Merge pull request #908 from ghoshbishakh/pep8change

Fix pep8 errors in viz

dipy/viz/colormap.py

@@ -117,7 +117,7 @@ def boys2rgb(v):
     hh5 = 6 * xy / 5.5
     hh6 = (1 / 1.176) * .125 * (35 * z4 - 30 * z2 + 3)
     hh7 = 2.5 * x * (7 * z3 - 3 * z) / 3.737
-    hh8 = 2.5 * y * (7 * z3 - 3 * z)/3.737
+    hh8 = 2.5 * y * (7 * z3 - 3 * z) / 3.737
     hh9 = ((x2 - y2) * 7.5 * (7 * z2 - 1)) / 15.85
     hh10 = ((2 * xy) * (7.5 * (7 * z2 - 1))) / 15.85
     hh11 = 105 * (4 * x3 * z - 3 * xz * (1 - z2)) / 59.32
@@ -149,7 +149,7 @@ def boys2rgb(v):
     X = X + hh8 * ss67
 
     X = X + hh10 * cc89
-    X = X + hh9 *  ss89
+    X = X + hh9 * ss89
 
     Y = 0.0
 
@@ -227,7 +227,7 @@ def orient2rgb(v):
 
     if v.ndim == 2:
         orientn = np.sqrt(v[:, 0] ** 2 + v[:, 1] ** 2 + v[:, 2] ** 2)
-        orientn.shape = orientn.shape+(1,)
+        orientn.shape = orientn.shape + (1,)
         orient = np.abs(v / orientn)
 
     return orient

dipy/viz/fvtk.py

@@ -1,8 +1,10 @@
 ''' Fvtk module implements simple visualization functions using VTK.
 
 The main idea is the following:
-A window can have one or more renderers. A renderer can have none, one or more actors. Examples of actors are a sphere, line, point etc.
-You basically add actors in a renderer and in that way you can visualize the forementioned objects e.g. sphere, line ...
+A window can have one or more renderers. A renderer can have none,
+one or more actors. Examples of actors are a sphere, line, point etc.
+You basically add actors in a renderer and in that way you can
+visualize the forementioned objects e.g. sphere, line ...
 
 Examples
 ---------
@@ -284,15 +286,17 @@ def volume(vol, voxsz=(1.0, 1.0, 1.0), affine=None, center_origin=1,
         As given by volumeimages.
     center_origin : int {0,1}
         It considers that the center of the volume is the
-        point ``(-vol.shape[0]/2.0+0.5,-vol.shape[1]/2.0+0.5,-vol.shape[2]/2.0+0.5)``.
+        point ``(-vol.shape[0]/2.0+0.5,-vol.shape[1]/2.0+0.5,
+            -vol.shape[2]/2.0+0.5)``.
     info : int {0,1}
         If 1 it prints out some info about the volume, the method and the
         dataset.
     trilinear : int {0,1}
         Use trilinear interpolation, default 1, gives smoother rendering. If
         you want faster interpolation use 0 (Nearest).
     maptype : int {0,1}
-        The maptype is a very important parameter which affects the raycasting algorithm in use for the rendering.
+        The maptype is a very important parameter which affects the
+        raycasting algorithm in use for the rendering.
         The options are:
         If 0 then vtkVolumeTextureMapper2D is used.
         If 1 then vtkVolumeRayCastFunction is used.
@@ -437,8 +441,12 @@ def volume(vol, voxsz=(1.0, 1.0, 1.0), affine=None, center_origin=1,
     if affine is not None:
 
         aff = vtk.vtkMatrix4x4()
-        aff.DeepCopy((affine[0, 0], affine[0, 1], affine[0, 2], affine[0, 3], affine[1, 0], affine[1, 1], affine[1, 2], affine[1, 3], affine[2, 0], affine[
-                     2, 1], affine[2, 2], affine[2, 3], affine[3, 0], affine[3, 1], affine[3, 2], affine[3, 3]))
+        aff.DeepCopy((affine[0, 0], affine[0, 1], affine[0, 2],
+                      affine[0, 3], affine[1, 0], affine[1, 1],
+                      affine[1, 2], affine[1, 3], affine[2, 0],
+                      affine[2, 1], affine[2, 2], affine[2, 3],
+                      affine[3, 0], affine[3, 1], affine[3, 2],
+                      affine[3, 3]))
         # aff.DeepCopy((affine[0,0],affine[0,1],affine[0,2],0,affine[1,0],affine[1,1],affine[1,2],0,affine[2,0],affine[2,1],affine[2,2],0,affine[3,0],affine[3,1],affine[3,2],1))
         # aff.DeepCopy((affine[0,0],affine[0,1],affine[0,2],127.5,affine[1,0],affine[1,1],affine[1,2],-127.5,affine[2,0],affine[2,1],affine[2,2],-127.5,affine[3,0],affine[3,1],affine[3,2],1))
 
@@ -472,7 +480,9 @@ def volume(vol, voxsz=(1.0, 1.0, 1.0), affine=None, center_origin=1,
         # changeFilter.SetInput(im)
         if center_origin:
             changeFilter.SetOutputOrigin(
-                -vol.shape[0] / 2.0 + 0.5, -vol.shape[1] / 2.0 + 0.5, -vol.shape[2] / 2.0 + 0.5)
+                -vol.shape[0] / 2.0 + 0.5,
+                -vol.shape[1] / 2.0 + 0.5,
+                -vol.shape[2] / 2.0 + 0.5)
             print('ChangeFilter ', changeFilter.GetOutputOrigin())
 
     opacity = vtk.vtkPiecewiseFunction()
@@ -673,7 +683,9 @@ def contour(vol, voxsz=(1.0, 1.0, 1.0), affine=None, levels=[50],
     return ass
 
 
-lowercase_cm_name = {'blues':'Blues', 'accent':'Accent'}
+lowercase_cm_name = {'blues': 'Blues', 'accent': 'Accent'}
+
+
 def create_colormap(v, name='jet', auto=True):
     """Create colors from a specific colormap and return it
     as an array of shape (N,3) where every row gives the corresponding
@@ -907,14 +919,15 @@ def peaks(peaks_dirs, peaks_values=None, scale=2.2, colors=(1, 0, 0)):
                 pv = 1.
 
             symm = np.vstack((-peaks_dirs[ijk][i] * pv + xyz,
-                               peaks_dirs[ijk][i] * pv + xyz))
+                              peaks_dirs[ijk][i] * pv + xyz))
 
             list_dirs.append(symm)
 
     return line(list_dirs, colors)
 
 
-def tensor(evals, evecs, scalar_colors=None, sphere=None, scale=2.2, norm=True):
+def tensor(evals, evecs, scalar_colors=None,
+           sphere=None, scale=2.2, norm=True):
     """Plot many tensors as ellipsoids simultaneously.
 
     Parameters

dipy/viz/projections.py

@@ -8,16 +8,14 @@
 import numpy as np
 import scipy.interpolate as interp
 from ..utils.optpkg import optional_package
+import dipy.core.geometry as geo
+from dipy.testing import doctest_skip_parser
 
 matplotlib, has_mpl, setup_module = optional_package("matplotlib")
 plt, _, _ = optional_package("matplotlib.pyplot")
 tri, _, _ = optional_package("matplotlib.tri")
 bm, has_basemap, _ = optional_package("mpl_toolkits.basemap")
 
-import dipy.core.geometry as geo
-
-from dipy.testing import doctest_skip_parser
-
 
 @doctest_skip_parser
 def sph_project(vertices, val, ax=None, vmin=None, vmax=None, cmap=None,
@@ -45,7 +43,8 @@ def sph_project(vertices, val, ax=None, vmin=None, vmax=None, cmap=None,
 
     triang : Whether to display the plot triangulated as a pseudo-color plot.
 
-    boundary : Whether to draw the boundary around the projection in a black line
+    boundary : Whether to draw the boundary around the projection
+    in a black line
 
     Returns
     -------
@@ -76,10 +75,12 @@ def sph_project(vertices, val, ax=None, vmin=None, vmax=None, cmap=None,
         m.drawmapboundary()
 
     # Rotate the coordinate system so that you are looking from the north pole:
-    verts_rot = np.array(np.dot(np.matrix([[0,0,-1],[0,1,0],[1,0,0]]), vertices))
+    verts_rot = np.array(
+        np.dot(np.matrix([[0, 0, -1], [0, 1, 0], [1, 0, 0]]), vertices))
 
-    # To get the orthographic projection, when the first coordinate is positive:
-    neg_idx = np.where(verts_rot[0]>0)
+    # To get the orthographic projection, when the first coordinate is
+    # positive:
+    neg_idx = np.where(verts_rot[0] > 0)
 
     # rotate the entire bvector around to point in the other direction:
     verts_rot[:, neg_idx] *= -1
@@ -102,18 +103,18 @@ def sph_project(vertices, val, ax=None, vmin=None, vmax=None, cmap=None,
     else:
         cmap_data = cmap._segmentdata
         red_interp, blue_interp, green_interp = (
-        interp.interp1d(np.array(cmap_data[gun])[:,0],
-                        np.array(cmap_data[gun])[:,1]) for gun in
-                                                  ['red', 'blue','green'])
+            interp.interp1d(np.array(cmap_data[gun])[:, 0],
+                            np.array(cmap_data[gun])[:, 1]) for gun in
+            ['red', 'blue', 'green'])
 
-        r = (val - my_min)/float(my_max-my_min)
+        r = (val - my_min) / float(my_max - my_min)
 
         # Enforce the maximum and minumum boundaries, if there are values
         # outside those boundaries:
-        r[r<0]=0
-        r[r>1]=1
+        r[r < 0] = 0
+        r[r > 1] = 1
 
-        for this_x, this_y, this_r in zip(x,y,r):
+        for this_x, this_y, this_r in zip(x, y, r):
             red = red_interp(this_r)
             blue = blue_interp(this_r)
             green = green_interp(this_r)
@@ -127,8 +128,7 @@ def sph_project(vertices, val, ax=None, vmin=None, vmax=None, cmap=None,
         pos = ax.get_position()
         l, b, w, h = pos.bounds
         # setup colorbar axes
-        cax = fig.add_axes([l+w+0.075, b, 0.05, h], frameon=False)
-        fig.colorbar(mappable, cax=cax) # draw colorbar
+        cax = fig.add_axes([l + w + 0.075, b, 0.05, h], frameon=False)
+        fig.colorbar(mappable, cax=cax)  # draw colorbar
 
     return ax
-

dipy/viz/regtools.py

@@ -17,6 +17,7 @@ def _tile_plot(imgs, titles, **kwargs):
 
     return fig
 
+
 def overlay_images(img0, img1, title0='', title_mid='', title1='', fname=None):
     r""" Plot two images one on top of the other using red and green channels.
 
@@ -49,8 +50,8 @@ def overlay_images(img0, img1, title0='', title_mid='', title1='', fname=None):
         image is not saved.
     """
     # Normalize the input images to [0,255]
-    img0 = 255*((img0 - img0.min()) / (img0.max() - img0.min()))
-    img1 = 255*((img1 - img1.min()) / (img1.max() - img1.min()))
+    img0 = 255 * ((img0 - img0.min()) / (img0.max() - img0.min()))
+    img1 = 255 * ((img1 - img1.min()) / (img1.max() - img1.min()))
 
     # Create the color images
     img0_red = np.zeros(shape=(img0.shape) + (3,), dtype=np.uint8)
@@ -65,14 +66,15 @@ def overlay_images(img0, img1, title0='', title_mid='', title1='', fname=None):
     overlay[..., 1] = img1
 
     fig = _tile_plot([img0_red, overlay, img1_green],
-                      [title0, title_mid, title1])
+                     [title0, title_mid, title1])
 
     # If a file name was given, save the figure
     if fname is not None:
         fig.savefig(fname, bbox_inches='tight')
 
     return fig
 
+
 def draw_lattice_2d(nrows, ncols, delta):
     r"""Create a regular lattice of nrows x ncols squares.
 
@@ -99,15 +101,15 @@ def draw_lattice_2d(nrows, ncols, delta):
         C = 1 + (delta + 1) * ncols
     """
     lattice = np.ndarray((1 + (delta + 1) * nrows,
-                         1 + (delta + 1) * ncols),
+                          1 + (delta + 1) * ncols),
                          dtype=np.float64)
 
     # Fill the lattice with "white"
     lattice[...] = 127
 
     # Draw the horizontal lines in "black"
     for i in range(nrows + 1):
-        lattice[i*(delta + 1), :] = 0
+        lattice[i * (delta + 1), :] = 0
 
     # Draw the vertical lines in "black"
     for j in range(ncols + 1):
@@ -278,15 +280,16 @@ def plot_slices(V, slice_indices=None, fname=None):
     V : array, shape (S, R, C)
         the 3D volume to extract the slices from
     slice_indices : array, shape (3,) (optional)
-        the indices of the sagital (slice_indices[0]), coronal (slice_indices[1])
+        the indices of the sagital (slice_indices[0]), coronal
+        (slice_indices[1])
         and axial (slice_indices[2]) slices to be displayed. If None, the
         middle slices along each direction are displayed.
     fname : string (optional)
         the name of the file to save the figure to. If None (default), the
         figure is not saved to disk.
     """
     if slice_indices is None:
-        slice_indices = np.array(V.shape)//2
+        slice_indices = np.array(V.shape) // 2
 
     # Normalize the intensities to [0, 255]
     sh = V.shape
@@ -299,15 +302,16 @@ def plot_slices(V, slice_indices=None, fname=None):
     sagittal = np.asarray(V[slice_indices[0], :, :]).astype(np.uint8).T
 
     fig = _tile_plot([axial, coronal, sagittal],
-                      ['Axial', 'Coronal', 'Sagittal'],
-                      cmap=plt.cm.gray, origin='lower')
+                     ['Axial', 'Coronal', 'Sagittal'],
+                     cmap=plt.cm.gray, origin='lower')
 
     # Save the figure if requested
     if fname is not None:
         fig.savefig(fname, bbox_inches='tight')
 
     return fig
 
+
 def overlay_slices(L, R, slice_index=None, slice_type=1, ltitle='Left',
                    rtitle='Right', fname=None):
     r"""Plot three overlaid slices from the given volumes.
@@ -354,19 +358,19 @@ def overlay_slices(L, R, slice_index=None, slice_type=1, ltitle='Left',
     # the slices (note the transpositions)
     if slice_type is 0:
         if slice_index is None:
-            slice_index = sh[0]//2
+            slice_index = sh[0] // 2
         colorImage = np.zeros(shape=(sh[2], sh[1], 3), dtype=np.uint8)
         ll = np.asarray(L[slice_index, :, :]).astype(np.uint8).T
         rr = np.asarray(R[slice_index, :, :]).astype(np.uint8).T
     elif slice_type is 1:
         if slice_index is None:
-            slice_index = sh[1]//2
+            slice_index = sh[1] // 2
         colorImage = np.zeros(shape=(sh[2], sh[0], 3), dtype=np.uint8)
         ll = np.asarray(L[:, slice_index, :]).astype(np.uint8).T
         rr = np.asarray(R[:, slice_index, :]).astype(np.uint8).T
     elif slice_type is 2:
         if slice_index is None:
-            slice_index = sh[2]//2
+            slice_index = sh[2] // 2
         colorImage = np.zeros(shape=(sh[1], sh[0], 3), dtype=np.uint8)
         ll = np.asarray(L[:, :, slice_index]).astype(np.uint8).T
         rr = np.asarray(R[:, :, slice_index]).astype(np.uint8).T
@@ -382,8 +386,8 @@ def overlay_slices(L, R, slice_index=None, slice_type=1, ltitle='Left',
     colorImage[..., 1] = rr * (rr > rr[0, 0])
 
     fig = _tile_plot([ll, colorImage, rr],
-                      [ltitle, 'Overlay', rtitle],
-                      cmap=plt.cm.gray, origin='lower')
+                     [ltitle, 'Overlay', rtitle],
+                     cmap=plt.cm.gray, origin='lower')
 
     # Save the figure to disk, if requested
     if fname is not None:

dipy/viz/widget.py

@@ -18,7 +18,7 @@ def slider(iren, ren, callback, min_value=0, max_value=255, value=125,
            size=(50, 0),
            label_format="%0.0lf",
            color=(0.5, 0.5, 0.5),
-           selected_color = (0.9, 0.2, 0.1)):
+           selected_color=(0.9, 0.2, 0.1)):
     """ A 2D slider widget
 
     Parameters
@@ -133,8 +133,10 @@ def get_value(self):
     def _place_widget(obj, event):
         slider.place(ren)
 
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.StartEvent, _place_widget)
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.ModifiedEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.StartEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.ModifiedEvent, _place_widget)
 
     return slider
 
@@ -218,8 +220,10 @@ def place(self, renderer):
     def _place_widget(obj, event):
         button.place(ren)
 
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.StartEvent, _place_widget)
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.ModifiedEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.StartEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.ModifiedEvent, _place_widget)
 
     return button
 
@@ -315,8 +319,10 @@ def place(self, renderer):
     def _place_widget(obj, event):
         text_widget.place(ren)
 
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.StartEvent, _place_widget)
-    iren.GetRenderWindow().AddObserver(vtk.vtkCommand.ModifiedEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.StartEvent, _place_widget)
+    iren.GetRenderWindow().AddObserver(
+        vtk.vtkCommand.ModifiedEvent, _place_widget)
 
     text_widget.On()