EBImage crop failure
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.2 years ago
Hello Michael, EBImage represents images as multidimensional arrays. Color images are usually represented as 3-dimensional ones, where the third dimension contains the color components. >From your example, it seems that are you are manipulating 3-dimensional arrays, explaining why "a[1:120,50:120]" fails. Use "a[1:120,50:120,]" instead to crop images. Is the image you are working with is a grayscale one ? In this case, you are maybe manipulating an image that was stored as a color one, explaining your array has 3 dimensions. Doing "a = Image(a[,,1], color=Grayscale)" will fix this. Hope this helps, Cheers, Greg --- Gregoire Pau EMBL Research officer http://www.embl.de/~gpau/ On 28/08/2011 15:22, Michael Cole wrote: > Using the latest version of EBImage and ver 8:6.6.9.7-5 of ImageMagick (debian > package) several EBImage operations fail. > > In particular, cropping an image with: > a<-readImage("xxxxxxxx") > a[1:120,50:120] # fails with "incorrect number of dimensions"] > > I can get cropped images by doing: > a[1:120,50:120,1] # display gives correct region with a red mask > a[1:120,50:120,c(1,0,0)] # display gives correct region with a red mask > a[1:120,50:120,c(1,0,1)] # display gives correct region with a yellow mask > a[1:120,50:120,c(1,1,1)] # display gives correct region as grayscale > a[1:120,50:120,c(0,1,1)] # display gives correct region with a yellow mask > > and so on. > > Has there been a change in EBImage that is not reflected in the documentation? > > I am trying to build histograms for each color channel to build classification > models. > > > Thanks, > > Michael > > _______________________________________________ > 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
EBImage EBImage • 704 views
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Michael Cole ▴ 20
@michael-cole-4824
Last seen 7.2 years ago
Thanks Gregoire, The images are color. Can I assume img[1:200, 1:200,x] gives a cropped image in red,blue,green where x={1,2,3}? Michael On Fri, Sep 2, 2011 at 3:10 AM, Gregoire Pau <gregoire.pau at="" embl.de=""> wrote: > Hello Michael, > > EBImage represents images as multidimensional arrays. Color images are > usually represented as 3-dimensional ones, where the third dimension > contains the color components. > > From your example, it seems that are you are manipulating 3-dimensional > arrays, explaining why "a[1:120,50:120]" fails. Use "a[1:120,50:120,]" > instead to crop images. > > Is the image you are working with is a grayscale one ? In this case, you > are maybe manipulating an image that was stored as a color one, > explaining your array has 3 dimensions. Doing "a = Image(a[,,1], > color=Grayscale)" will fix this. > > Hope this helps, > Cheers, > > Greg > --- > Gregoire Pau > EMBL Research officer > http://www.embl.de/~gpau/ > > On 28/08/2011 15:22, Michael Cole wrote: >> Using the latest version of EBImage and ver 8:6.6.9.7-5 of ImageMagick (debian >> package) several EBImage operations fail. >> >> In particular, cropping an image with: >> a<-readImage("xxxxxxxx") >> a[1:120,50:120] # fails with "incorrect number of dimensions"] >> >> I can get cropped images by doing: >> a[1:120,50:120,1] # display gives correct region with a red mask >> a[1:120,50:120,c(1,0,0)] # display gives correct region with a red mask >> a[1:120,50:120,c(1,0,1)] # display gives correct region with a yellow mask >> a[1:120,50:120,c(1,1,1)] # display gives correct region as grayscale >> a[1:120,50:120,c(0,1,1)] # display gives correct region with a yellow mask >> >> and so on. >> >> Has there been a change in EBImage that is not reflected in the documentation? >> >> I am trying to build histograms for each color channel to build classification >> models. >> >> >> Thanks, >> >> Michael >> >> _______________________________________________ >> 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 > -- Michael Cole m.cole at rutgers.edu
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Dear Michael Michael Cole scripsit 09/02/2011 06:22 PM: > Thanks Gregoire, > > The images are color. Can I assume img[1:200, 1:200,x] gives a cropped > image in red,blue,green where x={1,2,3}? Yes. What do you get when you type (a <- readImage("xxxxxxxx")) Wolfgang > Michael > > > On Fri, Sep 2, 2011 at 3:10 AM, Gregoire Pau<gregoire.pau at="" embl.de=""> wrote: >> Hello Michael, >> >> EBImage represents images as multidimensional arrays. Color images are >> usually represented as 3-dimensional ones, where the third dimension >> contains the color components. >> >> From your example, it seems that are you are manipulating 3-dimensional >> arrays, explaining why "a[1:120,50:120]" fails. Use "a[1:120,50:120,]" >> instead to crop images. >> >> Is the image you are working with is a grayscale one ? In this case, you >> are maybe manipulating an image that was stored as a color one, >> explaining your array has 3 dimensions. Doing "a = Image(a[,,1], >> color=Grayscale)" will fix this. >> >> Hope this helps, >> Cheers, >> >> Greg >> --- >> Gregoire Pau >> EMBL Research officer >> http://www.embl.de/~gpau/ >> >> On 28/08/2011 15:22, Michael Cole wrote: >>> Using the latest version of EBImage and ver 8:6.6.9.7-5 of ImageMagick (debian >>> package) several EBImage operations fail. >>> >>> In particular, cropping an image with: >>> a<-readImage("xxxxxxxx") >>> a[1:120,50:120] # fails with "incorrect number of dimensions"] >>> >>> I can get cropped images by doing: >>> a[1:120,50:120,1] # display gives correct region with a red mask >>> a[1:120,50:120,c(1,0,0)] # display gives correct region with a red mask >>> a[1:120,50:120,c(1,0,1)] # display gives correct region with a yellow mask >>> a[1:120,50:120,c(1,1,1)] # display gives correct region as grayscale >>> a[1:120,50:120,c(0,1,1)] # display gives correct region with a yellow mask >>> >>> and so on. >>> >>> Has there been a change in EBImage that is not reflected in the documentation? >>> >>> I am trying to build histograms for each color channel to build classification >>> models. >>> >>> >>> Thanks, >>> >>> Michael >>> >>> _______________________________________________ >>> 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 >> > > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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