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I'm needing reading some research papers whose formats are almost pdf.However I cannot find a good pdf reader which can make some notes while reading. Currently I use xournal however there seems not many choices when I want to make different comments. There exists another problem:the comments made is actually on another layer so other pdf readers cannot recongnize it. "Export to PDF" seems a little rude for me.

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Try okular. But it will face the same problem of layers. –  user14517 Mar 13 '12 at 6:45
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@Nunoxic, okular's comments are not portable - i.e. comments made with okular are not attached to the PDF and not viewable with other readers. I asked a similar question on TeX.SE: How to annotate PDF files generated by pdflatex? –  maxschlepzig Mar 13 '12 at 8:54
    
That's what I meant by layers. Its irritating that there is no good markup tool. –  user14517 Mar 13 '12 at 9:36
    
Wikipedia also only knows of Okular and Xournal...unfortunately –  sr_ Mar 13 '12 at 12:03
    
Thanks very much! –  Hongxu Chen Mar 14 '12 at 6:01

4 Answers 4

up vote 7 down vote accepted

[lib]poppler recently gained support for the annotations defined in the newer Adobe PDF specifications, and this has been implemented in evince. Unfortunately, it still lacks some features, such as the ability to delete annotations (IIRC, this is due to lack of support from poppler, not evince), and I had some issues regarding editing already existing comments (but I didn't have time to debug these properly).

So, on one hand, evince has, through poppler, support for standard, built-in PDF annotations, OTOH said support is not (yet) perfect.

This should also mean that other tools using poppler may get this kind of feature in the near future.

One thing you may find annoying is the lack of a "save" feature. It drives me mad, having to use "Save as" each time I want to save a copy of the annotations (I used windows (non-NT) some years ago, so I still have, once in a while, this strong urge to save my work frequently) — but, anyway, evince is intended as a viewer, not an editor, so enforcing "Save as" is really the way to fit this into their UI metaphor.

About portability, depending on where you go, maybe it suffices if the tool lets you grab the "annotation layer". I remember walking through a layered annotation tool for postscript many years ago (and at that time it was already old code, which would need some work to build) — if I get the time and I find myself needing PDF/postscript annotation tools again, I may go looking after that so that I can hack it...

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Since Version 0.17, Okular supports annotations saved to the PDF file. For this to work, you need to have a Okular compiled against a recent version of libpoppler (0.20+, this should be the case in any up to date linux distribution), and you need to use the "Save as..." command - otherwise the annotations are just saved to Okular's config directory, and only accessible by Okular itself.

This is proper PDF annotation, and can be edited by other PDF annotators, and extracted by other tools. For example, the annotations can be extracted to notes in Zotero using ZotFile.

Okular currently supports saving the following annotation types to PDF:

  • Pop-up notes
  • Inline notes
  • Text highlighting
  • Text underlining
  • Freehand lines
  • Polygons
  • Ellipses
  • Rectangles

Each type of annotation can have a text note attached. This appears to be most of the annotation types supported by the PDF specification.

Okular also supports "Stamp" annotations (adding an image), and these annotations do not save correctly to the PDF - the image does not appear, but any text annotation does get saved, as a kind of hidden pop-up note.

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Good news, thanks! –  Hongxu Chen Nov 4 '13 at 7:05
    
It should be noted, however, that the comment types are quite restricted and not much better than what evince offers (it's only highlighting and popup notes that can be exported to PDF, as far as I can remember). –  Glutanimate Nov 4 '13 at 14:31
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@Glutanimate: No, that's not true, Okular supports at least: pop-up notes, inline notes, text highlighting, text underlining, freehand lines, polygons, ellipses and rectangles, and each type of annotation can have a text note attached. I just tried it, and it worked fine opening the annotations in PDF-Xchange Viewer. –  naught101 Nov 5 '13 at 1:29
    
@naught101 Oh, that's great! I must admit the last time I tried out the PDF annotation support in Okular it was just when it was released. I am happy to hear that so much progress has been made since then. –  Glutanimate Nov 5 '13 at 14:57

This might not be the satisfying answer you are looking for, but PDF-XChange reader has never given me any qualms under WINE and it is by far the most powerful third-party PDF Editor out there (almost reaches feature parity with Adobe Acrobat Pro).

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Maybe have a look at pdfedit, a Freeware PDF Editor that can delinearize a PDF file to make it editable.

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I don't want to edit pdf file,just make some comments.pdfedit seems not a good pdf editing tool for me as well. –  Hongxu Chen Mar 13 '12 at 8:32

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