Re: Stack Aligner does not work in a macro with AstroImageJ V5

Posted by GeorgeF on Mar 28, 2023; 6:55pm
URL: http://astroimagej.170.s1.nabble.com/Stack-Aligner-does-not-work-in-a-macro-with-AstroImageJ-V5-tp2180p2195.html

Hi Kevin

Sorry about time taken to reply - I have been setting up part of the main macro to test - yes run as a simple statement it works - however I kept adding code back up the macro and reached a point which caused it to fail.

MasterFlats = "X\:\\Master\\Flats\\" +  Fdate + "\\" + Filter + "\\";
                        MasterFlatImage = MasterFlats + "\\mflat.fits";  // need to get stats from this file
                        open(MasterFlatImage);
                        // get max values
                        //other work on master flat
                        // ... but removed for this test
                        close("*");
                       
  file = CalEntry;
                       
            list = getFileList(CalEntry);
  i = list.length;
                        print ("Loading Sequence");
                    //    file = "X:\\Images\\Variable Stars\\R Mon (VSX18829)\\2023-03-07\\B\\gain_300\\Calibrated";
                        // file = "X:\\Images\\R Mon (VSX18829)\\2023-03-07\\B\\gain_300\\Calibrated";
                        print ("Sequence File " + file);
                        // 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..");
                       
                        selectWindow("Calibrated");
                        run("Stack Aligner", "first=1 last=i radius=8 inner=14 outer=21 use=false use_0=false use_1=false allow=false use_2=true remove=false align=false show=false");
                               
                        print("Waiting for Align stack to complete");
                        Alignwait = 0;
  while ((isOpen("Aligned_") == false) && (Alignwait < 20)){ // again we have an asynchronous process we have to wait for
                        wait(5000);
            print("waiting...");
                        Alignwait = Alignwait + 1;
      }

THIS PART OF THE MACRO FAILS

aij.log

Exception in thread "pool-1-thread-1" java.lang.NullPointerException: Cannot invoke "ij.ImagePlus.getProcessor()" because "this.imp" is null
        at astroj.AstroStackWindow.setAstroProcessor(AstroStackWindow.java:5425)
        at astroj.AstroStackWindow.setAstroProcessor(AstroStackWindow.java:5421)
        at Astronomy.Astronomy_Listener.lambda$imageUpdated$0(Astronomy_Listener.java:72)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.base/java.lang.Thread.run(Unknown Source)
Exception in thread "pool-1-thread-2" java.lang.NullPointerException: Cannot invoke "ij.ImagePlus.setRoi(ij.gui.Roi)" because "this.imp" is null
        at astroj.AstroStackWindow.getBiSliderStatistics(AstroStackWindow.java:5363)
        at astroj.AstroStackWindow.updatePanelValues(AstroStackWindow.java:5505)
        at astroj.AstroStackWindow.setAstroProcessor(AstroStackWindow.java:5465)
        at astroj.AstroStackWindow.setAstroProcessor(AstroStackWindow.java:5421)
        at Astronomy.Astronomy_Listener.lambda$imageUpdated$0(Astronomy_Listener.java:72)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.base/java.lang.Thread.run(Unknown Source)


Reason appears to be the
 
open(MasterFlatImage);
close("*");

remove this and it appears to work???
Regards

George