refObsids = [1342240316, 1342240317]
 
obsids = [1342240316, 1342240317, 1342240276, 1342240278]

calTree = getCalTree(obs=getObservation(obsids[0], useHsa=True, instrument="PACS"))

"""
  Make a copy of the reference frames
"""
for i in range(len(refObsids)/2):
   cameraName = camera
   try:
     referenceFitsFile = dataDir + str(refObsids[2*i]) +  "-" + str(refObsids[2*i+1])  +  "-" + cameraName + ".fits"
     referenceFrames = FitsArchive().load(referenceFitsFile)
   except:
     if cameraName == "blue": 
       cameraName = "green"
     referenceFitsFile = dataDir + str(refObsids[2*i]) +  "-" + str(refObsids[2*i+1])  +  "-" + cameraName + ".fits"
     referenceFrames = FitsArchive().load(referenceFitsFile)
   outputFitsFile = dataDir + str(refObsids[2*i]) +  "-" + str(refObsids[2*i+1])  +  "-" + cameraName + "-aligned.fits"
   FitsArchive().save(outputFitsFile, referenceFrames)

"""
  Align the rest of the frames
"""
for i in range(len(obsids)/4):
   """
    Load the frames and align them
   """
   cameraName = camera
   try:
     referenceFitsFile = dataDir + str(obsids[4*i]) +  "-" + str(obsids[4*i + 1])  +  "-" + cameraName + "-aligned.fits"
     referenceFrames = FitsArchive().load(referenceFitsFile)
   except:
     if cameraName == "blue": 
       cameraName = "green"
     referenceFitsFile = dataDir + str(obsids[4*i]) +  "-" + str(obsids[4*i + 1])  +  "-" + cameraName + "-aligned.fits"
     referenceFrames = FitsArchive().load(referenceFitsFile)
   fitsFile = dataDir + str(obsids[4*i + 2]) +  "-" + str(obsids[4*i + 3])  +  "-" + cameraName + ".fits"
   frames = FitsArchive().load(fitsFile)
   referenceFrames.setActive("Scanamorphos_NonOverlapMask", True)
   frames.setActive("Scanamorphos_NonOverlapMask", True)
   referenceFrames, frames = scanamorphosAlignFrames(referenceFrames, frames, calTree=calTree, createMask=False)
   referenceFrames.setActive("Scanamorphos_NonOverlapMask", False)
   frames.setActive("Scanamorphos_NonOverlapMask", False)
   
   """
     Write the fits files
   """
   outputFitsFile = dataDir + str(obsids[4*i + 2]) +  "-" + str(obsids[4*i + 3])  +  "-" + cameraName + "-aligned.fits"
   FitsArchive().save(outputFitsFile, frames)
   del(referenceFrames, frames)