Re: [R] Making TIFF images with rtiff

From: Inman, Brant A. M.D. <Inman.Brant_at_mayo.edu>
Date: Fri 12 Jan 2007 - 14:16:52 GMT

Thanks to all the responders. Here are some replies to the comments:

  1. Concerning the term TIFF "format". It may be that the journals are misusing the term TIFF, but it would also appear that wikipedia is as well. The first sentence in the wiki link sent below states:

"Tagged Image File FORMAT (abbreviated TIFF) is a file FORMAT for mainly storing images, including photographs and line art."

Either way, the semantics of the word TIFF are probably not that important for the current query. If a publisher wants images in TIFF, I would like to provide them in that format, regardless of whether or not I deem the request proper. After all they are the publishing experts!

2) Converting PNGs to TIFFs with Photoshop. This is principally what I have done in the past that has given the poor results that I have noted. I thought that it could be something that I was specifically doing wrong so I consulted the medical imaging and design department of my institution (Mayo Clinic) which informed me that there is often a loss of information, some times quite large, in these types of image format conversions. They suggested that it is best to work with the TIFFs from the start if possible, which is why I am trying to explore this option in R. It is interesting that my imaging department was able to convert the WMF format to TIFF with much better success. However, since Photoshop does not support WMFs, I am unable to do this myself. I have downloaded ImageMagick and will try that.

3)Lack of gratitude by R users.
It is interesting to note upon reviewing the R-help files that many queries (perhaps even the majority?) do, in fact, convey gratitude. Unfortunately, I have also noted that there are several messages from R developers that appear to feel underappreciated. I suspect that one reason that R is experiencing an explosion of users is precisely that people appreciate and value the donation of free time provided by statistical experts--such as Harrell, Weigand, Ripley and Kort in this thread--for the development of accurate and powerful statistical software. Furthermore, the support provided for the software in the form of R-help is outstanding, again something that I think is part of the package deal that is attracting new users to R. In other words, one should not assume a general lack of gratitude on behalf of R-help users but should see the growth of R as evidence that the software and its developpers/supporters are indeed greatly valued. I do not think that R would be used much if people did not appreciate the nice packages, functions and help provided. Indeed, those of us that have access to multiple software programs (I have access to JMP, SPSS, SPLUS and SAS) choose R as our primary method of analysis because we feel that the sharing environment supported by CRAN is a better way of doing statistical computing. Enough said.

4)Flexible journal policies.
Of 4 papers that I have submitted in the last 3 months for publication in 3 journals (all to cancer related journals), all were subjected to online file checkers that forced me to upload TIFF files instead of PDFs. Not only do they check the format, but also various other resolution related items. In other words, I would not have even made it past the online submission stage if I only PDFs to work with.

5)Using the bitmap function to make TIFFs. This sounds like a very attractive option. I have tried this option using the simple code below:



attach(cars)
plot(speed ~ dist) # Simple plot to test bitmap(file='C:\\...\\test.tif',type = "tifflzw", res = 1200)

Error in system(paste(gsexe, "-help"), intern = TRUE, invisible = TRUE) :

        gswin32c.exe not found


Despite what the error message suggests, I do have a functional Ghostscript 8.54 program installed on my Windows XP machine with the executable found in the directory: C:\Program Files\gs\gs8.54\bin\gswin32c. I am not sure why R is not finding the program. I tried making a Windows environmental variable, R_GSCMD, with this system address but that did not have any success. Does the gswin32c file need to be in my R PATH?

Brant Inman
Mayo Clinic



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