import sys
import os
import re
import os.path
import glob
import shutil
from optparse import OptionParser

#-------------------------------------------------------------------------------
# the main function
def main():
    # usage, parse parameters
    usage = "usage: %prog [options] arg"
    parser = OptionParser( usage )

    # option to debug and verbose
    parser.add_option( "-v", "--verbose",
      action="store_true", dest="verbose" )

    # options to control files
    parser.add_option( "-l", "--list", type="string", dest="directoryList", help="list of elastix output directories" )
    parser.add_option( "-o", "--output", type="string", dest="outputDirectory", help="output base directory" )

    (options, args) = parser.parse_args()

    # Check if option -l is given
    if options.directoryList == None :
      parser.error( "The option directory list (-l) should be given" )

    # Check if option -d is given
    if options.outputDirectory == None :
      parser.error( "The option output directory (-o) should be given" )

    if not os.path.exists( options.outputDirectory ) :
      print( "The output directory " + options.outputDirectory + " does not exist. Create it before running" )

    # Convert string -l to list
    dirList = options.directoryList.split( ' ' )
    # Add everything not processed
    dirList.extend( args );

    for directory in dirList:
      # Find the largest TransformParameters.?.txt
      inputFileNames = glob.glob( os.path.join( directory, "TransformParameters.?.txt" ) );
      inputFileNames.sort( reverse = True );
      inputFileName = inputFileNames[0];

      # Create a name for the output file name
      directory = re.sub( '\/$', '', directory )
      dir_part = list( os.path.split( directory ) ).pop()
      dir_part = dir_part.replace( "elastix_run_", "", 1 )
      outputFileName = "TransformParameters_" + dir_part + ".txt"
      outputFileName = os.path.join( options.outputDirectory, outputFileName )
      print( outputFileName );

      # Copy the results as the new baselines
      shutil.copy( inputFileName, outputFileName )

    return 0

#-------------------------------------------------------------------------------
if __name__ == '__main__':
    sys.exit(main())