STY: autopep8 on source code.

Author: Ben Cipollini

nibabel/affines.py

@@ -214,7 +214,7 @@ def append_diag(aff, steps, starts=()):
         starts = np.zeros(n_steps, dtype=steps.dtype)
     elif len(starts) != n_steps:
         raise ValueError('Steps should have same length as starts')
-    old_n_out, old_n_in = aff.shape[0]-1, aff.shape[1]-1
+    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)
@@ -223,7 +223,7 @@ def append_diag(aff, steps, starts=()):
     aff_plus[:old_n_out, -1] = aff[:old_n_out, -1]
     # Add new diagonal elements
     for i, el in enumerate(steps):
-        aff_plus[old_n_out+i, old_n_in+i] = el
+        aff_plus[old_n_out + i, old_n_in + i] = el
     # Add translations for new affine, plus last 1
     aff_plus[old_n_out:, -1] = list(starts) + [1]
     return aff_plus

nibabel/analyze.py

@@ -107,7 +107,7 @@
     ('session_error', 'i2'),
     ('regular', 'S1'),
     ('hkey_un0', 'S1')
-    ]
+]
 image_dimension_dtd = [
     ('dim', 'i2', (8,)),
     ('vox_units', 'S4'),
@@ -127,7 +127,7 @@
     ('verified', 'i4'),
     ('glmax', 'i4'),
     ('glmin', 'i4')
-    ]
+]
 data_history_dtd = [
     ('descrip', 'S80'),
     ('aux_file', 'S24'),
@@ -147,7 +147,7 @@
     ('omin', 'i4'),
     ('smax', 'i4'),
     ('smin', 'i4')
-    ]
+]
 
 # Full header numpy dtype combined across sub-fields
 header_dtype = np.dtype(header_key_dtd + image_dimension_dtd +
@@ -606,7 +606,7 @@ def get_data_shape(self):
         ndims = dims[0]
         if ndims == 0:
             return 0,
-        return tuple(int(d) for d in dims[1:ndims+1])
+        return tuple(int(d) for d in dims[1:ndims + 1])
 
     def set_data_shape(self, shape):
         ''' Set shape of data
@@ -624,18 +624,18 @@ def set_data_shape(self, shape):
         dims[:] = 1
         dims[0] = ndims
         try:
-            dims[1:ndims+1] = shape
+            dims[1:ndims + 1] = shape
         except (ValueError, OverflowError):
             # numpy 1.4.1 at least generates a ValueError from trying to set a
             # python long into an int64 array (dims are int64 for nifti2)
             values_fit = False
         else:
-            values_fit = np.all(dims[1:ndims+1] == shape)
+            values_fit = np.all(dims[1:ndims + 1] == shape)
         # Error if we did not succeed setting dimensions
         if not values_fit:
             raise HeaderDataError('shape %s does not fit in dim datatype' %
                                   (shape,))
-        self._structarr['pixdim'][ndims+1:] = 1.0
+        self._structarr['pixdim'][ndims + 1:] = 1.0
 
     def get_base_affine(self):
         ''' Get affine from basic (shared) header fields
@@ -659,8 +659,8 @@ def get_base_affine(self):
         hdr = self._structarr
         dims = hdr['dim']
         ndim = dims[0]
-        return shape_zoom_affine(hdr['dim'][1:ndim+1],
-                                 hdr['pixdim'][1:ndim+1],
+        return shape_zoom_affine(hdr['dim'][1:ndim + 1],
+                                 hdr['pixdim'][1:ndim + 1],
                                  self.default_x_flip)
 
     get_best_affine = get_base_affine
@@ -691,7 +691,7 @@ def get_zooms(self):
         if ndim == 0:
             return (1.0,)
         pixdims = hdr['pixdim']
-        return tuple(pixdims[1:ndim+1])
+        return tuple(pixdims[1:ndim + 1])
 
     def set_zooms(self, zooms):
         ''' Set zooms into header fields
@@ -708,7 +708,7 @@ def set_zooms(self, zooms):
         if np.any(zooms < 0):
             raise HeaderDataError('zooms must be positive')
         pixdims = hdr['pixdim']
-        pixdims[1:ndim+1] = zooms[:]
+        pixdims[1:ndim + 1] = zooms[:]
 
     def as_analyze_map(self):
         """ Return header as mapping for conversion to Analyze types
@@ -794,7 +794,7 @@ def set_slope_inter(self, slope, inter=None):
             If float, value must be 0.0 or we raise a ``HeaderTypeError``
         '''
         if ((slope in (None, 1) or np.isnan(slope)) and
-            (inter in (None, 0) or np.isnan(inter))):
+                (inter in (None, 0) or np.isnan(inter))):
             return
         raise HeaderTypeError('Cannot set slope != 1 or intercept != 0 '
                               'for Analyze headers')

nibabel/batteryrunners.py

@@ -175,6 +175,7 @@ def __len__(self):
 
 
 class Report(object):
+
     def __init__(self,
                  error=Exception,
                  problem_level=0,

nibabel/casting.py

@@ -272,7 +272,7 @@ def type_info(np_type):
     if not np_type in (np.longdouble, np.longcomplex) or width not in (16, 32):
         raise FloatingError('We had not expected type %s' % np_type)
     if (vals == (1, 1, 16) and on_powerpc() and
-        _check_maxexp(np.longdouble, 1024)):
+            _check_maxexp(np.longdouble, 1024)):
         # double pair on PPC.  The _check_nmant routine does not work for this
         # type, hence the powerpc platform check instead
         ret.update(dict(nmant=106, width=width))
@@ -664,7 +664,7 @@ def best_float():
     except FloatingError:
         return np.float64
     if (long_info['nmant'] > type_info(np.float64)['nmant'] and
-        machine() != 'sparc64'):  # sparc has crazy-slow float128
+            machine() != 'sparc64'):  # sparc has crazy-slow float128
         return np.longdouble
     return np.float64
 

nibabel/checkwarns.py

@@ -19,6 +19,7 @@
 
 
 class ErrorWarnings(error_warnings):
+
     def __init__(self, *args, **kwargs):
         warnings.warn('ErrorWarnings is deprecated and will be removed in '
                       'nibabel v3.0; use nibabel.testing.error_warnings.',
@@ -27,6 +28,7 @@ def __init__(self, *args, **kwargs):
 
 
 class IgnoreWarnings(suppress_warnings):
+
     def __init__(self, *args, **kwargs):
         warnings.warn('IgnoreWarnings is deprecated and will be removed in '
                       'nibabel v3.0; use nibabel.testing.suppress_warnings.',

nibabel/data.py

@@ -33,6 +33,7 @@ class BomberError(DataError, AttributeError):
 
 class Datasource(object):
     ''' Simple class to add base path to relative path '''
+
     def __init__(self, base_path):
         ''' Initialize datasource
 
@@ -87,7 +88,7 @@ def list_files(self, relative=True):
         out_list = list()
         for base, dirs, files in os.walk(self.base_path):
             if relative:
-                base = base[len(self.base_path)+1:]
+                base = base[len(self.base_path) + 1:]
             for filename in files:
                 out_list.append(pjoin(base, filename))
         return out_list
@@ -97,6 +98,7 @@ class VersionedDatasource(Datasource):
     ''' Datasource with version information in config file
 
     '''
+
     def __init__(self, base_path, config_filename=None):
         ''' Initialize versioned datasource
 
@@ -239,8 +241,8 @@ def find_data_dir(root_dirs, *names):
         if os.path.isdir(pth):
             return pth
     raise DataError('Could not find datasource "%s" in data path "%s"' %
-                   (ds_relative,
-                    os.path.pathsep.join(root_dirs)))
+                    (ds_relative,
+                     os.path.pathsep.join(root_dirs)))
 
 
 def make_datasource(pkg_def, **kwargs):
@@ -304,6 +306,7 @@ def make_datasource(pkg_def, **kwargs):
 
 class Bomber(object):
     ''' Class to raise an informative error when used '''
+
     def __init__(self, name, msg):
         self.name = name
         self.msg = msg
@@ -350,7 +353,7 @@ def datasource_or_bomber(pkg_def, **options):
         return Bomber(sys_relpath, str(e))
     # check version
     if (version is None or
-        LooseVersion(ds.version) >= LooseVersion(version)):
+            LooseVersion(ds.version) >= LooseVersion(version)):
         return ds
     if 'name' in pkg_def:
         pkg_name = pkg_def['name']

nibabel/deprecated.py

@@ -24,6 +24,7 @@ class ModuleProxy(object):
     when you do attribute access and return the attributes of the imported
     module.
     """
+
     def __init__(self, module_name):
         self._module_name = module_name
 

nibabel/dft.py

@@ -57,10 +57,11 @@ def __init__(self, series, i, si):
 
     def __str__(self):
         fmt = 'expecting instance number %d, got %d'
-        return fmt % (self.i+1, self.si.instance_number)
+        return fmt % (self.i + 1, self.si.instance_number)
 
 
 class _Study(object):
+
     def __init__(self, d):
         self.uid = d['uid']
         self.date = d['date']
@@ -93,6 +94,7 @@ def patient_name_or_uid(self):
 
 
 class _Series(object):
+
     def __init__(self, d):
         self.uid = d['uid']
         self.study = d['study']
@@ -160,7 +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('reading %d/%d' % (i + 1, len(self.storage_instances)))
             d = self.storage_instances[i].dicom()
             data[i, :, :] = d.pixel_array
 
@@ -190,7 +192,7 @@ def as_nifti(self):
         m = ((pdi * cosi[0], pdj * cosj[0], pdk * cosk[0], pos_1[0]),
              (pdi * cosi[1], pdj * cosj[1], pdk * cosk[1], pos_1[1]),
              (pdi * cosi[2], pdj * cosj[2], pdk * cosk[2], pos_1[2]),
-             (            0,             0,             0,        1))
+             (0, 0, 0, 1))
 
         m = numpy.array(m)
 
@@ -212,6 +214,7 @@ def nifti_size(self):
 
 
 class _StorageInstance(object):
+
     def __init__(self, d):
         self.uid = d['uid']
         self.instance_number = d['instance_number']
@@ -238,6 +241,7 @@ def dicom(self):
 
 class _db_nochange:
     """context guard for read-only database access"""
+
     def __enter__(self):
         self.c = DB.cursor()
         return self.c
@@ -251,6 +255,7 @@ def __exit__(self, type, value, traceback):
 
 class _db_change:
     """context guard for database access requiring a commit"""
+
     def __enter__(self):
         self.c = DB.cursor()
         return self.c

nibabel/ecat.py

@@ -117,7 +117,7 @@
     ('data_units', '32S'),
     ('septa_state', np.uint16),
     ('fill', '12S')
-    ]
+]
 hdr_dtype = np.dtype(main_header_dtd)
 
 
@@ -384,7 +384,7 @@ def read_mlist(fileobj, endianness):
             mlist = []
             return mlist
         # Use all but first housekeeping row
-        mlists.append(rows[1:n_rows+1])
+        mlists.append(rows[1:n_rows + 1])
         mlist_index += n_rows
         if mlist_block_no <= 2:  # should block_no in (1, 2) be an error?
             break
@@ -467,7 +467,7 @@ def get_series_framenumbers(mlist):
     try:
         for frame_stored, (true_order, _) in frames_order.items():
             # frame as stored in file -> true number in series
-            frame_dict[frame_stored] = trueframenumbers[true_order]+1
+            frame_dict[frame_stored] = trueframenumbers[true_order] + 1
         return frame_dict
     except:
         raise IOError('Error in header or mlist order unknown')
@@ -571,7 +571,7 @@ def get_frame_affine(self, frame=0):
 
         dims = self.get_shape(frame)
         # get translations from center of image
-        origin_offset = (np.array(dims)-1) / 2.0
+        origin_offset = (np.array(dims) - 1) / 2.0
         aff = np.diag(zooms)
         aff[:3, -1] = -origin_offset * zooms[:-1] + np.array([x_off, y_off,
                                                               z_off])
@@ -664,6 +664,7 @@ class EcatImageArrayProxy(object):
     The array proxy allows us to freeze the passed fileobj and
     header such that it returns the expected data array.
     '''
+
     def __init__(self, subheader):
         self._subheader = subheader
         self._data = None
@@ -706,7 +707,7 @@ def __getitem__(self, sliceobj):
         slice3 = sliceobj[ax_inds[3]]
         # We will load volume by volume.  Make slicer into volume by dropping
         # index over the volume axis
-        in_slicer = sliceobj[:ax_inds[3]] + sliceobj[ax_inds[3]+1:]
+        in_slicer = sliceobj[:ax_inds[3]] + sliceobj[ax_inds[3] + 1:]
         # int index for 4th axis, load one slice
         if isinstance(slice3, Integral):
             data = self._subheader.data_from_fileobj(frame_mapping[slice3][0])
@@ -868,16 +869,16 @@ def from_file_map(klass, file_map):
         hdr_fid = hdr_file.get_prepare_fileobj(mode='rb')
         header = klass._header.from_fileobj(hdr_fid)
         hdr_copy = header.copy()
-        ### LOAD MLIST
+        # LOAD MLIST
         mlist = np.zeros((header['num_frames'], 4), dtype=np.int32)
         mlist_data = read_mlist(hdr_fid, hdr_copy.endianness)
         mlist[:len(mlist_data)] = mlist_data
-        ### LOAD SUBHEADERS
+        # LOAD SUBHEADERS
         subheaders = klass._subheader(hdr_copy, mlist, hdr_fid)
-        ### LOAD DATA
-        ##  Class level ImageArrayProxy
+        # LOAD DATA
+        # Class level ImageArrayProxy
         data = klass.ImageArrayProxy(subheaders)
-        ## Get affine
+        # Get affine
         if not subheaders._check_affines():
             warnings.warn('Affines different across frames, loading affine '
                           'from FIRST frame', UserWarning)
@@ -961,7 +962,7 @@ def to_file_map(self, file_map=None):
             image = self._subheader.raw_data_from_fileobj(index)
 
             # Write frame images
-            self._write_data(image, imgf, pos+2, endianness='>')
+            self._write_data(image, imgf, pos + 2, endianness='>')
 
             # Move to dictionnary offset and write dictionnary entry
             self._write_data(mlist[index], imgf, entry_pos, endianness='>')