Merge pull request #45 from pnlbwh/py3k

More Python 3 updates, fix #41

.gitignore

@@ -13,3 +13,4 @@ htmlcov
 ## The Pycharm internal directory.
 .idea
 build
+cover

.travis.yml

@@ -1,8 +1,7 @@
 language: python
 matrix:
   include:
-    python: "2.7"
-  allow_failures:
+    - python: "2.7"
     - python: "3.5"
     - python: "3.6"
 

requirements.txt

@@ -1,5 +1,5 @@
 numpy>=1.6
 nose>=1.2
 nibabel>=2.0
+six>=1.10
 numpydoc
-six

scripts/tract_math

@@ -7,12 +7,8 @@ import traceback
 
 import warnings
 
-
-def custom_formatwarning(msg, *a):
-    # ignore everything except the message
-    return '\nWarning: ' + str(msg) + '\n'
-
-warnings.formatwarning = custom_formatwarning
+import os, sys
+# sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
 
 
 def tract_math_operation(help_text, needs_one_tract=True):
@@ -66,7 +62,7 @@ def main():
     """
 
     operations_names = operations.keys()
-    operations_names.sort()
+    operations_names = sorted(operations_names)
     for f in operations_names:
         usage += '\t%s %s\n' % (f, operations[f].help_text)
 
@@ -103,19 +99,19 @@ def main():
                 # filename, tractography instance) to tractography list.
                 tractography.append((f.name, tractography_from_files(f.name)))
         except IOError as e:
-            print >>sys.stderr, "Error reading file ", f.name, "(%s)" % repr(e)
+            # print >>sys.stderr, "Error reading file ", f.name, "(%s)" % repr(e)
+            print(sys.stderr, "Error reading file ", f.name, "(%s)" % repr(e))
 
     if args.operation in operations:
         try:
             operations[args.operation](
                 tractography, *args.operation_parameters)
-        except TractMathWrongArgumentsError, e:
+        except TractMathWrongArgumentsError as e:
             traceback.print_exc(file=sys.stdout)
             parser.error('\n\n' + str(e))
         except TypeError:
             traceback.print_exc(file=sys.stdout)
-            parser.error(
-                "\n\nError: Wrong number of parameters for the operation")
+            parser.error("\n\nError: Wrong number of parameters for the operation")
 
     else:
         parser.error("\n\nOperation not found")

scripts/tract_querier

@@ -66,14 +66,14 @@ def main():
             bounding_box_affine_transform = np.fromstring(
                 options.bounding_box_affine_transform, sep=','
             ).reshape(4, 4)
-            print "Affine transform:"
-            print bounding_box_affine_transform
+            print("Affine transform:")
+            print(bounding_box_affine_transform)
         except ValueError:
             parser.error("Matrix format not valid")
     else:
         bounding_box_affine_transform = None
 
-    print "Loading files"
+    print("Loading files")
 
     # Search order precidence for .qry files
     # 1. Command line options specified are respected first
@@ -106,7 +106,7 @@ def main():
 
     try:
         if os.path.exists(options.queries_string):
-            query_script = file(options.queries_string).read()
+            query_script = open(options.queries_string).read()
             query_filename = options.queries_string
         else:
             found = False
@@ -116,7 +116,7 @@ def main():
                     found = True
                     break
             if found:
-                query_script = file(file_).read()
+                query_script = open(file_).read()
                 query_filename = file_
             else:
                 query_script = options.queries_string
@@ -129,10 +129,10 @@ def main():
         )
 
         tract_querier.queries_syntax_check(query_file_body)
-    except tract_querier.TractQuerierSyntaxError as e:
-        parser.error(e.value)
-    except tract_querier.TractographySpatialIndexing as e:
+    except tract_querier.TractQuerierSyntaxError or tract_querier.TractographySpatialIndexing as e:
         parser.error(e.value)
+    # except tract_querier.TractographySpatialIndexing as e:
+    #     parser.error(e.value)
 
     labels_nii = nibabel.load(options.atlas_file_name)
     img = labels_nii.get_data()
@@ -169,7 +169,7 @@ def main():
     else:
         tractography_extra_kwargs = {}
 
-    print "Calculating labels and crossings"
+    print("Calculating labels and crossings")
     affine_ijk_2_ras = labels_nii.get_affine()
     tracts = tr.tracts()
 
@@ -186,13 +186,13 @@ def main():
     )
 
     if not options.interactive:
-        print "Computing queries"
+        print("Computing queries")
         evaluated_queries = tract_querier.eval_queries(
             query_file_body,
             tractography_spatial_indexing,
         )
 
-        query_names = evaluated_queries.keys()
+        query_names = list(evaluated_queries.keys())
         if options.query_selection != '':
             selected_queries = set(options.query_selection.lower().split(','))
             query_names = list(set(query_names) & set(selected_queries))
@@ -225,7 +225,7 @@ def main():
 
 def save_query(query_name, tractography, options, evaluated_queries, extension='.vtk', extra_kwargs={}):
     tract_numbers = evaluated_queries[query_name]
-    print "\tQuery %s: %.6d" % (query_name, len(tract_numbers))
+    print("\tQuery %s: %.6d" % (query_name, len(tract_numbers)))
     if tract_numbers:
         filename = options.output_file_name + "_" + query_name + extension
         save_tractography_file(

tract_querier/aabb.py

@@ -230,7 +230,7 @@ def buildTree_old(self, allboxes, indices=None, leafPointers=None, parent=None,
             boxes = allboxes[indices, :]
 
         if verbose:
-            print '*******************************************'
+            print('*******************************************')
 
         dimensions = len(boxes[0]) / 2
 
@@ -265,8 +265,8 @@ def buildTree_old(self, allboxes, indices=None, leafPointers=None, parent=None,
             rightIndices = indices[n:]
 
         if verbose:
-            print "Left: ", leftIndices
-            print "Right: ", rightIndices
+            print(("Left: ", leftIndices))
+            print(("Right: ", rightIndices))
         n = self.node(box, indices.copy(), parent=parent)
         n.left = self.buildTree(
             allboxes, leftIndices, parent=n, leafPointers=leafPointers)

tract_querier/code_util/__init__.py

@@ -1,3 +1,6 @@
+from six import add_metaclass
+
+
 class DocStringInheritor(type):
 
     '''A variation on
@@ -33,8 +36,9 @@ class Foo(object):
             def frobnicate(self):
                 pass
 
+        @add_metaclass(DocStringInheritor)
         class Bar(Foo):
-            __metaclass__ = DocStringInheritor
+            pass
         self.assertEqual(Bar.__doc__, object.__doc__)
         self.assertEqual(Bar().__doc__, object.__doc__)
         self.assertEqual(Bar.frobnicate.__doc__, None)
@@ -46,8 +50,10 @@ class Foo(object):
 
             def frobnicate(self):
                 'Frobnicate this gonk.'
+
+        @add_metaclass(DocStringInheritor)
         class Bar(Foo):
-            __metaclass__ = DocStringInheritor
+            pass
         self.assertEqual(Foo.__doc__, 'Foo')
         self.assertEqual(Foo().__doc__, 'Foo')
         self.assertEqual(Bar.__doc__, 'Foo')
@@ -64,8 +70,9 @@ def frobnicate(self):
         class Bar(Foo):
             pass
 
+        @add_metaclass(DocStringInheritor)
         class Baz(Bar):
-            __metaclass__ = DocStringInheritor
+            pass
         self.assertEqual(Baz.__doc__, 'Foo')
         self.assertEqual(Baz().__doc__, 'Foo')
         self.assertEqual(Baz.frobnicate.__doc__, 'Frobnicate this gonk.')
@@ -77,8 +84,10 @@ class Foo(object):
 
             def frobnicate(self):
                 'Frobnicate this gonk.'
+
+        @add_metaclass(DocStringInheritor)
         class Bar(Foo):
-            __metaclass__ = DocStringInheritor
+            pass
 
         class Baz(Bar):
             pass

tract_querier/nipype/utils.py

@@ -4,7 +4,7 @@
 
 import os
 import glob
-from itertools import izip
+
 
 from nipype.interfaces.base import (TraitedSpec, traits)
 from nipype.interfaces.ants import utils
@@ -218,7 +218,7 @@ def _format_arg(self, name, spec, value):
                         'must be 1 or the same as '
                         'input images'
                     )
-                for template, reference, weight in izip(
+                for template, reference, weight in zip(
                     self._internal['reference_images'],
                     self._internal['input_images'],
                     self._internal['metric_weights'],