From e57c406d3c4eac67c68ac86bffb2d9bad6bc0be4 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 12 Oct 2018 12:44:13 +0100
Subject: [PATCH] RF: Avoid various warnings
---
fsl/data/image.py | 3 ++-
fsl/data/imagewrapper.py | 11 ++++++-----
fsl/utils/transform.py | 14 +++++++-------
3 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 036d0575e..1b407a3f7 100644
--- a/fsl/data/image.py
+++ b/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
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index eccf85184..b73cb879a 100644
--- a/fsl/data/imagewrapper.py
+++ b/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, :, :]
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index 2a5610dd8..f574eaa76 100644
--- a/fsl/utils/transform.py
+++ b/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))
--
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