morphmet
Fri, 11 Dec 2009 12:50:38 -0800
-------- Original Message -------- Subject: Re: Morphometrics using R Date: Fri, 11 Dec 2009 19:23:08 GMT From: Joseph Kunkel <j...@bio.umass.edu> To: morphmet@morphometrics.org CC: Joseph Kunkel <j...@bio.umass.edu> References: <4b2288b4.4060...@morphometrics.org> With respect to the image file formats readable by R it should be noted that R has been a little conservative on reading files that are lossy or of ill defined content such as TIFFs and indexed images such as PNGs but has provided ways of printing output of images to such files for a long time. While it is nice to now be able to read such files into R for useful and decorative reasons the younger or beginning R user should know the evils of the TIFF, PNG and JPEG formats from a quantitative perspective. The TIFF file format produced by various softwares does not always conform to a standard that can be read by a good Graphic Image Manipulation Program. Some hardware companies produce image TIFFs that can only be read by their own software based on the ease of implementing your own custom format according to the TIFF standard. The JPEG is often used as a lossy (compressed to the point of irreversible data loss) file for compactness but each time it is saved it may lose more resolution unless the user is careful not to modify it. The PNG file is indexed with a color palette and although it may contain all the image detail that you want, the numbers that are used to index the palette are likely meaningless as data. The preferred image input for R has been the less well known PNM, PPM, PGM, PBM file formats which provide non-lossy binary, grey scale or RGB images that can be save in ASCII or binary file format. These formats are good for data that you want to be able to read and want to be rational in their construction. You could read these files with a word processor if you had a mind to. They have the benefit of being non-lossy in data as well as having the benefit of being a standard format that many software packages can read (GIMP, R) and manipulate unlike plain ill defined raster images that do not have dimension or layer information well specified. If landmarks are one's main objective and the image is of sufficient non-degraded resolution then by all means use the TIFF, PNG and JPEG formats. But be mindful of the reasons that R has been slow to develop libraries to read these formats. Joe Kunkel On Dec 11, 2009, at 7:00 PM, morphmet wrote:
-------- Original Message -------- Subject: Re: Morphometrics using R Date: Fri, 11 Dec 2009 17:41:56 GMT From: Kevin Middleton <k...@csusb.edu> To: morphmet@morphometrics.org References: <4b210421.2080...@morphometrics.org>I am attempting to learn how to do morphometrics on R using the book from Julien Claude and to visualize the jpegs I need to install the package rimage. However, the package will not install ("error: C++ compiler cannot create executables") and it automatically uninstalls the package. It is quoted as being "ORPHANED" on the website. Is there a comparable package for jpegs on R that anyone knows of? Thanks!Both the biOps (http://cran.r-project.org/web/packages/biOps/index.html ) and ReadImages (http://cran.r-project.org/web/packages/ReadImages/index.html ) packages have jpeg reading functions.Kevin ------------------------------------------------- Kevin M. Middleton Department of Biology California State University San Bernardino -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
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Joseph G. Kunkel, Professor Biology Department University of Massachusetts Amherst Amherst MA 01003 http://www.bio.umass.edu/biology/kunkel/ -- Replies will be sent to the list. For more information visit http://www.morphometrics.org