OT: Annotating PDF & Org

OT: Annotating PDF & Org

[Russell Adams]

Given the emacs and Org oriented nature of this group, I'd like to
know if anyone has found a good Orgish (ie: portable, text, etc) to
annotate PDFs?

Features would be items like highlighting blocks, adding notes
(margins or "sticky" notes), and saving to either a sidecar file in a
text format (ala Org) or directly appending the PDF.

Thanks.

------------------------------------------------------------------
Russell Adams                            RLAdams@AdamsInfoServ.com

PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

Re: OT: Annotating PDF & Org

[Vincent Beffara]

> Given the emacs and Org oriented nature of this group, I'd like to
> know if anyone has found a good Orgish (ie: portable, text, etc) to
> annotate PDFs?
>
> Features would be items like highlighting blocks, adding notes
> (margins or "sticky" notes), and saving to either a sidecar file in a
> text format (ala Org) or directly appending the PDF.

Not portable probably, but Skim (a very nice PDF viewer for Mac OS X)
supports notes in an xml file next to the PDF, and something like this
would make sense in a more general setting. Maybe using the same spec to
be compatible?

(Skim can then reexport everything as a single PDF file if needed, but a
nice use-case for what you suggest would be something like personal
org-mode reading notes on an article for which keeping them separate
would make more sense.)

      /v

-- 
Vincent Beffara

Re: OT: Annotating PDF & Org

[Russell Adams]

On Mon, May 06, 2013 at 03:53:05PM +0200, Vincent Beffara wrote:
>
> Not portable probably, but Skim (a very nice PDF viewer for Mac OS X)
> supports notes in an xml file next to the PDF, and something like this
> would make sense in a more general setting. Maybe using the same spec to
> be compatible?
>
> (Skim can then reexport everything as a single PDF file if needed, but a
> nice use-case for what you suggest would be something like personal
> org-mode reading notes on an article for which keeping them separate
> would make more sense.)

An excellent suggestion! I am on Linux, but I wasn't specific about
platform because I was hoping to see how other tools worked across
different platforms.

I'll go read up on it.

Thanks.

------------------------------------------------------------------
Russell Adams                            RLAdams@AdamsInfoServ.com

PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

Re: OT: Annotating PDF & Org

[Ramon Diaz-Uriarte]

On Mon, 6 May 2013 08:39:07 -0500,Russell Adams <RLAdams@AdamsInfoServ.Com> wrote:
> Given the emacs and Org oriented nature of this group, I'd like to
> know if anyone has found a good Orgish (ie: portable, text, etc) to
> annotate PDFs?

> Features would be items like highlighting blocks, adding notes
> (margins or "sticky" notes), and saving to either a sidecar file in a
> text format (ala Org) or directly appending the PDF.


I am not sure this will be of much help since the annotations, etc, are
not originally saved in a sidecar file but this is basically what I do:

- Annotate/highlight the PDF, keeping the annotations in the PDF itself
  (when on the computer I use Okular, and "Save As"; if in the tablet, I
  use ezPDF or similar). I emphasize this: the annotations are in the PDF
  itself (i.e., if you open the PDF with evince, acrobat reader, whatever,
  you'll see them there).

- Extract the annotations from my complete collection of PDFs (nightly
  cron job), storing all of them in an org file, with a link to the
  PDF. (I do the extraction with Leela
  ---https://github.com/TrilbyWhite/Leela---, which I find is more
  reliable than poppler-based approaches, such as that in recoll).


So the orgish part is just the second one, but it works for me: I can
search all of my annotations and jump directly to the PDF, from a single
org file from within Emacs.

Highlights? Nope, it does not work as Leela does not extract them and I
could not find another tool to do it automagically. Recoll will extract
all text from PDFs (not the annotations, though), so I can search for
specific text on my complete PDF collection using recoll. But that ain't
orgish at all ;-) and it is decoupled from the previous approach.



A few more details, and some ugly R code that I use to do this are
available here: http://ligarto.org/rdiaz/Zotero-Mendeley-Tablet.html#sec-9


Best,


R.


> Thanks.

> ------------------------------------------------------------------
> Russell Adams                            RLAdams@AdamsInfoServ.com

> PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

> Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02@gmail.com
       ramon.diaz@iib.uam.es

http://ligarto.org/rdiaz

Re: OT: Annotating PDF & Org

[Russell Adams]

On Tue, May 07, 2013 at 11:36:31PM +0200, Ramon Diaz-Uriarte wrote:
> - Annotate/highlight the PDF, keeping the annotations in the PDF itself
>   (when on the computer I use Okular, and "Save As"; if in the tablet, I
>   use ezPDF or similar). I emphasize this: the annotations are in the PDF
>   itself (i.e., if you open the PDF with evince, acrobat reader, whatever,
>   you'll see them there).

My understanding was that Okular didn't update the PDF, it had a
mini-database. You're saying if you save the PDF again it'll combine
the annotations?

------------------------------------------------------------------
Russell Adams                            RLAdams@AdamsInfoServ.com

PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

Re: OT: Annotating PDF & Org

[Ramon Diaz-Uriarte]

On Tue, 7 May 2013 16:39:42 -0500,Russell Adams <RLAdams@AdamsInfoServ.Com> wrote:
> On Tue, May 07, 2013 at 11:36:31PM +0200, Ramon Diaz-Uriarte wrote:
> > - Annotate/highlight the PDF, keeping the annotations in the PDF itself
> >   (when on the computer I use Okular, and "Save As"; if in the tablet, I
> >   use ezPDF or similar). I emphasize this: the annotations are in the PDF
> >   itself (i.e., if you open the PDF with evince, acrobat reader, whatever,
> >   you'll see them there).

> My understanding was that Okular didn't update the PDF, it had a
> mini-database. You're saying if you save the PDF again it'll combine
> the annotations?

It used to be that Okular saved the annotations in an external file
(located at ~/.kde/share/apps/okular/docdata or similar), I think as an
XML file (if memory serves me well). You can still do that, but as of some
recent version of Okular (0.15?  which you might need to compile yourself,
depending on your Linux distro), you can also save the annotations and
highlights in the PDF itself (the PDF, not the "okular document").

From the okular docs:
http://docs.kde.org/stable/en/kdegraphics/okular/annotations.html


The long thread, extending back in time five years, about this feature
request, etc

https://bugs.kde.org/show_bug.cgi?id=151614



I am not sure what you mean by "combine the annotations". But if you do
"Save As", you can save the annotations in the PDF itself. You can, I
guess, do both things (save in the external file, and save in the PDF),
but I've never done that.  

Note, though, that incorporating annotations in the PDF itself, which
means you use the "Save As", is somewhat of a pain, because by default the
file name and directory are not reasonable, in my opinion; see this
feature request: https://bugs.kde.org/show_bug.cgi?id=319042. (This is why
I now do most of my paper reading/PDF annotation in the tablet, even if I
have no keyboard there).


By the way, as of now (or a month or so back, at most), evince can save
annotations in the PDF itself, but will not highlight.


Best,

R.


> ------------------------------------------------------------------
> Russell Adams                            RLAdams@AdamsInfoServ.com

> PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

> Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02@gmail.com
       ramon.diaz@iib.uam.es

http://ligarto.org/rdiaz

Re: OT: Annotating PDF & Org

[Paul Rudin]

Russell Adams <RLAdams-oD4XmFtju8vuCfmLQ01/GwC/G2K4zDHf@public.gmane.org> writes:

> Given the emacs and Org oriented nature of this group, I'd like to
> know if anyone has found a good Orgish (ie: portable, text, etc) to
> annotate PDFs?
>
> Features would be items like highlighting blocks, adding notes
> (margins or "sticky" notes), and saving to either a sidecar file in a
> text format (ala Org) or directly appending the PDF.


I realise this doesn't answer your question exactly, but I use xournal
for adding highlights and notes to pdfs on linux. It does save the notes
in a "sidecar file", but its not a text file. There's an option to save
a new pdf with the annotations included.

Re: OT: Annotating PDF & Org

[Karl Voit]

* Russell Adams <RLAdams@AdamsInfoServ.Com> wrote:
> Given the emacs and Org oriented nature of this group, I'd like to
> know if anyone has found a good Orgish (ie: portable, text, etc) to
> annotate PDFs?

Please take a look at [1] for how I am extracting PDF annotations to
my reference management done with Org-mode.

  1. https://github.com/novoid/extract_pdf_annotations_to_orgmode
-- 
mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode:
       > get Memacs from https://github.com/novoid/Memacs <

https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on github

Re: OT: Annotating PDF & Org

[Scott Randby]

On 05/07/2013 11:02 PM, Paul Rudin wrote:
> Russell Adams <RLAdams@AdamsInfoServ.Com> writes:
> 
>> Given the emacs and Org oriented nature of this group, I'd like to
>> know if anyone has found a good Orgish (ie: portable, text, etc) to
>> annotate PDFs?
>>
>> Features would be items like highlighting blocks, adding notes
>> (margins or "sticky" notes), and saving to either a sidecar file in a
>> text format (ala Org) or directly appending the PDF.
> 
> 
> I realise this doesn't answer your question exactly, but I use xournal
> for adding highlights and notes to pdfs on linux. It does save the notes
> in a "sidecar file", but its not a text file. There's an option to save
> a new pdf with the annotations included.

I've also used Xournal for marking up and adding notes to PDF files, but
the new PDF is blurry if the original PDF came from a LaTeX file.

Scott Randby

Re: OT: Annotating PDF & Org

[Ramon Diaz-Uriarte]

To set the (new) record straight:

> On Tue, 7 May 2013 00:44 Ramon Diaz-Uriarte <rdiaz02 <at> gmail.com> writes:

(...)

[Talking about Okular]

> Note, though, that incorporating annotations in the PDF itself, which
> means you use the "Save As", is somewhat of a pain, because by default the
> file name and directory are not reasonable, in my opinion; see this
> feature request: https://bugs.kde.org/show_bug.cgi?id=319042. (This is why
> I now do most of my paper reading/PDF annotation in the tablet, even if I
> have no keyboard there).


As of 45 minutes ago that is no longer the case, because the bug has been
fixed/the request has been honored.

https://projects.kde.org/projects/kde/kdegraphics/okular/repository/revisions/460502d1240ae5eaa865b3e2873a23322b836ebf

https://bugs.kde.org/show_bug.cgi?id=319042



R.



(...)

On Tue, 7 May 2013 16:39:42 -0500,Russell Adams <RLAdams@AdamsInfoServ.Com> wrote:
> On Tue, May 07, 2013 at 11:36:31PM +0200, Ramon Diaz-Uriarte wrote:
> > - Annotate/highlight the PDF, keeping the annotations in the PDF itself
> >   (when on the computer I use Okular, and "Save As"; if in the tablet, I
> >   use ezPDF or similar). I emphasize this: the annotations are in the PDF
> >   itself (i.e., if you open the PDF with evince, acrobat reader, whatever,
> >   you'll see them there).

> My understanding was that Okular didn't update the PDF, it had a
> mini-database. You're saying if you save the PDF again it'll combine
> the annotations?

> ------------------------------------------------------------------
> Russell Adams                            RLAdams@AdamsInfoServ.com

> PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

> Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02@gmail.com
       ramon.diaz@iib.uam.es

http://ligarto.org/rdiaz