Texmaker not displaying properly and offset annotations

[hunter1749]

Just like nasser1, I come from this post in need of displaying annotations (mainly scribbles made over PDFs) in LaTeX documents. I've had some trouble running it (probably should've restarted my Windows). Eventually I found out that executing initexmf --update-fndb in command prompt solved my issue with the package not being recognised, so hopefully that helps anyone else in the future.
It now works great, however I did notice some flaws (probably not happening just on my end).

1. As a user of Texmaker, the built-in PDF viewer does not display annotations (there is an extra warning though Annotations may have changed. Rerun to get annotations right), so I have to either open an external PDF viewer or work with the TeXworks editor (no warning here), where the annotations are visible. I do realise that it's likely Texmaker's problem, so any recommendations about alternative PDF viewers would be appreciated (extra light external PDF viewers or similar).
2. At first I thought that the annotations weren't editable anymore after being included in the LaTeX document, but then I noticed I had altered the PDFs' scale through \includegraphics[scale = 0.5]{my.pdf}. I assume this option is still viable? Anyway, that's perfectly fine behaviour by me, I wouldn't really want to have editable annotations at such small scale anyway, so I changed them all to their default scale of 1.0. Then it again appeared like it should, but I had trouble selecting the annotations. Here's the example I'm talking about. When looking at the PDF in PDFgear, everything is displayed properly as I mentioned, but the positions are offset for some reason. Possibly because there's two PDFs next to each other (it's always the left PDF that's offset a lot, the right one is not that bad)? Just tried with a single annotated PDF in a row instead of two and it's still offset a bit. This happens both with Texmaker and TeXworks, obviously. I think I'd might prefer it if there was an option to just display the annotations (at least the ones like these scribbles) and remove the ability to edit them afterwards in the final LaTeX document.

[AndreasMatthias]

Could you create a short example (short but complete LateX file) showing the misaligned annotations, please? It's hard to tell what's going wrong without seeing the LaTeX source and the included PDF.

Though scaling of PDFs should work basically, there are still a lot of things that might go wrong. It's very hard to hook into the scaling algorithm of LaTeX (graphicx). It would be much easier if LaTeX would restrict itself to using setmatrix for each and every scaling. But it's using \useimageresource for scaling as well and it's imossible to hook into \useimageresource. You can only hook before or after 'useimageresource. That's why I try to hook into \includegraphics during processing of its scale option, which works reliably most of the time. But if you put \includegraphics into a \scalebox , i.e. if you scale from the outside of \includegraphics, things will go wrong.

[hunter1749]

Sure, I'll use PDFgear again, because Acrobat just draws a big rectangle when selecting an annotation so it's not as obvious. Also you will see that I did find where one of the scaled down PDFs was, but it really offset it. That's the first video, the second one is for the normal scale. Here's the LaTeX file (using minipage, but I get these results using subfigure too) and I can also include the PDF later. It's also worth mentioning that the offsets change each time I reopen the made PDF. I apologise if there are any obvious mistakes, but I try to make the most out of my limited LaTeX experience.

\documentclass[a4paper, 12pt]{report}
\usepackage[margin = 3cm]{geometry}
\usepackage{graphicx}
\usepackage{flare}
\usepackage{lipsum}

\pagestyle{empty}

\begin{document}
	
	\lipsum[6]
	
	\begin{center}
	
		\begin{figure}[h]
		
			\begin{center}
			
				\begin{minipage}{0.3\textwidth}
					\begin{center}
						\includegraphics[scale = 0.5]{Pic1.pdf}
					\end{center}
				\end{minipage}
				\begin{minipage}{0.3\textwidth}
					\begin{center}
						\includegraphics[scale = 0.5]{Pic2.pdf}
					\end{center}
				\end{minipage}
				\begin{minipage}{0.3\textwidth}
					\begin{center}
						\includegraphics[scale = 0.5]{Pic1.pdf}
					\end{center}
				\end{minipage}
				\caption{Three pictures at scale = 0.5 and 0.3\textbackslash textwidth because 0.33 breaks it.}
				
			\end{center}
				
		\end{figure}
			
	\end{center}
	
	\lipsum[6]
	
	\begin{center}
	
		\begin{figure}[h]
		
			\begin{center}
			
				\begin{minipage}{0.4\textwidth}
					\begin{center}
						\includegraphics[scale = 1]{Pic1.pdf}
					\end{center}
				\end{minipage}
				\begin{minipage}{0.4\textwidth}
					\begin{center}
						\includegraphics[scale = 1]{Pic2.pdf}
					\end{center}
				\end{minipage}
				\caption{Two pictures at scale = 1 and 0.4\textbackslash textwidth because 0.5 breaks it.}
			
			\end{center}
				
		\end{figure}
			
	\end{center}
	
\end{document}

PDF (temporary link): https://we.tl/t-FbyTlnB7Gb.

[AndreasMatthias]

Thank you for this example. It seems like some parts of the attachment are not copied (adjusted) correctly. I will look into it.

Could you please provide Pic1.pdf and Pic2.pdf as well? This would be great for testing.

[hunter1749]

I thought you might need them, here's (again temporary) the link for both Pic1.pdf and Pic2.pdf. Looking closer at Pic2.pdf again, it seems that it is slightly offset even before using your package. I would assume that is because I used different brushes on it within my eink tablet's PDF app. In Pic1.pdf however, I used the basic pencil brush from the PDF app and unlike Pic2.pdf, the PDF annotation doesn't seem offset. What I do basically is get the PDFs made with tikz (and made smaller with geometry) on the eink tablet, then draw over them there, and export back so I can put them into a LaTeX document.

[AndreasMatthias]

Thanks for the files. I see that the bounding box of the appearance dictionary is wrong. I'll try to fix this. However, this doesn't seem to be the only issue. There's still something wrong, even after correcting the bounding box manually. Let's see.

[hunter1749]

Thanks for dedication. I've tried the following, more general example

%Previous document code with two and three pictures.
\lipsum[6]
	
	\begin{center}
	
		\begin{figure}[h]
			\begin{center}		
				\includegraphics[scale = 1]{Pic1.pdf}
				\caption{Placeholder picture.}
			\end{center}
		\end{figure}
	
	\end{center}	
	
\lipsum[3]
%End of document code.

as well, but it seems to be having the same issue with offsets. The only thing that comes to my mind is that the smaller dimensions of PDFs, customised with geometry, mess up the locations and so none of the compositions work in the end.

I've tried removing the lipsum package, which made the above example with one picture less offset. Once I even managed to align it as it should be when I had the right amount of dummy text around it. The rows with two and three pictures are still offset with no noticeable difference. Even after getting rid of all Badbox - Overfull \hbox . . . warnings, it doesn't help.

Then the only warning that remains in Texmaker is Warning - Annotations may have changed. Rerun to get annotations right, which doesn't appear in TeXworks.

The other weird thing is that TeXworks also (in these same conditions) produces no offsets on the above example with one picture, but in that same LaTeX document, the other two compositions remained offset. I found this pretty inconsistant though, and probably doesn't mean much, however it is true that TeXworks never displays the annotations warning.

[AndreasMatthias]

This bug is in my source code. So far I do not know how to fix it. But it's definitely nothing that you can change from within your LaTeX document. I'll have to fix it in the source.
These annotations causing problems here are using so called "appearance streams" which are stored in two or more separate PDF object. In contrast to simple annotations which consist of just one PDF object. And my code doesn't seem to handle these multi-layer PDF objects correctly.

[AndreasMatthias]

The cache file (*.flr) was not updated correctly. I've fixed it.

Please, download the new release.

[hunter1749]

Sorry, but the link in readme doesn't work, says Not Found.
Since you're familiar with PDF annotations, I've got one more thing to ask, somewhat unrelated to the current topic. If I ever wanted to flatten the PDF, perhaps to prevent someone from being able to accidentally grab drawn annotations while scrolling my annotated PDF, what would the best option for that be? I've tried with PDFtk, but it turns out it only flattens forms. On the other hand, print previews that give you flattened PDF to print, flatten the entire document, including the ability to select text. The only solution I've found so far is online, and I'd much prefer it to have this done offline somehow.

I've found the .zip on the releases page and copied over 11 .lua and 1 .sty files to tex/latex/flare, replacing the old ones. The results indeed seem a lot closer now than what they were before, thanks!

[AndreasMatthias]

Thanks, I forgot to create the TDS-packaged ZIP file. Now, the link is working.

A lot of tools provide means to flatten PDFs. But the results might differ greatly. Not all tools know how to handle all kinds of annotations. One way to go is using Ghostscript and convert the PDF to PS and back to PDF again like this:

pdf2ps Pic1.pdf - | ps2pdf - Pic1_flatten.pdf