[Skim-app-users] Skim-app-users Digest, Vol 96, Issue 15

Discussion:

Josh Carney

2015-05-21 13:43:07 UTC

Thanks for your reply, Jan.
When I wrote "unsearchable" I was simply referring to the interface practice that I use most frequently in dealing with such PDFs. That is, using the command+f option to search for a particular sequence of characters, or in the case of DevonThink, searching the text of the document alongside that of others in aggregate form.
As you allude to, the problem is actually greater than this. Though I can select and even highlight text in this file for annotation, attempts to copy it end up in some sort of strange tab-like space being entered in the paste area. This can only be deleted by removing textual elements on either side of it. (That is, it can't simply be backed-over and deleted--in such attempts, the cursor just won't move.) No characters display in the copied "text," just a space that might be about 20 characters (an estimate) long.
If this is a frequent problem with the PDFKit I guess I should count myself lucky. Any ideas on what makes a particular PDF more likely to display such behavior? (This particular error is very repeatable with this particular file.)
Best wishes,
Josh

Subject: Skim-app-users Digest, Vol 96, Issue 15
Date: Thu, 21 May 2015 12:02:11 +0000
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1. Re: search disables after export save (Jan David Hauck)
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Message: 1
Date: Wed, 20 May 2015 10:28:10 -0700
Subject: Re: [Skim-app-users] search disables after export save
To: For general discussion about using Skim
Content-Type: text/plain; charset="iso-8859-1"
What do you mean by "unsearchable"?
Can you select text from the file? Can you copy?
If you copy text from the file into a text document, does it display
correctly or are the characters scrambled?
I've come across the latter when modifying scanned and OCR'ed PDFs in
Preview. For some reason PDFKit frequently screws up the character mapping
of scanned pdfs. This has been a problem for probably a decade now and
Apple has been unable to fix it.
Jan

Thanks for your reply, Christiaan. In answer to your question, yes, that's
just what I meant. In terms of the PDFKit it looks like you're right: I
replicated the issue with Preview and I don't get the issue with Acrobat
Pro. I'm very glad to hear this is an exception, though I'm still curious
to know if others have experienced a similar problem. I'm wondering if
there's a way to anticipate what PDFs might be prone to this sort of
behavior.
Josh

Hello,
My apologies in advance if this has been covered before. I didn't find

it discussed in my forum search under the terms I selected.

I have at least one PDF (an article downloaded from project muse) that

becomes unsearchable after I save with the"export - as PDF - with embedded
notes" option. That is, after I attempt to shift from Skim format to a
format in which my annotations are available to other PDF applications. For
those who might be interested and have access, the article is available at
https://muse.jhu.edu/journals/journal_of_middle_east_womens_studies/v005/5.2.barzilai-lumbroso.pdf

The issue is repeatable with this item, but is not occurring with some

of the other articles I recently worked with. That said, it has me
concerned, as I only became aware of the phenomenon when searching this
particular article. I generally annotate, export as PDF, and store my
articles in the DevonThink Pro Office database, where I often search them
in aggregate rather than on an article-by-article basis. So I might not
know if there are other instances of similar behavior.

Is this behavior familiar and, if so, do you have any suggestions for

dealing with it? For the time being I will re-annotate this particular PDF
in Acrobat Pro or another program, since I need to have the annotations
visible across a variety of platforms, but I would prefer to stick to the
Skim-based workflow that I have.

Thanks in advance for any thoughts you might be able to offer.
Josh

Do you mean that when you open a file that was exported with embedded
notes it becomes unsearchable? I have not heard about that. But it is also
something we cannot do anything about. It's really Apple's problem. That is
because the PDF is saved by Apple's PDFKit, which for us is a black box, we
have no influence over how that is done, and regularly has problems (that's
an important reason why we don't use it by default.) For sure, this must be
an exception. Also, it would be true for other PDFKit based apps, like
Preview.
Christiaan
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Jan David Hauck

2015-05-21 17:40:02 UTC

Permalink

Post by Josh Carney
Any ideas on what makes a particular PDF more likely to display such

behavior?

I've come across the problem with scanned PDFs as well as with LaTeX
generated PDFs.
When I would modify them in Preview (e.g., deleting a page, rearranging
pages, extracting pages, etc.) then the character mapping would get lost
and there is no way to recover from that (other than regenerating the
PDF). That's why I only use Acrobat if I have to edit PDFs (although it
sucks, because all the drag and drop functions in Preview are much easier).

Post by Josh Carney
Thanks for your reply, Jan.
When I wrote "unsearchable" I was simply referring to the interface
practice that I use most frequently in dealing with such PDFs. That is,
using the command+f option to search for a particular sequence of
characters, or in the case of DevonThink, searching the text of the
document alongside that of others in aggregate form.
As you allude to, the problem is actually greater than this. Though I can
select and even highlight text in this file for annotation, attempts to
copy it end up in some sort of strange tab-like space being entered in the
paste area. This can only be deleted by removing textual elements on either
side of it. (That is, it can't simply be backed-over and deleted--in such
attempts, the cursor just won't move.) No characters display in the copied
"text," just a space that might be about 20 characters (an estimate) long.
If this is a frequent problem with the PDFKit I guess I should count
myself lucky. Any ideas on what makes a particular PDF more likely to
display such behavior? (This particular error is very repeatable with this
particular file.)
Best wishes,
Josh

mapping

of scanned pdfs. This has been a problem for probably a decade now and
Apple has been unable to fix it.
Jan

Thanks for your reply, Christiaan. In answer to your question, yes,

that's

just what I meant. In terms of the PDFKit it looks like you're right: I
replicated the issue with Preview and I don't get the issue with

Acrobat

Pro. I'm very glad to hear this is an exception, though I'm still

curious

to know if others have experienced a similar problem. I'm wondering if
there's a way to anticipate what PDFs might be prone to this sort of
behavior.
Josh

Hello,
My apologies in advance if this has been covered before. I didn't

find

it discussed in my forum search under the terms I selected.

I have at least one PDF (an article downloaded from project muse)

that

becomes unsearchable after I save with the"export - as PDF - with

embedded

notes" option. That is, after I attempt to shift from Skim format to a
format in which my annotations are available to other PDF

applications. For

those who might be interested and have access, the article is

available at
https://muse.jhu.edu/journals/journal_of_middle_east_womens_studies/v005/5.2.barzilai-lumbroso.pdf

The issue is repeatable with this item, but is not occurring with

some

them

in aggregate rather than on an article-by-article basis. So I might not
know if there are other instances of similar behavior.

Is this behavior familiar and, if so, do you have any suggestions for

dealing with it? For the time being I will re-annotate this particular

PDF

in Acrobat Pro or another program, since I need to have the annotations
visible across a variety of platforms, but I would prefer to stick to

the

Skim-based workflow that I have.

Thanks in advance for any thoughts you might be able to offer.
Josh

Do you mean that when you open a file that was exported with embedded
notes it becomes unsearchable? I have not heard about that. But it is

also

something we cannot do anything about. It's really Apple's problem.

That is

because the PDF is saved by Apple's PDFKit, which for us is a black

box, we

have no influence over how that is done, and regularly has problems

(that's

an important reason why we don't use it by default.) For sure, this

must be

an exception. Also, it would be true for other PDFKit based apps, like
Preview.
Christiaan

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Jan Jakob Bornheim

2015-05-22 15:30:16 UTC

Permalink

Post by Josh Carney

Post by Josh Carney
Any ideas on what makes a particular PDF more likely to display such

behavior?
I've come across the problem with scanned PDFs as well as with LaTeX
generated PDFs.
When I would modify them in Preview (e.g., deleting a page, rearranging
pages, extracting pages, etc.) then the character mapping would get lost
and there is no way to recover from that (other than regenerating the
PDF). That's why I only use Acrobat if I have to edit PDFs (although it
sucks, because all the drag and drop functions in Preview are much easier).

For me it happens if I have a combination of a non-standard embedded fonts
and non-English characters, such as Umlauts.

I can only speculate, but I wonder whether you, Jan, have it happening
because you use something akin to Adobe's ClearScan (
http://blogs.adobe.com/acrolaw/2009/05/better_pdf_ocr_clearscan_is_smal/)
when creating OCRd PDFs, which would result in non-standard fonts being
embedded. I think some scanners might even do that automatically (wasn't
there one that would randomly confuse characters?). I just tried it by
using the ClearScan OCR setting in Adobe for the first time on a text in
French (lots of accents, PDFKit can't handle them at all, try copy and
pasting them!), and sure enough I had my first ever scanned PDF that would
become corrupted by PDFKit. With all my other scans, I have always left the
picture layer intact and just let Adobe or OCRKit add a text layer. These
PDFs would not be corrupted by PDFKit.

JJ

Post by Josh Carney

mapping

of scanned pdfs. This has been a problem for probably a decade now and
Apple has been unable to fix it.
Jan

Thanks for your reply, Christiaan. In answer to your question, yes,

that's
I

replicated the issue with Preview and I don't get the issue with

Acrobat

Pro. I'm very glad to hear this is an exception, though I'm still

curious

to know if others have experienced a similar problem. I'm wondering if
there's a way to anticipate what PDFs might be prone to this sort of
behavior.
Josh

Hello,
My apologies in advance if this has been covered before. I didn't

find

it discussed in my forum search under the terms I selected.

I have at least one PDF (an article downloaded from project muse)

that

becomes unsearchable after I save with the"export - as PDF - with

embedded

notes" option. That is, after I attempt to shift from Skim format to a
format in which my annotations are available to other PDF

applications. For

those who might be interested and have access, the article is

available at
https://muse.jhu.edu/journals/journal_of_middle_east_womens_studies/v005/5.2.barzilai-lumbroso.pdf

The issue is repeatable with this item, but is not occurring with

some

of the other articles I recently worked with. That said, it has me
concerned, as I only became aware of the phenomenon when searching

this

particular article. I generally annotate, export as PDF, and store my
articles in the DevonThink Pro Office database, where I often search

them

in aggregate rather than on an article-by-article basis. So I might

not

know if there are other instances of similar behavior.

Is this behavior familiar and, if so, do you have any suggestions

for

dealing with it? For the time being I will re-annotate this

particular PDF

in Acrobat Pro or another program, since I need to have the

annotations

visible across a variety of platforms, but I would prefer to stick to

the

Skim-based workflow that I have.

Thanks in advance for any thoughts you might be able to offer.
Josh

Do you mean that when you open a file that was exported with embedded
notes it becomes unsearchable? I have not heard about that. But it is

also

something we cannot do anything about. It's really Apple's problem.

That is

because the PDF is saved by Apple's PDFKit, which for us is a black

box, we

have no influence over how that is done, and regularly has problems

(that's

an important reason why we don't use it by default.) For sure, this

must be

an exception. Also, it would be true for other PDFKit based apps, like
Preview.
Christiaan

------------------------------------------------------------------------------

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Physical-Virtual-Cloud

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One dashboard for servers and applications across

Physical-Virtual-Cloud

Widest out-of-the-box monitoring support with 50+ applications
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Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
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End of Skim-app-users Digest, Vol 96, Issue 15
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