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: