Merge branch 'mnt/warnings' into 'main'

MNT: Remove some obsolete warning suppression logic, and suppress nibabel warning when converting to NIFTI2

See merge request fsl/fslpy!406

CHANGELOG.rst

@@ -26,6 +26,15 @@ Changed
   (!405).
 
 
+Fixed
+^^^^^
+
+
+* Updated the ```immv``/``imcp`` scripts to honour the ``$FSLOUTPUTTYPE``
+  environment variable more closely - conversions between NIFTI1 and
+  NIFTI2 were not being performed correctly (!405).
+
+
 3.13.3 (Monday 17th July 2023)
 ------------------------------
 

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__)

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

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(

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(