readImage(system.file("images", "lena-color.png", >>> package="EBImage")); >>> range(x) >> >> [1] 0.01176471 1.00000000 >> >> # (b) Image object with intensities in [0,1] >>> >>> y<- readImage(system.file('images', 'nuclei.tif', package='EBImage')) >>> range(y) >> >> [1] 0 1 >> >> # (c) Image object with large negative and positive intensities >>> >>> z<- Image(rnorm(300*300*3),dim=c(300,300,3), colormode='Color') >>> range(z) >> >> [1] -4.661843 ?4.353772 >> >> All three Image:s can be displayed using display(). >> >> I assume the colors in 'z' are rescaled/renormalized to (R,G,B) \in >> [0,1]x[0,1]x[0,1], but how? >> >> BTW, I went through the EBImage docs, but I cannot find any >> information on what range the intensities should have. ?I only >> inferred from the examples that [0,1] seems to be the scale, but the >> above 'z' puzzles me. >> >> Thanks, >> >> Henrik >> >>> library(EBImage) >> >> Loading required package: abind >> Warning message: >> package 'EBImage' was built under R version 2.15.0 >>> >>> sessionInfo() >> >> R version 2.14.2 Patched (2012-02-29 r58590) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] EBImage_3.11.2 abind_1.4-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Best wishes > ? ? ? ?Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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