Merge pull request #1243 from larsoner/deps

MAINT: Deprecations

Author: effigies

nibabel/__init__.py

@@ -39,7 +39,7 @@
 
 # module imports
 from . import analyze as ana
-from . import ecat, imagestats, mriutils
+from . import ecat, imagestats, mriutils, orientations
 from . import nifti1 as ni1
 from . import spm2analyze as spm2
 from . import spm99analyze as spm99

nibabel/nicom/utils.py

@@ -1,8 +1,6 @@
 """Utilities for working with DICOM datasets
 """
 
-from numpy.compat.py3k import asstr
-
 
 def find_private_section(dcm_data, group_no, creator):
     """Return start element in group `group_no` given creator name `creator`
@@ -31,15 +29,20 @@ def find_private_section(dcm_data, group_no, creator):
     """
     if hasattr(creator, 'search'):
         match_func = creator.search
-    else:  # assume string / bytes
-        match_func = asstr(creator).__eq__
+    else:
+        if isinstance(creator, bytes):
+            creator = creator.decode('latin-1')
+        match_func = creator.__eq__
     # Group elements assumed ordered by tag (groupno, elno)
     for element in dcm_data.group_dataset(group_no):
         elno = element.tag.elem
         if elno > 0xFF:
             break
         if element.VR not in ('LO', 'OB'):
             continue
-        if match_func(asstr(element.value)):
+        val = element.value
+        if isinstance(val, bytes):
+            val = val.decode('latin-1')
+        if match_func(val):
             return elno * 0x100
     return None

nibabel/nifti1.py

@@ -17,7 +17,6 @@
 
 import numpy as np
 import numpy.linalg as npl
-from numpy.compat.py3k import asstr
 
 from . import analyze  # module import
 from .arrayproxy import get_obj_dtype
@@ -1405,7 +1404,7 @@ def get_intent(self, code_repr='label'):
             raise TypeError('repr can be "label" or "code"')
         n_params = len(recoder.parameters[code]) if known_intent else 0
         params = (float(hdr['intent_p%d' % (i + 1)]) for i in range(n_params))
-        name = asstr(hdr['intent_name'].item())
+        name = hdr['intent_name'].item().decode('latin-1')
         return label, tuple(params), name
 
     def set_intent(self, code, params=(), name='', allow_unknown=False):
@@ -1741,7 +1740,7 @@ def _chk_magic(hdr, fix=False):
         magic = hdr['magic'].item()
         if magic in (hdr.pair_magic, hdr.single_magic):
             return hdr, rep
-        rep.problem_msg = f'magic string "{asstr(magic)}" is not valid'
+        rep.problem_msg = f'magic string {magic.decode("latin1")!r} is not valid'
         rep.problem_level = 45
         if fix:
             rep.fix_msg = 'leaving as is, but future errors are likely'

nibabel/streamlines/trk.py

@@ -7,7 +7,6 @@
 import warnings
 
 import numpy as np
-from numpy.compat.py3k import asstr
 
 import nibabel as nib
 from nibabel.openers import Opener
@@ -180,7 +179,7 @@ def decode_value_from_name(encoded_name):
     value : int
         Value decoded from the name.
     """
-    encoded_name = asstr(encoded_name)
+    encoded_name = encoded_name.decode('latin1')
     if len(encoded_name) == 0:
         return encoded_name, 0
 
@@ -740,14 +739,18 @@ def __str__(self):
                     vars[attr] = vars[hdr_field]
 
         nb_scalars = self.header[Field.NB_SCALARS_PER_POINT]
-        scalar_names = [asstr(s) for s in vars['scalar_name'][:nb_scalars] if len(s) > 0]
+        scalar_names = [
+            s.decode('latin-1') for s in vars['scalar_name'][:nb_scalars] if len(s) > 0
+        ]
         vars['scalar_names'] = '\n  '.join(scalar_names)
         nb_properties = self.header[Field.NB_PROPERTIES_PER_STREAMLINE]
-        property_names = [asstr(s) for s in vars['property_name'][:nb_properties] if len(s) > 0]
+        property_names = [
+            s.decode('latin-1') for s in vars['property_name'][:nb_properties] if len(s) > 0
+        ]
         vars['property_names'] = '\n  '.join(property_names)
         # Make all byte strings into strings
         # Fixes recursion error on Python 3.3
-        vars = {k: asstr(v) if hasattr(v, 'decode') else v for k, v in vars.items()}
+        vars = {k: v.decode('latin-1') if hasattr(v, 'decode') else v for k, v in vars.items()}
         return """\
 MAGIC NUMBER: {MAGIC_NUMBER}
 v.{version}

nibabel/tests/test_nifti1.py

@@ -251,7 +251,7 @@ def test_magic_offset_checks(self):
         fhdr, message, raiser = self.log_chk(hdr, 45)
         assert fhdr['magic'] == b'ooh'
         assert (
-            message == 'magic string "ooh" is not valid; '
+            message == "magic string 'ooh' is not valid; "
             'leaving as is, but future errors are likely'
         )
         # For pairs, any offset is OK, but should be divisible by 16

nibabel/tests/test_openers.py

@@ -17,7 +17,6 @@
 from unittest import mock
 
 import pytest
-from numpy.compat.py3k import asbytes, asstr
 from packaging.version import Version
 
 from ..deprecator import ExpiredDeprecationError
@@ -342,10 +341,10 @@ def test_iter():
         for input, does_t in files_to_test:
             with Opener(input, 'wb') as fobj:
                 for line in lines:
-                    fobj.write(asbytes(line + os.linesep))
+                    fobj.write(str.encode(line + os.linesep))
             with Opener(input, 'rb') as fobj:
                 for back_line, line in zip(fobj, lines):
-                    assert asstr(back_line).rstrip() == line
+                    assert back_line.decode().rstrip() == line
             if not does_t:
                 continue
             with Opener(input, 'rt') as fobj:

nibabel/tests/test_scripts.py

@@ -228,7 +228,7 @@ def test_nib_nifti_dx():
     expected = f"""Picky header check output for "{dirty_hdr}"
 
 pixdim[0] (qfac) should be 1 (default) or -1
-magic string "" is not valid
+magic string '' is not valid
 sform_code 11776 not valid"""
     # Split strings to remove line endings
     assert stdout == expected