I got the debug messages as follows:

(base) ➜  TeXmacs /Applications/TeXmacs.app/Contents/MacOS/TeXmacs --debug-convert

TeXmacs] debug-convert, Loading dictionary corktounicode
TeXmacs] debug-convert, Loading dictionary cork-unicode-oneway
TeXmacs] debug-convert, Loading dictionary tmuniversaltounicode
TeXmacs] debug-convert, Loading dictionary symbol-unicode-oneway
TeXmacs] debug-convert, Loading dictionary symbol-unicode-fallback
TeXmacs] debug-convert, Loading dictionary symbol-unicode-math
TeXmacs] debug-convert, Loading dictionary corktounicode
TeXmacs] debug-convert, Loading dictionary unicode-cork-oneway
TeXmacs] debug-convert, Loading dictionary tmuniversaltounicode
TeXmacs] debug-convert, Loading dictionary unicode-symbol-oneway
TeXmacs] debug-convert, Loading dictionary corktounicode
TeXmacs] debug-convert, Loading dictionary cork-unicode-oneway
TeXmacs] debug-convert, Loading dictionary tmuniversaltounicode
TeXmacs] debug-convert, Loading dictionary symbol-unicode-oneway
TeXmacs] debug-convert, Loading dictionary symbol-unicode-math
TeXmacs] With linked TrueType support
2023-08-31 17:33:21.252 TeXmacs[11824:307101] +[CATransaction synchronize] called within transaction
TeXmacs] debug-convert, image_size not cached for :/Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, hummus_pdf_image_info:
TeXmacs] debug-convert, image =/Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, crop box={0, 80.0089, 0, 80.0089}
TeXmacs] debug-convert, w,h={80, 80}
TeXmacs] debug-convert, degrees image rotated :0
TeXmacs] debug-convert, dx,dy={-0, -0}
TeXmacs] debug-convert, image_to_png ...  using gs
TeXmacs] debug-convert, gs_to_png using gs
TeXmacs] debug-convert, image_size in cache for /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, 80 x 80
TeXmacs] debug-convert, w=446 h=446
TeXmacs] debug-convert, bbw=80 bbh=80
TeXmacs] debug-convert,  res =401 * 401
TeXmacs] debug-convert, "/Applications/TeXmacs.app/Contents/Resources/share/TeXmacs/bin/gs" -dQUIET -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pngalpha -dGraphicsAlphaBits=4 -dTextAlphaBits=4 -g446x446 -sOutputFile=/Users/yuliang/.TeXmacs/system/tmp/11824/tmp_741378756.png -r401x401 -dUseCropBox /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, answer :
2023-08-31 17:33:57.361 TeXmacs[11824:307101] +[CATransaction synchronize] called within transaction
TeXmacs] debug-convert, image_size in cache for /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, 80 x 80
TeXmacs] debug-convert, image_size in cache for /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, 80 x 80
TeXmacs] debug-convert, image_to_png ...  using gs
TeXmacs] debug-convert, gs_to_png using gs
TeXmacs] debug-convert, image_size in cache for /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, 80 x 80
TeXmacs] debug-convert, w=446 h=446
TeXmacs] debug-convert, bbw=80 bbh=80
TeXmacs] debug-convert,  res =401 * 401
TeXmacs] debug-convert, "/Applications/TeXmacs.app/Contents/Resources/share/TeXmacs/bin/gs" -dQUIET -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pngalpha -dGraphicsAlphaBits=4 -dTextAlphaBits=4 -g446x446 -sOutputFile=/Users/yuliang/.TeXmacs/system/tmp/11824/tmp_20891602.png -r401x401 -dUseCropBox /Users/yuliang/Computer/TeXmacs/pdf-image-cropped/logo.pdf
TeXmacs] debug-convert, answer :


comment #10:

> Still not reproduced on Linux.
>
> texmacs --debug-convert
>
> Then I link the image. I first have a file load dialog with preview, which triggers the creation of a png thumbnail (This probably does not occur on MacOs)
>
> TeXmacs] debug-convert, image preview :[/tmp/logo.pdf]
> TeXmacs] debug-convert, image_size not cached for :/tmp/logo.pdf
> TeXmacs] debug-convert, hummus_pdf_image_info:
> TeXmacs] debug-convert, image =/tmp/logo.pdf
> TeXmacs] debug-convert, crop box={0, 80.0089, 0, 80.0089}
> TeXmacs] debug-convert, w,h={80, 80}
> TeXmacs] debug-convert, degrees image rotated :0
> TeXmacs] debug-convert, dx,dy={-0, -0}
> TeXmacs] debug-convert, image_to_png ...  using gs
> TeXmacs] debug-convert, gs_to_png using gs
> TeXmacs] debug-convert, image_size in cache for /tmp/logo.pdf
> TeXmacs] debug-convert, 80 x 80
> TeXmacs] debug-convert, "gs" -dQUIET -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pngalpha -dGraphicsAlphaBits=4 -dTextAlphaBits=4 -g98x98 -sOutputFile=/home/pj/.TeXmacs/system/tmp/146465/tmp_1135913469.png -dUseCropBox -dPDFFitPage /tmp/logo.pdf
> TeXmacs] debug-convert, answer :
>
> When I confirm the dialog, the image is actually inserted and a png is created for on-screen display:
>
> TeXmacs] debug-convert, image_size in cache for /tmp/logo.pdf
> TeXmacs] debug-convert, 80 x 80
> TeXmacs] debug-convert, qt loading image /tmp/logo.pdf
> TeXmacs] debug-convert, image_to_png ...  using gs
> TeXmacs] debug-convert, gs_to_png using gs
> TeXmacs] debug-convert, image_size in cache for /tmp/logo.pdf
> TeXmacs] debug-convert, 80 x 80
> TeXmacs] debug-convert, "gs" -dQUIET -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pngalpha -dGraphicsAlphaBits=4 -dTextAlphaBits=4 -g132x132 -sOutputFile=/home/pj/.TeXmacs/system/tmp/146465/tmp_1149413475.png -dUseCropBox -dPDFFitPage /tmp/logo.pdf
> TeXmacs] debug-convert, answer :
>
> Now, I delete logo.pdf and rename logo-large.pdf to logo.pdf. Then I do Tools>Update>Pictures. This clears the size cache, all cached bitmaps and reloads all images. On the console, this gives:
>
> TeXmacs] debug-convert, image_size not cached for :/tmp/logo.pdf
> TeXmacs] debug-convert, hummus_pdf_image_info:
> TeXmacs] debug-convert, image =/tmp/logo.pdf
> TeXmacs] debug-convert, crop box={0, 241.627, 0, 247.227}
> TeXmacs] debug-convert, w,h={241, 247}
> TeXmacs] debug-convert, degrees image rotated :0
> TeXmacs] debug-convert, dx,dy={-0, -0}
> TeXmacs] debug-convert, qt loading image /tmp/logo.pdf
> TeXmacs] debug-convert, image_to_png ...  using gs
> TeXmacs] debug-convert, gs_to_png using gs
> TeXmacs] debug-convert, image_size in cache for /tmp/logo.pdf
> TeXmacs] debug-convert, 241 x 247
> TeXmacs] debug-convert, "gs" -dQUIET -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pngalpha -dGraphicsAlphaBits=4 -dTextAlphaBits=4 -g132x132 -sOutputFile=/home/pj/.TeXmacs/system/tmp/146465/tmp_1720702465.png -dUseCropBox -dPDFFitPage /tmp/logo.pdf
> TeXmacs] debug-convert, answer :
>
> So the new image size is correctly determined and the new image displays correctly, with no crop.
>
> But like I said, image handling is different in MacOS... I reopen and change the Summary so as to make this apparent:
>
> Linked PDF images get cropped -> cached pdf image sizes not properly refreshed on MacOs, images get cropped

I attached two images of different sizes. How to reproduce the bug:

1. New document
2. Link logo.pdf
3. Remove logo.pdf and rename logo-large.pdf to logo.pdf
4. Update Pictures
5. Observe the image get cropped

I got error messages in the console, but I can't copy them. (--debug-convert in the terminal is not working).

BTW, can you reopen this bug?

comment #8:

> Right, this unexpected. However, not having access to a MacOs machine for reproducing and investigating your issue, I'd really need the full debug->convert output to retrace what goes wrong there (in order to understand how/why the cached size content was incorrectly determined). Since you suspect some interaction/confusion between images, having the tm file and all the images could be useful too.

(file #55100, file #55101)

The bug appeared again in another document. I turned on the debug menu and activate debug->convert. The error message says something like "image size blahblah in cache 1000x300", which is wrong, because my image is 1000x400. My previous image in this Figure is 1000x300.

comment #6:

> The bug seems to have disappeared, so I close it.
>

Sorry for the late reply. Now I can't reproduce it either. But it occurs in another document previously. I also run the app in the debug mode by running the suggested commands, and I didn't see any error messages. I will investigate it further later.

comment #4:

> I cannot reproduce in Debian, either. However, this is not entirely surprising since image handling can be different on MacOS, according to the c++ code... Jadelight, can you please turn on the debug menu and activate debug->convert entry before importing the image (as an alternative, you can start texmacs with the --debug-convert command line option), and report here the corresponding debug output?

The submitter reports on the forum:
"Apple M2 Max, OS 13.4.1 (22F82). TeXmacs 2.1.2, installed from the latest build in github.
Sometimes the images are not cropped but padded with more a big white space, and the issue can get fixed by restarting TeXmacs."

I can't reproduce this on my system (Fedora Linux, TeXmacs 2.1.2). Perhaps it depends on the Qt version or platform?

BTW, the pdf is created in matlab by the "exportgraphics" command. The problem occurs only if I choose 'image' as the value for the option 'ContentType'. If I choose 'vector', then the image is displayed correctly.