From 379ded01bb419d1a72fb4543078fb802a9abb6dd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 30 Aug 2023 10:36:43 +0100
Subject: [PATCH] MNT: Remove some obsolete warning suppression. Suppress
nibabel warning when converting to NIFTI2
---
fsl/scripts/atlasq.py | 17 +++--------------
fsl/scripts/fsl_ents.py | 8 ++------
fsl/scripts/imcp.py | 15 ++++++++-------
fsl/scripts/immv.py | 15 ++++++++-------
4 files changed, 21 insertions(+), 34 deletions(-)
diff --git a/fsl/scripts/atlasq.py b/fsl/scripts/atlasq.py
index b0ef32a94..9e887e688 100644
--- a/fsl/scripts/atlasq.py
+++ b/fsl/scripts/atlasq.py
@@ -19,20 +19,9 @@ import warnings
import logging
import numpy as np
-# if h5py <= 2.7.1 is installed,
-# it will be imported via nibabel,
-# and will cause a numpy warning
-# to be emitted.
-with warnings.catch_warnings():
- warnings.filterwarnings("ignore", category=FutureWarning)
- import fsl.data.image as fslimage
-
-# If wx is not present, then fsl.utils.platform
-# will complain that it is not present.
-logging.getLogger('fsl.utils.platform').setLevel(logging.ERROR)
-
-import fsl.data.atlases as fslatlases # noqa
-import fsl.version as fslversion # noqa
+import fsl.data.image as fslimage
+import fsl.data.atlases as fslatlases
+import fsl.version as fslversion
log = logging.getLogger(__name__)
diff --git a/fsl/scripts/fsl_ents.py b/fsl/scripts/fsl_ents.py
index 1590c9b44..2f9a4a0b1 100644
--- a/fsl/scripts/fsl_ents.py
+++ b/fsl/scripts/fsl_ents.py
@@ -16,12 +16,8 @@ import warnings
import numpy as np
-# See atlasq.py for explanation
-with warnings.catch_warnings():
- warnings.filterwarnings("ignore", category=FutureWarning)
-
- import fsl.data.fixlabels as fixlabels
- import fsl.data.melodicanalysis as melanalysis
+import fsl.data.fixlabels as fixlabels
+import fsl.data.melodicanalysis as melanalysis
DTYPE = np.float64
diff --git a/fsl/scripts/imcp.py b/fsl/scripts/imcp.py
index d2fcc1eda..6ae4d26da 100755
--- a/fsl/scripts/imcp.py
+++ b/fsl/scripts/imcp.py
@@ -14,15 +14,11 @@ The :func:`main` function is essentially a wrapper around the
import os.path as op
import sys
-import warnings
+import logging
import fsl.utils.path as fslpath
-
-# See atlasq.py for explanation
-with warnings.catch_warnings():
- warnings.filterwarnings("ignore", category=FutureWarning)
- import fsl.utils.imcp as imcp
- import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
usage = """Usage:
@@ -57,6 +53,11 @@ def main(argv=None):
print(usage)
return 1
+ # When converting to NIFTI2, nibabel
+ # emits an annoying message via log.warning:
+ # sizeof_hdr should be 540; set sizeof_hdr to 540
+ logging.getLogger('nibabel').setLevel(logging.ERROR)
+
try:
srcs = [fslimage.fixExt(s) for s in srcs]
srcs = fslpath.removeDuplicates(
diff --git a/fsl/scripts/immv.py b/fsl/scripts/immv.py
index febe42274..0ebfb575d 100755
--- a/fsl/scripts/immv.py
+++ b/fsl/scripts/immv.py
@@ -15,15 +15,11 @@ The :func:`main` function is essentially a wrapper around the
import os.path as op
import sys
-import warnings
+import logging
import fsl.utils.path as fslpath
-
-# See atlasq.py for explanation
-with warnings.catch_warnings():
- warnings.filterwarnings("ignore", category=FutureWarning)
- import fsl.utils.imcp as imcp
- import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.data.image as fslimage
usage = """Usage:
@@ -58,6 +54,11 @@ def main(argv=None):
print(usage)
return 1
+ # When converting to NIFTI2, nibabel
+ # emits an annoying message via log.warning:
+ # sizeof_hdr should be 540; set sizeof_hdr to 540
+ logging.getLogger('nibabel').setLevel(logging.ERROR)
+
try:
srcs = [fslimage.fixExt(s) for s in srcs]
srcs = fslpath.removeDuplicates(
--
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