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Commitbf14770

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committed
ENH: Add type annotations to pacify mypy
1 parentbea81f3 commitbf14770

22 files changed

+93
-81
lines changed

‎nibabel/analyze.py‎

Lines changed: 10 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -81,14 +81,17 @@
8181
can be loaded with and without a default flip, so the saved zoom will not
8282
constrain the affine.
8383
"""
84+
from __future__importannotations
85+
86+
fromtypingimportType
8487

8588
importnumpyasnp
8689

8790
from .arrayproxyimportArrayProxy
8891
from .arraywritersimportArrayWriter,WriterError,get_slope_inter,make_array_writer
8992
from .batteryrunnersimportReport
9093
from .fileholdersimportcopy_file_map
91-
from .spatialimagesimportHeaderDataError,HeaderTypeError,SpatialImage
94+
from .spatialimagesimportHeaderDataError,HeaderTypeError,SpatialHeader,SpatialImage
9295
from .volumeutilsimport (
9396
apply_read_scaling,
9497
array_from_file,
@@ -131,7 +134,7 @@
131134
('glmax','i4'),
132135
('glmin','i4'),
133136
]
134-
data_history_dtd= [
137+
data_history_dtd:list[tuple[str,str]|tuple[str,str,tuple[int, ...]]]= [
135138
('descrip','S80'),
136139
('aux_file','S24'),
137140
('orient','S1'),
@@ -172,7 +175,7 @@
172175
data_type_codes=make_dt_codes(_dtdefs)
173176

174177

175-
classAnalyzeHeader(LabeledWrapStruct):
178+
classAnalyzeHeader(LabeledWrapStruct,SpatialHeader):
176179
"""Class for basic analyze header
177180
178181
Implements zoom-only setting of affine transform, and no image
@@ -892,11 +895,11 @@ def may_contain_header(klass, binaryblock):
892895
classAnalyzeImage(SpatialImage):
893896
"""Class for basic Analyze format image"""
894897

895-
header_class=AnalyzeHeader
898+
header_class:Type[AnalyzeHeader]=AnalyzeHeader
896899
_meta_sniff_len=header_class.sizeof_hdr
897-
files_types= (('image','.img'), ('header','.hdr'))
898-
valid_exts= ('.img','.hdr')
899-
_compressed_suffixes= ('.gz','.bz2','.zst')
900+
files_types:tuple[tuple[str,str], ...]= (('image','.img'), ('header','.hdr'))
901+
valid_exts:tuple[str, ...]= ('.img','.hdr')
902+
_compressed_suffixes:tuple[str, ...]= ('.gz','.bz2','.zst')
900903

901904
makeable=True
902905
rw=True

‎nibabel/benchmarks/bench_arrayproxy_slicing.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626

2727
# if memory_profiler is installed, we get memory usage results
2828
try:
29-
frommemory_profilerimportmemory_usage
29+
frommemory_profilerimportmemory_usage# type: ignore
3030
exceptImportError:
3131
memory_usage=None
3232

‎nibabel/brikhead.py‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@
2727
am aware) always be >= 1. This permits sub-brick indexing common in AFNI
2828
programs (e.g., example4d+orig'[0]').
2929
"""
30+
from __future__importannotations
3031

3132
importos
3233
importre
@@ -476,9 +477,9 @@ class AFNIImage(SpatialImage):
476477
True
477478
"""
478479

479-
header_class=AFNIHeader
480-
valid_exts= ('.brik','.head')
481-
files_types= (('image','.brik'), ('header','.head'))
480+
header_class:type=AFNIHeader
481+
valid_exts:tuple[str, ...]= ('.brik','.head')
482+
files_types:tuple[tuple[str,str], ...]= (('image','.brik'), ('header','.head'))
482483
_compressed_suffixes= ('.gz','.bz2','.Z','.zst')
483484
makeable=False
484485
rw=False

‎nibabel/casting.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
Most routines work round some numpy oddities in floating point precision and
44
casting. Others work round numpy casting to and from python ints
55
"""
6+
from __future__importannotations
67

78
importwarnings
89
fromnumbersimportIntegral
@@ -110,7 +111,7 @@ def float_to_int(arr, int_type, nan2zero=True, infmax=False):
110111

111112

112113
# Cache range values
113-
_SHARED_RANGES= {}
114+
_SHARED_RANGES:dict[tuple[type,type],tuple[np.number,np.number]]= {}
114115

115116

116117
defshared_range(flt_type,int_type):

‎nibabel/cmdline/dicomfs.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@ class dummy_fuse:
2525

2626

2727
try:
28-
importfuse
28+
importfuse# type: ignore
2929

3030
uid=os.getuid()
3131
gid=os.getgid()

‎nibabel/ecat.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,7 @@
5050

5151
from .arraywritersimportmake_array_writer
5252
from .filesliceimportcanonical_slicers,predict_shape,slice2outax
53-
from .spatialimagesimportSpatialImage
53+
from .spatialimagesimportSpatialHeader,SpatialImage
5454
from .volumeutilsimportarray_from_file,make_dt_codes,native_code,swapped_code
5555
from .wrapstructimportWrapStruct
5656

@@ -243,7 +243,7 @@
243243
patient_orient_neurological= [1,3,5,7]
244244

245245

246-
classEcatHeader(WrapStruct):
246+
classEcatHeader(WrapStruct,SpatialHeader):
247247
"""Class for basic Ecat PET header
248248
249249
Sub-parts of standard Ecat File

‎nibabel/externals/netcdf.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -871,6 +871,7 @@ def __setattr__(self, attr, value):
871871
pass
872872
self.__dict__[attr]=value
873873

874+
@property
874875
defisrec(self):
875876
"""Returns whether the variable has a record dimension or not.
876877
@@ -881,16 +882,15 @@ def isrec(self):
881882
882883
"""
883884
returnbool(self.data.shape)andnotself._shape[0]
884-
isrec=property(isrec)
885885

886+
@property
886887
defshape(self):
887888
"""Returns the shape tuple of the data variable.
888889
889890
This is a read-only attribute and can not be modified in the
890891
same manner of other numpy arrays.
891892
"""
892893
returnself.data.shape
893-
shape=property(shape)
894894

895895
defgetValue(self):
896896
"""

‎nibabel/filebasedimages.py‎

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,11 @@
77
#
88
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
99
"""Common interface for any image format--volume or surface, binary or xml."""
10+
from __future__importannotations
1011

1112
importio
1213
fromcopyimportdeepcopy
14+
fromtypingimportType
1315
fromurllibimportrequest
1416

1517
from .fileholdersimportFileHolder
@@ -144,14 +146,14 @@ class FileBasedImage:
144146
work.
145147
"""
146148

147-
header_class=FileBasedHeader
148-
_meta_sniff_len=0
149-
files_types= (('image',None),)
150-
valid_exts= ()
151-
_compressed_suffixes= ()
149+
header_class:Type[FileBasedHeader]=FileBasedHeader
150+
_meta_sniff_len:int=0
151+
files_types:tuple[tuple[str,str|None], ...]= (('image',None),)
152+
valid_exts:tuple[str, ...]= ()
153+
_compressed_suffixes:tuple[str, ...]= ()
152154

153-
makeable=True# Used in test code
154-
rw=True# Used in test code
155+
makeable:bool=True# Used in test code
156+
rw:bool=True# Used in test code
155157

156158
def__init__(self,header=None,extra=None,file_map=None):
157159
"""Initialize image

‎nibabel/freesurfer/mghformat.py‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,10 @@
1010
1111
Author: Krish Subramaniam
1212
"""
13+
from __future__importannotations
14+
1315
fromos.pathimportsplitext
16+
fromtypingimportType
1417

1518
importnumpyasnp
1619

@@ -21,7 +24,7 @@
2124
from ..fileholdersimportFileHolder
2225
from ..filename_parserimport_stringify_path
2326
from ..openersimportImageOpener
24-
from ..spatialimagesimportHeaderDataError,SpatialImage
27+
from ..spatialimagesimportHeaderDataError,SpatialHeader,SpatialImage
2528
from ..volumeutilsimportRecoder,array_from_file,array_to_file,endian_codes
2629
from ..wrapstructimportLabeledWrapStruct
2730

@@ -87,7 +90,7 @@ class MGHError(Exception):
8790
"""
8891

8992

90-
classMGHHeader(LabeledWrapStruct):
93+
classMGHHeader(LabeledWrapStruct,SpatialHeader):
9194
"""Class for MGH format header
9295
9396
The header also consists of the footer data which MGH places after the data
@@ -461,7 +464,7 @@ def diagnose_binaryblock(klass, binaryblock, endianness=None):
461464
classMGHImage(SpatialImage,SerializableImage):
462465
"""Class for MGH format image"""
463466

464-
header_class=MGHHeader
467+
header_class:Type[MGHHeader]=MGHHeader
465468
valid_exts= ('.mgh','.mgz')
466469
# Register that .mgz extension signals gzip compression
467470
ImageOpener.compress_ext_map['.mgz']=ImageOpener.gz_def

‎nibabel/gifti/gifti.py‎

Lines changed: 8 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -11,10 +11,12 @@
1111
The Gifti specification was (at time of writing) available as a PDF download
1212
from http://www.nitrc.org/projects/gifti/
1313
"""
14+
from __future__importannotations
1415

1516
importbase64
1617
importsys
1718
importwarnings
19+
fromtypingimportType
1820

1921
importnumpyasnp
2022

@@ -577,7 +579,7 @@ class GiftiImage(xml.XmlSerializable, SerializableImage):
577579
# The parser will in due course be a GiftiImageParser, but we can't set
578580
# that now, because it would result in a circular import. We set it after
579581
# the class has been defined, at the end of the class definition.
580-
parser=None
582+
parser:Type[xml.XmlParser]
581583

582584
def__init__(
583585
self,
@@ -832,17 +834,18 @@ def _to_xml_element(self):
832834
GIFTI.append(dar._to_xml_element())
833835
returnGIFTI
834836

835-
defto_xml(self,enc='utf-8'):
837+
defto_xml(self,enc='utf-8')->bytes:
836838
"""Return XML corresponding to image content"""
837839
header=b"""<?xml version="1.0" encoding="UTF-8"?>
838840
<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">
839841
"""
840842
returnheader+super().to_xml(enc)
841843

842844
# Avoid the indirection of going through to_file_map
843-
to_bytes=to_xml
845+
defto_bytes(self,enc='utf-8'):
846+
returnself.to_xml(enc=enc)
844847

845-
defto_file_map(self,file_map=None):
848+
defto_file_map(self,file_map=None,enc='utf-8'):
846849
"""Save the current image to the specified file_map
847850
848851
Parameters
@@ -858,7 +861,7 @@ def to_file_map(self, file_map=None):
858861
iffile_mapisNone:
859862
file_map=self.file_map
860863
withfile_map['image'].get_prepare_fileobj('wb')asf:
861-
f.write(self.to_xml())
864+
f.write(self.to_xml(enc=enc))
862865

863866
@classmethod
864867
deffrom_file_map(klass,file_map,buffer_size=35000000,mmap=True):

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