STY: Manual, blue-compatible touchups

[git-blame-ignore-rev]

Author: effigies

nibabel/analyze.py

@@ -785,7 +785,7 @@ def set_slope_inter(self, slope, inter=None):
         """
         if (slope in (None, 1) or np.isnan(slope)) and (inter in (None, 0) or np.isnan(inter)):
             return
-        raise HeaderTypeError('Cannot set slope != 1 or intercept != 0 ' 'for Analyze headers')
+        raise HeaderTypeError('Cannot set slope != 1 or intercept != 0 for Analyze headers')
 
     @classmethod
     def _get_checks(klass):

nibabel/arraywriters.py

@@ -454,7 +454,7 @@ def _range_scale(self, in_min, in_max):
         if self._out_dtype.kind == 'u':
             if in_min < 0 and in_max > 0:
                 raise WriterError(
-                    'Cannot scale negative and positive ' 'numbers to uint without intercept'
+                    'Cannot scale negative and positive numbers to uint without intercept'
                 )
             if in_max <= 0:  # All input numbers <= 0
                 self.slope = in_min / out_max

nibabel/brikhead.py

@@ -104,9 +104,7 @@ def _unpack_var(var):
     TEMPLATE_SPACE ORIG
     """
 
-    err_msg = (
-        'Please check HEAD file to ensure it is AFNI compliant. ' f'Offending attribute:\n{var}'
-    )
+    err_msg = f'Please check HEAD file to ensure it is AFNI compliant. Offending attribute:\n{var}'
     atype, aname = TYPE_RE.findall(var), NAME_RE.findall(var)
     if len(atype) != 1:
         raise AFNIHeaderError(f'Invalid attribute type entry in HEAD file. {err_msg}')
@@ -354,13 +352,7 @@ def _calc_zooms(self):
         origin", and second giving "Time step (TR)".
         """
         xyz_step = tuple(np.abs(self.info['DELTA']))
-        t_step = self.info.get(
-            'TAXIS_FLOATS',
-            (
-                0,
-                0,
-            ),
-        )
+        t_step = self.info.get('TAXIS_FLOATS', (0, 0))
         if len(t_step) > 0:
             t_step = (t_step[1],)
         return xyz_step + t_step

nibabel/casting.py

@@ -259,15 +259,15 @@ def type_info(np_type):
     if vals in (
         (112, 15, 16),  # binary128
         (info_64.nmant, info_64.nexp, 8),  # float64
-        (63, 15, 12),
-        (63, 15, 16),
-    ):  # Intel extended 80
+        (63, 15, 12),  # Intel extended 80
+        (63, 15, 16),  # Intel extended 80
+    ):
         return ret  # these are OK without modification
     # The remaining types are longdoubles with bad finfo values.  Some we
     # correct, others we wait to hear of errors.
     # We start with float64 as basis
     ret = type_info(np.float64)
-    if vals in ((52, 15, 12), (52, 15, 16)):  # windows float96  # windows float128?
+    if vals in ((52, 15, 12), (52, 15, 16)):  # windows float96 / windows float128?
         # On windows 32 bit at least, float96 is Intel 80 storage but operating
         # at float64 precision. The finfo values give nexp == 15 (as for intel
         # 80) but in calculations nexp in fact appears to be 11 as for float64
@@ -298,7 +298,13 @@ def type_info(np_type):
         if np_type is np.longcomplex:
             max_val += 0j
         ret = dict(
-            min=-max_val, max=max_val, nmant=112, nexp=15, minexp=-16382, maxexp=16384, width=width
+            min=-max_val,
+            max=max_val,
+            nmant=112,
+            nexp=15,
+            minexp=-16382,
+            maxexp=16384,
+            width=width,
         )
     else:  # don't recognize the type
         raise FloatingError(f'We had not expected long double type {np_type} with info {info}')

nibabel/cifti2/cifti2.py

@@ -70,7 +70,7 @@ class Cifti2HeaderError(Exception):
 
 CIFTI_MODEL_TYPES = (
     'CIFTI_MODEL_TYPE_SURFACE',  # Modeled using surface vertices
-    'CIFTI_MODEL_TYPE_VOXELS',  # Modeled using voxels.
+    'CIFTI_MODEL_TYPE_VOXELS',  # Modeled using voxels
 )
 
 CIFTI_SERIESUNIT_TYPES = ('SECOND', 'HERTZ', 'METER', 'RADIAN')
@@ -662,7 +662,7 @@ def __init__(self, name=None, voxel_indices_ijk=None, vertices=None):
         self.vertices = vertices if vertices is not None else []
         for val in self.vertices:
             if not isinstance(val, Cifti2Vertices):
-                raise ValueError(('Cifti2Parcel vertices must be instances of ' 'Cifti2Vertices'))
+                raise ValueError(('Cifti2Parcel vertices must be instances of Cifti2Vertices'))
 
     @property
     def voxel_indices_ijk(self):
@@ -1237,7 +1237,7 @@ def _validate_new_mim(self, value):
         a2md = self._get_indices_from_mim(value)
         if not set(self.mapped_indices).isdisjoint(a2md):
             raise Cifti2HeaderError(
-                'Indices in this Cifti2MatrixIndicesMap ' 'already mapped in this matrix'
+                'Indices in this Cifti2MatrixIndicesMap already mapped in this matrix'
             )
 
     def __setitem__(self, key, value):
@@ -1412,7 +1412,13 @@ class Cifti2Image(DataobjImage, SerializableImage):
     rw = True
 
     def __init__(
-        self, dataobj=None, header=None, nifti_header=None, extra=None, file_map=None, dtype=None
+        self,
+        dataobj=None,
+        header=None,
+        nifti_header=None,
+        extra=None,
+        file_map=None,
+        dtype=None,
     ):
         """Initialize image
 
@@ -1485,7 +1491,7 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
                 cifti_header = item.get_content()
                 break
         else:
-            raise ValueError('NIfTI2 header does not contain a CIFTI-2 ' 'extension')
+            raise ValueError('NIfTI2 header does not contain a CIFTI-2 extension')
 
         # Construct cifti image.
         # Use array proxy object where possible

nibabel/cifti2/cifti2_axes.py

@@ -665,7 +665,7 @@ def __add__(self, other):
                 not np.allclose(other.affine, affine) or other.volume_shape != shape
             ):
                 raise ValueError(
-                    'Trying to concatenate two BrainModels defined ' 'in a different brain volume'
+                    'Trying to concatenate two BrainModels defined in a different brain volume'
                 )
 
         nvertices = dict(self.nvertices)
@@ -1008,7 +1008,7 @@ def __add__(self, other):
                 not np.allclose(other.affine, affine) or other.volume_shape != shape
             ):
                 raise ValueError(
-                    'Trying to concatenate two ParcelsAxis defined ' 'in a different brain volume'
+                    'Trying to concatenate two ParcelsAxis defined in a different brain volume'
                 )
         nvertices = dict(self.nvertices)
         for name, value in other.nvertices.items():

nibabel/cifti2/tests/test_new_cifti2.py

@@ -20,14 +20,27 @@
     suppress_warnings,
 )
 
-affine = [[-1.5, 0, 0, 90], [0, 1.5, 0, -85], [0, 0, 1.5, -71], [0, 0, 0, 1.0]]
+affine = [
+    [-1.5, 0, 0, 90],
+    [0, 1.5, 0, -85],
+    [0, 0, 1.5, -71],
+    [0, 0, 0, 1.0],
+]
 
 dimensions = (120, 83, 78)
 
 number_of_vertices = 30000
 
 brain_models = [
-    ('CIFTI_STRUCTURE_THALAMUS_LEFT', [[60, 60, 60], [61, 59, 60], [61, 60, 59], [80, 90, 92]]),
+    (
+        'CIFTI_STRUCTURE_THALAMUS_LEFT',
+        [
+            [60, 60, 60],
+            [61, 59, 60],
+            [61, 60, 59],
+            [80, 90, 92],
+        ],
+    ),
     ('CIFTI_STRUCTURE_CORTEX_LEFT', [0, 1000, 1301, 19972, 27312]),
     ('CIFTI_STRUCTURE_CORTEX_RIGHT', [207]),
 ]
@@ -107,7 +120,17 @@ def check_geometry_map(mapping):
 
 
 parcels = [
-    ('volume_parcel', ([[60, 60, 60], [61, 59, 60], [61, 60, 59], [80, 90, 92]],)),
+    (
+        'volume_parcel',
+        (
+            [
+                [60, 60, 60],
+                [61, 59, 60],
+                [61, 60, 59],
+                [80, 90, 92],
+            ],
+        ),
+    ),
     (
         'surface_parcel',
         (
@@ -117,7 +140,13 @@ def check_geometry_map(mapping):
     ),
     (
         'mixed_parcel',
-        ([[71, 81, 39], [53, 21, 91]], ('CIFTI_STRUCTURE_CORTEX_LEFT', [71, 88, 999])),
+        (
+            [
+                [71, 81, 39],
+                [53, 21, 91],
+            ],
+            ('CIFTI_STRUCTURE_CORTEX_LEFT', [71, 88, 999]),
+        ),
     ),
     ('single_element', ([[71, 81, 39]], ('CIFTI_STRUCTURE_CORTEX_LEFT', [40]))),
 ]
@@ -196,9 +225,19 @@ def check_scalar_map(mapping):
     (
         'first_name',
         {'meta_key': 'some_metadata'},
-        {0: ('label0', (0.1, 0.3, 0.2, 0.5)), 1: ('new_label', (0.5, 0.3, 0.1, 0.4))},
+        {
+            0: ('label0', (0.1, 0.3, 0.2, 0.5)),
+            1: ('new_label', (0.5, 0.3, 0.1, 0.4)),
+        },
+    ),
+    (
+        'another name',
+        {},
+        {
+            0: ('???', (0, 0, 0, 0)),
+            1: ('great region', (0.4, 0.1, 0.23, 0.15)),
+        },
     ),
-    ('another name', {}, {0: ('???', (0, 0, 0, 0)), 1: ('great region', (0.4, 0.1, 0.23, 0.15))}),
 ]
 
 
@@ -472,7 +511,7 @@ def test_pconnseries():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(4, 4, 13)
     img = ci.Cifti2Image(data, hdr)
-    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_' 'PARCELLATED_SERIES')
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pconnseries.nii')
@@ -496,7 +535,7 @@ def test_pconnscalar():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(4, 4, 2)
     img = ci.Cifti2Image(data, hdr)
-    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_' 'PARCELLATED_SCALAR')
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pconnscalar.nii')

nibabel/cmdline/diff.py

@@ -51,15 +51,15 @@ def get_opt_parser():
                 '--header-fields',
                 dest='header_fields',
                 default='all',
-                help='Header fields (comma separated) to be printed as well' ' (if present)',
+                help='Header fields (comma separated) to be printed as well (if present)',
             ),
             Option(
                 '--ma',
                 '--data-max-abs-diff',
                 dest='data_max_abs_diff',
                 type=float,
                 default=0.0,
-                help='Maximal absolute difference in data between files' ' to tolerate.',
+                help='Maximal absolute difference in data between files to tolerate.',
             ),
             Option(
                 '--mr',

nibabel/cmdline/ls.py

@@ -20,7 +20,7 @@
 import nibabel.cmdline.utils
 from nibabel.cmdline.utils import _err, ap, safe_get, table2string, verbose
 
-__copyright__ = 'Copyright (c) 2011-18 Yaroslav Halchenko ' 'and NiBabel contributors'
+__copyright__ = 'Copyright (c) 2011-18 Yaroslav Halchenko and NiBabel contributors'
 __license__ = 'MIT'
 
 

nibabel/cmdline/nifti_dx.py

@@ -15,7 +15,7 @@
 import nibabel as nib
 
 __author__ = 'Matthew Brett'
-__copyright__ = 'Copyright (c) 2011-18 Matthew Brett ' 'and NiBabel contributors'
+__copyright__ = 'Copyright (c) 2011-18 Matthew Brett and NiBabel contributors'
 __license__ = 'MIT'
 
 

nibabel/cmdline/parrec2nii.py

@@ -44,10 +44,7 @@ def get_opt_parser():
             type='string',
             dest='outdir',
             default=None,
-            help=one_line(
-                """Destination directory for NIfTI files.
-                             Default: current directory."""
-            ),
+            help='Destination directory for NIfTI files. Default: current directory.',
         )
     )
     p.add_option(
@@ -81,10 +78,7 @@ def get_opt_parser():
             action='store_true',
             dest='bvs',
             default=False,
-            help=one_line(
-                """Output bvals/bvecs files in addition to NIFTI
-                   image."""
-            ),
+            help='Output bvals/bvecs files in addition to NIFTI image.',
         )
     )
     p.add_option(
@@ -207,7 +201,7 @@ def get_opt_parser():
             default=False,
             help=one_line(
                 """Do not discard the diagnostic Philips DTI
-                             trace volume, if it exists in the data."""
+                   trace volume, if it exists in the data."""
             ),
         )
     )
@@ -217,10 +211,7 @@ def get_opt_parser():
             action='store_true',
             dest='overwrite',
             default=False,
-            help=one_line(
-                """Overwrite file if it exists. Default:
-                             False"""
-            ),
+            help='Overwrite file if it exists. Default: False',
         )
     )
     p.add_option(