Convert TileConfiguration.registered.txt to a format TrakEM2 can load

convert-stitching-results.py

#!/usr/bin/env python

# This script takes the output of Stephan Preibisch's stitching plugins
# for 3D stacks and outputs tab separated data suitable for loading
# into TrakEM2.  What TrakEM2 expects is described here:
#
#   http://www.ini.uzh.ch/~acardona/trakem2_manual.html#importing_list

import sys, re

if len(sys.argv) != 1:
    print "Usage: %s < tile-configuration.txt > trakem2-tils.txt" % (sys.argv[0])
    sys.exit(1)

# A verbose regular expression to match the format of lines in
# TileConfiguration.registered.txt:

matcher = re.compile(r'''
  (\S+)               # Match the filename
  ;\s+;\s+            # Match semi-colons followed by whitespace
  \(                  # Match opening bracket
  ([-+0-9\.eE]+)      # A floating point number
  ,\s*                # A comma and zero or more spaces
  ([-+0-9\.eE]+)      # A floating point number
  ,\s*                # A comma and zero or more spaces
  ([-+0-9\.eE]+)      # A floating point number
  \s*\)               # Zero or more spaces, then a close bracket
''', re.VERBOSE)

for line in sys.stdin:
    m = matcher.match(line)
    if m:
        # Output all of the groups matched by the regular expression
        # joined by tabs.  I think TrakEM2 is just expecting fields
        # naively joined by tabs, rather than fields quoted properly
        # as in tab-separated data:
        print "\t".join(m.groups())