Merge pull request #1369 from DimitriPapadopoulos/preview

STY: Apply ruff preview rules

nibabel/analyze.py

@@ -699,7 +699,7 @@ def set_zooms(self, zooms):
         ndim = dims[0]
         zooms = np.asarray(zooms)
         if len(zooms) != ndim:
-            raise HeaderDataError('Expecting %d zoom values for ndim %d' % (ndim, ndim))
+            raise HeaderDataError(f'Expecting {ndim} zoom values for ndim {ndim}')
         if np.any(zooms < 0):
             raise HeaderDataError('zooms must be positive')
         pixdims = hdr['pixdim']
@@ -818,11 +818,11 @@ def _chk_datatype(klass, hdr, fix=False):
             dtype = klass._data_type_codes.dtype[code]
         except KeyError:
             rep.problem_level = 40
-            rep.problem_msg = 'data code %d not recognized' % code
+            rep.problem_msg = f'data code {code} not recognized'
         else:
             if dtype.itemsize == 0:
                 rep.problem_level = 40
-                rep.problem_msg = 'data code %d not supported' % code
+                rep.problem_msg = f'data code {code} not supported'
             else:
                 return hdr, rep
         if fix:

nibabel/cifti2/cifti2_axes.py

@@ -373,7 +373,7 @@ def from_mask(cls, mask, name='other', affine=None):
         else:
             raise ValueError(
                 'Mask should be either 1-dimensional (for surfaces) or '
-                '3-dimensional (for volumes), not %i-dimensional' % mask.ndim
+                f'3-dimensional (for volumes), not {mask.ndim}-dimensional'
             )
 
     @classmethod
@@ -1519,7 +1519,6 @@ def get_element(self, index):
             index = self.size + index
         if index >= self.size or index < 0:
             raise IndexError(
-                'index %i is out of range for SeriesAxis with size %i'
-                % (original_index, self.size)
+                f'index {original_index} is out of range for SeriesAxis with size {self.size}'
             )
         return self.start + self.step * index

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -72,7 +72,7 @@ def test_read_and_proxies():
 
 @needs_nibabel_data('nitest-cifti2')
 def test_version():
-    for i, dat in enumerate(datafiles):
+    for dat in datafiles:
         img = nib.load(dat)
         assert Version(img.header.version) == Version('2')
 

nibabel/cmdline/dicomfs.py

@@ -51,7 +51,7 @@ def __init__(self, fno):
         self.direct_io = False
 
     def __str__(self):
-        return 'FileHandle(%d)' % self.fno
+        return f'FileHandle({self.fno})'
 
 
 class DICOMFS(fuse.Fuse):
@@ -85,11 +85,11 @@ def get_paths(self):
                 series_info += f'UID: {series.uid}\n'
                 series_info += f'number: {series.number}\n'
                 series_info += f'description: {series.description}\n'
-                series_info += 'rows: %d\n' % series.rows
-                series_info += 'columns: %d\n' % series.columns
-                series_info += 'bits allocated: %d\n' % series.bits_allocated
-                series_info += 'bits stored: %d\n' % series.bits_stored
-                series_info += 'storage instances: %d\n' % len(series.storage_instances)
+                series_info += f'rows: {series.rows}\n'
+                series_info += f'columns: {series.columns}\n'
+                series_info += f'bits allocated: {series.bits_allocated}\n'
+                series_info += f'bits stored: {series.bits_stored}\n'
+                series_info += f'storage instances: {len(series.storage_instances)}\n'
                 d[series.number] = {
                     'INFO': series_info.encode('ascii', 'replace'),
                     f'{series.number}.nii': (series.nifti_size, series.as_nifti),

nibabel/cmdline/diff.py

@@ -266,7 +266,7 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
                 diffs1.append({'CMP': 'incompat'})
 
         if any(diffs1):
-            diffs['DATA(diff %d:)' % (i + 1)] = diffs1
+            diffs[f'DATA(diff {i + 1}:)'] = diffs1
 
     return diffs
 
@@ -293,7 +293,7 @@ def display_diff(files, diff):
     output += field_width.format('Field/File')
 
     for i, f in enumerate(files, 1):
-        output += '%d:%s' % (i, filename_width.format(os.path.basename(f)))
+        output += f'{i}:{filename_width.format(os.path.basename(f))}'
 
     output += '\n'
 

nibabel/cmdline/ls.py

@@ -73,7 +73,7 @@ def get_opt_parser():
                 action='store_true',
                 dest='all_counts',
                 default=False,
-                help='Output all counts, even if number of unique values > %d' % MAX_UNIQUE,
+                help=f'Output all counts, even if number of unique values > {MAX_UNIQUE}',
             ),
             Option(
                 '-z',
@@ -117,7 +117,7 @@ def proc_file(f, opts):
         row += ['']
 
     if hasattr(h, 'extensions') and len(h.extensions):
-        row += ['@l#exts: %d' % len(h.extensions)]
+        row += [f'@l#exts: {len(h.extensions)}']
     else:
         row += ['']
 
@@ -166,16 +166,16 @@ def proc_file(f, opts):
                 d = d.reshape(-1)
             if opts.stats:
                 # just # of elements
-                row += ['@l[%d]' % np.prod(d.shape)]
+                row += [f'@l[{np.prod(d.shape)}]']
                 # stats
                 row += [f'@l[{np.min(d):.2g}, {np.max(d):.2g}]' if len(d) else '-']
             if opts.counts:
                 items, inv = np.unique(d, return_inverse=True)
                 if len(items) > 1000 and not opts.all_counts:
-                    counts = _err('%d uniques. Use --all-counts' % len(items))
+                    counts = _err(f'{len(items)} uniques. Use --all-counts')
                 else:
                     freq = np.bincount(inv)
-                    counts = ' '.join('%g:%d' % (i, f) for i, f in zip(items, freq))
+                    counts = ' '.join(f'{i:g}:{f}' for i, f in zip(items, freq))
                 row += ['@l' + counts]
         except OSError as e:
             verbose(2, f'Failed to obtain stats/counts -- {e}')

nibabel/dft.py

@@ -162,7 +162,7 @@ def as_nifti(self):
         for i, si in enumerate(self.storage_instances):
             if i + 1 != si.instance_number:
                 raise InstanceStackError(self, i, si)
-            logger.info('reading %d/%d' % (i + 1, len(self.storage_instances)))
+            logger.info(f'reading {i + 1}/{len(self.storage_instances)}')
             d = self.storage_instances[i].dicom()
             data[i, :, :] = d.pixel_array
 

nibabel/ecat.py

@@ -309,14 +309,14 @@ def get_patient_orient(self):
         """
         code = self._structarr['patient_orientation'].item()
         if code not in self._patient_orient_codes:
-            raise KeyError('Ecat Orientation CODE %d not recognized' % code)
+            raise KeyError(f'Ecat Orientation CODE {code} not recognized')
         return self._patient_orient_codes[code]
 
     def get_filetype(self):
         """Type of ECAT Matrix File from code stored in header"""
         code = self._structarr['file_type'].item()
         if code not in self._ft_codes:
-            raise KeyError('Ecat Filetype CODE %d not recognized' % code)
+            raise KeyError(f'Ecat Filetype CODE {code} not recognized')
         return self._ft_codes[code]
 
     @classmethod

nibabel/fileslice.py

@@ -127,7 +127,7 @@ def canonical_slicers(sliceobj, shape, check_inds=True):
             if slicer < 0:
                 slicer = dim_len + slicer
             elif check_inds and slicer >= dim_len:
-                raise ValueError('Integer index %d to large' % slicer)
+                raise ValueError(f'Integer index {slicer} too large')
         can_slicers.append(slicer)
     # Fill out any missing dimensions
     if n_real < n_dim:

nibabel/freesurfer/io.py

@@ -427,7 +427,7 @@ def _read_annot_ctab_old_format(fobj, n_entries):
     for i in range(n_entries):
         # structure name length + string
         name_length = np.fromfile(fobj, dt, 1)[0]
-        name = np.fromfile(fobj, '|S%d' % name_length, 1)[0]
+        name = np.fromfile(fobj, f'|S{name_length}', 1)[0]
         names.append(name)
         # read RGBT for this entry
         ctab[i, :4] = np.fromfile(fobj, dt, 4)
@@ -465,13 +465,13 @@ def _read_annot_ctab_new_format(fobj, ctab_version):
     dt = _ANNOT_DT
     # This code works with a file version == 2, nothing else
     if ctab_version != 2:
-        raise Exception('Unrecognised .annot file version (%i)', ctab_version)
+        raise Exception(f'Unrecognised .annot file version ({ctab_version})')
     # maximum LUT index present in the file
     max_index = np.fromfile(fobj, dt, 1)[0]
     ctab = np.zeros((max_index, 5), dt)
     # orig_tab string length + string
     length = np.fromfile(fobj, dt, 1)[0]
-    np.fromfile(fobj, '|S%d' % length, 1)[0]  # Orig table path
+    np.fromfile(fobj, f'|S{length}', 1)[0]  # Orig table path
     # number of LUT entries present in the file
     entries_to_read = np.fromfile(fobj, dt, 1)[0]
     names = list()
@@ -480,7 +480,7 @@ def _read_annot_ctab_new_format(fobj, ctab_version):
         idx = np.fromfile(fobj, dt, 1)[0]
         # structure name length + string
         name_length = np.fromfile(fobj, dt, 1)[0]
-        name = np.fromfile(fobj, '|S%d' % name_length, 1)[0]
+        name = np.fromfile(fobj, f'|S{name_length}', 1)[0]
         names.append(name)
         # RGBT
         ctab[idx, :4] = np.fromfile(fobj, dt, 4)
@@ -525,7 +525,7 @@ def write(num, dtype=dt):
         def write_string(s):
             s = (s if isinstance(s, bytes) else s.encode()) + b'\x00'
             write(len(s))
-            write(s, dtype='|S%d' % len(s))
+            write(s, dtype=f'|S{len(s)}')
 
         # Generate annotation values for each ctab entry
         if fill_ctab:

nibabel/freesurfer/mghformat.py

@@ -281,7 +281,7 @@ def set_zooms(self, zooms):
         zooms = np.asarray(zooms)
         ndims = self._ndims()
         if len(zooms) > ndims:
-            raise HeaderDataError('Expecting %d zoom values' % ndims)
+            raise HeaderDataError(f'Expecting {ndims} zoom values')
         if np.any(zooms[:3] <= 0):
             raise HeaderDataError(
                 f'Spatial (first three) zooms must be positive; got {tuple(zooms[:3])}'

nibabel/gifti/gifti.py

@@ -522,7 +522,7 @@ def _to_xml_element(self):
             },
         )
         for di, dn in enumerate(self.dims):
-            data_array.attrib['Dim%d' % di] = str(dn)
+            data_array.attrib[f'Dim{di}'] = str(dn)
 
         if self.meta is not None:
             data_array.append(self.meta._to_xml_element())

nibabel/gifti/parse_gifti_fast.py

@@ -284,8 +284,8 @@ def EndElementHandler(self, name):
         if name == 'GIFTI':
             if hasattr(self, 'expected_numDA') and self.expected_numDA != self.img.numDA:
                 warnings.warn(
-                    'Actual # of data arrays does not match '
-                    '# expected: %d != %d.' % (self.expected_numDA, self.img.numDA)
+                    'Actual # of data arrays does not match # expected: '
+                    f'{self.expected_numDA} != {self.img.numDA}.'
                 )
             # remove last element of the list
             self.fsm_state.pop()

nibabel/gifti/util.py

@@ -10,7 +10,7 @@
 from ..volumeutils import Recoder
 
 # Translate dtype.kind char codes to XML text output strings
-KIND2FMT = {'i': '%i', 'u': '%i', 'f': '%10.6f', 'c': '%10.6f', 'V': ''}
+KIND2FMT = {'i': '%d', 'u': '%d', 'f': '%10.6f', 'c': '%10.6f', 'V': ''}
 
 array_index_order_codes = Recoder(
     (

nibabel/nicom/csareader.py

@@ -179,7 +179,7 @@ def get_vector(csa_dict, tag_name, n):
     if len(items) == 0:
         return None
     if len(items) != n:
-        raise ValueError('Expecting %d vector' % n)
+        raise ValueError(f'Expecting {n} vector')
     return np.array(items)
 
 

nibabel/nicom/dicomreaders.py

@@ -131,7 +131,7 @@ def slices_to_series(wrappers):
                 break
         else:  # no match in current volume lists
             volume_lists.append([dw])
-    print('We appear to have %d Series' % len(volume_lists))
+    print(f'We appear to have {len(volume_lists)} Series')
     # second pass
     out_vol_lists = []
     for vol_list in volume_lists:
@@ -143,7 +143,7 @@ def slices_to_series(wrappers):
                 out_vol_lists += _third_pass(vol_list)
                 continue
         out_vol_lists.append(vol_list)
-    print('We have %d volumes after second pass' % len(out_vol_lists))
+    print(f'We have {len(out_vol_lists)} volumes after second pass')
     # final pass check
     for vol_list in out_vol_lists:
         zs = [s.slice_indicator for s in vol_list]

nibabel/nicom/dicomwrappers.py

@@ -565,7 +565,7 @@ def applies(self, dcm_wrp) -> bool:
                 warnings.warn(
                     'A multi-stack file was passed without an explicit filter, just using lowest StackID'
                 )
-                self._selected = sorted(stack_ids)[0]
+                self._selected = min(stack_ids)
             return True
         return False
 

nibabel/nicom/tests/test_dicomwrappers.py

@@ -991,8 +991,8 @@ def test_scale_data(self):
         assert_array_equal(data * 3 - 2, MFW(fake_mf)._scale_data(data))
         # Decimals are OK
         for frame in frames:
-            frame.PixelValueTransformationSequence[0].RescaleSlope = Decimal('3')
-            frame.PixelValueTransformationSequence[0].RescaleIntercept = Decimal('-2')
+            frame.PixelValueTransformationSequence[0].RescaleSlope = Decimal(3)
+            frame.PixelValueTransformationSequence[0].RescaleIntercept = Decimal(-2)
         assert_array_equal(data * 3 - 2, MFW(fake_mf)._scale_data(data))
         # A per-frame RWV scaling takes precedence over per-frame PixelValueTransformation
         for frame in frames:

nibabel/nifti1.py

@@ -1559,7 +1559,7 @@ def get_intent(self, code_repr='label'):
         else:
             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))
+        params = (float(hdr[f'intent_p{i}']) for i in range(1, n_params + 1))
         name = hdr['intent_name'].item().decode('latin-1')
         return label, tuple(params), name
 
@@ -1632,8 +1632,8 @@ def set_intent(self, code, params=(), name='', allow_unknown=False):
         hdr['intent_name'] = name
         all_params = [0] * 3
         all_params[: len(params)] = params[:]
-        for i, param in enumerate(all_params):
-            hdr['intent_p%d' % (i + 1)] = param
+        for i, param in enumerate(all_params, start=1):
+            hdr[f'intent_p{i}'] = param
 
     def get_slice_duration(self):
         """Get slice duration
@@ -1911,7 +1911,7 @@ def _chk_offset(hdr, fix=False):
             return hdr, rep
         if magic == hdr.single_magic and offset < hdr.single_vox_offset:
             rep.problem_level = 40
-            rep.problem_msg = 'vox offset %d too low for single file nifti1' % offset
+            rep.problem_msg = f'vox offset {int(offset)} too low for single file nifti1'
             if fix:
                 hdr['vox_offset'] = hdr.single_vox_offset
                 rep.fix_msg = f'setting to minimum value of {hdr.single_vox_offset}'
@@ -1943,7 +1943,7 @@ def _chk_xform_code(klass, code_type, hdr, fix):
         if code in recoder.value_set():
             return hdr, rep
         rep.problem_level = 30
-        rep.problem_msg = '%s %d not valid' % (code_type, code)
+        rep.problem_msg = f'{code_type} {code} not valid'
         if fix:
             hdr[code_type] = 0
             rep.fix_msg = 'setting to 0'

nibabel/orientations.py

@@ -124,7 +124,7 @@ def ornt_transform(start_ornt, end_ornt):
                 result[start_in_idx, :] = [end_in_idx, flip]
                 break
         else:
-            raise ValueError('Unable to find out axis %d in start_ornt' % end_out_idx)
+            raise ValueError(f'Unable to find out axis {end_out_idx} in start_ornt')
     return result
 
 
@@ -322,7 +322,7 @@ def axcodes2ornt(axcodes, labels=None):
            [ 2.,  1.]])
     """
     labels = list(zip('LPI', 'RAS')) if labels is None else labels
-    allowed_labels = sum([list(L) for L in labels], []) + [None]
+    allowed_labels = sum(map(list, labels), [None])
     if len(allowed_labels) != len(set(allowed_labels)):
         raise ValueError(f'Duplicate labels in {allowed_labels}')
     if not set(axcodes).issubset(allowed_labels):

nibabel/spatialimages.py

@@ -267,7 +267,7 @@ def set_zooms(self, zooms: Sequence[float]) -> None:
         shape = self.get_data_shape()
         ndim = len(shape)
         if len(zooms) != ndim:
-            raise HeaderDataError('Expecting %d zoom values for ndim %d' % (ndim, ndim))
+            raise HeaderDataError(f'Expecting {ndim} zoom values for ndim {ndim}')
         if any(z < 0 for z in zooms):
             raise HeaderDataError('zooms must be positive')
         self._zooms = zooms

nibabel/streamlines/tests/test_array_sequence.py

@@ -79,7 +79,7 @@ def test_creating_arraysequence_from_list(self):
         # List of ndarrays.
         N = 5
         for ndim in range(1, N + 1):
-            common_shape = tuple([SEQ_DATA['rng'].randint(1, 10) for _ in range(ndim - 1)])
+            common_shape = tuple(SEQ_DATA['rng'].randint(1, 10) for _ in range(ndim - 1))
             data = generate_data(nb_arrays=5, common_shape=common_shape, rng=SEQ_DATA['rng'])
             check_arr_seq(ArraySequence(data), data)
 

nibabel/tests/test_funcs.py

@@ -23,7 +23,7 @@
 
 def _as_fname(img):
     global _counter
-    fname = 'img%3d.nii' % _counter
+    fname = f'img{_counter:3d}.nii'
     _counter = _counter + 1
     save(img, fname)
     return fname

nibabel/tests/test_nifti1.py

@@ -578,12 +578,12 @@ def test_slice_times(self):
         with pytest.raises(HeaderDataError):
             # all None
             hdr.set_slice_times((None,) * len(times))
-        n_mid_times = times[:]
+        n_mid_times = times.copy()
         n_mid_times[3] = None
         with pytest.raises(HeaderDataError):
             # None in middle
             hdr.set_slice_times(n_mid_times)
-        funny_times = times[:]
+        funny_times = times.copy()
         funny_times[3] = 0.05
         with pytest.raises(HeaderDataError):
             # can't get single slice duration