old_contents: import vigra
  import argparse
  import numpy as np
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser(description='Take two tiff files, one for the sporozite channel and one for the nucleus channel, \
              and create two files needed for further processing: a 3-channel hdf5 volume and a 1-channel nucleus HDF5.',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
      parser.add_argument('--sporo', required=True, type=str, dest='sporoFilename',
                          help='Filename of the sporozyte tiff')
      parser.add_argument('--nucleus', required=True, type=str, dest='nucleusFilename',
                          help='Filename of the nucleus tiff')
      parser.add_argument('--3channel-out', type=str, dest='threeChannelOut', required=True, help='Filename of the resulting 3 channel HDF5')
      parser.add_argument('--nucleus-channel-out', type=str, dest='nucleusChannelOut', required=True, help='Filename of the resulting nucleus channel HDF5')
  
      args = parser.parse_args()
  
      sporoChannel = vigra.impex.readVolume(args.sporoFilename)
      nucleusChannel = vigra.impex.readVolume(args.nucleusFilename)
      resultVolume = np.zeros((nucleusChannel.shape[0], nucleusChannel.shape[1], nucleusChannel.shape[2], 3), dtype='float32')
      resultVolume[...,1] = sporoChannel[...,0]
      resultVolume[...,2] = nucleusChannel[...,0]
      resultVolume = np.swapaxes(resultVolume, 2, 0)
      nucleusChannel = np.swapaxes(nucleusChannel, 2, 0)
      vigra.impex.writeHDF5(resultVolume, args.threeChannelOut, 'exported_data')
      vigra.impex.writeHDF5(nucleusChannel, args.nucleusChannelOut, 'exported_data')
  
new_contents: import vigra
  import argparse
  import numpy as np
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser(description='Take two tiff files, one for the sporozite channel and one for the nucleus channel, \
              and create two files needed for further processing: a 3-channel hdf5 volume and a 1-channel nucleus HDF5.',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
      parser.add_argument('--sporo', required=True, type=str, dest='sporoFilename',
                          help='Filename of the sporozyte tiff')
      parser.add_argument('--nucleus', required=True, type=str, dest='nucleusFilename',
                          help='Filename of the nucleus tiff')
      parser.add_argument('--3channel-out', type=str, dest='threeChannelOut', required=True, help='Filename of the resulting 3 channel HDF5')
      parser.add_argument('--nucleus-channel-out', type=str, dest='nucleusChannelOut', required=True, help='Filename of the resulting nucleus channel HDF5')
  
      # TODO: save without vigra, normalize data and save as uint8, add axes ordering parameters
  
      args = parser.parse_args()
  
      sporoChannel = vigra.impex.readVolume(args.sporoFilename)
      nucleusChannel = vigra.impex.readVolume(args.nucleusFilename)
      resultVolume = np.zeros((nucleusChannel.shape[0], nucleusChannel.shape[1], nucleusChannel.shape[2], 3), dtype='float32')
      resultVolume[...,1] = sporoChannel[...,0]
      resultVolume[...,2] = nucleusChannel[...,0]
      resultVolume = np.swapaxes(resultVolume, 2, 0)
      nucleusChannel = np.swapaxes(nucleusChannel, 2, 0)
      vigra.impex.writeHDF5(resultVolume, args.threeChannelOut, 'exported_data')
      vigra.impex.writeHDF5(nucleusChannel, args.nucleusChannelOut, 'exported_data')
  
subject: Add todos for sporo data prep