STY: Manual, blue-compatible touchups

[git-blame-ignore-rev]

Author: effigies

nibabel/analyze.py

@@ -394,8 +394,8 @@ def from_header(klass, header=None, check=True):
             obj.set_data_dtype(orig_code)
         except HeaderDataError:
             raise HeaderDataError(
-                f'Input header {header.__class__} has '
-                f"datatype {header.get_value_label('datatype')} "
+                f'Input header {header.__class__} has datatype '
+                f'{header.get_value_label("datatype")} '
                 f'but output header {klass} does not support it'
             )
         obj.set_data_dtype(header.get_data_dtype())
@@ -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

@@ -432,7 +432,7 @@ 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

@@ -58,7 +58,12 @@
 }
 
 space_codes = Recoder(
-    ((0, 'unknown', ''), (1, 'scanner', 'ORIG'), (3, 'talairach', 'TLRC'), (4, 'mni', 'MNI')),
+    (
+        (0, 'unknown', ''),
+        (1, 'scanner', 'ORIG'),
+        (3, 'talairach', 'TLRC'),
+        (4, 'mni', 'MNI'),
+    ),
     fields=('code', 'label', 'space'),
 )
 
@@ -104,9 +109,7 @@ 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}')
@@ -119,8 +122,7 @@ def _unpack_var(var):
             attr = [atype(f) for f in attr.split()]
         except ValueError:
             raise AFNIHeaderError(
-                'Failed to read variable from HEAD file '
-                f'due to improper type casting. {err_msg}'
+                f'Failed to read variable from HEAD file due to improper type casting. {err_msg}'
             )
     else:
         # AFNI string attributes will always start with open single quote and
@@ -354,13 +356,7 @@ 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

@@ -70,10 +70,15 @@ 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')
+CIFTI_SERIESUNIT_TYPES = (
+    'SECOND',
+    'HERTZ',
+    'METER',
+    'RADIAN',
+)
 
 CIFTI_BRAIN_STRUCTURES = (
     'CIFTI_STRUCTURE_ACCUMBENS_LEFT',
@@ -662,7 +667,7 @@ 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 +1242,7 @@ 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 +1417,13 @@ 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 +1496,7 @@ 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/parse_cifti2.py

@@ -335,7 +335,7 @@ def StartElementHandler(self, name, attrs):
                 raise Cifti2HeaderError(
                     'Volume element can only be a child of the CIFTI-2 MatrixIndicesMap element'
                 )
-            dimensions = tuple([int(val) for val in attrs['VolumeDimensions'].split(',')])
+            dimensions = tuple(int(val) for val in attrs['VolumeDimensions'].split(','))
             volume = Cifti2Volume(volume_dimensions=dimensions)
             mim.append(volume)
             self.fsm_state.append('Volume')

nibabel/cifti2/tests/test_axes.py

@@ -128,7 +128,9 @@ def test_brain_models():
     assert (bml[4].vertex == [2, 9, 14]).all()
 
     for bm, label, is_surface in zip(
-        bml, ['ThalamusRight', 'Other', 'cortex_left', 'Other'], (False, False, True, True)
+        bml,
+        ['ThalamusRight', 'Other', 'cortex_left', 'Other'],
+        (False, False, True, True),
     ):
         assert np.all(bm.surface_mask == ~bm.volume_mask)
         structures = list(bm.iter_structures())
@@ -176,18 +178,27 @@ def test_brain_models():
 
     # Test the constructor
     bm_vox = axes.BrainModelAxis(
-        'thalamus_left', voxel=np.ones((5, 3), dtype=int), affine=np.eye(4), volume_shape=(2, 3, 4)
+        'thalamus_left',
+        voxel=np.ones((5, 3), dtype=int),
+        affine=np.eye(4),
+        volume_shape=(2, 3, 4),
     )
     assert np.all(bm_vox.name == ['CIFTI_STRUCTURE_THALAMUS_LEFT'] * 5)
     assert np.array_equal(bm_vox.vertex, np.full(5, -1))
     assert np.array_equal(bm_vox.voxel, np.full((5, 3), 1))
     with pytest.raises(ValueError):
         # no volume shape
-        axes.BrainModelAxis('thalamus_left', voxel=np.ones((5, 3), dtype=int), affine=np.eye(4))
+        axes.BrainModelAxis(
+            'thalamus_left',
+            voxel=np.ones((5, 3), dtype=int),
+            affine=np.eye(4),
+        )
     with pytest.raises(ValueError):
         # no affine
         axes.BrainModelAxis(
-            'thalamus_left', voxel=np.ones((5, 3), dtype=int), volume_shape=(2, 3, 4)
+            'thalamus_left',
+            voxel=np.ones((5, 3), dtype=int),
+            volume_shape=(2, 3, 4),
         )
     with pytest.raises(ValueError):
         # incorrect name
@@ -207,7 +218,11 @@ def test_brain_models():
         )
     with pytest.raises(ValueError):
         # no voxels or vertices
-        axes.BrainModelAxis('thalamus_left', affine=np.eye(4), volume_shape=(2, 3, 4))
+        axes.BrainModelAxis(
+            'thalamus_left',
+            affine=np.eye(4),
+            volume_shape=(2, 3, 4),
+        )
     with pytest.raises(ValueError):
         # incorrect voxel shape
         axes.BrainModelAxis(
@@ -218,7 +233,9 @@ def test_brain_models():
         )
 
     bm_vertex = axes.BrainModelAxis(
-        'cortex_left', vertex=np.ones(5, dtype=int), nvertices={'cortex_left': 20}
+        'cortex_left',
+        vertex=np.ones(5, dtype=int),
+        nvertices={'cortex_left': 20},
     )
     assert np.array_equal(bm_vertex.name, ['CIFTI_STRUCTURE_CORTEX_LEFT'] * 5)
     assert np.array_equal(bm_vertex.vertex, np.full(5, 1))
@@ -227,11 +244,15 @@ def test_brain_models():
         axes.BrainModelAxis('cortex_left', vertex=np.ones(5, dtype=int))
     with pytest.raises(ValueError):
         axes.BrainModelAxis(
-            'cortex_left', vertex=np.ones(5, dtype=int), nvertices={'cortex_right': 20}
+            'cortex_left',
+            vertex=np.ones(5, dtype=int),
+            nvertices={'cortex_right': 20},
         )
     with pytest.raises(ValueError):
         axes.BrainModelAxis(
-            'cortex_left', vertex=-np.ones(5, dtype=int), nvertices={'cortex_left': 20}
+            'cortex_left',
+            vertex=-np.ones(5, dtype=int),
+            nvertices={'cortex_left': 20},
         )
 
     # test from_mask errors
@@ -244,7 +265,10 @@ def test_brain_models():
 
     # tests error in adding together or combining as ParcelsAxis
     bm_vox = axes.BrainModelAxis(
-        'thalamus_left', voxel=np.ones((5, 3), dtype=int), affine=np.eye(4), volume_shape=(2, 3, 4)
+        'thalamus_left',
+        voxel=np.ones((5, 3), dtype=int),
+        affine=np.eye(4),
+        volume_shape=(2, 3, 4),
     )
     bm_vox + bm_vox
     assert (bm_vertex + bm_vox)[: bm_vertex.size] == bm_vertex
@@ -289,7 +313,10 @@ def test_brain_models():
 
     # test equalities
     bm_vox = axes.BrainModelAxis(
-        'thalamus_left', voxel=np.ones((5, 3), dtype=int), affine=np.eye(4), volume_shape=(2, 3, 4)
+        'thalamus_left',
+        voxel=np.ones((5, 3), dtype=int),
+        affine=np.eye(4),
+        volume_shape=(2, 3, 4),
     )
     bm_other = deepcopy(bm_vox)
     assert bm_vox == bm_other

nibabel/cifti2/tests/test_cifti2.py

@@ -79,10 +79,7 @@ def test_cifti2_metadata():
 
     with pytest.raises(KeyError):
         md.difference_update({'a': 'aval', 'd': 'dval'})
-    assert (
-        md.to_xml().decode('utf-8')
-        == '<MetaData><MD><Name>b</Name><Value>bval</Value></MD></MetaData>'
-    )
+    assert md.to_xml() == b'<MetaData><MD><Name>b</Name><Value>bval</Value></MD></MetaData>'
 
 
 def test__float_01():
@@ -195,8 +192,7 @@ def test_cifti2_parcel():
 
     assert len(pl.vertices) == 0
     assert (
-        pl.to_xml().decode('utf-8')
-        == '<Parcel Name="region"><VoxelIndicesIJK>1 2 3</VoxelIndicesIJK></Parcel>'
+        pl.to_xml() == b'<Parcel Name="region"><VoxelIndicesIJK>1 2 3</VoxelIndicesIJK></Parcel>'
     )
 
 
@@ -207,7 +203,7 @@ def test_cifti2_vertices():
 
     vs.brain_structure = 'CIFTI_STRUCTURE_OTHER'
 
-    assert vs.to_xml().decode('utf-8') == '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER" />'
+    assert vs.to_xml() == b'<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER" />'
 
     assert len(vs) == 0
     vs.extend(np.array([0, 1, 2]))
@@ -217,10 +213,7 @@ def test_cifti2_vertices():
     with pytest.raises(ValueError):
         vs.insert(1, 'a')
 
-    assert (
-        vs.to_xml().decode('utf-8')
-        == '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
-    )
+    assert vs.to_xml() == b'<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
 
     vs[0] = 10
     assert vs[0] == 10
@@ -254,7 +247,7 @@ def test_cifti2_vertexindices():
         vi.to_xml()
     vi.extend(np.array([0, 1, 2]))
     assert len(vi) == 3
-    assert vi.to_xml().decode('utf-8') == '<VertexIndices>0 1 2</VertexIndices>'
+    assert vi.to_xml() == b'<VertexIndices>0 1 2</VertexIndices>'
 
     with pytest.raises(ValueError):
         vi[0] = 'a'

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -11,6 +11,7 @@
 from os.path import dirname
 from os.path import join as pjoin
 
+import numpy as np
 import pytest
 from numpy.testing import assert_array_almost_equal
 from packaging.version import Version
@@ -249,12 +250,17 @@ def test_read_geometry():
             assert from_file.voxel_indices_ijk[-1] == expected[3]
     assert current_index == img.shape[1]
 
-    expected_affine = [[-2, 0, 0, 90], [0, 2, 0, -126], [0, 0, 2, -72], [0, 0, 0, 1]]
+    expected_affine = [
+        [-2, 0, 0, 90],
+        [0, 2, 0, -126],
+        [0, 0, 2, -72],
+        [0, 0, 0, 1],
+    ]
     expected_dimensions = (91, 109, 91)
-    assert (
-        geometry_mapping.volume.transformation_matrix_voxel_indices_ijk_to_xyz.matrix
-        == expected_affine
-    ).all()
+    assert np.array_equal(
+        geometry_mapping.volume.transformation_matrix_voxel_indices_ijk_to_xyz.matrix,
+        expected_affine,
+    )
     assert geometry_mapping.volume.volume_dimensions == expected_dimensions