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Chabot Denis

2007-May-22 10:32 UTC

[R] Reducing the size of pdf graphics files produced with R

Hi,

Without trying to print 1000000 points (see <http:// 
finzi.psych.upenn.edu/R/Rhelp02a/archive/42105.html>), I often print  
maps for which I do not want to loose too much of coastline detail,  
and/or plots with 1000-5000 points (yes, some are on top of each  
other, but using transparency (i.e. rgb colors with alpha  
information) this actually comes through as useful information.

But the files are large (not as large as in the thread above of  
course, 800 KB to about 2 MB), especially when included in a LaTeX  
document by the dozen.

Acrobat (not the reader, the full program) has an option "reduce file  
size". I don't know what it does, but it shrinks most of my plots to  
about 30% or original size, and I cannot detect any loss of detail  
even when zooming several times. But it is a pain to do this with  
Acrobat when you generate many plots... And you need to buy Acrobat.

Is this something the pdf device could do in a future version? I  
tried the "million points" example from the thread above and the 55  
MB file was reduced to 6.9 MB, an even better shrinking I see on my  
usual plots.


Denis Chabot

Prof Brian Ripley

2007-May-22 16:47 UTC

head link

[R] Reducing the size of pdf graphics files produced with R

>From the help page
      'pdf' writes uncompressed PDF.  It is primarily intended for
      producing PDF graphics for inclusion in other documents, and
      PDF-includers such as 'pdftex' are usually able to handle
      compression.

If you are able to contribute a stream compressor, R will produce smaller 
plots.  Otherwise it is unlikely to happen (and it any case would be a
smaller contribution than that of the author of pdf(), who is quite happy 
with external compressors).

Acrobat does other things (not all of which it tells you about), but 
compression is the main advantage.

On Tue, 22 May 2007, Chabot Denis wrote:
> Hi,
>
> Without trying to print 1000000 points (see <http://
> finzi.psych.upenn.edu/R/Rhelp02a/archive/42105.html>), I often print
> maps for which I do not want to loose too much of coastline detail,
> and/or plots with 1000-5000 points (yes, some are on top of each
> other, but using transparency (i.e. rgb colors with alpha
> information) this actually comes through as useful information.
>
> But the files are large (not as large as in the thread above of
> course, 800 KB to about 2 MB), especially when included in a LaTeX
> document by the dozen.
>
> Acrobat (not the reader, the full program) has an option "reduce file
> size". I don't know what it does, but it shrinks most of my plots
to
> about 30% or original size, and I cannot detect any loss of detail
> even when zooming several times. But it is a pain to do this with
> Acrobat when you generate many plots... And you need to buy Acrobat.
>
> Is this something the pdf device could do in a future version? I
> tried the "million points" example from the thread above and the
55
> MB file was reduced to 6.9 MB, an even better shrinking I see on my
> usual plots.
>
>
> Denis Chabot
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Sundar Dorai-Raj

2007-May-22 17:19 UTC

head link

[R] Reducing the size of pdf graphics files produced with R

You need not buy Acrobat. There are two free software programs that will 
compress pdf files:

http://www.cutepdf.com
http://www.cs.wisc.edu/~ghost/ (and in particular GSView)

They both allow several levels of compression.

Thanks,

--sundar

Chabot Denis said the following on 5/22/2007 3:32 AM:> Hi,
> 
> Without trying to print 1000000 points (see <http:// 
> finzi.psych.upenn.edu/R/Rhelp02a/archive/42105.html>), I often print  
> maps for which I do not want to loose too much of coastline detail,  
> and/or plots with 1000-5000 points (yes, some are on top of each  
> other, but using transparency (i.e. rgb colors with alpha  
> information) this actually comes through as useful information.
> 
> But the files are large (not as large as in the thread above of  
> course, 800 KB to about 2 MB), especially when included in a LaTeX  
> document by the dozen.
> 
> Acrobat (not the reader, the full program) has an option "reduce file
> size". I don't know what it does, but it shrinks most of my plots
to
> about 30% or original size, and I cannot detect any loss of detail  
> even when zooming several times. But it is a pain to do this with  
> Acrobat when you generate many plots... And you need to buy Acrobat.
> 
> Is this something the pdf device could do in a future version? I  
> tried the "million points" example from the thread above and the
55
> MB file was reduced to 6.9 MB, an even better shrinking I see on my  
> usual plots.
> 
> 
> Denis Chabot
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Waichler, Scott R

2007-May-23 14:24 UTC

head link

[R] Reducing the size of pdf graphics files produced with R

> as you are using MacOS X, you'll have ghostscript installed anyway. so
> try in R `dev2bitmap' with `type =pdfwrite'. I believe `gs'
_does_
> include compression. a quick test showed at least a reduction by about
> a factor of 2 relative to `pdf()'. probably one can fiddle with the
> ghostscript settings (cf. e.g. `Ps2pdf.htm' in the ghostscipt 
> docs: you
> can adjust the resolution for images in the pdf file) to
> improve this, so as a last resort you could indeed export the graphics
> as postscript and do the conversion to `pdf' by adjusting the
`ps2pdf'
> switches. but even with the default settings the pdf produced via
> dev2bitmap/ghostscript is the better solution. apart from file size I
> by and then ran into problems when converting `pdf()' output to
> postscript later on, for instance.
Can you give an example of dev2bitmap usage?  I tried using it in place
of a pdf() statement.  An X11 window opened and my figure flew by, but I
didn't get the file output.  I also used dev2bitmap after opening a
pdf() and just before the dev.off() statement, since the help says it
works on the "current device", but again no written output.  What am I
doing wrong?

I tried:
  dev2bitmap(file = plotfile2, type="pdfwrite", width=8.5, height=11,
pointsize=12)
  print(myplot())
  dev.off()

and

  pdf(file = plotfile, paper="letter", width=8.5, height=11,
pointsize=12)
  print(myplot())
  dev2bitmap(file = plotfile2, type="pdfwrite", width=8.5, height=11,
pointsize=12)
  dev.off()

Thanks,
Scott Waichler
scott.waichler _at_ pnl.gov

Chabot Denis

2007-May-24 14:59 UTC

head link

[R] Reducing the size of pdf graphics files produced with R

Hi again,

Many of you have suggested other means than pdf device and/or  
conversion/compression of pdf outside of R.

I ran some tests on a small, a medium-size and a large figure. Here I  
summarize the results, which depend very much on the original  
graphics file. Please note that I wish to retain a vector-based  
graphic file.

You'll find at the end of this message the R program used to produce  
the graphics files.

Starting with a small size graphic file: in order, these were  
produced by

1) postscript device
2) pdf device
3) bitmap device (pdf output)
4) dev2bitmap, pdf output, from a quartz window
5) quartz device saved to pdf via command quarts.save
6) quartz device saved to pdf via save menu in R gui

-rw-r--r--   1 chabotd  chabotd    243446 May 23 21:00 test_ps_from_R.ps
-rw-r--r--   1 chabotd  chabotd    572513 May 23 21:00  
test_pdf_from_R.pdf
-rw-r--r--   1 chabotd  chabotd    600106 May 24 09:21  
test_pdf_bitmapR.pdf
-rw-r--r--   1 chabotd  chabotd    600050 May 24 09:22  
test_dev2bitmap.pdf
-rw-r--r--   1 chabotd  chabotd   1657446 May 23 21:00  
test_pdf_from_quartz.save.pdf
-rw-r--r--   1 chabotd  chabotd    572634 May 23 21:01  
test_pdf_from_quartz.menu.pdf

These show how "test_pdf_from_R.pdf" can be shrunk outside of R
1) the command pdftk
2) opening the pdf in any Mac OS X pdf viewer and doing "print to  
compressed pdf"

-rw-r--r--   1 chabotd  chabotd     68742 May 24 09:25  
test_pdf_pdftk.pdf
-rw-r--r--   1 chabotd  chabotd    100660 May 23 21:16  
test_pdf_print_to_comppdf.pdf

Finally, these show 3 conversions from postscript to pdf outside of R
1) command ps2pdf
2) command epstopdf
3) command pstopdf

-rw-r--r--   1 chabotd  chabotd    566626 May 23 21:12  
test_ps_ps2pdf.pdf
-rw-r--r--   1 chabotd  chabotd    566587 May 24 10:21  
test_ps_epstopdf.pdf
-rw-r--r--   1 chabotd  chabotd   1939788 May 24 10:20  
test_ps_pstopdf.pdf

For this first example, all pdf produced directly within R were of  
similar size, except one (quartz.save) that was 3x larger. Producing  
a postscript file and transforming it into pdf resulted in no  
significant saving. However pdf output from R can be shrunk (here to  
12% of original size) with pdftk. So far I found no adverse effect of  
this shrinking.

I did the same with a larger graphic, this example came from Dave  
Watson. Using the same blocks as above:

Produced with R:
-rw-r--r--   1 chabotd  chabotd    854320 May 24 09:08  
mauna_ps_from_R.eps
-rw-r--r--   1 chabotd  chabotd   1000504 May 24 09:08  
mauna_pdf_from_R.pdf
-rw-r--r--   1 chabotd  chabotd     96737 May 24 09:08  
mauna_pdf_bitmapR.pdf
-rw-r--r--   1 chabotd  chabotd     97236 May 24 09:17  
mauna_dev2bitmap.pdf
-rw-r--r--   1 chabotd  chabotd    468195 May 24 09:08  
mauna_pdf_from_quartz.save.pdf
-rw-r--r--   1 chabotd  chabotd    999853 May 24 09:09  
mauna_pdf_from_quartz.menu.pdf

PS to pdf outside of R
-rw-r--r--   1 chabotd  chabotd     95024 May 24 09:11  
mauna_ps_ps2pdf.pdf
-rw-r--r--   1 chabotd  chabotd    603021 May 24 10:40  
mauna_ps_pstopdf.pdf
-rw-r--r--   1 chabotd  chabotd     95015 May 24 10:40  
mauna_ps_epstopdf.pdf

pdf transformation outside of R
-rw-r--r--   1 chabotd  chabotd    104487 May 24 09:12  
mauna_pdf_pdftk.pdf
-rw-r--r--   1 chabotd  chabotd    134663 May 24 09:23  
mauna_print_to_comppdf.pdf

For this example, different methods of producing pdf within R had  
very different file sizes. The two methods based on quartz performed  
in reverse order compare to the previous example. Overall, using  
bitmap device or postscript-transformed-to-pdf outside of R produced  
files about 10% the size of the file produced by pdf device. But the  
latter could be shrunk almost as much using pdftk.

Finally, a larger-size example:
Produced with R:
-rw-r--r--   1 chabotd  chabotd   1426330 May 23 20:54 fig_ps_from_R.ps
-rw-r--r--   1 chabotd  chabotd   3384788 May 23 20:54  
fig_pdf_from_R.pdf
-rw-r--r--   1 chabotd  chabotd   3494689 May 24 09:03  
fig_pdf_bitmapR.pdf
-rw-r--r--   1 chabotd  chabotd   3494689 May 24 10:46  
fig_dev2bitmap.pdf
-rw-r--r--   1 chabotd  chabotd   3384832 May 23 20:54  
fig_pdf_from_quartz.menu.pdf
-rw-r--r--   1 chabotd  chabotd   9583552 May 23 20:52  
fig_pdf_from_quartz.save.pdf

PS to pdf outside of R
-rw-r--r--   1 chabotd  chabotd   3356223 May 23 21:12 fig_ps_ps2pdf.pdf
-rw-r--r--   1 chabotd  chabotd  11397461 May 23 23:51  
fig_ps_pstopdf.pdf
-rw-r--r--   1 chabotd  chabotd   3354762 May 23 23:55  
fig_ps_epstopdf.pdf

pdf transformation outside of R
-rw-r--r--   1 chabotd  chabotd    379307 May 23 22:31  
fig_pdf_comptk.pdf
-rw-r--r--   1 chabotd  chabotd    520509 May 24 00:19  
fig_pdf_print_to_comppdf.pdf

This time, as in the first example, there was little benefit going  
the bitmap device or ps to pdf route. Only shrinking the pdf with  
pdftk was effective. So examples with a lot of objects on the plot do  
not seem to benefit from postscript use, but one example with few  
objects (but objects that were "filled, don't know if it matters) did.

I have never done this in R, but could the pdftk command be run from  
within a R script? This would allow one to compress automatically  
when needed.

Thank you all for the suggestions,

Denis

##############  R program that produced the above files  
#################
# example 1, small
pdf(file="test_pdf_from_R.pdf", w=5, h=5, version="1.4",  
bg="transparent")
plot(rnorm(10000), rnorm(10000))
dev.off()

postscript(file="test_ps_from_R.ps", width=5, height=5,
paper="special")
plot(rnorm(10000), rnorm(10000))
dev.off()

bitmap(file = "test_pdf_bitmapR.pdf", width=5, height=5, type =  
"pdfwrite")
plot(rnorm(10000), rnorm(10000))
dev.off()

plot(rnorm(10000), rnorm(10000))
quartz.save(file="test_pdf_from_quartz.save.pdf",
type="pdf")
dev2bitmap(file="test_dev2bitmap.pdf", width=5, height=5,  
type="pdfwrite")
# here I also manually saved the quartz graphics and called it  
"test_pdf_from_quartz.menu.pdf"


# Example from Dave Watson


postscript(file = "mauna_ps_from_R.eps", width=5, height=5,  
horizontal=FALSE, paper="special", onefile=FALSE)
filled.contour(volcano, color=terrain.colors, asp=1)
title(main="volcano data: filled contour map")
dev.off()

pdf(file = "mauna_pdf_from_R.pdf", width=5, height=5)
filled.contour(volcano, color=terrain.colors, asp=1)
title(main="volcano data: filled contour map")
dev.off()

bitmap(file = "mauna_pdf_bitmapR.pdf", width=5, height=5, type =  
"pdfwrite")
filled.contour(volcano, color=terrain.colors, asp=1)
title(main="volcano data: filled contour map")
dev.off()

# on mac os x only
quartz(w=5, h=5)
filled.contour(volcano, color=terrain.colors, asp=1)
title(main="volcano data: filled contour map")
dev2bitmap(file="mauna_dev2bitmap.pdf", width=5, height=5,  
type="pdfwrite")
quartz.save(file="mauna_pdf_from_quartz.save.pdf",
type="pdf")
# here I also manually saved the quartz graphics and called it  
"mauna_pdf_from_quartz.menu.pdf"



# example 3, large

x <- rep(1:99, 20)

c <- 0
for (a in 1:3) {
   for (b in c(0.7, 0.9) ) {
   c<-c+1
   nam <- paste("Y", c, sep="")
   assign(nam, a + b*x + rnorm(length(x),20,10))
   }
   }
the.data <- data.frame(Y1, Y2, Y3, Y4, Y5, Y6)
rm(Y1, Y2, Y3, Y4, Y5, Y6)


pdf(file="fig_pdf_from_R.pdf", w=8, h=8, version="1.4",  
bg="transparent")
pairs(the.data)
dev.off()

postscript(file="fig_ps_from_R.ps", width=8, height=8,
paper="special")
pairs(the.data)
dev.off()

bitmap(file = "fig_pdf_bitmapR.pdf", width=8, height=8, type =  
"pdfwrite")
pairs(the.data)
dev.off()

# on mac os x only
quartz(w=8, h=8)
pairs(the.data)
dev2bitmap(file="fig_dev2bitmap.pdf", width=8, height=8,  
type="pdfwrite")
quartz.save(file="fig_pdf_from_quartz.savev2.pdf",
type="pdf")
# here I also manually saved the quartz graphics and called it  
"fig_pdf_from_quartz.menu.pdf"

Paul Hiemstra

2008-Feb-07 10:52 UTC

head link

[R] Reducing the size of pdf graphics files produced with R

Hi all,

Maybe a bit late, but I found a way that worked great for me.

In windows, download CutePDF
In linux (debian for me), install CUPS and cups-pdf

Open your pdf with a viewer and print to CutePDF or cups-pdf. Both 
support a range of compression options. I use cups-pdf and reduced an R 
output file of 3.6 mb to 0.9 mb. Much better if you want to include in a 
Latex article

cheers,
Paul

Chabot Denis wrote:> Hi,
>
> Without trying to print 1000000 points (see <http:// 
> finzi.psych.upenn.edu/R/Rhelp02a/archive/42105.html>), I often print  
> maps for which I do not want to loose too much of coastline detail,  
> and/or plots with 1000-5000 points (yes, some are on top of each  
> other, but using transparency (i.e. rgb colors with alpha  
> information) this actually comes through as useful information.
>
> But the files are large (not as large as in the thread above of  
> course, 800 KB to about 2 MB), especially when included in a LaTeX  
> document by the dozen.
>
> Acrobat (not the reader, the full program) has an option "reduce file
> size". I don't know what it does, but it shrinks most of my plots
to
> about 30% or original size, and I cannot detect any loss of detail  
> even when zooming several times. But it is a pain to do this with  
> Acrobat when you generate many plots... And you need to buy Acrobat.
>
> Is this something the pdf device could do in a future version? I  
> tried the "million points" example from the thread above and the
55
> MB file was reduced to 6.9 MB, an even better shrinking I see on my  
> usual plots.
>
>
> Denis Chabot
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>   

-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: 	+31302535773
Fax:	+31302531145
http://intamap.geo.uu.nl/~paul

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