EBImage: alpha plane in grey scale
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@samuel-granjeaud-iricim-3718
Last seen 7.7 years ago
Hello, I am using EBImage to convert matrix to tiff grey scale. And I would like to read them directly in ImageJ. Unfortunately such image contains an extra plane that is not needed and not supported by ImageJ. This alpha plane seems to be automatically added at the creation of the image in the C code (I guess). In ImageMagick API, this is referred as "matte" http://www.imagemagick.org/api/magick-image.php#MagickSetImageMatte If I am not wrong, it would be nice if this alpha plane could be removed in next release. Regards, Samuel ~$ R --vanilla R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(EBImage) Loading required package: abind > a <- matrix(10,20,20) > b <- Image(a) > b Image colormode: Grayscale storage.mode: double dim: 20 20 nb.total.frames: 1 nb.render.frames: 1 imageData(object)[1:5,1:6]: [,1] [,2] [,3] [,4] [,5] [,6] [1,] 10 10 10 10 10 10 [2,] 10 10 10 10 10 10 [3,] 10 10 10 10 10 10 [4,] 10 10 10 10 10 10 [5,] 10 10 10 10 10 10 > writeImage(b,"b.tif") > system("tiffinfo b.tif") TIFF Directory at offset 0x6c (108) Image Width: 20 Image Length: 20 Resolution: 72, 72 pixels/inch Bits/Sample: 1 Compression Scheme: None Photometric Interpretation: min-is-black Extra Samples: 1<unassoc-alpha> FillOrder: msb-to-lsb Orientation: row 0 top, col 0 lhs Samples/Pixel: 2 Rows/Strip: 1638 Planar Configuration: single image plane DocumentName: b.tif Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org > system("convert b.tif +matte c.tif") > system("tiffinfo c.tif") TIFF Directory at offset 0x44 (68) Image Width: 20 Image Length: 20 Resolution: 72, 72 pixels/inch Bits/Sample: 1 Compression Scheme: None Photometric Interpretation: min-is-black FillOrder: msb-to-lsb Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 2730 Planar Configuration: single image plane DocumentName: c.tif Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EBImage_3.6.0 abind_1.1-0
convert EBImage convert EBImage • 1.0k views
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.7 years ago
Hello Samuel, EBImage uses ImageMagick's WriteImage() to write images and doesn't do anything more. Image format is guessed by ImageMagick from the file name and the dynamic range of the image. As an example, the following code creates a random uniform 16-bit grayscale TIFF 20x20 image: > library("EBImage") > a = matrix(runif(20*20), 20, 20) > display(a) > writeImage(a, "a.tiff") Your example uses an image with only one color and ImageMagick (and therefore EBImage) uses the 1-bit mode of the TIFF image format to write it. The bug you are facing seems to come from the fact that ImageJ does not support the 1-bit TIFF image format. In the future, it would be nice to have more control in the output image format. But, in the meanwhile, just use more colors to force EBImage to use the 16-bit format. Hope this helps, Best regards, Greg --- Gregoire Pau EMBL Research officer http://www.embl.de/~gpau/ On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote: > Hello, > > I am using EBImage to convert matrix to tiff grey scale. And I would > like to read them directly in ImageJ. Unfortunately such image contains > an extra plane that is not needed and not supported by ImageJ. This > alpha plane seems to be automatically added at the creation of the image > in the C code (I guess). In ImageMagick API, this is referred as "matte" > http://www.imagemagick.org/api/magick-image.php#MagickSetImageMatte > > If I am not wrong, it would be nice if this alpha plane could be removed > in next release. > > Regards, > Samuel > > ~$ R --vanilla > > R version 2.12.1 (2010-12-16) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(EBImage) > Loading required package: abind > > a <- matrix(10,20,20) > > b <- Image(a) > > b > Image > colormode: Grayscale > storage.mode: double > dim: 20 20 > nb.total.frames: 1 > nb.render.frames: 1 > > imageData(object)[1:5,1:6]: > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 10 10 10 10 10 10 > [2,] 10 10 10 10 10 10 > [3,] 10 10 10 10 10 10 > [4,] 10 10 10 10 10 10 > [5,] 10 10 10 10 10 10 > > > writeImage(b,"b.tif") > > system("tiffinfo b.tif") > TIFF Directory at offset 0x6c (108) > Image Width: 20 Image Length: 20 > Resolution: 72, 72 pixels/inch > Bits/Sample: 1 > Compression Scheme: None > Photometric Interpretation: min-is-black > Extra Samples: 1<unassoc-alpha> > FillOrder: msb-to-lsb > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 2 > Rows/Strip: 1638 > Planar Configuration: single image plane > DocumentName: b.tif > Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org > > system("convert b.tif +matte c.tif") > > system("tiffinfo c.tif") > TIFF Directory at offset 0x44 (68) > Image Width: 20 Image Length: 20 > Resolution: 72, 72 pixels/inch > Bits/Sample: 1 > Compression Scheme: None > Photometric Interpretation: min-is-black > FillOrder: msb-to-lsb > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 2730 > Planar Configuration: single image plane > DocumentName: c.tif > Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 > LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] > LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] > LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] EBImage_3.6.0 abind_1.1-0 > > _______________________________________________ > 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
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Hello, Sometimes we build examples that do not reflect our minds. Sorry I was wrong in putting the same value in the matrix. Nevertheless, the runif matrix leads to the same result in respect to my point. As tiffinfo enlights it, there is an extra plane (aka ExtraSamples) in the tiff, that leads to a SamplePerPixel value of 2. Now BitsPerSample are 16 of course. Best regards. > library(EBImage) Loading required package: abind > a = matrix(runif(20*20), 20, 20) > writeImage(a, "a.tiff") > system("tiffinfo a.tiff") TIFF Directory at offset 0x648 (1608) Image Width: 20 Image Length: 20 Resolution: 72, 72 pixels/inch Bits/Sample: 16 Compression Scheme: None Photometric Interpretation: min-is-black Extra Samples: 1<unassoc-alpha> FillOrder: msb-to-lsb Orientation: row 0 top, col 0 lhs Samples/Pixel: 2 Rows/Strip: 102 Planar Configuration: single image plane DocumentName: a.tiff Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org Gregoire Pau wrote: > Hello Samuel, > > EBImage uses ImageMagick's WriteImage() to write images and doesn't do > anything more. Image format is guessed by ImageMagick from the file > name and the dynamic range of the image. As an example, the following > code creates a random uniform 16-bit grayscale TIFF 20x20 image: > > library("EBImage") > > a = matrix(runif(20*20), 20, 20) > > display(a) > > writeImage(a, "a.tiff") > > Your example uses an image with only one color and ImageMagick (and > therefore EBImage) uses the 1-bit mode of the TIFF image format to > write it. The bug you are facing seems to come from the fact that > ImageJ does not support the 1-bit TIFF image format. > > In the future, it would be nice to have more control in the output > image format. But, in the meanwhile, just use more colors to force > EBImage to use the 16-bit format. > > Hope this helps, > Best regards, > > Greg > --- > Gregoire Pau > EMBL Research officer > http://www.embl.de/~gpau/ > > On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote: >> Hello, >> >> I am using EBImage to convert matrix to tiff grey scale. And I would >> like to read them directly in ImageJ. Unfortunately such image contains >> an extra plane that is not needed and not supported by ImageJ. This >> alpha plane seems to be automatically added at the creation of the image >> in the C code (I guess). In ImageMagick API, this is referred as "matte" >> http://www.imagemagick.org/api/magick-image.php#MagickSetImageMatte >> >> If I am not wrong, it would be nice if this alpha plane could be removed >> in next release. >> >> Regards, >> Samuel >> >> ~$ R --vanilla >> >> R version 2.12.1 (2010-12-16) >> Copyright (C) 2010 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > library(EBImage) >> Loading required package: abind >> > a <- matrix(10,20,20) >> > b <- Image(a) >> > b >> Image >> colormode: Grayscale >> storage.mode: double >> dim: 20 20 >> nb.total.frames: 1 >> nb.render.frames: 1 >> >> imageData(object)[1:5,1:6]: >> [,1] [,2] [,3] [,4] [,5] [,6] >> [1,] 10 10 10 10 10 10 >> [2,] 10 10 10 10 10 10 >> [3,] 10 10 10 10 10 10 >> [4,] 10 10 10 10 10 10 >> [5,] 10 10 10 10 10 10 >> >> > writeImage(b,"b.tif") >> > system("tiffinfo b.tif") >> TIFF Directory at offset 0x6c (108) >> Image Width: 20 Image Length: 20 >> Resolution: 72, 72 pixels/inch >> Bits/Sample: 1 >> Compression Scheme: None >> Photometric Interpretation: min-is-black >> Extra Samples: 1<unassoc-alpha> >> FillOrder: msb-to-lsb >> Orientation: row 0 top, col 0 lhs >> Samples/Pixel: 2 >> Rows/Strip: 1638 >> Planar Configuration: single image plane >> DocumentName: b.tif >> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >> > system("convert b.tif +matte c.tif") >> > system("tiffinfo c.tif") >> TIFF Directory at offset 0x44 (68) >> Image Width: 20 Image Length: 20 >> Resolution: 72, 72 pixels/inch >> Bits/Sample: 1 >> Compression Scheme: None >> Photometric Interpretation: min-is-black >> FillOrder: msb-to-lsb >> Orientation: row 0 top, col 0 lhs >> Samples/Pixel: 1 >> Rows/Strip: 2730 >> Planar Configuration: single image plane >> DocumentName: c.tif >> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >> > sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 >> LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] >> LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] >> LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] EBImage_3.6.0 abind_1.1-0 >> >> _______________________________________________ >> 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 >
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Hello Samuel, Running the following code on my system: > library("EBImage") > a = matrix(runif(20*20), 20, 20) > writeImage(a, "a.tiff") > system("tiffinfo a.tiff") Gives me: Image Width: 20 Image Length: 20 Resolution: 72, 72 pixels/inch Bits/Sample: 16 Compression Scheme: None Photometric Interpretation: min-is-black FillOrder: msb-to-lsb Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 204 Planar Configuration: single image plane Page Number: 0-1 DocumentName: a.tiff Software: ImageMagick 6.5.7-8 2010-12-02 Q16 Only one sample per pixel is present here. I am using EBImage 3.7.1 and ImageMagick 6.5.7. It seems that your version of ImageMagick is very old and is likely the cause of the extra alpha layer. I guess updating it will solve your problem. Hope this helps, Best, Greg --- Gregoire Pau EMBL Research Officer http://www.embl.de/~gpau/ On 28/02/11 14:35, Samuel GRANJEAUD - IR/ICIM wrote: > Hello, > > Sometimes we build examples that do not reflect our minds. Sorry I was > wrong in putting the same value in the matrix. Nevertheless, the runif > matrix leads to the same result in respect to my point. As tiffinfo > enlights it, there is an extra plane (aka ExtraSamples) in the tiff, > that leads to a SamplePerPixel value of 2. Now BitsPerSample are 16 of > course. > > Best regards. > > > library(EBImage) > Loading required package: abind > > a = matrix(runif(20*20), 20, 20) > > writeImage(a, "a.tiff") > > system("tiffinfo a.tiff") > TIFF Directory at offset 0x648 (1608) > Image Width: 20 Image Length: 20 > Resolution: 72, 72 pixels/inch > Bits/Sample: 16 > Compression Scheme: None > Photometric Interpretation: min-is-black > Extra Samples: 1<unassoc-alpha> > FillOrder: msb-to-lsb > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 2 > Rows/Strip: 102 > Planar Configuration: single image plane > DocumentName: a.tiff > Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org > > > Gregoire Pau wrote: >> Hello Samuel, >> >> EBImage uses ImageMagick's WriteImage() to write images and doesn't do >> anything more. Image format is guessed by ImageMagick from the file >> name and the dynamic range of the image. As an example, the following >> code creates a random uniform 16-bit grayscale TIFF 20x20 image: >> > library("EBImage") >> > a = matrix(runif(20*20), 20, 20) >> > display(a) >> > writeImage(a, "a.tiff") >> >> Your example uses an image with only one color and ImageMagick (and >> therefore EBImage) uses the 1-bit mode of the TIFF image format to >> write it. The bug you are facing seems to come from the fact that >> ImageJ does not support the 1-bit TIFF image format. >> >> In the future, it would be nice to have more control in the output >> image format. But, in the meanwhile, just use more colors to force >> EBImage to use the 16-bit format. >> >> Hope this helps, >> Best regards, >> >> Greg >> --- >> Gregoire Pau >> EMBL Research officer >> http://www.embl.de/~gpau/ >> >> On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote: >>> Hello, >>> >>> I am using EBImage to convert matrix to tiff grey scale. And I would >>> like to read them directly in ImageJ. Unfortunately such image contains >>> an extra plane that is not needed and not supported by ImageJ. This >>> alpha plane seems to be automatically added at the creation of the image >>> in the C code (I guess). In ImageMagick API, this is referred as "matte" >>> http://www.imagemagick.org/api/magick- image.php#MagickSetImageMatte >>> >>> If I am not wrong, it would be nice if this alpha plane could be removed >>> in next release. >>> >>> Regards, >>> Samuel >>> >>> ~$ R --vanilla >>> >>> R version 2.12.1 (2010-12-16) >>> Copyright (C) 2010 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> > library(EBImage) >>> Loading required package: abind >>> > a <- matrix(10,20,20) >>> > b <- Image(a) >>> > b >>> Image >>> colormode: Grayscale >>> storage.mode: double >>> dim: 20 20 >>> nb.total.frames: 1 >>> nb.render.frames: 1 >>> >>> imageData(object)[1:5,1:6]: >>> [,1] [,2] [,3] [,4] [,5] [,6] >>> [1,] 10 10 10 10 10 10 >>> [2,] 10 10 10 10 10 10 >>> [3,] 10 10 10 10 10 10 >>> [4,] 10 10 10 10 10 10 >>> [5,] 10 10 10 10 10 10 >>> >>> > writeImage(b,"b.tif") >>> > system("tiffinfo b.tif") >>> TIFF Directory at offset 0x6c (108) >>> Image Width: 20 Image Length: 20 >>> Resolution: 72, 72 pixels/inch >>> Bits/Sample: 1 >>> Compression Scheme: None >>> Photometric Interpretation: min-is-black >>> Extra Samples: 1<unassoc-alpha> >>> FillOrder: msb-to-lsb >>> Orientation: row 0 top, col 0 lhs >>> Samples/Pixel: 2 >>> Rows/Strip: 1638 >>> Planar Configuration: single image plane >>> DocumentName: b.tif >>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>> > system("convert b.tif +matte c.tif") >>> > system("tiffinfo c.tif") >>> TIFF Directory at offset 0x44 (68) >>> Image Width: 20 Image Length: 20 >>> Resolution: 72, 72 pixels/inch >>> Bits/Sample: 1 >>> Compression Scheme: None >>> Photometric Interpretation: min-is-black >>> FillOrder: msb-to-lsb >>> Orientation: row 0 top, col 0 lhs >>> Samples/Pixel: 1 >>> Rows/Strip: 2730 >>> Planar Configuration: single image plane >>> DocumentName: c.tif >>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>> > sessionInfo() >>> R version 2.12.1 (2010-12-16) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 >>> LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] >>> LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] >>> LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> other attached packages: >>> [1] EBImage_3.6.0 abind_1.1-0 >>> >>> _______________________________________________ >>> 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 >> >
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Hello Gregoire, Good news, you got the answer. Thanks a lot, Samuel Gregoire Pau wrote: > Hello Samuel, > > Running the following code on my system: > > library("EBImage") > > a = matrix(runif(20*20), 20, 20) > > writeImage(a, "a.tiff") > > system("tiffinfo a.tiff") > > Gives me: > Image Width: 20 Image Length: 20 > Resolution: 72, 72 pixels/inch > Bits/Sample: 16 > Compression Scheme: None > Photometric Interpretation: min-is-black > FillOrder: msb-to-lsb > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 204 > Planar Configuration: single image plane > Page Number: 0-1 > DocumentName: a.tiff > Software: ImageMagick 6.5.7-8 2010-12-02 Q16 > > Only one sample per pixel is present here. I am using EBImage 3.7.1 > and ImageMagick 6.5.7. It seems that your version of ImageMagick is > very old and is likely the cause of the extra alpha layer. I guess > updating it will solve your problem. > > Hope this helps, > > Best, > > Greg > --- > Gregoire Pau > EMBL Research Officer > http://www.embl.de/~gpau/ > > On 28/02/11 14:35, Samuel GRANJEAUD - IR/ICIM wrote: >> Hello, >> >> Sometimes we build examples that do not reflect our minds. Sorry I was >> wrong in putting the same value in the matrix. Nevertheless, the runif >> matrix leads to the same result in respect to my point. As tiffinfo >> enlights it, there is an extra plane (aka ExtraSamples) in the tiff, >> that leads to a SamplePerPixel value of 2. Now BitsPerSample are 16 of >> course. >> >> Best regards. >> >> > library(EBImage) >> Loading required package: abind >> > a = matrix(runif(20*20), 20, 20) >> > writeImage(a, "a.tiff") >> > system("tiffinfo a.tiff") >> TIFF Directory at offset 0x648 (1608) >> Image Width: 20 Image Length: 20 >> Resolution: 72, 72 pixels/inch >> Bits/Sample: 16 >> Compression Scheme: None >> Photometric Interpretation: min-is-black >> Extra Samples: 1<unassoc-alpha> >> FillOrder: msb-to-lsb >> Orientation: row 0 top, col 0 lhs >> Samples/Pixel: 2 >> Rows/Strip: 102 >> Planar Configuration: single image plane >> DocumentName: a.tiff >> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >> >> >> Gregoire Pau wrote: >>> Hello Samuel, >>> >>> EBImage uses ImageMagick's WriteImage() to write images and doesn't do >>> anything more. Image format is guessed by ImageMagick from the file >>> name and the dynamic range of the image. As an example, the following >>> code creates a random uniform 16-bit grayscale TIFF 20x20 image: >>> > library("EBImage") >>> > a = matrix(runif(20*20), 20, 20) >>> > display(a) >>> > writeImage(a, "a.tiff") >>> >>> Your example uses an image with only one color and ImageMagick (and >>> therefore EBImage) uses the 1-bit mode of the TIFF image format to >>> write it. The bug you are facing seems to come from the fact that >>> ImageJ does not support the 1-bit TIFF image format. >>> >>> In the future, it would be nice to have more control in the output >>> image format. But, in the meanwhile, just use more colors to force >>> EBImage to use the 16-bit format. >>> >>> Hope this helps, >>> Best regards, >>> >>> Greg >>> --- >>> Gregoire Pau >>> EMBL Research officer >>> http://www.embl.de/~gpau/ >>> >>> On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote: >>>> Hello, >>>> >>>> I am using EBImage to convert matrix to tiff grey scale. And I would >>>> like to read them directly in ImageJ. Unfortunately such image >>>> contains >>>> an extra plane that is not needed and not supported by ImageJ. This >>>> alpha plane seems to be automatically added at the creation of the >>>> image >>>> in the C code (I guess). In ImageMagick API, this is referred as >>>> "matte" >>>> http://www.imagemagick.org/api/magick- image.php#MagickSetImageMatte >>>> >>>> If I am not wrong, it would be nice if this alpha plane could be >>>> removed >>>> in next release. >>>> >>>> Regards, >>>> Samuel >>>> >>>> ~$ R --vanilla >>>> >>>> R version 2.12.1 (2010-12-16) >>>> Copyright (C) 2010 The R Foundation for Statistical Computing >>>> ISBN 3-900051-07-0 >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>>> You are welcome to redistribute it under certain conditions. >>>> Type 'license()' or 'licence()' for distribution details. >>>> >>>> Natural language support but running in an English locale >>>> >>>> R is a collaborative project with many contributors. >>>> Type 'contributors()' for more information and >>>> 'citation()' on how to cite R or R packages in publications. >>>> >>>> Type 'demo()' for some demos, 'help()' for on-line help, or >>>> 'help.start()' for an HTML browser interface to help. >>>> Type 'q()' to quit R. >>>> >>>> > library(EBImage) >>>> Loading required package: abind >>>> > a <- matrix(10,20,20) >>>> > b <- Image(a) >>>> > b >>>> Image >>>> colormode: Grayscale >>>> storage.mode: double >>>> dim: 20 20 >>>> nb.total.frames: 1 >>>> nb.render.frames: 1 >>>> >>>> imageData(object)[1:5,1:6]: >>>> [,1] [,2] [,3] [,4] [,5] [,6] >>>> [1,] 10 10 10 10 10 10 >>>> [2,] 10 10 10 10 10 10 >>>> [3,] 10 10 10 10 10 10 >>>> [4,] 10 10 10 10 10 10 >>>> [5,] 10 10 10 10 10 10 >>>> >>>> > writeImage(b,"b.tif") >>>> > system("tiffinfo b.tif") >>>> TIFF Directory at offset 0x6c (108) >>>> Image Width: 20 Image Length: 20 >>>> Resolution: 72, 72 pixels/inch >>>> Bits/Sample: 1 >>>> Compression Scheme: None >>>> Photometric Interpretation: min-is-black >>>> Extra Samples: 1<unassoc-alpha> >>>> FillOrder: msb-to-lsb >>>> Orientation: row 0 top, col 0 lhs >>>> Samples/Pixel: 2 >>>> Rows/Strip: 1638 >>>> Planar Configuration: single image plane >>>> DocumentName: b.tif >>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>>> > system("convert b.tif +matte c.tif") >>>> > system("tiffinfo c.tif") >>>> TIFF Directory at offset 0x44 (68) >>>> Image Width: 20 Image Length: 20 >>>> Resolution: 72, 72 pixels/inch >>>> Bits/Sample: 1 >>>> Compression Scheme: None >>>> Photometric Interpretation: min-is-black >>>> FillOrder: msb-to-lsb >>>> Orientation: row 0 top, col 0 lhs >>>> Samples/Pixel: 1 >>>> Rows/Strip: 2730 >>>> Planar Configuration: single image plane >>>> DocumentName: c.tif >>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>>> > sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 >>>> LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] >>>> LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] >>>> LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> other attached packages: >>>> [1] EBImage_3.6.0 abind_1.1-0 >>>> >>>> _______________________________________________ >>>> 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 >>> >> >
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