Problem with "Summarize Annotations" as Markdown

“Summarize Annotation → Markdown” creates unexpected result.

Problem description

I have a PDF containing this text:

In DEVONthink I highlight a few words like this:

When I create the annotation summary it returns the correct result:

Now I see that my highlight is not complete and I extend it like this:

Now the annotation summary looks like this:

Problem is:

  • DEVONthink falsely assumes that my extended highlight is actually two highlights
  • adds the last letter i to the first highlight although it was not originally highlighted by extending my highlight in the PDF
  • cuts the first letter from the second highlight, although it was highlighted

This can be much weirder when I annotate and highlight on my iPad and generate the annotation summary later when the last word of a highlighted sentence is added as the first word to the sentence in the annotation summary. Highlighting on my iPad with the Apple Pencil often requests extending the highlight because sometimes the first word is omitted by the first try to highlight.

Expected result

I would rather expect an annotation summary like this:

DEVONthink should assume that continuing highlighted text results in one quotation in the annotation summary file.

Environment: latest releases of DEVONthink, DTTG, MacOS Sonoma and iPadOS

Are you truly using two different colors? I could see where that might be interpreted as two different highlights.

No, both are yellow. The light green only appears once the moment when I mark it (in yellow). Afterwards the complete highlight is yellow.

Presumably if you unhighlight it all and then re-highlight it all as one phrase it then changes back to one highlight?

yes, it does

Then it seems to me the behavior is reasonable

There are arguably reasons why you might want those to be two separate annotations

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no, I think as long as the yellow highlight is continuing it should be interpreted as 1 highlight. When I want to mark two neighbouring highlights as different highlights I use different methods of highlighting (different colour, underlining or an non-highlighted space between etc.)

If you want to make it 1 highlight, then when you extend the highlight start somewhere in the middle of the first highlight. That will modify your first annotation as you prefer.

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Tried it but that removes the first highlight completely.

Another weird example how Devonthink interprets a single yellow highlight (left: highlighted part in PDF, right: annotation generated by DEVONthink):

Have you tried the Highlights app on the Mac app store? It plays very well with Devonthink and is fairly universally accepted as the best annotation/highlighting UI for creating, editing, and/or summarizing annotations.

I use DT3 for simple/brief annotations but use Highlights for any sort of long-form, detailed, or serious work. I have even pondered if I should use it as my default PDF reader but it does not support tabs for multiple PDFs so it probably is not usable for that purpose; but for viewing or annotating a single PDF it is superb.

A copy of the annotated PDF document would be useful, the annotations seem to be completely different.

Attached is another PDF where the first highlight results in corrupt annotation. Also attached: annotation summary as created by Devonthink (converted to PDF).

The Only Thing More Dangerous Than Authoritarianism - The Atlantic.pdf (396.7 KB)
Annotation summary.pdf (32.5 KB)

Which app did you use to highlight the document? The internal order of the highlights is a mess and the creator of the PDF document is actually Safari?!?

Thanks for checking!

Browser is Safari (most of the times I use the Safari reader mode for PDF prints to DEVONthink) and I annotate/highlight in the DTTG-PDF editor on my iPad using the Apple Pencil.

I don’t agree with this, and agree with @rkaplan’s comment that the behaviour is reasonable.

There’s already a mechanic for editing a highlight if you need to increase its size (and that mechanic is the same across multiple apps, e.g. Kindle, Readwise’s Reader, various native PDF programs). It would not make sense for DevonThink to handle highlights differently to other common apps, but in any case if I put two individual highlights next to each other, I don’t want them merging. If I wanted one highlight, I would’ve edited the first one as designed. I regularly highlight two sentences that are next to each other, but are separate points.

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I just found out that if I long-press on a highlight it displays 2 markers which I can use to increase or decrease the highlight. That is just what I was looking for!
But following @rkaplan ‘s advice I am also giving the HighLights app a try (and it looks great!)

Highlights is a great app. I had a problem with it not remembering my reading place, so it was fine for short papers but got annoying quickly with long reports. That was last summer though and I imagine they’ve fixed that by now.

I mostly use DTTG’s interface, but when I need something fancier I use PDFExpert (the free version). I only really need the highlighter tool, the textbox tool and sometimes the pen tool if I feel like shaking things up a bit, so most PDF apps would meet my needs (as long as they use standard annotation functions, I am very strict about that!). What I like about PDFExpert is you can remove the tools you don’t need from the toolbar, which means you can strip out all the visual clutter (you can also hide the toolbar if you don’t want it at all, and move its location to different screen edges).

I went on a quest to find a different process for handling my PDFs, but after a year I’ve mostly ended up back where I started, in DTTG with PDFExpert when I feel like it :joy: (I’m sure there is a lesson here about tweaking our tech set-ups, but no matter how much we are warned it’s a lesson we have to learn for ourselves, over and over again in some cases…)