"run Byte Swapper" issue when importing FLIR JPG

[gtatters]

"run Byte Swapper" issue when importing FLIR JPG

[gtatters]

Can you confirm you have installed Byte Swapper? Assuming you have, the error is associated when a user tries to run byte swapper without an image present.

Next time importing it, could you select the "keep default byte order" option at the top of the window just to make sure it successfully can convert and load the image into FIJI first, before running byte swapper.

Also, if you can send a sample of the image or verify that the image loads and operates properly on your version of ThermimageJ. Most common issue I have is people unknowingly loading non-radiometric jpgs.

Also, ThermimageJ won't work with ATS-JPGs - these are formatted differently than other FLIR radiometric jpgs.

[coatej]

Hi Glenn. Just heard back from my colleague. Byte Swapper is definitely installed. He tried the "keep default byte order" option and this error popped up instead of the previously posted one:

The image loads on my version on ThermImageJ, yes. Here's a sample too.

[gtatters]

the image loads fine for me. But if the issue is with the byte swapper plug in on your colleague's computer, I don't know what I can do to help. the language is a macro language, calling many routines within FIJI that should be tested separately. One thing I do advise is to avoid using folder names with white space since the cross-platform compatibility for folder pathing in FIJI is tricky and I am not sure I have it working in all cases.

[gtatters]

Could you try opening this image into FIJI (don't use ThermimageJ to import it) and then verifying if the Byte Swapper works on it? If it doesn't work then it means the issue is with how you have installed Byte Swapper, and you might need to contact the author of that plugin. You said in the opening message that you can't call Byte Swapper from the Plugins menu, which suggests it is not functioning, and ThermimageJ assumes it is functioning.

[gtatters]

With byte swapper the image should toggle back and forth between these two uploaded versions. While the second one looks dark and washed out, that is simply due to the 16 bit span of the radiance values, squished into the grayscale image space.

[gtatters]

so, I could replicate nearly the same error you mention in the first post simply by deleting Byte Swapper.class from the Plug-ins folder, suggesting that the Byte Swapper file is not in plug-ins folder. Please verify that the .class file is in the plug-ins folder but it seems to me that the issue is not one with ThermimageJ.

[coatej]

Thanks for taking a good look here! I really appreciate your efforts. I'll get back to you as soon as I've heard from my colleague.

[coatej]

Okay, so he's spent the better part of the day looking into this, and still no luck unfortunately, we've hit a wall.

Byte Swapper is definitely within the plug-ins folder, see below screenshot.

Regarding the point about just opening image with fiji and then applying byte swapper, this is the issue which came up:

So he's now tried uninstalling and deleting everything and starting from scratch. Exiftool, ffpmeg, and perl all verified using bash commands. However perl split.pl script not accessible, see below screenshot. Do you know where/how to change this in the .ijm file?

[gtatters]

ack! That seems over kill to remove and restart. When I asked for you to try byte swapper on its own, I meant to try it on one of the 16 bit greyscale images I attached not the colourised jpg you attached above. The split.pl file is on this repository website, just download all the files and follow the install instructions or my install video.

[gtatters]

to change the paths to conform to the user's installation settings, somewhere around about line 110 in the .ijm file are the various variables that need to be set. This is outlined on the repository installation section:
https://github.com/gtatters/ThermImageJ#setting-and-verifying-paths-to-command-line-tools

[coatej]

Hi Glenn,

Thanks again for your help here. So after the uninstall and reinstall (we got all the paths working in the end) we attempted your Byte Swapper suggestion with the image you attached. Byte Swapper was able to be called from the plugins menu and it works on images opened through Fiji, toggling between the two.

However, when uploading through thermimageJ this error still appears:

[gtatters]

I notice that you have installed FIJI on a university machine Onedrive account? I haven't had much success using these machines because these routines are making read/write operations and need complete write access. If this is the issue, I can't really help with that. I also notice you installed exiftool.exe in an unusual location rather than the default one indicated on the exiftool website. Have you verified that windows has given full access to exiftool at the command line?

[coatej]

Hi Glenn,
Great news!! You were right about the OneDrive causing issues with analysis. My colleague moved where the FLIR images were stored to his C drive and voila, it worked. Thanks so much for sticking through with us while we fumbled around for the answer! All good now.

[gtatters]

Great! I'll close this now. I'm guessing that "synced" drives are aliased differently than actual folders on the local machine.