COMP: making sure python move operations work

Also with python 2.7.

Testing/elx_compare_landmarks.py

@@ -78,7 +78,7 @@ def main():
   for line in f1 :
     f2.write( line.strip().split(';')[4].strip().strip( "OutputPoint = [ " ).rstrip( " ]" ) + "\n" );
   f1.close(); f2.close();
-  shutil.rename( landmarkstemp, landmarks1full ); # for later inspection
+  shutil.move( landmarkstemp, landmarks1full ); # for later inspection
 
   #
   # Transform the fixed image landmarks by the baseline result
@@ -95,7 +95,7 @@ def main():
   for line in f1 :
     f2.write( line.strip().split(';')[4].strip().strip( "OutputPoint = [ " ).rstrip( " ]" ) + "\n" );
   f1.close(); f2.close();
-  shutil.rename( landmarkstemp, landmarks2full ); # for later inspection
+  shutil.move( landmarkstemp, landmarks2full ); # for later inspection
 
   # Compute the distance between all transformed landmarks
   f1 = open( landmarks1, 'r' ); f2 = open( landmarks2, 'r' );

Testing/elx_compare_overlap.py

@@ -1,6 +1,7 @@
 import sys, subprocess
 import os
 import os.path
+import shutil
 import re
 import glob
 from optparse import OptionParser
@@ -71,6 +72,7 @@ def main():
   seg_defm = os.path.join( options.directory, "segmentation_deformed.mha" );
   subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName ],
     stdout=subprocess.PIPE );
+  os.remove( seg_defm );
   shutil.move( seg, seg_defm );
 
   #
@@ -92,6 +94,7 @@ def main():
   seg_defb = os.path.join( options.directory, "segmentation_baseline.mha" );
   subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName_b ],
     stdout=subprocess.PIPE );
+  os.remove( seg_defb );
   shutil.move( seg, seg_defb );
 
   # Compute the overlap between baseline segmentation and deformed moving segmentation