Merge pull request #1213 from effigies/typ/loadsave

TYP: Annotate loadsave and image header classes

nibabel/analyze.py

@@ -83,8 +83,6 @@
 """
 from __future__ import annotations
 
-from typing import Type
-
 import numpy as np
 
 from .arrayproxy import ArrayProxy
@@ -895,7 +893,8 @@ def may_contain_header(klass, binaryblock):
 class AnalyzeImage(SpatialImage):
     """Class for basic Analyze format image"""
 
-    header_class: Type[AnalyzeHeader] = AnalyzeHeader
+    header_class: type[AnalyzeHeader] = AnalyzeHeader
+    header: AnalyzeHeader
     _meta_sniff_len = header_class.sizeof_hdr
     files_types: tuple[tuple[str, str], ...] = (('image', '.img'), ('header', '.hdr'))
     valid_exts: tuple[str, ...] = ('.img', '.hdr')

nibabel/brikhead.py

@@ -475,6 +475,7 @@ class AFNIImage(SpatialImage):
     """
 
     header_class = AFNIHeader
+    header: AFNIHeader
     valid_exts = ('.brik', '.head')
     files_types = (('image', '.brik'), ('header', '.head'))
     _compressed_suffixes = ('.gz', '.bz2', '.Z', '.zst')

nibabel/cifti2/cifti2.py

@@ -1411,6 +1411,7 @@ class Cifti2Image(DataobjImage, SerializableImage):
     """Class for single file CIFTI-2 format image"""
 
     header_class = Cifti2Header
+    header: Cifti2Header
     valid_exts = Nifti2Image.valid_exts
     files_types = Nifti2Image.files_types
     makeable = False

nibabel/ecat.py

@@ -751,7 +751,7 @@ class EcatImage(SpatialImage):
     valid_exts = ('.v',)
     files_types = (('image', '.v'), ('header', '.v'))
 
-    _header: EcatHeader
+    header: EcatHeader
     _subheader: EcatSubHeader
 
     ImageArrayProxy = EcatImageArrayProxy

nibabel/filebasedimages.py

@@ -12,7 +12,6 @@
 import io
 import typing as ty
 from copy import deepcopy
-from typing import Type
 from urllib import request
 
 from ._compression import COMPRESSION_ERRORS
@@ -158,8 +157,7 @@ class FileBasedImage:
     work.
     """
 
-    header_class: Type[FileBasedHeader] = FileBasedHeader
-    _header: FileBasedHeader
+    header_class: type[FileBasedHeader] = FileBasedHeader
     _meta_sniff_len: int = 0
     files_types: tuple[ExtensionSpec, ...] = (('image', None),)
     valid_exts: tuple[str, ...] = ()

nibabel/freesurfer/mghformat.py

@@ -462,6 +462,7 @@ class MGHImage(SpatialImage, SerializableImage):
     """Class for MGH format image"""
 
     header_class = MGHHeader
+    header: MGHHeader
     valid_exts = ('.mgh', '.mgz')
     # Register that .mgz extension signals gzip compression
     ImageOpener.compress_ext_map['.mgz'] = ImageOpener.gz_def

nibabel/imageclasses.py

@@ -7,9 +7,13 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Define supported image classes and names"""
+from __future__ import annotations
+
 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
@@ -21,7 +25,7 @@
 from .spm99analyze import Spm99AnalyzeImage
 
 # Ordered by the load/save priority.
-all_image_classes = [
+all_image_classes: list[type[FileBasedImage]] = [
     Nifti1Pair,
     Nifti1Image,
     Nifti2Pair,
@@ -41,7 +45,7 @@
 # Image classes known to require spatial axes to be first in index ordering.
 # When adding an image class, consider whether the new class should be listed
 # here.
-KNOWN_SPATIAL_FIRST = (
+KNOWN_SPATIAL_FIRST: tuple[type[FileBasedImage], ...] = (
     Nifti1Pair,
     Nifti1Image,
     Nifti2Pair,
@@ -55,7 +59,7 @@
 )
 
 
-def spatial_axes_first(img):
+def spatial_axes_first(img: DataobjImage) -> bool:
     """True if spatial image axes for `img` always precede other axes
 
     Parameters

nibabel/loadsave.py

@@ -8,7 +8,10 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # module imports
 """Utilities to load and save image objects"""
+from __future__ import annotations
+
 import os
+import typing as ty
 
 import numpy as np
 
@@ -22,7 +25,18 @@
 _compressed_suffixes = ('.gz', '.bz2', '.zst')
 
 
-def _signature_matches_extension(filename):
+if ty.TYPE_CHECKING:  # pragma: no cover
+    from .filebasedimages import FileBasedImage
+    from .filename_parser import FileSpec
+
+    P = ty.ParamSpec('P')
+
+    class Signature(ty.TypedDict):
+        signature: bytes
+        format_name: str
+
+
+def _signature_matches_extension(filename: FileSpec) -> tuple[bool, str]:
     """Check if signature aka magic number matches filename extension.
 
     Parameters
@@ -42,7 +56,7 @@ def _signature_matches_extension(filename):
        the empty string otherwise.
 
     """
-    signatures = {
+    signatures: dict[str, Signature] = {
         '.gz': {'signature': b'\x1f\x8b', 'format_name': 'gzip'},
         '.bz2': {'signature': b'BZh', 'format_name': 'bzip2'},
         '.zst': {'signature': b'\x28\xb5\x2f\xfd', 'format_name': 'ztsd'},
@@ -64,7 +78,7 @@ def _signature_matches_extension(filename):
     return False, f'File {filename} is not a {format_name} file'
 
 
-def load(filename, **kwargs):
+def load(filename: FileSpec, **kwargs) -> FileBasedImage:
     r"""Load file given filename, guessing at file type
 
     Parameters
@@ -126,7 +140,7 @@ def guessed_image_type(filename):
     raise ImageFileError(f'Cannot work out file type of "{filename}"')
 
 
-def save(img, filename, **kwargs):
+def save(img: FileBasedImage, filename: FileSpec, **kwargs) -> None:
     r"""Save an image to file adapting format to `filename`
 
     Parameters
@@ -161,19 +175,17 @@ def save(img, filename, **kwargs):
     from .nifti1 import Nifti1Image, Nifti1Pair
     from .nifti2 import Nifti2Image, Nifti2Pair
 
-    klass = None
-    converted = None
-
+    converted: FileBasedImage
     if type(img) == Nifti1Image and lext in ('.img', '.hdr'):
-        klass = Nifti1Pair
+        converted = Nifti1Pair.from_image(img)
     elif type(img) == Nifti2Image and lext in ('.img', '.hdr'):
-        klass = Nifti2Pair
+        converted = Nifti2Pair.from_image(img)
     elif type(img) == Nifti1Pair and lext == '.nii':
-        klass = Nifti1Image
+        converted = Nifti1Image.from_image(img)
     elif type(img) == Nifti2Pair and lext == '.nii':
-        klass = Nifti2Image
+        converted = Nifti2Image.from_image(img)
     else:  # arbitrary conversion
-        valid_klasses = [klass for klass in all_image_classes if ext in klass.valid_exts]
+        valid_klasses = [klass for klass in all_image_classes if lext in klass.valid_exts]
         if not valid_klasses:  # if list is empty
             raise ImageFileError(f'Cannot work out file type of "{filename}"')
 
@@ -186,13 +198,9 @@ def save(img, filename, **kwargs):
                 break
             except Exception as e:
                 err = e
-        # ... and if none of them work, raise an error.
-        if converted is None:
+        else:
             raise err
 
-    # Here, we either have a klass or a converted image.
-    if converted is None:
-        converted = klass.from_image(img)
     converted.to_filename(filename, **kwargs)
 
 

nibabel/minc1.py

@@ -10,7 +10,6 @@
 from __future__ import annotations
 
 from numbers import Integral
-from typing import Type
 
 import numpy as np
 
@@ -307,7 +306,8 @@ class Minc1Image(SpatialImage):
     load.
     """
 
-    header_class: Type[MincHeader] = Minc1Header
+    header_class: type[MincHeader] = Minc1Header
+    header: MincHeader
     _meta_sniff_len: int = 4
     valid_exts: tuple[str, ...] = ('.mnc',)
     files_types: tuple[tuple[str, str], ...] = (('image', '.mnc'),)

nibabel/minc2.py

@@ -150,6 +150,7 @@ class Minc2Image(Minc1Image):
     # MINC2 does not do compressed whole files
     _compressed_suffixes = ()
     header_class = Minc2Header
+    header: Minc2Header
 
     @classmethod
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):

nibabel/nifti1.py

@@ -14,7 +14,6 @@
 
 import warnings
 from io import BytesIO
-from typing import Type
 
 import numpy as np
 import numpy.linalg as npl
@@ -90,8 +89,8 @@
 # datatypes not in analyze format, with codes
 if have_binary128():
     # Only enable 128 bit floats if we really have IEEE binary 128 longdoubles
-    _float128t: Type[np.generic] = np.longdouble
-    _complex256t: Type[np.generic] = np.longcomplex
+    _float128t: type[np.generic] = np.longdouble
+    _complex256t: type[np.generic] = np.longcomplex
 else:
     _float128t = np.void
     _complex256t = np.void
@@ -1817,7 +1816,8 @@ class Nifti1PairHeader(Nifti1Header):
 class Nifti1Pair(analyze.AnalyzeImage):
     """Class for NIfTI1 format image, header pair"""
 
-    header_class: Type[Nifti1Header] = Nifti1PairHeader
+    header_class: type[Nifti1Header] = Nifti1PairHeader
+    header: Nifti1Header
     _meta_sniff_len = header_class.sizeof_hdr
     rw = True
 

nibabel/parrec.py

@@ -1253,6 +1253,7 @@ class PARRECImage(SpatialImage):
     """PAR/REC image"""
 
     header_class = PARRECHeader
+    header: PARRECHeader
     valid_exts = ('.rec', '.par')
     files_types = (('image', '.rec'), ('header', '.par'))
 

nibabel/spatialimages.py

@@ -476,6 +476,7 @@ class SpatialImage(DataobjImage):
     ImageSlicer: type[SpatialFirstSlicer] = SpatialFirstSlicer
 
     _header: SpatialHeader
+    header: SpatialHeader
 
     def __init__(
         self,

nibabel/spm2analyze.py

@@ -128,6 +128,7 @@ class Spm2AnalyzeImage(spm99.Spm99AnalyzeImage):
     """Class for SPM2 variant of basic Analyze image"""
 
     header_class = Spm2AnalyzeHeader
+    header: Spm2AnalyzeHeader
 
 
 load = Spm2AnalyzeImage.from_filename

nibabel/spm99analyze.py

@@ -227,6 +227,7 @@ class Spm99AnalyzeImage(analyze.AnalyzeImage):
     """Class for SPM99 variant of basic Analyze image"""
 
     header_class = Spm99AnalyzeHeader
+    header: Spm99AnalyzeHeader
     files_types = (('image', '.img'), ('header', '.hdr'), ('mat', '.mat'))
     has_affine = True
     makeable = True