The workshop materials are a couple of years old and would be potentially misleading today.
> I have many of these working in ImageJ1 but would like to always have
> the option of fast, headless execution after prototype development. In
> ImageJ1, I end up having adapt a lot of the source code to make
> display optional. This work is part of a larger plan to make my data
> analysis more reproducible.
Fantastic. The basic idea of ImageJ2 along those lines is to implement your algorithms as parameterized commands, which declare their inputs and outputs explicitly rather than relying on something like ImageJ1's GenericDialog. Then they can be called from a variety of contexts.
That said, please understand that the ImageJ2 data model is still under development. One relatively safe option would be to use the new parameterized plugin and script framework, but stick to ImageJ1 data structures (i.e., ij.* classes) for the time being. (E.g.: @Parameter ImagePlus inputs)
Happy to assist if you have any further questions about it.
First let me thank you for your tireless work on Fiji/ImageJ. I noticed that you were the co-author with Johannes Schindelin (who I understand is on sabbatical) on the ImageJ2 Scripting and Plug-In Workshop. The link to the support material here:
does not work. I was wondering if electronic copies of the presentation slides and support material were available. I learn best by example...
I have had some success in developing Jython scripts for ImageJ1 but would like to transition to ImageJ2. My goal is to process series of images for several applications (e.g. particle sizing and montaging images from X-ray EDS maps with custom hue lookup tables.) I have many of these working in ImageJ1 but would like to always have the option of fast, headless execution after prototype development. In ImageJ1, I end up having adapt a lot of the source code to make display optional. This work is part of a larger plan to make my data analysis more reproducible. The basic idea would be to be able to reproduce an analysis from a make file.