RF: Avoid various warnings

fsl/data/image.py

@@ -814,7 +814,8 @@ class Image(Nifti):
         if indexed is not False:
             warnings.warn('The indexed argument is deprecated '
                           'and has no effect',
-                          category=DeprecationWarning)
+                          category=DeprecationWarning,
+                          stacklevel=2)
 
         if loadData:
             threaded = False

fsl/data/imagewrapper.py

@@ -37,9 +37,10 @@ get their definitions straight:
 """
 
 
-import logging
-import collections
-import itertools as it
+import                    logging
+import                    collections
+import collections.abc as abc
+import itertools       as it
 
 import numpy     as np
 import nibabel   as nib
@@ -689,7 +690,7 @@ class ImageWrapper(notifier.Notifier):
 
             # If we are slicing a scalar, the
             # assigned value has to be scalar.
-            if expNdims == 0 and isinstance(values, collections.Sequence):
+            if expNdims == 0 and isinstance(values, abc.Sequence):
 
                 if len(values) > 1:
                     raise IndexError('Invalid assignment: [{}] = {}'.format(
@@ -828,7 +829,7 @@ def sliceObjToSliceTuple(sliceobj, shape):
 
     # The sliceobj could be a single sliceobj
     # or integer, instead of a tuple
-    if not isinstance(sliceobj, collections.Sequence):
+    if not isinstance(sliceobj, abc.Sequence):
         sliceobj = [sliceobj]
 
     # Turn e.g. array[6] into array[6, :, :]

fsl/utils/transform.py

@@ -34,9 +34,9 @@ And a few more functions are provided for working with vectors:
    normalise
 """
 
-import numpy        as np
-import numpy.linalg as linalg
-import collections
+import numpy           as np
+import numpy.linalg    as linalg
+import collections.abc as abc
 
 
 def invert(x):
@@ -94,7 +94,7 @@ def scaleOffsetXform(scales, offsets):
     :returns:     A ``numpy.float32`` array of size :math:`4 \\times 4`.
     """
 
-    oktypes = (collections.Sequence, np.ndarray)
+    oktypes = (abc.Sequence, np.ndarray)
 
     if not isinstance(scales,  oktypes): scales  = [scales]
     if not isinstance(offsets, oktypes): offsets = [offsets]
@@ -398,7 +398,7 @@ def axisBounds(shape,
     if axes is None:
         axes = [0, 1, 2]
 
-    elif not isinstance(axes, collections.Iterable):
+    elif not isinstance(axes, abc.Iterable):
         scalar = True
         axes   = [axes]
 
@@ -507,13 +507,13 @@ def _fillPoints(p, axes):
     or an ``N*2`` or ``N*3`` array.
     """
 
-    if not isinstance(p, collections.Iterable): p = [p]
+    if not isinstance(p, abc.Iterable): p = [p]
 
     p = np.array(p)
 
     if axes is None: return p
 
-    if not isinstance(axes, collections.Iterable): axes = [axes]
+    if not isinstance(axes, abc.Iterable): axes = [axes]
 
     if p.ndim == 1:
         p = p.reshape((len(p), 1))