          logger.debug("Timelapse enabled: %s", kwargs)
          return kwargs
  
      def get_images(self):
          """ Check the image dirs exist, contain images and return the image
          objects """
          logger.debug("Getting image paths")
          images = dict()
          for side in ("a", "b"):
              image_dir = getattr(self.args, "input_{}".format(side))
 
</s> remove         """ Set the alignments path to input dirs if not provided """
 </s> add         """ Set the alignments path to input folder if not provided """ </s> remove         """ Set timelapse paths if requested """
 </s> add         """ Set time-lapse paths if requested """ </s> remove             self.output.warning("Running without root/admin privileges")
 </s> add             self.output.info("Running without root/admin privileges") </s> remove         """ Monitor stdin for keypress """
 </s> add         """ Monitor stdin for key press """ </s> remove                 alignments_path = os.path.join(image_path, "alignments.json")
 </s> add                 alignments_path = os.path.join(image_path, "alignments.fsa")
        """ Check the image folders exist, contain images and return the image
          logger.debug("Timelapse enabled: %s", kwargs)
          return kwargs
  
      def get_images(self):
        """ Check the image folders exist, contain images and return the image
          objects """
          logger.debug("Getting image paths")
          images = dict()
          for side in ("a", "b"):
              image_dir = getattr(self.args, "input_{}".format(side))
keep keep keep keep replace keep keep keep keep keep
 Minor Fixes

scripts.train - default to .fsa alignments file
setup.py - Lower non-root message to info level 
scripts/train.py