Stack Aligner does not work in a macro with AstroImageJ V5

Posted by GeorgeF on Mar 21, 2023; 3:54pm
URL: http://astroimagej.170.s1.nabble.com/Stack-Aligner-does-not-work-in-a-macro-with-AstroImageJ-V5-tp2180.html

Previously 3.4. version I used this extract (from a very large macro which processes all my data in batch mode)

print ("Loading Sequence");
                        // I have preset that stack aligning will be done by WCS
                        call("ij.Prefs.set","stackAligner.useWCSOnly","true");
  run("Image Sequence...", "open=&file number=i starting=1 increment=1 scale=100 file=[] or=[] sort");
                        print("Images loaded..");
                        run("Align Stack", "first=1 last=i radius=8 inner=14 outer=21 use show");
                        print("Waiting for Align stack to complete");


Decided that it was probably time to upgrade to V5 and had a few false starts but started to get things working - however I am attempting to run with the latest daily build v5 and tells me "Align Stack" not found and sure enough it is not in the Astromony list of commands. I believe the correct name has always been Stack Aligner however using Macro record for running this just returned  run("Stack Aligner") - no parameters, ok, BUT if you run in a macro it STOPS and wants an OK button to be pressed. Not much use in a batch macro which will want to do this many times during the course of a run. Up to this point the transition to V5 was working but I have no work around for this problem?
Regards
George