[R] Artifacts in pdf() of image() (w/o comments)

[Mark Wardle]

It may be worth outputting postscript and converting to PDF from
there. Although Preview can do this, it may be worth looking at
Ghostscript which *may* not have simila problems.

I have also had PDFs which have displayed well in Preview and open
source tools and have been garbled in Adobe Acrobat, so the problems
aren't limited to Preview.

Best wishes,

Mark

On 13/08/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
> Michael Kubovy wrote:
> > On Aug 12, 2007, at 6:24 AM, Duncan Murdoch wrote:
> >
> >
> >> Michael Kubovy wrote:
> >>
> >>> Dear r-helpers,
> >>>
> >>> In my previous message there were comments in the code that may
> >>> have  made cutting and pasting awkward. Here it is w/o them.
> >>>
> >>> I have two questions:
> >>>
> >>> (1) The following produces a pdf with artifacts. How do I prevent
> >>> them?
> >>>
> >>>
> >> What artifacts do you see?  It looks like a smoothly varying field
> >> when produced by R 2.5.1 and viewed in Acrobat Reader 6.0 on Windows.
> >>
> >> Duncan Murdoch
> >>
> >>> require(grDevices)
> >>> imSize <- 200
> >>> lambda <- 10
> >>> theta <- 15
> >>> sigma <- 40
> >>> x <- 1:imSize
> >>> x0 <- x / imSize -.5
> >>> freq = imSize/lambda
> >>> xf = x0 * freq * 2 * pi
> >>> f <- function(x, y){r <- -((x^2 + y^2)/(sigma ^2)); exp(r)}
> >>> z <- outer(xf, xf, f)
> >>> f1 <- function(x, y){cos(.1 * x)}
> >>> z1 <- outer(xf, xf, f1)
> >>> pdf('gabor.pdf')
> >>> image(xf, xf, z * z1, col = gray(250:1000/1000),
> >>> xlab = '', ylab =  '', bty = 'n', axes = FALSE, asp = 1)
> >>> dev.off()
> >>>
> >
> > I'm working on a Mac. You're right, Acrobat 6.05 renders the figure
> > nicely, but when it's included in a LaTeX-produced pdf or viewed with
> > the Mac Preview program, a grid of fine white lines is superimposed
> > on the figure. So I believe that it's a matter of aliasing, which I
> > might be able to prevent by adjusting the parameters of the figures.
> > I just don't know enough to figure this out, and would appreciate
> > guidance.
> I see the artifacts in Preview on a Mac too.  So it looks to me like a
> Mac bug.
>
> Preview is actually pretty poor at graphics display; see
> <http://www.geuz.org/pipermail/gl2ps/2007/000223.html>.
>
> My only suggestion is not to use Preview.
>
> Duncan Murdoch
>
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-- 
Dr. Mark Wardle
Clinical research fellow and specialist registrar, Neurology
Cardiff, UK