Added support for Python 3

Author: MarcCote

nibabel/streamlines/compact_list.py

@@ -110,7 +110,7 @@ def extend(self, elements):
             lengths = elements._lengths
         else:
             self._data = np.concatenate([self._data] + list(elements), axis=0)
-            lengths = map(len, elements)
+            lengths = list(map(len, elements))
 
         idx = self._offsets[-1] + self._lengths[-1] if len(self) > 0 else 0
         self._lengths.extend(lengths)

nibabel/streamlines/tests/test_compact_list.py

@@ -17,7 +17,7 @@ class TestCompactList(unittest.TestCase):
     def setUp(self):
         rng = np.random.RandomState(42)
         self.data = [rng.rand(rng.randint(10, 50), 3) for _ in range(10)]
-        self.lengths = map(len, self.data)
+        self.lengths = list(map(len, self.data))
         self.clist = CompactList(self.data)
 
     def test_creating_empty_compactlist(self):
@@ -31,7 +31,7 @@ def test_creating_empty_compactlist(self):
     def test_creating_compactlist_from_list(self):
         rng = np.random.RandomState(42)
         data = [rng.rand(rng.randint(10, 50), 3) for _ in range(10)]
-        lengths = map(len, data)
+        lengths = list(map(len, data))
 
         clist = CompactList(data)
         assert_equal(len(clist), len(data))
@@ -54,7 +54,7 @@ def test_creating_compactlist_from_list(self):
     def test_creating_compactlist_from_generator(self):
         rng = np.random.RandomState(42)
         data = [rng.rand(rng.randint(10, 50), 3) for _ in range(10)]
-        lengths = map(len, data)
+        lengths = list(map(len, data))
 
         gen = (e for e in data)
         clist = CompactList(gen)
@@ -78,7 +78,7 @@ def test_creating_compactlist_from_generator(self):
     def test_creating_compactlist_from_compact_list(self):
         rng = np.random.RandomState(42)
         data = [rng.rand(rng.randint(10, 50), 3) for _ in range(10)]
-        lengths = map(len, data)
+        lengths = list(map(len, data))
 
         clist = CompactList(data)
         clist2 = CompactList(clist)
@@ -152,7 +152,7 @@ def test_compactlist_extend(self):
         rng = np.random.RandomState(1234)
         shape = self.clist.shape
         new_data = [rng.rand(rng.randint(10, 50), *shape) for _ in range(5)]
-        lengths = map(len, new_data)
+        lengths = list(map(len, new_data))
         clist.extend(new_data)
         assert_equal(len(clist), len(self.clist)+len(new_data))
         assert_array_equal(clist._offsets[-len(new_data):],
@@ -187,7 +187,7 @@ def test_compactlist_getitem(self):
             assert_array_equal(self.clist[i], e)
 
         # Get multiple items (this will create a view).
-        clist_view = self.clist[range(len(self.clist))]
+        clist_view = self.clist[list(range(len(self.clist)))]
         assert_true(clist_view is not self.clist)
         assert_true(clist_view._data is self.clist._data)
         assert_true(clist_view._offsets is not self.clist._offsets)

nibabel/streamlines/trk.py

@@ -13,6 +13,7 @@
 
 from nibabel.affines import apply_affine
 from nibabel.openers import Opener
+from nibabel.py3k import asbytes, asstr
 from nibabel.volumeutils import (native_code, swapped_code)
 
 from .compact_list import CompactList
@@ -276,7 +277,7 @@ def write(self, tractogram):
             property_name = k
             if nb_values > 1:
                 # Use the last to bytes of the name to store the nb of values associated to this data_for_streamline.
-                property_name = k[:18].ljust(18, '\x00') + '\x00' + np.array(nb_values, dtype=np.int8).tostring()
+                property_name = asbytes(k[:18].ljust(18, '\x00')) + b'\x00' + np.array(nb_values, dtype=np.int8).tostring()
 
             self.header['property_name'][i] = property_name
 
@@ -298,7 +299,7 @@ def write(self, tractogram):
             scalar_name = k
             if nb_values > 1:
                 # Use the last to bytes of the name to store the nb of values associated to this data_for_streamline.
-                scalar_name = k[:18].ljust(18, '\x00') + '\x00' + np.array(nb_values, dtype=np.int8).tostring()
+                scalar_name = asbytes(k[:18].ljust(18, '\x00')) + b'\x00' + np.array(nb_values, dtype=np.int8).tostring()
 
             self.header['scalar_name'][i] = scalar_name
 
@@ -314,7 +315,7 @@ def write(self, tractogram):
         # If the voxel order implied by the affine does not match the voxel
         # order in the TRK header, change the orientation.
         # voxel (affine) -> voxel (header)
-        header_ornt = self.header[Field.VOXEL_ORDER]
+        header_ornt = asstr(self.header[Field.VOXEL_ORDER])
         affine_ornt = "".join(nib.orientations.aff2axcodes(self.header[Field.VOXEL_TO_RASMM]))
         header_ornt = nib.orientations.axcodes2ornt(header_ornt)
         affine_ornt = nib.orientations.axcodes2ornt(affine_ornt)
@@ -589,7 +590,7 @@ def load(cls, fileobj, lazy_load=False):
         # If the voxel order implied by the affine does not match the voxel
         # order in the TRK header, change the orientation.
         # voxel (header) -> voxel (affine)
-        header_ornt = trk_reader.header[Field.VOXEL_ORDER]
+        header_ornt = asstr(trk_reader.header[Field.VOXEL_ORDER])
         affine_ornt = "".join(nib.orientations.aff2axcodes(trk_reader.header[Field.VOXEL_TO_RASMM]))
         header_ornt = nib.orientations.axcodes2ornt(header_ornt)
         affine_ornt = nib.orientations.axcodes2ornt(affine_ornt)
@@ -601,12 +602,12 @@ def load(cls, fileobj, lazy_load=False):
         # voxel -> rasmm
         affine = np.dot(trk_reader.header[Field.VOXEL_TO_RASMM], affine)
 
-
         # Find scalars and properties name
         data_per_point_slice = {}
         if trk_reader.header[Field.NB_SCALARS_PER_POINT] > 0:
             cpt = 0
             for scalar_name in trk_reader.header['scalar_name']:
+                scalar_name = asstr(scalar_name)
                 if len(scalar_name) == 0:
                     continue
 
@@ -626,6 +627,7 @@ def load(cls, fileobj, lazy_load=False):
         if trk_reader.header[Field.NB_PROPERTIES_PER_STREAMLINE] > 0:
             cpt = 0
             for property_name in trk_reader.header['property_name']:
+                property_name = asstr(property_name)
                 if len(property_name) == 0:
                     continue