Comments (14)
from thermimagej.
are you getting this error running the sample csq I provide? https://github.com/gtatters/ThermImageJ/blob/master/SampleFiles.zip
It is possible that my perl split script needs adjusting for your file type. I could take a look at a sample file of yours if you are able to send it to me?
from thermimagej.
from thermimagej.
ok. so, that suggests an install problem, so sending me file might not help yet. Can you verify whether the split.pl script was copied to your FIJI/scripts folder, according to the (brief) instructions.
from thermimagej.
from thermimagej.
and the installation checks? did they produce errors? I'd need to know that exiftool, perl and ffmpeg are installed properly.
from thermimagej.
I haven't tested on Catalina yet (I've been delaying the update to get bugs out of the os), but I doubt that is the issue. Unfortunately, I won't update to Catalina until the end of semester to avoid sudden loss of function during teaching. Hopefully I can diagnose the problem one error at a time.
from thermimagej.
Hmm..i just noticed in your error message that FIJI seems to think that the split.pl is in a different subfolder than Fiji/scripts. But on line 57 of the toolset, I know I scan for where your ImageJ folder is. Can you confirm the precise path location of your FIJI install? I would advise you place FIJI in a folder that you have read+write permission. Usually on a Mac, FIJI goes directly in the Application folder:
i.e.
/Applications/FIJI
thus, the scripts would be:
/Applications/FIJI/scripts
I don't know if this will affect functionality or not.
from thermimagej.
from thermimagej.
Aha! FIJI is Just ImageJ. The circular acronym doesn't really help! Glad you figured it out, because I would not have known.
I do need to add some error checking for file/folder executions and some more informative error messages. Eventually I'll have that up in the install instructions.
Thanks for filing the issue. At least I'll know what trips users up.
from thermimagej.
from thermimagej.
I would like that as well! With colleagues, outside of this software, we are trying to get Machine learning roi coding working, but it won't likely be part of ThermimageJ. Early days yet for that.
But at least you can use ThermimageJ to extract or convert CSQ files into a format where you might do that in another environment.
As for ROI saving...that seems like some kind of feature that ImageJ might already have, but I know what you mean. That is probably beyond my skills for the time being. You could probably use ImageJ masking features to remove all parts of the image space that are below or above your threshold temperature. I am less likely to develop those features, much as they would be nice to have!
from thermimagej.
in terms of a moving ROI...there are Tracker or Tracking plugins that you might be able to get to work that are available in FIJI. Once you have the ROIs registered, I think those plugins allow you to extract certain types of info like mean, max or median intensity scores (which would be temperature if you ran the conversions).
from thermimagej.
from thermimagej.
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from thermimagej.