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|
From: Gregory Lee <grlee77@gmail.com>
Date: Tue, 29 Nov 2022 00:50:13 -0500
Subject: [PATCH] Handle new warnings introduced in NumPy 1.24 (#6637)
* ignore warning about deprecated int0 arising from SciPy<1.9.4 in one test case
This warning appears with NumPy>=1.24 where np.int0 has been deprecated
* ignore warning about deprecated np.bool8 in dtype utilities
This warning appears with NumPy>=1.24 where np.bool8 has been deprecated
* bump tolerance of float64 case in test_ciede2000_dE
uncertain why this was needed for NumPy>=1.24
* refactor relabel_sequential to avoid a new NumPy RuntimeWarning
* use explicit astype call to avoid a DeprecationWarning in Cascade
* Apply suggestions from code review
Co-authored-by: Brett M. Morris <morrisbrettm@gmail.com>
Co-authored-by: Mark Harfouche <mark.harfouche@gmail.com>
---
skimage/_shared/testing.py | 9 +++++++++
skimage/color/tests/test_delta_e.py | 3 +--
skimage/feature/_cascade.pyx | 4 +++-
skimage/feature/tests/test_cascade.py | 1 +
skimage/segmentation/_join.py | 5 ++++-
skimage/util/dtype.py | 13 +++++++++++--
skimage/util/tests/test_dtype.py | 2 +-
7 files changed, 30 insertions(+), 7 deletions(-)
diff --git a/skimage/_shared/testing.py b/skimage/_shared/testing.py
index 64b5856..e7da493 100644
--- a/skimage/_shared/testing.py
+++ b/skimage/_shared/testing.py
@@ -285,6 +285,15 @@ def setup_test():
category=DeprecationWarning
)
+ # ignore dtype deprecation warning from NumPy arising from use of SciPy
+ # as a reference in test_watershed09. Should be fixed in scipy>=1.9.4
+ # https://github.com/scipy/scipy/commit/da3ff893b9ac161938e11f9bcd5380e09cf03150
+ warnings.filterwarnings(
+ 'default',
+ message=('`np.int0` is a deprecated alias for `np.intp`'),
+ category=DeprecationWarning
+ )
+
def teardown_test():
"""Default package level teardown routine for skimage tests.
diff --git a/skimage/color/tests/test_delta_e.py b/skimage/color/tests/test_delta_e.py
index 7472126..304346f 100644
--- a/skimage/color/tests/test_delta_e.py
+++ b/skimage/color/tests/test_delta_e.py
@@ -30,8 +30,7 @@ def test_ciede2000_dE(dtype, channel_axis):
dE2 = deltaE_ciede2000(lab1, lab2, channel_axis=channel_axis)
assert dE2.dtype == _supported_float_type(dtype)
- rtol = 1e-2 if dtype == np.float32 else 1e-4
- assert_allclose(dE2, data['dE'], rtol=rtol)
+ assert_allclose(dE2, data['dE'], rtol=1e-2)
def load_ciede2000_data():
diff --git a/skimage/feature/_cascade.pyx b/skimage/feature/_cascade.pyx
index 2556584..7f3914b 100644
--- a/skimage/feature/_cascade.pyx
+++ b/skimage/feature/_cascade.pyx
@@ -909,7 +909,9 @@ cdef class Cascade:
feature_number = int(internal_nodes[0])
# list() is for Python3 fix here
lut_array = list(map(lambda x: int(x), internal_nodes[1:]))
- lut = np.asarray(lut_array, dtype='uint32')
+ # Cast via astype to avoid warning about integer wraparound.
+ # see: https://github.com/scikit-image/scikit-image/issues/6638
+ lut = np.asarray(lut_array).astype(np.uint32)
# Copy array to the main LUT array
for i in range(8):
diff --git a/skimage/feature/tests/test_cascade.py b/skimage/feature/tests/test_cascade.py
index 5d5263a..bf541d6 100644
--- a/skimage/feature/tests/test_cascade.py
+++ b/skimage/feature/tests/test_cascade.py
@@ -2,6 +2,7 @@ import skimage.data as data
from skimage.feature import Cascade
+
def test_detector_astronaut():
# Load the trained file from the module root.
diff --git a/skimage/segmentation/_join.py b/skimage/segmentation/_join.py
index d22bff4..dcf68f0 100644
--- a/skimage/segmentation/_join.py
+++ b/skimage/segmentation/_join.py
@@ -1,4 +1,5 @@
import numpy as np
+
from ..util._map_array import map_array, ArrayMap
@@ -128,6 +129,8 @@ def relabel_sequential(label_field, offset=1):
else:
out_vals = np.arange(offset, offset+len(in_vals))
input_type = label_field.dtype
+ if input_type.kind not in "iu":
+ raise TypeError("label_field must have an integer dtype")
# Some logic to determine the output type:
# - we don't want to return a smaller output type than the input type,
@@ -142,7 +145,7 @@ def relabel_sequential(label_field, offset=1):
if input_type.itemsize < required_type.itemsize:
output_type = required_type
else:
- if input_type.type(out_vals[-1]) == out_vals[-1]:
+ if out_vals[-1] < np.iinfo(input_type).max:
output_type = input_type
else:
output_type = required_type
diff --git a/skimage/util/dtype.py b/skimage/util/dtype.py
index 23e4452..064f9a0 100644
--- a/skimage/util/dtype.py
+++ b/skimage/util/dtype.py
@@ -1,6 +1,8 @@
-import numpy as np
+import warnings
from warnings import warn
+import numpy as np
+
__all__ = ['img_as_float32', 'img_as_float64', 'img_as_float',
'img_as_int', 'img_as_uint', 'img_as_ubyte',
@@ -24,12 +26,19 @@ _integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max)
for t in _integer_types}
dtype_range = {bool: (False, True),
np.bool_: (False, True),
- np.bool8: (False, True),
float: (-1, 1),
np.float_: (-1, 1),
np.float16: (-1, 1),
np.float32: (-1, 1),
np.float64: (-1, 1)}
+
+with warnings.catch_warnings():
+ warnings.filterwarnings('ignore', category=DeprecationWarning)
+
+ # np.bool8 is a deprecated alias of np.bool_
+ if hasattr(np, 'bool8'):
+ dtype_range[np.bool8] = (False, True)
+
dtype_range.update(_integer_ranges)
_supported_types = list(dtype_range.keys())
diff --git a/skimage/util/tests/test_dtype.py b/skimage/util/tests/test_dtype.py
index e7b4529..f8804e4 100644
--- a/skimage/util/tests/test_dtype.py
+++ b/skimage/util/tests/test_dtype.py
@@ -109,7 +109,7 @@ def test_copy():
def test_bool():
img_ = np.zeros((10, 10), bool)
- img8 = np.zeros((10, 10), np.bool8)
+ img8 = np.zeros((10, 10), np.bool_)
img_[1, 1] = True
img8[1, 1] = True
for (func, dt) in [(img_as_int, np.int16),
|
