Export MatrixPlot graphics to PDF

Question

I am trying to export a plot generated by MatrixPlot to PDF but am having problems with the way the exported PDF is rendered.

  mPlot = MatrixPlot[length, 
  Epilog -> {Cyan, 
    MapIndexed[If[#1 != 0, Text[#1, Reverse[#2 - 1/2]]] &, 
     Reverse[number], {2}]}, Mesh -> True, 
  FrameTicks -> {{Table[i, {i, 9}], 
     MapIndexed[{First[#2], regionCodes[[#1]]} &, 
      Table[i, {i, 9}]]}, {Table[i, {i, 9}], 
     MapIndexed[{First[#2], Rotate[regionCodes[[#1]], 90 Degree]} &, 
      Table[i, {i, 9}]]}}, ColorFunctionScaling -> False, 
  PlotRange -> {Min[length], Max[length]}]

The matrices length (plotted as shades of gray in the figure below), number (shown as the cyan numbers in the figure below), and regionCodes have the following values

length = {{0, 0, 0, 0, 0, 0, 0, 0, 0}, {0, 0.079774, 0.0545131, 
   0.0484267, 0.0614324, 0.0627509, 0.0572262, 0.0424639, 0}, {0, 0, 
   0.0600802, 0.100418, 0.0615561, 0.0737833, 0.0732888, 0.0624553, 
   0}, {0, 0, 0, 0.0740108, 0.0559982, 0.0666054, 0.0749018, 
   0.0493431, 0}, {0, 0, 0, 0, 0.0774839, 0.0554172, 0.0564699, 
   0.0491287, 0}, {0, 0, 0, 0, 0, 0.0798436, 0.0643044, 0.0606039, 
   0}, {0, 0, 0, 0, 0, 0, 0.107009, 0.0713126, 0}, {0, 0, 0, 0, 0, 0, 
   0, 0.0951722, 0}, {0, 0, 0, 0, 0, 0, 0, 0, 0}}
number = {{0, 0, 0, 0, 0, 0, 0, 0, 0}, {0, 37, 53, 21, 778, 1064, 228,
    15, 0}, {0, 0, 27, 40, 761, 1164, 272, 21, 0}, {0, 0, 0, 7, 331, 
   507, 125, 9, 0}, {0, 0, 0, 0, 5935, 12430, 2917, 245, 0}, {0, 0, 0,
    0, 0, 10665, 4323, 393, 0}, {0, 0, 0, 0, 0, 0, 664, 90, 0}, {0, 0,
    0, 0, 0, 0, 0, 7, 0}, {0, 0, 0, 0, 0, 0, 0, 0, 0}}
regionCodes = {"New England", "Middle Atlantic", "East North Central",
   "West North Central", "South Atlantic", "East South Central", 
  "West South Central", "Mountain", "Pacific"}

This is length//MatrixForm

enter image description here

And this is number//MatrixForm

enter image description here

The plot looks like this when shown in Mathematica enter image description here

But the exported PDF is rendered as follows (shown in OS X Preview) enter image description here

There is a lot of shading and (and anti-aliasing?) going on (it shouldn't!). The only solution I have come up with is to rasterize the plot before exporting it. It does the job, but I don't consider it very elegant.

Export["regionIBD_MatrixPlot.pdf", Rasterize[mPlot, ImageResolution -> 600], ImageSize -> Full]

The funny thing is that if I export it as TIFF, it renders correctly. Is there a way to export the plot as a vector graphics and not as a bitmap?

Are you using version 10? There have been other complaints about PDF export issues in v10 so this may be part of a larger problem. I couldn't test it in v9 since some definitions are not present in the post. — mfvonh, Aug 26 '14 at 18:29
Thanks. Yes, I am using version 10. I'll look up other comments, in case there are already workarounds posted. — darXider, Aug 26 '14 at 18:30
Have a look here there are some nice strategies concerning vectors for simple graphics and/or high resolution rasterized image. And please post code and data, if people are willing to help this is very helpful. — , Aug 26 '14 at 18:36
Thanks @Lou. I've already read that thread. The method suggested there in the first answer (by @Heike) involves rasterizing the image, although when I used "AllowRasterization" -> True, it produced the same shaded(!) PDF, hence my use of Rasterize[].
Oh, and I have posted code and data! Is it not readable? Did I use an incorrect format? — darXider, Aug 26 '14 at 18:41
Code is ok, but if I'm not mistaken regionCodes, length and number can not be copied, are not as data but as image uploaded. People will not write off your data. — , Aug 26 '14 at 18:49
exporting to EPS and using epstopdf produced the same old shaded PDF. — darXider, Aug 26 '14 at 19:20
duplicate of http://mathematica.stackexchange.com/questions/11273/pdf-exports-of-arrayplots-are-fuzzy-os-x/11283#11283 ? — chris, Aug 26 '14 at 21:20
^ more or less! it's the same problem (fuzziness in OS X Preview), but I also do see the same problem in Adobe Reader, and changing Rendering options there hasn't fixed it for me. — darXider, Aug 26 '14 at 21:59

score 8 · Accepted Answer · 2014-08-27T16:17:44.290

8

To long for a comment, but looks great on "10.0 for Mac OS X x86 (64-bit) (June 29, 2014)" with AR, Preview and Skim. Shut-down and restart your system and try with an alternative viewer ...

enter image description here

Edit

@Jens response is fantastic, right? The procedure improves the resolution dramatically and even reduced the size.

enter image description here

I was able to test both algorithms on iMac & MacBookRetina (Home) and iMac (work). No difference, still the same results. The PDF's I opened on W7 & W8 with AR without significant differences between Mac and W be seen.

I am also "R" user and therefore use X11 and Cairo. On my Mac the Cairo Engine is the PDF Creator (I guess?). I wanted to share this information with the community.

Maybe this Information leads to a new question with even better answers.

edited Aug 27 '14 at 16:17

answered Aug 26 '14 at 19:22

Oh, cool! Your answer made me think that maybe the problem is indeed in Preview, so I looked at its Preferences and in the PDF tab, there is an option "Smooth test and line art"; unchecking it fixed the issue. Thanks a lot! – darXider Aug 26 '14 at 19:29
You are most welcome, to check the settings and preferences is always a good thing :) – Aug 26 '14 at 19:35
True! I just tried Adobe Acrobat, and it does the same weird smoothing/shading (and I haven't been able to fix it yet!). – darXider Aug 26 '14 at 19:37
@darXider You should upvote Lou's answer :) – mfvonh Aug 26 '14 at 20:33
i tried, really, but i have less than 15 reputations, and it prevented me! sorry, but i'm only a n00b here ;) – darXider Aug 26 '14 at 20:34
@darXider Oh oops. No big deal, I just thought maybe you had forgotten. Welcome to the site. – mfvonh Aug 26 '14 at 21:12
ok! upvoted now. thanks Lou and @mfvonh. – darXider Aug 26 '14 at 22:00
@Lou: just to double-check! did you have to turn off any anti-aliasing/smoothing options in Skim and/or Adobe Reader (assuming that's what you meant by "AR" in your answer)? i tried Skim as well, and i had to turn off that option. in the figure you posted, is that option on or off? – darXider Aug 26 '14 at 22:29

score 7 · Answer 2 · edited Apr 13 '17 at 12:55

7

I see this problem too, and I found it is fixed in Skim and Preview by using this function:

rasterTrick[plot_] := 
 Show[plot, 
  Prolog -> {Opacity[0], Texture[{{{0, 0, 0, 0}}}], 
    VertexTextureCoordinates -> {{0, 0}, {1, 0}, {1, 1}}, 
    Polygon[{{0, 0}, {.1, 0}, {.1, .1}}]}]

Export["regionIBD_MatrixPlot1.pdf", mPlot // rasterTrick]

The convenience function rasterTrick is from my answer to Avoiding grid lines inside filled area in RegionPlot exported as PDF.

edited Apr 13 '17 at 12:55

Community

1

answered Aug 27 '14 at 06:47

Jens

97,245
7
213
499

fantastic! it fixes things in Preview, Skim, and Adobe Reader. – darXider Aug 27 '14 at 15:10
I tend to testify this answer is Jens-sastic. – Aug 27 '14 at 16:23
@Lou New dictionary item - "jens-sastic (adj.): awkward and painful solution to a problem that shouldn't exist in the first place" – Jens Aug 27 '14 at 18:32
I just remembered that I had asked a closely related question myself in 2012, and that this answer also applies there: Color ramp banding in PDFKit when exporting Raster image Inset to PDF. – Jens Aug 27 '14 at 18:45
Your solution works for me as well, but the exported graphic is still a bit more fuzzy than if I save it as png for example. Is there a way to improve the level of fuzzyness based on your code (even if it increases the size of the pdf)? – Sulli Nov 18 '14 at 13:16

score 5 · Answer 3 · edited Apr 13 '17 at 12:55

A similar problem is being discussed in this thread. I'll copy my method of going around it here, in case someone stumbles on this thread through searches.

I have been saving a file wit MatrixPlot (using Save As...-> PDF), and have encountered a similar problem.

Turns out, MatrixPlot (and similar) data is being exported as a bitmap, which gets blurred in Adobe Reader 9 (which I have), even if "Smooth line art" and "Smooth images" is unchecked in preferences. The PDF showed fine in Okular, but that is probably just the lack of smoothing in that viewer.

I have found the solution on Inkscape forums. Open the PDF file in a text editor, and locate the following line:

/Interpolate true

Change it to the following:

/Interpolate false

Et voilà! The problem is solved, and the PDF shows fine in Adobe Reader, without blurring.

thanks for the information! that's very useful. – darXider Nov 25 '14 at 23:49 — darXider, Nov 25 '14 at 23:49

Export MatrixPlot graphics to PDF

3 Answers3

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