ENH: Add type annotations to pacify mypy

Author: effigies

nibabel/analyze.py

@@ -81,6 +81,9 @@
 can be loaded with and without a default flip, so the saved zoom will not
 constrain the affine.
 """
+from __future__ import annotations
+
+from typing import Type
 
 import numpy as np
 
@@ -131,7 +134,7 @@
     ('glmax', 'i4'),
     ('glmin', 'i4'),
 ]
-data_history_dtd = [
+data_history_dtd: list[tuple[str, str] | tuple[str, str, tuple[int, ...]]] = [
     ('descrip', 'S80'),
     ('aux_file', 'S24'),
     ('orient', 'S1'),
@@ -892,11 +895,11 @@ def may_contain_header(klass, binaryblock):
 class AnalyzeImage(SpatialImage):
     """Class for basic Analyze format image"""
 
-    header_class = AnalyzeHeader
+    header_class: Type[AnalyzeHeader] = AnalyzeHeader
     _meta_sniff_len = header_class.sizeof_hdr
-    files_types = (('image', '.img'), ('header', '.hdr'))
-    valid_exts = ('.img', '.hdr')
-    _compressed_suffixes = ('.gz', '.bz2', '.zst')
+    files_types: tuple[tuple[str, str], ...] = (('image', '.img'), ('header', '.hdr'))
+    valid_exts: tuple[str, ...] = ('.img', '.hdr')
+    _compressed_suffixes: tuple[str, ...] = ('.gz', '.bz2', '.zst')
 
     makeable = True
     rw = True

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -26,7 +26,7 @@
 
 # if memory_profiler is installed, we get memory usage results
 try:
-    from memory_profiler import memory_usage
+    from memory_profiler import memory_usage  # type: ignore
 except ImportError:
     memory_usage = None
 

nibabel/brikhead.py

@@ -27,6 +27,7 @@
 am aware) always be >= 1. This permits sub-brick indexing common in AFNI
 programs (e.g., example4d+orig'[0]').
 """
+from __future__ import annotations
 
 import os
 import re
@@ -476,9 +477,9 @@ class AFNIImage(SpatialImage):
     True
     """
 
-    header_class = AFNIHeader
-    valid_exts = ('.brik', '.head')
-    files_types = (('image', '.brik'), ('header', '.head'))
+    header_class: type = AFNIHeader
+    valid_exts: tuple[str, ...] = ('.brik', '.head')
+    files_types: tuple[tuple[str, str], ...] = (('image', '.brik'), ('header', '.head'))
     _compressed_suffixes = ('.gz', '.bz2', '.Z', '.zst')
     makeable = False
     rw = False

nibabel/casting.py

@@ -3,6 +3,7 @@
 Most routines work round some numpy oddities in floating point precision and
 casting.  Others work round numpy casting to and from python ints
 """
+from __future__ import annotations
 
 import warnings
 from numbers import Integral
@@ -110,7 +111,7 @@ def float_to_int(arr, int_type, nan2zero=True, infmax=False):
 
 
 # Cache range values
-_SHARED_RANGES = {}
+_SHARED_RANGES : dict[tuple[type, type], tuple[np.number, np.number]] = {}
 
 
 def shared_range(flt_type, int_type):

nibabel/cmdline/dicomfs.py

@@ -25,7 +25,7 @@ class dummy_fuse:
 
 
 try:
-    import fuse
+    import fuse  # type: ignore
 
     uid = os.getuid()
     gid = os.getgid()

nibabel/externals/netcdf.py

@@ -871,6 +871,7 @@ def __setattr__(self, attr, value):
             pass
         self.__dict__[attr] = value
 
+    @property
     def isrec(self):
         """Returns whether the variable has a record dimension or not.
 
@@ -881,16 +882,15 @@ def isrec(self):
 
         """
         return bool(self.data.shape) and not self._shape[0]
-    isrec = property(isrec)
 
+    @property
     def shape(self):
         """Returns the shape tuple of the data variable.
 
         This is a read-only attribute and can not be modified in the
         same manner of other numpy arrays.
         """
         return self.data.shape
-    shape = property(shape)
 
     def getValue(self):
         """

nibabel/filebasedimages.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Common interface for any image format--volume or surface, binary or xml."""
+from __future__ import annotations
 
 import io
 from copy import deepcopy
@@ -144,14 +145,14 @@ class FileBasedImage:
     work.
     """
 
-    header_class = FileBasedHeader
-    _meta_sniff_len = 0
-    files_types = (('image', None),)
-    valid_exts = ()
-    _compressed_suffixes = ()
+    header_class: type = FileBasedHeader
+    _meta_sniff_len: int = 0
+    files_types: tuple[tuple[str, str | None], ...] = (('image', None),)
+    valid_exts: tuple[str, ...] = ()
+    _compressed_suffixes: tuple[str, ...] = ()
 
-    makeable = True  # Used in test code
-    rw = True  # Used in test code
+    makeable: bool = True  # Used in test code
+    rw: bool = True  # Used in test code
 
     def __init__(self, header=None, extra=None, file_map=None):
         """Initialize image

nibabel/gifti/gifti.py

@@ -11,10 +11,12 @@
 The Gifti specification was (at time of writing) available as a PDF download
 from http://www.nitrc.org/projects/gifti/
 """
+from __future__ import annotations
 
 import base64
 import sys
 import warnings
+from typing import Type
 
 import numpy as np
 
@@ -577,7 +579,7 @@ class GiftiImage(xml.XmlSerializable, SerializableImage):
     # The parser will in due course be a GiftiImageParser, but we can't set
     # that now, because it would result in a circular import.  We set it after
     # the class has been defined, at the end of the class definition.
-    parser = None
+    parser: Type[xml.XmlParser]
 
     def __init__(
         self,
@@ -832,17 +834,18 @@ def _to_xml_element(self):
             GIFTI.append(dar._to_xml_element())
         return GIFTI
 
-    def to_xml(self, enc='utf-8'):
+    def to_xml(self, enc='utf-8') -> bytes:
         """Return XML corresponding to image content"""
         header = b"""<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">
 """
         return header + super().to_xml(enc)
 
     # Avoid the indirection of going through to_file_map
-    to_bytes = to_xml
+    def to_bytes(self, enc='utf-8'):
+        return self.to_xml(enc=enc)
 
-    def to_file_map(self, file_map=None):
+    def to_file_map(self, file_map=None, enc='utf-8'):
         """Save the current image to the specified file_map
 
         Parameters
@@ -858,7 +861,7 @@ def to_file_map(self, file_map=None):
         if file_map is None:
             file_map = self.file_map
         with file_map['image'].get_prepare_fileobj('wb') as f:
-            f.write(self.to_xml())
+            f.write(self.to_xml(enc=enc))
 
     @classmethod
     def from_file_map(klass, file_map, buffer_size=35000000, mmap=True):

nibabel/minc1.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Read MINC1 format images"""
+from __future__ import annotations
 
 from numbers import Integral
 
@@ -305,11 +306,11 @@ class Minc1Image(SpatialImage):
     load.
     """
 
-    header_class = Minc1Header
+    header_class: type = Minc1Header
     _meta_sniff_len = 4
     valid_exts = ('.mnc',)
     files_types = (('image', '.mnc'),)
-    _compressed_suffixes = ('.gz', '.bz2', '.zst')
+    _compressed_suffixes: tuple[str, ...] = ('.gz', '.bz2', '.zst')
 
     makeable = True
     rw = False

nibabel/minc2.py

@@ -25,6 +25,8 @@
 
     mincstats my_funny.mnc
 """
+from __future__ import annotations
+
 import numpy as np
 
 from .minc1 import Minc1File, Minc1Image, MincError, MincHeader
@@ -148,14 +150,14 @@ class Minc2Image(Minc1Image):
     """
 
     # MINC2 does not do compressed whole files
-    _compressed_suffixes = ()
+    _compressed_suffixes: tuple[str, ...] = ()
     header_class = Minc2Header
 
     @classmethod
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         # Import of h5py might take awhile for MPI-enabled builds
         # So we are importing it here "on demand"
-        import h5py
+        import h5py  # type: ignore
 
         holder = file_map['image']
         if holder.filename is None:

nibabel/nicom/dicomwrappers.py

@@ -127,8 +127,6 @@ class Wrapper:
     is_multiframe = False
     b_matrix = None
     q_vector = None
-    b_value = None
-    b_vector = None
 
     def __init__(self, dcm_data):
         """Initialize wrapper

nibabel/nifti1.py

@@ -10,8 +10,11 @@
 
 NIfTI1 format defined at http://nifti.nimh.nih.gov/nifti-1/
 """
+from __future__ import annotations
+
 import warnings
 from io import BytesIO
+from typing import Type
 
 import numpy as np
 import numpy.linalg as npl
@@ -86,8 +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 = np.longdouble
-    _complex256t = np.longcomplex
+    _float128t: Type[np.generic] = np.longdouble
+    _complex256t: Type[np.generic] = np.longcomplex
 else:
     _float128t = np.void
     _complex256t = np.void
@@ -1813,7 +1816,7 @@ class Nifti1PairHeader(Nifti1Header):
 class Nifti1Pair(analyze.AnalyzeImage):
     """Class for NIfTI1 format image, header pair"""
 
-    header_class = Nifti1PairHeader
+    header_class: Type[Nifti1Header] = Nifti1PairHeader
     _meta_sniff_len = header_class.sizeof_hdr
     rw = True
 
@@ -1844,9 +1847,7 @@ def __init__(self, dataobj, affine, header=None, extra=None, file_map=None, dtyp
             self._affine2header()
 
     # Copy docstring
-    __init__.__doc__ = (
-        analyze.AnalyzeImage.__init__.__doc__
-        + """
+    __init__.__doc__ = f"""{analyze.AnalyzeImage.__init__.__doc__}
         Notes
         -----
 
@@ -1859,7 +1860,6 @@ def __init__(self, dataobj, affine, header=None, extra=None, file_map=None, dtyp
         :meth:`set_qform` methods can be used to update the codes after an image
         has been created - see those methods, and the :ref:`manual
         <default-sform-qform-codes>` for more details.  """
-    )
 
     def update_header(self):
         """Harmonize header with image data and affine

nibabel/openers.py

@@ -20,7 +20,7 @@
 
 # is indexed_gzip present and modern?
 try:
-    import indexed_gzip as igzip
+    import indexed_gzip as igzip  # type: ignore
 
     version = igzip.__version__
 

nibabel/parrec.py

@@ -1338,7 +1338,7 @@ def from_filename(
             strict_sort=strict_sort,
         )
 
-    load = from_filename
+    load = from_filename  # type: ignore
 
 
-load = PARRECImage.load
+load = PARRECImage.from_filename

nibabel/pydicom_compat.py

@@ -7,7 +7,7 @@
 without error, and always defines:
 
 * have_dicom : True if we can import pydicom or dicom;
-* pydicom : pydicom module or dicom module or None of not importable;
+* pydicom : pydicom module or dicom module or None if not importable;
 * read_file : ``read_file`` function if pydicom or dicom module is importable
   else None;
 * tag_for_keyword : ``tag_for_keyword`` function if pydicom or dicom module
@@ -19,26 +19,27 @@
 
 A deprecated copy is available here for backward compatibility.
 """
+from __future__ import annotations
+from .optpkg import optional_package
+from typing import Callable
+from types import ModuleType
 
 # Module has (apparently) unused imports; stop flake8 complaining
 # flake8: noqa
 
 from .deprecated import deprecate_with_version
 
-have_dicom = True
-pydicom = read_file = tag_for_keyword = Sequence = None
+pydicom, have_dicom, _ = optional_package('pydicom')
 
-try:
-    import pydicom
-except ImportError:
-    have_dicom = False
-else:  # pydicom module available
+read_file: Callable | None = None
+tag_for_keyword: Callable | None = None
+Sequence: type | None = None
+
+if have_dicom:
     # Values not imported by default
-    import pydicom.values
+    import pydicom.values  # type: ignore
     from pydicom.dicomio import read_file
     from pydicom.sequence import Sequence
-
-if have_dicom:
     tag_for_keyword = pydicom.datadict.tag_for_keyword
 
 

nibabel/spatialimages.py

@@ -129,6 +129,7 @@
     >>> np.all(img3.get_fdata(dtype=np.float32) == data)
     True
 """
+from __future__ import annotations
 
 import numpy as np
 
@@ -400,7 +401,7 @@ def slice_affine(self, slicer):
 class SpatialImage(DataobjImage):
     """Template class for volumetric (3D/4D) images"""
 
-    header_class = SpatialHeader
+    header_class: type = SpatialHeader
     ImageSlicer = SpatialFirstSlicer
 
     def __init__(self, dataobj, affine, header=None, extra=None, file_map=None):

nibabel/spm99analyze.py

@@ -274,7 +274,7 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
             contents = matf.read()
         if len(contents) == 0:
             return ret
-        import scipy.io as sio
+        import scipy.io as sio  # type: ignore
 
         mats = sio.loadmat(BytesIO(contents))
         if 'mat' in mats:  # this overrides a 'M', and includes any flip