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Currently I need to highlight certain sections in PDFs. These highlights would need to be saved. What tools are out there to do this on Ubuntu?

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Have you looked at PDF edit from USC? –  Mitch May 23 '12 at 16:54
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Have just tried pdfedit, ugly gui, no highlighting tools. It is not what i wanted. (if you are sure, give me instructions about how to do that with that pdfedit) –  Anwar Shah May 23 '12 at 18:03
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I tried it, too. It has such tools in the toolbar above the text, but it didn't work as expected: When I tried to highlight text in a pdf I made with LibreOffice the area above the text became highlighted ... But than saving it the highlighting also is visible with Evince for example, although at the wrong place. → Not really a solution. –  Jakob May 23 '12 at 18:09
    
Google docs. I know it sounds like a cop-out at first, but it works and it will definitely be cross-platform. You can even download the result as a PDF containing the annotations you made –  cxrodgers Jun 25 '13 at 10:07

20 Answers 20

up vote 54 down vote accepted

Okular supports PDF annotations.

To save the highliting/annotations directly in the PDF document, choose "File" -> "Save as..." and create a new PDF which will contain your edits.

Edit: Inkscape supports PDF editing and most people seem not to be aware of this so I'm adding it to the answer.

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Brilliant! Just what I was looking for! :) –  ssanj Aug 7 '10 at 3:45
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Okular stores annotations and highlights outside of the edited document (it seems to be a Poppler limitation!) okular.kde.org/faq.php#addedannotationsinpdf This means that changes are only visible from Okular, on the machine they were created. –  Syzygy Aug 22 '11 at 23:10
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@downvoters: at least have the courtesy to specify why you're downvoting the answer. –  Li Lo Oct 26 '11 at 13:59
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Inkscape allowed me to highlight text as well as 'redact' some personal information from a PDF by drawing opaque boxes over the text. Excellent solution, took ~30 seconds to install, about the same amount of time to edit my one page PDF. Thanks Li Lo! –  OpensourceFool Jan 6 '13 at 22:48
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Okular can now save annotations to PDFs, see askubuntu.com/questions/1529/how-can-i-highlight-pdfs/… –  Thomas Arildsen May 14 '13 at 9:29

Actually, none of these solutions work half as well as anything on Windows or Mac OS. Okular stores annotations separately, so you lose them if you move or rename the pdf or if you want to view it on another computer. Mendeley only supports yellow highlighting and importing pdfs into inkscape or openoffice is pretty inconvenient if you want to read a paper and simply make some annotations.

Fortunately, there are some free pdf viewers for Windows that work flawlessly with wine (If you find wine too complicated, use PlayOnLinux - a great front end for wine configuration). One of the best of those viewers is the PDFXChange Viewer by Tracker Software. There is a free version that comes with a ton of annotation features, session saving etc. Grab it here:

http://www.tracker-software.com/product/downloads

And check out this screenshot:

http://www.tracker-software.com/image/Viewer1%28684%29_300x0.jpg

I really whish there was a working open source linux alternative (xournal is good, but too limited). But for the time being, I am happy with using wine.

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I'm sure Inkscape, pdfedit, or okular work at least half as well as some packages on MacOS or Windows. –  belacqua Mar 20 '11 at 22:27
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+1: This is, so far, the only good option. It works great in Wine, mod some Unity-specific bugs that are getting fixed, and supports a wide collection of document markup options. –  Syzygy Aug 22 '11 at 23:08
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I normally use Foxit_PDF_Editor on Wine –  blvdeer Jan 11 '13 at 18:44
    
I would like to add that PDFXChange Viewer does not work well with all Wine versions. For example with 64bit Wine 1.6 (and 1.5, I believe) it crashes when trying to save (and on other occasions). I found Wine 1.4 32bit to be perfectly working though. –  onse Sep 13 '13 at 14:45
    
Okular can now store the annotations in the pdf itself –  Karthik Nov 12 '13 at 23:16

xournal is also some software which you use for this task.

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xournal only saves the highlights in a xournal-specific format (basically converts the PDF to images, and highlights there) –  Syzygy Aug 22 '11 at 22:10
    
then what about the okular, it also save file in okular specific format –  Anwar Shah Jun 20 '12 at 9:46
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@Szygy :In contrast to okular xournal can however export the annotations to PDF –  Glutanimate Sep 16 '12 at 9:42
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I just used Xournal for annotating a PDF file, and exported the annotated version to PDF, and it worked perfectly. –  Erel Segal Halevi Mar 20 '13 at 10:28
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@ErelSegalHalevi Please disregard my last comment. Recent revisions of Xournal do not rasterize the PDF. Both text and scalable vector elements are preserved. This make Xournal the best choice for PDF annotation by far. –  Glutanimate Apr 21 '13 at 19:22

Future version of Evince will support PDF annotation and highlight. Here you can see a video of the first partial implementation, made by Carlos Garcia Campos

If you want to try I think you need to have at least evince 2.32 and recompile yourself latest version of Poppler cloning from the git repository:

git clone git://git.freedesktop.org/git/poppler/poppler

Here the launchpad bug of this missing feature from evince (poppler packaged for Maverick isn't enough updated).

21 april 2011 - Update Evince in Natty now support by default annotations (not highlighting). Evince in Natty is 2.32, poppler is 0.16.4.

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I have 12.04, evince 3.4.0, poppler 0.18.4, and I can't find the annotation feature in the menus... –  Erel Segal Halevi Mar 20 '13 at 9:29

There is a package called pdfedit that can do this.

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Note that pdfedit has been dropped from Ubuntu as of 12.10 –  Dustin Kirkland Dec 17 '12 at 22:22
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Also, on 12.04 there are some errors, such as, when trying to change the color or font. Also, pdfedit has no undo, which can be very frustrating, especially since the highlighing does not work as expected (highlights a full line instead of a single word). –  Erel Segal Halevi Mar 20 '13 at 9:27

The PDF viewer in Mendeley allows you to highlight and annotate pdfs.

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While Mendelay has a nice interface, the annotation abilities are limited (can only add sticky notes; no drawing or text boxes), and annotations and highlighting aren't saved in the document. –  Syzygy Aug 22 '11 at 23:06

There's a plugin for OpenOffice.org that does this.

http://extensions.services.openoffice.org/project/pdfimport

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For me the best solution was PDF X-Change Viewer.

It just installs and works flawlessly under Wine. (Source)

The only issue is that sometimes when you scroll fast it shows some white spaces over the text, that clear when you click or select a line in the document.

There is an option in the Edit menu under Preferences\Performance\Threads Usage: "Use synchronous mode of page rendering" which prevents those white spaces in mine.

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After years of asking for this, and after KDE 4.9 release, Okular is now capable to make annotations within the PDF itself, as this fixed bug and KDE's 4.9 release note states.

Unfortunately it seems that Ubuntu 12.04 users can't benefit from this new long demanded feature according to this bug. The good news is that it works under ubuntu 12.10 (which is due to be released)

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there are backport ppas to get this functionallity in 12.04: see askubuntu.com/questions/172126/… –  Uli Oct 18 '13 at 12:13

Jarnal is a good software that allows you to highlight

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I have got a workaround to this problem, but it is too localized. Using okular for reading a pdf file and then annotate by pressing F6 to bring Highlighting toolbar.

After annotating, you can save the file as document archive, which preserve the annotation. From File -> Export as -> Document Archive.

Note This file can only be opened by Okular.

Installing Okular: To install okular, issue this command in terminal :
sudo apt-get install okular

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I've tested PDF X-Change viewer and I experienced the same white space problem while scrolling. I'm currently using Foxit Reader 4.3 which works really flawlessly. Foxit 5 crashes with wine 1.3 but works fine with wine 1.4 and 1.5. The only minor bug is that when you add a text annotation, it will ask you if you want to download the dictionary. You simple click cancel and keep working. It will keep asking you just once every time you open Foxit.

I managed to make Foxit reader 4 my default pdf viewer but can open files by double clicking a pdf file only if Foxit is not open. With Foxit 5 this issue is solved too. See this thread: How do I set a wine program (ex. Foxit Reader for Windows) as the default program?

Hope the pdf annotation feature in evince improves to avoid using wine.

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I use an old version of Foxit Reader (the latest 4.x version from oldapps.com), and it works very well under Wine.

At the moment, there is no good native highlighting solution!

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I think that Xournal is the tool you're looking for. What you should do is exporting in PDF, and the changes will be saved in pdf.

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Maybe xournal (app to add annotations to pdf's files)

Click to install xournal

And okular save the hightlighting separetly then if you want to save the hightlighting you have to save the pdf like new file to save the hightlighting.

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I have tried saving as new file. Did you try that ? –  Anwar Shah May 23 '12 at 17:31
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This saves the highlighting to be part of the PDF in a way that can't be edited in other PDF editors, if I am correct. –  Syzygy May 23 '12 at 17:31
    
I really like Xournal but when you export Xournal annotations as PDF it saves an image of every page with the annotation. So when you send that pdf to someone else, they will not be able to search through it. Other than this main limitation, Xournal is pretty cool. –  Aras Aug 5 '12 at 7:55
    
I just used Xournal, and the file were saved as a searchable PDF. Excellent. –  Erel Segal Halevi Mar 20 '13 at 10:29

PDF Studio is, probably, the best solution. It is not free, but you can install it using the Ubuntu Software Center.

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Now you can actually export annotations to PDFs in Okular (this was not possible until recently): http://docs.kde.org/stable/en/kdegraphics/okular/annotations.html

It seems Okular has to be built with Poppler at least version 0.20. It works with Ubuntu 13.04.

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I had the same question but unfortunately I didn't arrive to any satisfactory answer, being okular the closest one (but as you say, it does not save the changes in the same file, which is a problem).

I finally decided to use "PDF-Xchange Viewer": that piece of program makes exactly what I wanted to do and does it well, but it has two problems: it is free but not opensource and there's no linux version, although it can be used in ubuntu via wine. I wish there were better ways to annotate PDFs and so on.

Maybe you could open an issue at okular developers so hopefully they can implement that feature in the nearly future.

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You should also try PDF Buddy, an online PDF editor that supports highlighting, annotation, and other common editing features. It's a fast and easy solution that works in any modern browser.

(Full disclosure: I'm a co-founder of PDF Buddy)

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I just tried pdfedit 0.4.5 for highlighting. Saved the document and opened in evince. The highlighting was centered properly. Looked like what I wanted.

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