Fixed Pycodestyle errors in fury/actors/odf_slicer.py, fury/actors/pe…

…ak.py, fury/actors/tensor.py, and fury/data/fetcher.py (#877)

* fix pycodestyle error: fetcher.py

* fix: pycodestyle error in peak.py and in odf_slice.py

* fix: "tensor.py:425:12: W605 invalid escape sequence '\D'"

* Fix formatting issues in OdfSlicerAct,,PeakActor and TensorActotr

fury/actors/odf_slicer.py

@@ -118,7 +118,7 @@ def display_extent(self, x1, x2, y1, y2, z1, z2):
         (inclusive).
         """
         mask = np.zeros(self.grid_shape, dtype=bool)
-        mask[x1 : x2 + 1, y1 : y2 + 1, z1 : z2 + 1] = True
+        mask[x1: x2 + 1, y1: y2 + 1, z1: z2 + 1] = True
         self.mask = mask
 
         self._update_mapper()
@@ -173,7 +173,10 @@ def update_sphere(self, vertices, faces, B):
         """Dynamically change the sphere used for SH to SF projection.
         """
         if self.B is None:
-            raise ValueError("Can't update sphere when using " 'SF coefficients.')
+            raise ValueError(
+                "Can't update sphere when using "
+                'SF coefficients.'
+                )
         self.vertices = vertices
         if self.affine is not None:
             self.w_verts = self.vertices.dot(self.affine[:3, :3])
@@ -242,8 +245,9 @@ def _get_all_vertices(self, offsets, sph_dirs, sf):
         if self.radial_scale:
             # apply SF amplitudes to all sphere
             # directions and offset each voxel
-            return np.tile(sph_dirs, (len(offsets), 1)) * sf.reshape(-1, 1) + np.repeat(
-                offsets, len(sph_dirs), axis=0
+            return (
+                np.tile(sph_dirs, (len(offsets), 1)) * sf.reshape(-1, 1)
+                + np.repeat(offsets, len(sph_dirs), axis=0)
             )
         # return scaled spheres offsetted by `offsets`
         return np.tile(sph_dirs, (len(offsets), 1)) * self.scale + np.repeat(
@@ -271,7 +275,8 @@ def _generate_color_for_vertices(self, sf):
                 range_sf = sf.max(axis=-1) - sf.min(axis=-1)
                 rescaled = sf - sf.min(axis=-1, keepdims=True)
                 rescaled[range_sf > 0] /= range_sf[range_sf > 0][..., None]
-                all_colors = create_colormap(rescaled.ravel(), self.colormap) * 255
+                all_colors = create_colormap(rescaled.ravel(), self.colormap) \
+                    * 255
             else:
                 all_colors = np.tile(
                     np.array(self.colormap).reshape(1, 3),

fury/actors/peak.py

@@ -91,9 +91,9 @@ def __init__(
                 xyz = np.asarray(center)
             else:
                 xyz = w_pos[idx, :]
-            valid_peaks = np.nonzero(np.abs(valid_dirs[idx, :, :]).max(axis=-1) > 0.0)[
-                0
-            ]
+            valid_peaks = np.nonzero(
+                    np.abs(valid_dirs[idx, :, :]).max(axis=-1) > 0.0
+                    )[0]
             for direction in valid_peaks:
                 if values is not None:
                     pv = values[center][direction]
@@ -152,14 +152,20 @@ def __init__(
             uniform vec3 lowRanges;
             uniform vec3 highRanges;
             """
-        orient_to_rgb = import_fury_shader(pjoin('utils', 'orient_to_rgb.glsl'))
+        orient_to_rgb = import_fury_shader(
+                pjoin('utils', 'orient_to_rgb.glsl')
+                )
         visible_cross_section = import_fury_shader(
             pjoin('interaction', 'visible_cross_section.glsl')
         )
-        visible_range = import_fury_shader(pjoin('interaction', 'visible_range.glsl'))
+        visible_range = import_fury_shader(
+                pjoin('interaction', 'visible_range.glsl')
+                )
 
         vs_dec = compose_shader([vs_var_dec, orient_to_rgb])
-        fs_dec = compose_shader([fs_var_dec, visible_cross_section, visible_range])
+        fs_dec = compose_shader(
+                [fs_var_dec, visible_cross_section, visible_range]
+                )
 
         vs_impl = """
             centerVertexMCVSOutput = center;
@@ -292,11 +298,13 @@ def _orientation_colors(points, cmap='rgb_standard'):
     """
     if cmap.lower() == 'rgb_standard':
         col_list = [
-            orient2rgb(points[i + 1] - points[i]) for i in range(0, len(points), 2)
+                orient2rgb(points[i + 1] - points[i])
+                for i in range(0, len(points), 2)
         ]
     elif cmap.lower() == 'boys_standard':
         col_list = [
-            boys2rgb(points[i + 1] - points[i]) for i in range(0, len(points), 2)
+            boys2rgb(points[i + 1] - points[i])
+            for i in range(0, len(points), 2)
         ]
     else:
         raise ValueError(
@@ -359,7 +367,8 @@ def _peaks_colors_from_points(points, colors=None, points_per_line=2):
         if len(colors) == num_lines:
             pnts_colors = np.repeat(colors, points_per_line, axis=0)
             if colors.ndim == 1:  # Scalar per line
-                color_array = numpy_support.numpy_to_vtk(pnts_colors, deep=True)
+                color_array = \
+                        numpy_support.numpy_to_vtk(pnts_colors, deep=True)
                 colors_are_scalars = True
             elif colors.ndim == 2:  # RGB(A) color per line
                 global_opacity = 1 if colors.shape[1] == 3 else -1
@@ -409,12 +418,18 @@ def _points_to_vtk_cells(points, points_per_line=2):
     this actor the creation of this array requires a 2 points padding
     between indices.
     """
-    offset = np.asarray(list(range(0, num_pnts + 1, points_per_line)), dtype=int)
+    offset = np.asarray(
+            list(range(0, num_pnts + 1, points_per_line)), dtype=int
+            )
 
     vtk_array_type = numpy_support.get_vtk_array_type(connectivity.dtype)
     cell_array.SetData(
-        numpy_support.numpy_to_vtk(offset, deep=True, array_type=vtk_array_type),
-        numpy_support.numpy_to_vtk(connectivity, deep=True, array_type=vtk_array_type),
+        numpy_support.numpy_to_vtk(
+            offset, deep=True, array_type=vtk_array_type
+            ),
+        numpy_support.numpy_to_vtk(
+            connectivity, deep=True, array_type=vtk_array_type
+            ),
     )
 
     cell_array.SetNumberOfCells(num_cells)

fury/actors/tensor.py

@@ -422,7 +422,7 @@ def main_dir_uncertainty(evals, evecs, signal, sigma, b_matrix):
     analysis described in [1]_. The idea is to estimate the variance of the
     main eigenvector which corresponds to the main direction of diffusion,
     directly from estimated D and its estimated covariance matrix
-    :math:`\Delta D` (see [2]_, equation 4). The angle :math:`\\Theta`
+    :math:`\\Delta D` (see [2]_, equation 4). The angle :math:`\\Theta`
     between the perturbed principal eigenvector of D,
     :math:`\\epsilon_1+\\Delta\\epsilon_1`, and the estimated eigenvector
     :math:`\\epsilon_1`, measures the angular deviation of the main fiber

fury/data/fetcher.py

@@ -26,8 +26,10 @@
 UW_RW_URL = \
     "https://digital.lib.washington.edu/researchworks/bitstream/handle/"
 
-NEW_ICONS_DATA_URL = \
-    "https://raw.githubusercontent.com/fury-gl/fury-data/master/icons/new_icons/"
+NEW_ICONS_DATA_URL = (
+    "https://raw.githubusercontent.com/fury-gl/fury-data/master/icons/"
+    "new_icons/"
+)
 
 CUBEMAP_DATA_URL = \
     "https://raw.githubusercontent.com/fury-gl/fury-data/master/cubemaps/"
@@ -181,7 +183,7 @@ def fetch_data(files, folder, data_size=None):
 
         Raises if the sha checksum of the file does not match the expected
         value. The downloaded file is not deleted when this error is raised.
-    
+
     """
     if not os.path.exists(folder):
         print("Creating new folder %s" % (folder))
@@ -316,7 +318,6 @@ async def _download(session, url, filename, size=None):
         Name of the downloaded file (e.g. BoxTextured.gltf)
     size : int, optional
         Length of the content in bytes
-    
     """
     if not os.path.exists(filename):
         print(f'Downloading: {filename}')
@@ -412,7 +413,7 @@ def fetch_gltf(name=None, mode='glTF'):
     -------
     filenames : tuple
         tuple of feteched filenames (list) and folder (str) path.
-    
+
     """
     if platform.system().lower() == "windows":
         asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
@@ -456,11 +457,13 @@ def fetch_gltf(name=None, mode='glTF'):
     ["circle-pressed.png", "circle.png", "delete-pressed.png", "delete.png",
      "drawing-pressed.png", "drawing.png", "line-pressed.png", "line.png",
      "polyline-pressed.png", "polyline.png", "quad-pressed.png", "quad.png",
-     "resize-pressed.png", "resize.png", "selection-pressed.png", "selection.png"],
+     "resize-pressed.png", "resize.png", "selection-pressed.png",
+     "selection.png"],
     ["circle-pressed.png", "circle.png", "delete-pressed.png", "delete.png",
      "drawing-pressed.png", "drawing.png", "line-pressed.png", "line.png",
      "polyline-pressed.png", "polyline.png", "quad-pressed.png", "quad.png",
-     "resize-pressed.png", "resize.png", "selection-pressed.png", "selection.png"],
+     "resize-pressed.png", "resize.png", "selection-pressed.png",
+     "selection.png"],
     ["CD859F244DF1BA719C65C869C3FAF6B8563ABF82F457730ADBFBD7CA72DDB7BC",
      "5896BDC9FF9B3D1054134D7D9A854677CE9FA4E64F494F156BB2E3F0E863F207",
      "937C46C25BC38B62021B01C97A4EE3CDE5F7C8C4A6D0DB75BF4E4CACE2AF1226",
@@ -718,7 +721,7 @@ def read_viz_gltf(fname, mode='glTF'):
     -------
     path : str
         Complete path of models.
-    
+
     """
     folder = pjoin(fury_home, 'glTF')
     model = pjoin(folder, fname)
@@ -741,7 +744,7 @@ def list_gltf_sample_models():
     model_names : list
         Lists the name of glTF sample from
         https://github.com/KhronosGroup/glTF-Sample-Models/tree/master/2.0
-    
+
     """
     DATA_DIR = pjoin(dirname(__file__), 'files')
     with open(pjoin(DATA_DIR, 'KhronosGltfSamples.json'), 'r') as f: