Merge branch 'master' into PERF

Author: effigies

nibabel/_compression.py

@@ -12,12 +12,13 @@
 
 import bz2
 import gzip
-import io
 import typing as ty
 
 from .optpkg import optional_package
 
 if ty.TYPE_CHECKING:
+    import io
+
     import indexed_gzip  # type: ignore[import]
     import pyzstd
 

nibabel/batteryrunners.py

@@ -252,7 +252,7 @@ def __str__(self):
     def message(self):
         """formatted message string, including fix message if present"""
         if self.fix_msg:
-            return '; '.join((self.problem_msg, self.fix_msg))
+            return f'{self.problem_msg}; {self.fix_msg}'
         return self.problem_msg
 
     def log_raise(self, logger, error_level=40):

nibabel/cifti2/cifti2.py

@@ -1570,7 +1570,7 @@ def to_file_map(self, file_map=None, dtype=None):
 
         self.update_headers()
         header = self._nifti_header
-        extension = Cifti2Extension(content=self.header.to_xml())
+        extension = Cifti2Extension.from_bytes(self.header.to_xml())
         header.extensions = Nifti1Extensions(
             ext for ext in header.extensions if not isinstance(ext, Cifti2Extension)
         )

nibabel/cifti2/parse_cifti2.py

@@ -40,19 +40,15 @@
 )
 
 
-class Cifti2Extension(Nifti1Extension):
+class Cifti2Extension(Nifti1Extension[Cifti2Header]):
     code = 32
 
-    def __init__(self, code=None, content=None):
-        Nifti1Extension.__init__(self, code=code or self.code, content=content)
-
-    def _unmangle(self, value):
+    def _unmangle(self, value: bytes) -> Cifti2Header:
         parser = Cifti2Parser()
         parser.parse(string=value)
-        self._content = parser.header
-        return self._content
+        return parser.header
 
-    def _mangle(self, value):
+    def _mangle(self, value: Cifti2Header) -> bytes:
         if not isinstance(value, Cifti2Header):
             raise ValueError('Can only mangle a Cifti2Header.')
         return value.to_xml()

nibabel/dataobj_images.py

@@ -14,14 +14,14 @@
 
 import numpy as np
 
-from .arrayproxy import ArrayLike
 from .deprecated import deprecate_with_version
 from .filebasedimages import FileBasedHeader, FileBasedImage
-from .fileholders import FileMap
 
 if ty.TYPE_CHECKING:
     import numpy.typing as npt
 
+    from .arrayproxy import ArrayLike
+    from .fileholders import FileMap
     from .filename_parser import FileSpec
 
 ArrayImgT = ty.TypeVar('ArrayImgT', bound='DataobjImage')

nibabel/ecat.py

@@ -957,7 +957,7 @@ def to_file_map(self, file_map=None):
         hdr.write_to(hdrf)
 
         # Write every frames
-        for index in range(0, self.header['num_frames']):
+        for index in range(self.header['num_frames']):
             # Move to subheader offset
             frame_offset = subheaders._get_frame_offset(index) - 512
             imgf.seek(frame_offset)

nibabel/fileholders.py

@@ -10,12 +10,14 @@
 
 from __future__ import annotations
 
-import io
 import typing as ty
 from copy import copy
 
 from .openers import ImageOpener
 
+if ty.TYPE_CHECKING:
+    import io
+
 
 class FileHolderError(Exception):
     pass

nibabel/gifti/gifti.py

@@ -374,7 +374,7 @@ def _to_xml_element(self):
     def print_summary(self):
         print('Dataspace: ', xform_codes.niistring[self.dataspace])
         print('XFormSpace: ', xform_codes.niistring[self.xformspace])
-        print('Affine Transformation Matrix: \n', self.xform)
+        print('Affine Transformation Matrix:\n', self.xform)
 
 
 def _data_tag_element(dataarray, encoding, dtype, ordering):

nibabel/gifti/tests/test_gifti.py

@@ -423,13 +423,14 @@ def test_gifti_coord(capsys):
     gcs.xform = None
     gcs.print_summary()
     captured = capsys.readouterr()
-    assert captured.out == '\n'.join(
-        [
-            'Dataspace:  NIFTI_XFORM_UNKNOWN',
-            'XFormSpace:  NIFTI_XFORM_UNKNOWN',
-            'Affine Transformation Matrix: ',
-            ' None\n',
-        ]
+    assert (
+        captured.out
+        == """\
+Dataspace:  NIFTI_XFORM_UNKNOWN
+XFormSpace:  NIFTI_XFORM_UNKNOWN
+Affine Transformation Matrix:
+ None
+"""
     )
     gcs.to_xml()
 

nibabel/imageclasses.py

@@ -10,11 +10,11 @@
 
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 from .analyze import AnalyzeImage
 from .brikhead import AFNIImage
 from .cifti2 import Cifti2Image
-from .dataobj_images import DataobjImage
-from .filebasedimages import FileBasedImage
 from .freesurfer import MGHImage
 from .gifti import GiftiImage
 from .minc1 import Minc1Image
@@ -25,6 +25,10 @@
 from .spm2analyze import Spm2AnalyzeImage
 from .spm99analyze import Spm99AnalyzeImage
 
+if TYPE_CHECKING:
+    from .dataobj_images import DataobjImage
+    from .filebasedimages import FileBasedImage
+
 # Ordered by the load/save priority.
 all_image_classes: list[type[FileBasedImage]] = [
     Nifti1Pair,