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.
[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
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...
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
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.
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).
It may sound strange, but my best choice till now is Foxit Reader for Windows running under Wine. Currently using version 126.96.36.1991 and having installed winetricks allfonts (see here why) it works like a charm. Wine version 1.9.8 on Fedora23-64bit.
You can do many many things and commenting (with sidebar listing of those comments course) is at its best. Saving does not require "Save as...". Given that the linuxversion of Foxit is feature-less and okular or evince still lack some features, its my best choice-combined with a native linux reader like Evince(for quick/secondary viewing). Only drawback: a bit slower than native linux pdf application.
I finally found that the pdf reader that mostly satisfied my requirement is the foxit reader on Linux. The download page is here. The annotation works seamlessly with other readers on Windows.
It still cannot compare with its windows counterpart, according to its feature comparison page.
The only problem is that when using
xdg-open xxx.pdf when setting the default reader to be foxit reader, it cannot locate the path correctly therefore I have to firstly open foxit reader and then use "File->Open" (Ctrl-O) to open the related pdf file.