Merge ce81257 into eb810c3

.coveragerc

@@ -2,6 +2,7 @@
 omit =
     *test_package*
     *test_*
+    *generate_test_results*
     *auto*
     *segmentation_stitch*
     *stack_np*

.gitignore

@@ -2,6 +2,13 @@ build-*
 tmp/
 data/
 cluster
+
+# Cython
+*.c
+*.so
+*.html
+
+# Python bytecode
 *.pyc
 .*.swp
 ipython_log.py*

Makefile

@@ -0,0 +1,7 @@
+clean:
+	 rm gala/features/*.{c,html,so}
+	 rm gala/*.{c,html,so}
+	 rm -rf build
+	 rm -rf gala.egg-info
+	 rm -rf dist
+	 rm -rf *.pyc */*.pyc */*/*.pyc

bin/comparestacks

@@ -1,3 +1,5 @@
+from __future__ import absolute_import
+from __future__ import print_function
 #!/usr/bin/env python
 
 import os
@@ -69,7 +71,7 @@ def main(argv):
 
     if args.relabel1:
         stack1_int, dummy1, dummy2 = ev.relabel_from_one(stack1_int)
-    print "Imported first stack"
+    print("Imported first stack")
 
 
     stackbase=args.stackbase
@@ -92,15 +94,15 @@ def main(argv):
 
     if args.relabelbase:
         stackbase_int, dummy1, dummy2 = ev.relabel_from_one(stackbase_int)
-    print "Imported base stack"
+    print("Imported base stack")
 
     if args.synapsejson != '':
         synaptic_vi, synaptic_comps = ev.make_synaptic_functions(args.synapsejson, [ev.split_vi_mem, ev.split_vi_mem])
         merge, split, stack1_bodies2, stack1_vis2, gt_bodies2, gt_vis2 = synaptic_vi(stack1_int, stackbase_int)
-        print "SynMergeSplit: " + str((merge, split))
+        print("SynMergeSplit: " + str((merge, split)))
     else:
         merge, split, stack1_bodies2, stack1_vis2, gt_bodies2, gt_vis2 = ev.split_vi_mem(stack1_int, stackbase_int)
-        print "MergeSplit: " + str((merge, split))
+        print("MergeSplit: " + str((merge, split)))
 
     data=[]
     database=[]

bin/gala-auto

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-evaluate

@@ -1,3 +1,5 @@
+from __future__ import absolute_import
+from __future__ import print_function
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable
@@ -10,7 +12,7 @@ pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
 # Python standard library
-import argparse, cPickle
+import argparse, six.moves.cPickle
 import subprocess as sp
 import logging
 
@@ -83,4 +85,4 @@ if __name__ == '__main__':
             vi = np.concatenate((np.array([args.threshold]), 
                 ev.split_vi(seg, gt)))[..., np.newaxis]
         imio.write_h5_stack(vi, segfn, group='vi')
-        print vi[:, :max(6, len(vi[0]))]
+        print(vi[:, :max(6, len(vi[0]))])

bin/gala-pixel

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-remove-inclusions

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-segment

@@ -1,16 +1,18 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable
 
 import os
 import sys
+from six.moves import map
 
 this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
 # Python standard library
-import argparse, cPickle
+import argparse, six.moves.cPickle
 import subprocess as sp
 import logging
 import functools

bin/gala-segmentation-pipeline

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-segmentation-stitch

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-test-package

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-train

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/gala-valprob

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 #!/usr/bin/env python
 
 # ensure imported package is local to this executable

bin/h5cat

@@ -1,3 +1,5 @@
+from __future__ import absolute_import
+from __future__ import print_function
 #!/usr/bin/env python
 
 import os, sys, argparse
@@ -20,18 +22,18 @@ if __name__ == '__main__':
 
     args = parser.parse_args()
     for fin in args.fin:
-        print '>>>', fin
+        print('>>>', fin)
         f = h5py.File(fin, 'r')
         if args.group is not None:
             groups = [args.group]
         else:
             groups = []
             f.visit(groups.append)
         for g in groups:
-            print '\n   ', g
+            print('\n   ', g)
             if type(f[g]) == h5py.highlevel.Dataset:
                 a = f[g]
-                print '      shape: ', a.shape, '\n      type: ', a.dtype
+                print('      shape: ', a.shape, '\n      type: ', a.dtype)
                 if args.verbose:
                     a = array(f[g])
-                    print a
+                    print(a)

gala/__init__.py

@@ -4,6 +4,7 @@
 
     Gala is a Python package for nD image segmentation. 
 """
+from __future__ import absolute_import
 
 import sys, logging
 if sys.version_info[:2] < (2,6):