Make mahotas work on Python 2.6 to 3.3 without 2to3

[cgohlke]

Looking at the output of 2to3, the mahotas code could be made compatible with Python 2.6 to 3.3 with few changes. Most changes are xrange->range. A few import, print and raise statements need to be updated.

This patch works for me on win-amd64, Python 2.6 to 3.3. I could work on a pull request later if there is interest.

diff --git a/mahotas/__init__.py b/mahotas/__init__.py
index 09a3b8f..1315571 100644
--- a/mahotas/__init__.py
+++ b/mahotas/__init__.py
@@ -5,6 +5,9 @@ Mahotas

 A package for computer vision in Python.
 '''
+
+from __future__ import print_function
+
 try:
     from .bbox import bbox, croptobbox
     from .center_of_mass import center_of_mass
@@ -25,14 +28,14 @@ try:

     from .tests import run as test

-    from mahotas_version import __version__
+    from .mahotas_version import __version__

-    import features
-    import morph
-    import segmentation
-except ImportError, e:
+    from . import features
+    from . import morph
+    from . import segmentation
+except ImportError as e:
     import sys
-    print >>sys.stderr, '''\
+    print('''\
 Could not import submodules (exact error was: %s).

 There are many reasons for this error the most common one is that you have
@@ -41,7 +44,7 @@ installed them (using `python setup.py install`) and then proceeded to test
 mahotas **without changing the current directory**.

 Try installing and then changing to another directory before importing mahotas.
-''' % e
+''' % e, file=sys.stderr)

diff --git a/mahotas/convolve.py b/mahotas/convolve.py
index 64c2826..4c08792 100644
--- a/mahotas/convolve.py
+++ b/mahotas/convolve.py
@@ -324,7 +324,7 @@ def gaussian_filter(array, sigma, order=0, mode='reflect', cval=0., out=None, ou
     sigmas = _normalize_sequence(array, sigma, 'gaussian_filter')
     output[...] = array[...]
     noutput = None
-    for axis in xrange(array.ndim):
+    for axis in range(array.ndim):
         sigma = sigmas[axis]
         order = orders[axis]
         noutput = gaussian_filter1d(output, sigma, axis, order, mode, cval, noutput)
@@ -342,7 +342,7 @@ def _wavelet_array(f, inline, func):

 def _wavelet_center_compute(oshape, border=0, dtype=None, cval=0.0):
-    for c in xrange(1, 16+border):
+    for c in range(1, 16+border):
         nshape = 2**(np.floor(np.log2(oshape))+c)
         delta = nshape - oshape
         delta //= 2
@@ -448,7 +448,7 @@ def haar(f, preserve_energy=True, inline=False):
         f /= 2.0
     return f

-_daubechies_codes = [('D%s' % ci) for ci in xrange(2,21,2)]
+_daubechies_codes = [('D%s' % ci) for ci in range(2,21,2)]
 def daubechies(f, code, inline=False):
     '''
     filtered = daubechies(f, code, inline=False)
diff --git a/mahotas/features/surf.py b/mahotas/features/surf.py
index c195a31..cf1b782 100644
--- a/mahotas/features/surf.py
+++ b/mahotas/features/surf.py
@@ -3,6 +3,7 @@
 #
 # License: MIT (see COPYING file)

+
 from __future__ import division
 import numpy as np
 from . import _surf
@@ -217,7 +218,9 @@ def show_surf(f, spoints, values=None, colors=None):
         x0 = int(x) - size//2
         x1 = x + size
         y1 = y + size
-        def rotate_around((p0,p1),(c0,c1), a):
+        def rotate_around(p, c, a):
+            (p0, p1) = p
+            (c0, c1) = c
             d0 = p0-c0
             d1 = p1 - c1
             d0,d1 = rotate(d0,d1,a)
diff --git a/mahotas/features/texture.py b/mahotas/features/texture.py
index 8f9ea11..448c06a 100644
--- a/mahotas/features/texture.py
+++ b/mahotas/features/texture.py
@@ -76,7 +76,7 @@ def haralick(f, ignore_zeros=False, preserve_haralick_bug=False, compute_14th_fe
     px_plus_y = np.empty(2*fm1, np.double)
     px_minus_y = np.empty(fm1, np.double)

-    for dir in xrange(nr_dirs):
+    for dir in range(nr_dirs):
         cooccurence(f, dir, cmat, symmetric=True)
         if ignore_zeros:
             cmat[0] = 0
@@ -222,7 +222,7 @@ def cooccurence(f, direction, output=None, symmetric=True):
     if len(f.shape) == 2:
         assert direction in (0,1,2,3), 'mahotas.texture.cooccurence: `direction` %s is not in range(4).' % direction
     elif len(f.shape) == 3:
-        assert direction in xrange(13), 'mahotas.texture.cooccurence: `direction` %s is not in range(13).' % direction
+        assert direction in range(13), 'mahotas.texture.cooccurence: `direction` %s is not in range(13).' % direction
     else:
         raise ValueError('mahotas.texture.cooccurence: cannot handle images of %s dimensions.' % len(f.shape))

diff --git a/mahotas/features/zernike.py b/mahotas/features/zernike.py
index 41825f4..9ce8888 100644
--- a/mahotas/features/zernike.py
+++ b/mahotas/features/zernike.py
@@ -83,11 +83,11 @@ def zernike_moments(im, radius, degree=8, cm=None):
     An.real = (Xn/Dn)
     An.imag = (Yn/Dn)

-    Ans = [An**p for p in xrange(2,degree+2)]
+    Ans = [An**p for p in range(2,degree+2)]
     Ans.insert(0, An) # An**1
     Ans.insert(0, np.ones_like(An)) # An**0
-    for n in xrange(degree+1):
-        for l in xrange(n+1):
+    for n in range(degree+1):
+        for l in range(n+1):
             if (n-l)%2 == 0:
                 z = _zernike.znl(Dn, Ans[l], frac_center, n, l)
                 zvalues.append(abs(z))
diff --git a/mahotas/io/__init__.py b/mahotas/io/__init__.py
index 3f0e640..ae2946a 100644
--- a/mahotas/io/__init__.py
+++ b/mahotas/io/__init__.py
@@ -33,7 +33,7 @@ try:
         from imread import imread, imsave
     except:
         from .freeimage import imread, imsave
-except OSError, e:
+except OSError as e:
     _error_message %= e
     imread = error_imread
     imsave = error_imsave
diff --git a/mahotas/labeled.py b/mahotas/labeled.py
index 6c66e7f..a45bc92 100644
--- a/mahotas/labeled.py
+++ b/mahotas/labeled.py
@@ -3,6 +3,7 @@
 # 
 # LICENSE: MIT

+
 from __future__ import division
 import numpy as np
 from .morph import get_structuring_elem
@@ -71,8 +72,8 @@ def remove_bordering(im, rsize=1, out=None, output=None):
         Subset of ``labeled``
     '''
     invalid = set()
-    index = [slice(None,None,None) for _ in xrange(im.ndim)]
-    for dim in xrange(im.ndim):
+    index = [slice(None,None,None) for _ in range(im.ndim)]
+    for dim in range(im.ndim):
         for bordering in (
                     slice(rsize),
                     slice(-rsize, None)
diff --git a/mahotas/morph.py b/mahotas/morph.py
index e9c73ce..4dff545 100644
--- a/mahotas/morph.py
+++ b/mahotas/morph.py
@@ -85,7 +85,7 @@ def get_structuring_elem(A,Bc):
     Bc = np.zeros((3,)*len(A.shape), dtype=A.dtype)
     centre = np.ones(len(A.shape))
     # This is pretty slow, but this should be a tiny array, so who cares
-    for i in xrange(Bc.size):
+    for i in range(Bc.size):
         pos = np.unravel_index(i, Bc.shape)
         pos -= centre
         if np.sum(np.abs(pos)) <= max1:
diff --git a/mahotas/polygon.py b/mahotas/polygon.py
index b44b6d5..4eef063 100644
--- a/mahotas/polygon.py
+++ b/mahotas/polygon.py
@@ -51,7 +51,7 @@ def line(p0, p1, canvas, color=1):
     error = dx/2.
     y = y0
     ystep = (+1 if y0 < y1 else -1)
-    for x in xrange(x0,x1+1):
+    for x in range(x0,x1+1):
         if steep:
             canvas[x,y] = color
         else:
@@ -83,7 +83,7 @@ def fill_polygon(polygon, canvas, color=1):
     min_y = min(y for y,x in polygon)
     max_y = max(y for y,x in polygon)
     polygon = [(float(y),float(x)) for y,x in polygon]
-    for y in xrange(min_y, max_y+1):
+    for y in range(min_y, max_y+1):
         nodes = []
         j = -1
         for i,p in enumerate(polygon):
diff --git a/mahotas/tests/test_euler.py b/mahotas/tests/test_euler.py
index d9e44bb..c77581e 100644
--- a/mahotas/tests/test_euler.py
+++ b/mahotas/tests/test_euler.py
@@ -3,9 +3,9 @@ from mahotas.euler import euler, _euler_lookup4, _euler_lookup8
 from nose.tools import raises

 def test_lookup():
-    Q1 = [np.array(q, np.bool) for q in [[0,0],[1,0]], [[0,0],[0,1]], [[0,1],[0,0]], [[1,0],[0,0]] ]
+    Q1 = [np.array(q, np.bool) for q in ([[0,0],[1,0]], [[0,0],[0,1]], [[0,1],[0,0]], [[1,0],[0,0]]) ]
     Q2 =  [(~q) for q in Q1]
-    Q3 = [np.array(q, np.bool) for q in [[0,1],[1,0]], [[1,0],[0,1]] ]
+    Q3 = [np.array(q, np.bool) for q in ([[0,1],[1,0]], [[1,0],[0,1]]) ]

     def _value(q, lookup):
         q = q.ravel()
diff --git a/mahotas/thresholding.py b/mahotas/thresholding.py
index ae26137..bd7c5de 100644
--- a/mahotas/thresholding.py
+++ b/mahotas/thresholding.py
@@ -75,7 +75,7 @@ def otsu(img, ignore_zeros=False):
     best = nB[0]*nO[0]*(mu_B-mu_O)*(mu_B-mu_O)
     bestT = 0

-    for T in xrange(1, Ng):
+    for T in range(1, Ng):
         if nB[T] == 0: continue
         if nO[T] == 0: break
         mu_B = (mu_B*nB[T-1] + T*hist[T]) / nB[T]

[luispedro]

I am not sure whether someone is still using 2.5, which is why I didn't do this myself.

[cgohlke]

OK. FWIW, on Windows with msvc compilers, I was never able to build mahotas for Python 2.5.

[luispedro]

FYI, I just committed something very similar (more hand-written, though).

I think it is Python 2.5 compatible: it uses stderr.write instead of print and sys.exc_info() to get the exception instead of of except type as name.