Merge branch 'release-0.1.13'

NEWS

@@ -1,3 +1,7 @@
+New in Version 0.1.13
+=====================
+* code changes to ensure python3 compatibility
+
 New in Version 0.1.12
 =====================
 * added the option -flip-images to ray_trace_crosshair in case you are working with a version of 

python/rotational_minctracc.py

@@ -33,7 +33,7 @@ def get_tempfile(suffix):
 
 def get_centre_of_gravity(file):
     lines = subprocess.check_output(["volume_cog", file])
-    line = lines.split('\n')[-2]
+    line = lines.decode().split('\n')[-2]
     cog = array(line.strip().split(" ")).astype("float32")
     return cog
 

python/smooth_vector

@@ -8,11 +8,9 @@
 # Created Aug 26, 2004
 
 import sys
-import string
 import os, tempfile
 import subprocess
 import re
-import exceptions
 from optparse import OptionParser, Option, OptionValueError
 
 program_name = 'smooth_vector.py'
@@ -43,8 +41,8 @@ def process_volume(input, output, options):
             subprocess.check_call(('mincblur -fwhm %f %s %s' % (options.fwhm, working, smooth_base[i])).split())
 
     subprocess.check_call(('mincconcat -clobber -concat_dimension vector_dimension %s %s'
-                          % (string.join(smoothed), output)).split())
-    subprocess.check_call(('rm -f %s %s' % (string.join(smoothed), working)).split())
+                          % (' '.join(smoothed), output)).split())
+    subprocess.check_call(('rm -f %s %s' % (' '.join(smoothed), working)).split())
 
 
 
@@ -54,7 +52,7 @@ def get_vector_length(input):
     # sometimes the file exists, but the MINC file has not been 
     # properly written out to disk, check for this:
     output = subprocess.check_output(["mincinfo", input], stderr=subprocess.STDOUT)
-    if re.search("Unable to open file", output):
+    if re.search(b"Unable to open file", output):
         sys.exit("\nError: can not read input file: '%s'\n" % input)
     length = int(subprocess.check_output(['mincinfo', '-dimlength', 'vector_dimension', input]))
     return length

setup.py

@@ -13,7 +13,7 @@
     m.Extension.__dict__ = m._Extension.__dict__
 
 setup(name="python-stuffs",
-      version='0.1.12',
+      version='0.1.13',
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",