type: Annotate SpatialImage subclasses with affine information

Author: effigies

nibabel/analyze.py

@@ -84,13 +84,15 @@
 
 from __future__ import annotations
 
+import typing as ty
+
 import numpy as np
 
 from .arrayproxy import ArrayProxy
 from .arraywriters import ArrayWriter, WriterError, get_slope_inter, make_array_writer
 from .batteryrunners import Report
 from .fileholders import copy_file_map
-from .spatialimages import HeaderDataError, HeaderTypeError, SpatialHeader, SpatialImage
+from .spatialimages import AffT, HeaderDataError, HeaderTypeError, SpatialHeader, SpatialImage
 from .volumeutils import (
     apply_read_scaling,
     array_from_file,
@@ -102,6 +104,13 @@
 )
 from .wrapstruct import LabeledWrapStruct
 
+if ty.TYPE_CHECKING:
+    from collections.abc import Mapping
+
+    from .arrayproxy import ArrayLike
+    from .filebasedimages import FileBasedHeader
+    from .fileholders import FileMap
+
 # Sub-parts of standard analyze header from
 # Mayo dbh.h file
 header_key_dtd = [
@@ -893,11 +902,12 @@ def may_contain_header(klass, binaryblock):
         return 348 in (hdr_struct['sizeof_hdr'], bs_hdr_struct['sizeof_hdr'])
 
 
-class AnalyzeImage(SpatialImage):
+class AnalyzeImage(SpatialImage[AffT]):
     """Class for basic Analyze format image"""
 
     header_class: type[AnalyzeHeader] = AnalyzeHeader
     header: 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')
@@ -908,7 +918,15 @@ class AnalyzeImage(SpatialImage):
 
     ImageArrayProxy = ArrayProxy
 
-    def __init__(self, dataobj, affine, header=None, extra=None, file_map=None, dtype=None):
+    def __init__(
+        self,
+        dataobj: ArrayLike,
+        affine: AffT,
+        header: FileBasedHeader | Mapping | None = None,
+        extra: Mapping | None = None,
+        file_map: FileMap | None = None,
+        dtype=None,
+    ) -> None:
         super().__init__(dataobj, affine, header, extra, file_map)
         # Reset consumable values
         self._header.set_data_offset(0)

nibabel/brikhead.py

@@ -35,7 +35,7 @@
 
 from .arrayproxy import ArrayProxy
 from .fileslice import strided_scalar
-from .spatialimages import HeaderDataError, ImageDataError, SpatialHeader, SpatialImage
+from .spatialimages import Affine, HeaderDataError, ImageDataError, SpatialHeader, SpatialImage
 from .volumeutils import Recoder
 
 # used for doc-tests
@@ -453,7 +453,7 @@ def get_volume_labels(self):
         return labels
 
 
-class AFNIImage(SpatialImage):
+class AFNIImage(SpatialImage[Affine]):
     """
     AFNI Image file
 

nibabel/ecat.py

@@ -43,17 +43,30 @@
 below).  It's not clear what the licenses are for these files.
 """
 
+from __future__ import annotations
+
 import warnings
 from numbers import Integral
+from typing import TYPE_CHECKING
 
 import numpy as np
 
 from .arraywriters import make_array_writer
 from .fileslice import canonical_slicers, predict_shape, slice2outax
-from .spatialimages import SpatialHeader, SpatialImage
+from .spatialimages import Affine, AffT, SpatialHeader, SpatialImage
 from .volumeutils import array_from_file, make_dt_codes, native_code, swapped_code
 from .wrapstruct import WrapStruct
 
+if TYPE_CHECKING:
+    from collections.abc import Mapping
+    from typing import Literal as L
+
+    import numpy.typing as npt
+
+    from .arrayproxy import ArrayLike
+    from .filebasedimages import FileBasedHeader
+    from .fileholders import FileMap
+
 BLOCK_SIZE = 512
 
 main_header_dtd = [
@@ -743,7 +756,7 @@ def __getitem__(self, sliceobj):
         return out_data
 
 
-class EcatImage(SpatialImage):
+class EcatImage(SpatialImage[AffT]):
     """Class returns a list of Ecat images, with one image(hdr/data) per frame"""
 
     header_class = EcatHeader
@@ -756,7 +769,16 @@ class EcatImage(SpatialImage):
 
     ImageArrayProxy = EcatImageArrayProxy
 
-    def __init__(self, dataobj, affine, header, subheader, mlist, extra=None, file_map=None):
+    def __init__(
+        self,
+        dataobj: ArrayLike,
+        affine: AffT,
+        header: FileBasedHeader | Mapping | None,
+        subheader: EcatSubHeader,
+        mlist: npt.NDArray[np.integer],
+        extra: Mapping | None = None,
+        file_map: FileMap | None = None,
+    ) -> None:
         """Initialize Image
 
         The image is a combination of
@@ -798,40 +820,38 @@ def __init__(self, dataobj, affine, header, subheader, mlist, extra=None, file_m
         >>> data4d.shape == (10, 10, 3, 1)
         True
         """
+        super().__init__(
+            dataobj=dataobj,
+            affine=affine,
+            header=header,
+            extra=extra,
+            file_map=file_map,
+        )
         self._subheader = subheader
         self._mlist = mlist
-        self._dataobj = dataobj
-        if affine is not None:
-            # Check that affine is array-like 4,4.  Maybe this is too strict at
-            # this abstract level, but so far I think all image formats we know
-            # do need 4,4.
-            affine = np.array(affine, dtype=np.float64, copy=True)
-            if not affine.shape == (4, 4):
-                raise ValueError('Affine should be shape 4,4')
-        self._affine = affine
-        if extra is None:
-            extra = {}
-        self.extra = extra
-        self._header = header
-        if file_map is None:
-            file_map = self.__class__.make_file_map()
-        self.file_map = file_map
-        self._data_cache = None
-        self._fdata_cache = None
+
+    # Override SpatialImage default, which attempts to set the
+    # affine in the header.
+    def update_header(self) -> None:
+        """Does nothing"""
 
     @property
-    def affine(self):
+    def affine(self) -> AffT:
         if not self._subheader._check_affines():
             warnings.warn(
                 'Affines different across frames, loading affine from FIRST frame', UserWarning
             )
         return self._affine
 
-    def get_frame_affine(self, frame):
+    def get_frame_affine(self, frame: int) -> Affine:
         """returns 4X4 affine"""
         return self._subheader.get_frame_affine(frame=frame)
 
-    def get_frame(self, frame, orientation=None):
+    def get_frame(
+        self,
+        frame: int,
+        orientation: L['neurological', 'radiological'] | None = None,
+    ) -> np.ndarray:
         """
         Get full volume for a time frame
 
@@ -847,16 +867,16 @@ def get_data_dtype(self, frame):
         return dt
 
     @property
-    def shape(self):
+    def shape(self) -> tuple[int, int, int, int]:
         x, y, z = self._subheader.get_shape()
         nframes = self._subheader.get_nframes()
         return (x, y, z, nframes)
 
-    def get_mlist(self):
+    def get_mlist(self) -> npt.NDArray[np.integer]:
         """get access to the mlist"""
         return self._mlist
 
-    def get_subheaders(self):
+    def get_subheaders(self) -> EcatSubHeader:
         """get access to subheaders"""
         return self._subheader
 

nibabel/freesurfer/mghformat.py

@@ -22,7 +22,7 @@
 from ..fileholders import FileHolder
 from ..filename_parser import _stringify_path
 from ..openers import ImageOpener
-from ..spatialimages import HeaderDataError, SpatialHeader, SpatialImage
+from ..spatialimages import Affine, HeaderDataError, SpatialHeader, SpatialImage
 from ..volumeutils import Recoder, array_from_file, array_to_file, endian_codes
 from ..wrapstruct import LabeledWrapStruct
 
@@ -459,7 +459,7 @@ def diagnose_binaryblock(klass, binaryblock, endianness=None):
         return '\n'.join([report.message for report in reports if report.message])
 
 
-class MGHImage(SpatialImage, SerializableImage):
+class MGHImage(SpatialImage[Affine], SerializableImage):
     """Class for MGH format image"""
 
     header_class = MGHHeader

nibabel/minc1.py

@@ -16,7 +16,7 @@
 
 from .externals.netcdf import netcdf_file
 from .fileslice import canonical_slicers
-from .spatialimages import SpatialHeader, SpatialImage
+from .spatialimages import Affine, SpatialHeader, SpatialImage
 
 _dt_dict = {
     ('b', 'unsigned'): np.uint8,
@@ -299,7 +299,7 @@ def may_contain_header(klass, binaryblock):
         return binaryblock[:4] == b'CDF\x01'
 
 
-class Minc1Image(SpatialImage):
+class Minc1Image(SpatialImage[Affine]):
     """Class for MINC1 format images
 
     The MINC1 image class uses the default header type, rather than a specific

nibabel/nifti1.py

@@ -35,13 +35,19 @@
 from .filebasedimages import ImageFileError, SerializableImage
 from .optpkg import optional_package
 from .quaternions import fillpositive, mat2quat, quat2mat
-from .spatialimages import HeaderDataError
+from .spatialimages import AffT, HeaderDataError
 from .spm99analyze import SpmAnalyzeHeader
 from .volumeutils import Recoder, endian_codes, make_dt_codes
 
 if ty.TYPE_CHECKING:
+    from collections.abc import Mapping
+
     import pydicom as pdcm
 
+    from .arrayproxy import ArrayLike
+    from .filebasedimages import FileBasedHeader
+    from .fileholders import FileMap
+
     have_dicom = True
     DicomDataset = pdcm.Dataset
 else:
@@ -1971,19 +1977,28 @@ class Nifti1PairHeader(Nifti1Header):
     is_single = False
 
 
-class Nifti1Pair(analyze.AnalyzeImage):
+class Nifti1Pair(analyze.AnalyzeImage[AffT]):
     """Class for NIfTI1 format image, header pair"""
 
     header_class: type[Nifti1Header] = Nifti1PairHeader
     header: Nifti1Header
+    _header: Nifti1Header
     _meta_sniff_len = header_class.sizeof_hdr
     rw = True
 
     # If a _dtype_alias has been set, it can only be resolved by inspecting
     # the data at serialization time
     _dtype_alias = None
 
-    def __init__(self, dataobj, affine, header=None, extra=None, file_map=None, dtype=None):
+    def __init__(
+        self,
+        dataobj: ArrayLike,
+        affine: AffT,
+        header: FileBasedHeader | Mapping | None = None,
+        extra: Mapping | None = None,
+        file_map: FileMap | None = None,
+        dtype=None,
+    ) -> None:
         # Special carve-out for 64 bit integers
         # See GitHub issues
         #  * https://github.com/nipy/nibabel/issues/1046
@@ -1994,7 +2009,7 @@ def __init__(self, dataobj, affine, header=None, extra=None, file_map=None, dtyp
         danger_dts = (np.dtype('int64'), np.dtype('uint64'))
         if header is None and dtype is None and get_obj_dtype(dataobj) in danger_dts:
             alert_future_error(
-                f'Image data has type {dataobj.dtype}, which may cause '
+                f'Image data has type {get_obj_dtype(dataobj)}, which may cause '
                 'incompatibilities with other tools.',
                 '5.0',
                 warning_rec='This warning can be silenced by passing the dtype argument'
@@ -2410,7 +2425,7 @@ def as_reoriented(self, ornt):
         return img
 
 
-class Nifti1Image(Nifti1Pair, SerializableImage):
+class Nifti1Image(Nifti1Pair[AffT], SerializableImage):
     """Class for single file NIfTI1 format image"""
 
     header_class = Nifti1Header

nibabel/nifti2.py

@@ -19,7 +19,7 @@
 from .batteryrunners import Report
 from .filebasedimages import ImageFileError
 from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
-from .spatialimages import HeaderDataError
+from .spatialimages import AffT, HeaderDataError
 
 r"""
 Header struct from : https://www.nitrc.org/forum/message.php?msg_id=3738
@@ -240,17 +240,19 @@ class Nifti2PairHeader(Nifti2Header):
     is_single = False
 
 
-class Nifti2Pair(Nifti1Pair):
+class Nifti2Pair(Nifti1Pair[AffT]):
     """Class for NIfTI2 format image, header pair"""
 
-    header_class = Nifti2PairHeader
+    header_class: type[Nifti2Header] = Nifti2PairHeader
+    header: Nifti2Header
     _meta_sniff_len = header_class.sizeof_hdr
 
 
-class Nifti2Image(Nifti1Image):
+class Nifti2Image(Nifti1Image[AffT]):
     """Class for single file NIfTI2 format image"""
 
-    header_class = Nifti2Header
+    header_class: type[Nifti2Header] = Nifti2Header
+    header: Nifti2Header
     _meta_sniff_len = header_class.sizeof_hdr
 
 

nibabel/parrec.py

@@ -134,7 +134,7 @@
 from .fileslice import fileslice, strided_scalar
 from .nifti1 import unit_codes
 from .openers import ImageOpener
-from .spatialimages import SpatialHeader, SpatialImage
+from .spatialimages import Affine, SpatialHeader, SpatialImage
 from .volumeutils import Recoder, array_from_file
 
 # PSL to RAS affine
@@ -1248,7 +1248,7 @@ def get_volume_labels(self):
         return sort_info
 
 
-class PARRECImage(SpatialImage):
+class PARRECImage(SpatialImage[Affine]):
     """PAR/REC image"""
 
     header_class = PARRECHeader

nibabel/spm2analyze.py

@@ -10,7 +10,8 @@
 
 import numpy as np
 
-from . import spm99analyze as spm99  # module import
+from . import spm99analyze as spm99
+from .spatialimages import AffT
 
 image_dimension_dtd = spm99.image_dimension_dtd.copy()
 image_dimension_dtd[image_dimension_dtd.index(('funused2', 'f4'))] = ('scl_inter', 'f4')
@@ -125,7 +126,7 @@ def may_contain_header(klass, binaryblock):
         )
 
 
-class Spm2AnalyzeImage(spm99.Spm99AnalyzeImage):
+class Spm2AnalyzeImage(spm99.Spm99AnalyzeImage[AffT]):
     """Class for SPM2 variant of basic Analyze image"""
 
     header_class = Spm2AnalyzeHeader