STY: blue

[git-blame-ignore-rev]

Author: effigies

nibabel/__init__.py

@@ -11,6 +11,7 @@
 
 from .pkg_info import __version__
 from .info import long_description as __doc__
+
 __doc__ += """
 Quickstart
 ==========
@@ -42,6 +43,7 @@
 from . import spm2analyze as spm2
 from . import nifti1 as ni1
 from . import ecat
+
 # object imports
 from .fileholders import FileHolder, FileHolderError
 from .loadsave import load, save
@@ -56,11 +58,15 @@
 from .cifti2 import Cifti2Header, Cifti2Image
 from .gifti import GiftiImage
 from .freesurfer import MGHImage
-from .funcs import (squeeze_image, concat_images, four_to_three,
-                    as_closest_canonical)
-from .orientations import (io_orientation, orientation_affine,
-                           flip_axis, OrientationError,
-                           apply_orientation, aff2axcodes)
+from .funcs import squeeze_image, concat_images, four_to_three, as_closest_canonical
+from .orientations import (
+    io_orientation,
+    orientation_affine,
+    flip_axis,
+    OrientationError,
+    apply_orientation,
+    aff2axcodes,
+)
 from .imageclasses import class_map, ext_map, all_image_classes
 from . import mriutils
 from . import streamlines
@@ -73,9 +79,15 @@ def get_info():
     return _get_pkg_info(os.path.dirname(__file__))
 
 
-def test(label=None, verbose=1, extra_argv=None,
-         doctests=False, coverage=False, raise_warnings=None,
-         timer=False):
+def test(
+    label=None,
+    verbose=1,
+    extra_argv=None,
+    doctests=False,
+    coverage=False,
+    raise_warnings=None,
+    timer=False,
+):
     """
     Run tests for nibabel using pytest
 
@@ -108,29 +120,30 @@ def test(label=None, verbose=1, extra_argv=None,
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     import pytest
+
     args = []
 
     if label is not None:
-        raise NotImplementedError("Labels cannot be set at present")
+        raise NotImplementedError('Labels cannot be set at present')
 
     verbose = int(verbose)
     if verbose > 0:
-        args.append("-" + "v" * verbose)
+        args.append('-' + 'v' * verbose)
     elif verbose < 0:
-        args.append("-" + "q" * -verbose)
+        args.append('-' + 'q' * -verbose)
 
     if extra_argv:
         args.extend(extra_argv)
     if doctests:
-        args.append("--doctest-modules")
+        args.append('--doctest-modules')
     if coverage:
-        args.extend(["--cov", "nibabel"])
+        args.extend(['--cov', 'nibabel'])
     if raise_warnings is not None:
-        raise NotImplementedError("Warning filters are not implemented")
+        raise NotImplementedError('Warning filters are not implemented')
     if timer:
-        raise NotImplementedError("Timing is not implemented")
+        raise NotImplementedError('Timing is not implemented')
 
-    args.extend(["--pyargs", "nibabel"])
+    args.extend(['--pyargs', 'nibabel'])
 
     return pytest.main(args=args)
 
@@ -158,9 +171,10 @@ def bench(label=None, verbose=1, extra_argv=None):
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     from pkg_resources import resource_filename
-    config = resource_filename("nibabel", "benchmarks/pytest.benchmark.ini")
+
+    config = resource_filename('nibabel', 'benchmarks/pytest.benchmark.ini')
     args = []
     if extra_argv is not None:
         args.extend(extra_argv)
-    args.extend(["-c", config])
+    args.extend(['-c', config])
     return test(label, verbose, extra_argv=args)

nibabel/affines.py

@@ -1,21 +1,22 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Utility routines for working with points and affine transforms
+"""Utility routines for working with points and affine transforms
 """
 import numpy as np
 
 from functools import reduce
 
 
 class AffineError(ValueError):
-    """ Errors in calculating or using affines """
+    """Errors in calculating or using affines"""
+
     # Inherits from ValueError to keep compatibility with ValueError previously
     # raised in append_diag
     pass
 
 
 def apply_affine(aff, pts, inplace=False):
-    """ Apply affine matrix `aff` to points `pts`
+    """Apply affine matrix `aff` to points `pts`
 
     Returns result of application of `aff` to the *right* of `pts`.  The
     coordinate dimension of `pts` should be the last.
@@ -142,7 +143,7 @@ def to_matvec(transform):
 
 
 def from_matvec(matrix, vector=None):
-    """ Combine a matrix and vector into an homogeneous affine
+    """Combine a matrix and vector into an homogeneous affine
 
     Combine a rotation / scaling / shearing matrix and translation vector into
     a transform in homogeneous coordinates.
@@ -185,14 +186,14 @@ def from_matvec(matrix, vector=None):
     nin, nout = matrix.shape
     t = np.zeros((nin + 1, nout + 1), matrix.dtype)
     t[0:nin, 0:nout] = matrix
-    t[nin, nout] = 1.
+    t[nin, nout] = 1.0
     if vector is not None:
         t[0:nin, nout] = vector
     return t
 
 
 def append_diag(aff, steps, starts=()):
-    """ Add diagonal elements `steps` and translations `starts` to affine
+    """Add diagonal elements `steps` and translations `starts` to affine
 
     Typical use is in expanding 4x4 affines to larger dimensions.  Nipy is the
     main consumer because it uses NxM affines, whereas we generally only use
@@ -236,8 +237,7 @@ def append_diag(aff, steps, starts=()):
         raise AffineError('Steps should have same length as starts')
     old_n_out, old_n_in = aff.shape[0] - 1, aff.shape[1] - 1
     # make new affine
-    aff_plus = np.zeros((old_n_out + n_steps + 1,
-                         old_n_in + n_steps + 1), dtype=aff.dtype)
+    aff_plus = np.zeros((old_n_out + n_steps + 1, old_n_in + n_steps + 1), dtype=aff.dtype)
     # Get stuff from old affine
     aff_plus[:old_n_out, :old_n_in] = aff[:old_n_out, :old_n_in]
     aff_plus[:old_n_out, -1] = aff[:old_n_out, -1]
@@ -250,7 +250,7 @@ def append_diag(aff, steps, starts=()):
 
 
 def dot_reduce(*args):
-    r""" Apply numpy dot product function from right to left on arrays
+    r"""Apply numpy dot product function from right to left on arrays
 
     For passed arrays :math:`A, B, C, ... Z` returns :math:`A \dot B \dot C ...
     \dot Z` where "." is the numpy array dot product.
@@ -270,7 +270,7 @@ def dot_reduce(*args):
 
 
 def voxel_sizes(affine):
-    r""" Return voxel size for each input axis given `affine`
+    r"""Return voxel size for each input axis given `affine`
 
     The `affine` is the mapping between array (voxel) coordinates and mm
     (world) coordinates.
@@ -308,7 +308,7 @@ def voxel_sizes(affine):
         but in general has length (N-1) where input `affine` is shape (M, N).
     """
     top_left = affine[:-1, :-1]
-    return np.sqrt(np.sum(top_left ** 2, axis=0))
+    return np.sqrt(np.sum(top_left**2, axis=0))
 
 
 def obliquity(affine):
@@ -340,7 +340,7 @@ def obliquity(affine):
 
 
 def rescale_affine(affine, shape, zooms, new_shape=None):
-    """ Return a new affine matrix with updated voxel sizes (zooms)
+    """Return a new affine matrix with updated voxel sizes (zooms)
 
     This function preserves the rotations and shears of the original
     affine, as well as the RAS location of the central voxel of the