Re: [O] OT: Annotating PDF Org
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 rlad...@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 Adamsrlad...@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: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
* Russell Adams rlad...@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: [O] OT: Annotating PDF Org
On 05/07/2013 11:02 PM, Paul Rudin wrote: Russell Adams rlad...@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: [O] OT: Annotating PDF Org
On Mon, 6 May 2013 08:39:07 -0500,Russell Adams rlad...@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 Adamsrlad...@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: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
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 Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3
Re: [O] OT: Annotating PDF Org
On Tue, 7 May 2013 16:39:42 -0500,Russell Adams rlad...@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 Adamsrlad...@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: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
Russell Adams rlad...@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.
[O] OT: Annotating PDF Org
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 Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3
Re: [O] OT: Annotating PDF Org
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: [O] OT: Annotating PDF Org
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 Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3
