Hi, I am coming from a Github error that has been resolved in its initial problem, but has shown I still need some help in terms of understanding how Fiji and the pyimagej wrapper works.
Above is the link to what has been said already on Github so I do not have to post the entirety of the background here. In short, I am trying to run a code in python that automates an imaging process which involves a rotational stage (with a python code I have already written and works separately), an EMCCD camera controlled by micromanager (which I cannot work on until later notice due to COVID), and the use of Fiji to work on the image that gets popped up once the camera takes the picture. The reason I am using Fiji in the first place, is typically during an experiment once the camera creates the image I save the image through Fiji then close it and wait for the next to open (we are doing tomography). I am new to coding in python and previously had simply written a script using Fiji’s scripting capabilities. This script works when I run it directly from Fiji. Since I don’t have the camera instead of a new image being produced I have been opening an existing image which has worked. However, when I try to execute this code in an anaconda environment using pyimagej and writing the script as referenced in my github link, it never seems to find an active image to save.
The last comment on my issue on github shows I may be going about this the wrong way. If there is another way to wait for an active image, save it, and close it that is much easier, I am all ears. I was just going with what I knew as I am new to coding.