In order to allow the macro recording to work, it shows a simpler version when called from a macro, this is on purpose, otherwise it would not work. Usually, it is supposed to be called with a lot of parameters so that it runs automatically.

However, when running the plugin afterwards from the menu, it still thinks that it is in plugin mode. The bug seems to be on the ImageJ/Fiji side, as the call

IJ.isMacro()

still returns true although it is called through the menu. Does anybody have an idea how this can happen?

Stephan,

You could try using IJ.macroRunning() instead of IJ.isMacro(). Here is the source for these two methods:

  /** Returns true if the run(), open() or newImage() method is executing. */
  public static boolean macroRunning() {
    return macroRunning;
  }

  /** Returns true if a macro is running, or if the run(),
      open() or newImage() method is executing. */
  public static boolean isMacro() {
    return macroRunning || Interpreter.getInstance()!=null;
  }

See https://github.com/fiji/Stitching/issues/1