I think it is an (intentional) limitation of ImageJ that the console window is not visible, as you rarely need it. I don’t know of any other way than activating it on the command line, perhaps someone else know this?
Thanks for the tip, I did not know this! I will try that.
Edit Plus is a great program! It is shareware at $35 but well worth the money, as it is easy to add syntax coloring and custom shortcuts for running your script in other applications. It is also easy to edit text as vertical selections, which is very useful when you have tables or repeating code lines. When working on computers that I do not own myself, I use Notepad++ as it is free. I have not checked out if that can also grab output as Edit Plus can, maybe it can as well.
Yes I tried it from Fiji first. Yes, the auto-completion feature works great!
A big problem is that my existing macros where I try to add CLIJ2 code get messed up if I try to edit them in the Fiji script editor. It is a line ending issue; whenever I add some text the line endings in that text is missing both in EditPlus and the ImageJ text editor. Perhaps this can be solved by setting the file format to Linux or Mac style from the start, I will check that out.
I like the simplicity and speed of ImageJ 1. I am a scientist and not a programmer, so cutting and pasting code found somewhere and just doing a “Compile and Run” makes it easy to write new or modify existing plugins. Since my work is purely project-based, I do not have the resources nor time to learn tools such as Maven or Eclipse.
Another and more important reason for me not using Fiji as my primary tool is that a majority of my workflow is based on launching code from somewhere else (command line on Windows, right-clicks in Explorer) and the very long launch time of Fiji (tens of seconds, often several minutes) slows my workflow a lot compared to ImageJ 1.x which launches in just a tiny fraction of a second. I usually launch ImageJ and close it for every single desired task (probably hundreds of times per day), which is started by right-clicking the data file or folder of interest in Windows and selecting what to do from a menu I have created there. This makes multi-tasking easy as I can have as many instances I want running parallel threads of batch macros without any cross-interference. I control what goes where using the -port option from my Windows scripts. Yes I know that much of this could be fixed by running everything in headless mode, but I like to see on screen how the macros proceed, so that I can take action if if something is wrong or will take too long time to execute.
Also, there are few of the bundled plugins in Fiji that are useful for me since I am a materials scientist and do not work with biology. I prefer to install single plugins that are useful to me (such as the 3D tools and CLIJ2) in ImageJ 1. This nearly always works fine; whenever there are dependencies I just copy the dependency jars as well over to ImageJ 1 and put them in the same subfolder. CLIJ1 worked fine this way when I tested it.
I still use Fiji as my first stop when testing stuff described or linked to from imagej.net. The Fiji update sites makes it very easy to install plugins with complex dependencies. Then I can test the plugins first to see if it is worth including in my workflow, as I did with CLIJ2.
Yes I have tried that. Reslicing is still slow under batch mode. I think the performance difference is only a few percent better. I also see that reslicing from left-right is much slower than top-down with the normal ImageJ methods. Perhaps the memory handling is done inefficiently?