#!/usr/bin/env python3

import os
import sys
from io import StringIO
from optparse import OptionParser

import numpy as np

import damask


scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID   = ' '.join([scriptName,damask.version])


#--------------------------------------------------------------------------------------------------
#                                MAIN
#--------------------------------------------------------------------------------------------------

parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Renumber sorted microstructure indices to 1,...,N.

""", version=scriptID)

(options, filenames) = parser.parse_args()


if filenames == []: filenames = [None]

for name in filenames:
  damask.util.report(scriptName,name)

  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)

  renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
  for i, oldID in enumerate(np.unique(geom.microstructure)):
    renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)

  damask.util.croak(geom.update(renumbered))
  geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))

  if name is None:
    sys.stdout.write(str(geom.show()))
  else:
    geom.to_file(name)