flake8, isort

Author: kip-hart

src/microstructpy/examples/docs_banner.py

@@ -3,10 +3,11 @@
 import os
 
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 import scipy.stats
 
+import microstructpy as msp
+
 
 def main():
     # Colors
@@ -61,7 +62,7 @@ def main():
     len_y = domain.width + 2 * off
     plt.figure(figsize=(k * len_x, k * len_y))
 
-    # Plot Seeds 
+    # Plot Seeds
     seed_colors = [phases[s.phase]['color'] for s in seeds]
     seeds.plot(color=seed_colors, alpha=0.8, edgecolor='k', linewidth=0.3)
     domain.plot(facecolor='none', edgecolor='k', linewidth=0.3)
@@ -111,7 +112,7 @@ def main():
     plt.gca().set_axis_off()
     plt.gca().get_xaxis().set_visible(False)
     plt.gca().get_yaxis().set_visible(False)
-    
+
     xlim, ylim = domain.limits
     xlim[0] -= off
     xlim[1] += 3 * off + 2 * domain.length

src/microstructpy/examples/foam.py

@@ -1,10 +1,11 @@
 import os
 
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 import scipy.stats
 
+import microstructpy as msp
+
 
 def main():
     # Create Directory
@@ -49,7 +50,7 @@ def main():
             while not good_pt:
                 trial_pt = trial_position(void_tess)
                 good_pt = check_pt(trial_pt, r, check_bkdwns)
-        
+
         seed.position = trial_pt
         bkdwns[i] = seed.breakdown
         seed.phase = 1
@@ -97,6 +98,7 @@ def pick_edge(void_tess):
     kp2 = facet[j - 1]
     return kp1, kp2
 
+
 def trial_position(void_tess):
     kp1, kp2 = pick_edge(void_tess)
     pt1 = void_tess.points[kp1]

src/microstructpy/examples/from_image.py

@@ -3,9 +3,9 @@
 
 import matplotlib.image as mpim
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 
+import microstructpy as msp
 
 # Read in image
 image_basename = 'aluminum_micro.png'

src/microstructpy/examples/grain_neighborhoods.py

@@ -3,11 +3,11 @@
 import os
 
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 import scipy.integrate
 import scipy.stats
 
+import microstructpy as msp
 
 # Define the domain
 domain = msp.geometry.Square(corner=(0, 0), side_length=10)
@@ -83,7 +83,7 @@
                                           max_volume=0.1)
 
 # Plot triangle mesh
-colors = ['C' + str(repl_seeds[a].phase) for a in tmesh.element_attributes]
+colors = ['C' + str(repl_seeds[att].phase) for att in tmesh.element_attributes]
 tmesh.plot(facecolors=colors, edgecolors='k', linewidth=0.2)
 
 plt.axis('square')

src/microstructpy/examples/logo.py

@@ -3,12 +3,12 @@
 import os
 
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 from matplotlib import collections
-from matplotlib.offsetbox import OffsetImage, AnnotationBbox
+from matplotlib.offsetbox import AnnotationBbox
+from matplotlib.offsetbox import OffsetImage
 
-__author__ = 'Kenneth (Kip) Hart'
+import microstructpy as msp
 
 
 def main(n_seeds, size_rng, pos_rng, k_lw):
@@ -106,14 +106,13 @@ def main(n_seeds, size_rng, pos_rng, k_lw):
     # Create the Logo
     logo_im = np.copy(plt_im)
 
-    xx, yy = np.meshgrid(np.arange(logo_im.shape[0]), np.arange(logo_im.shape[1]))
-    zz = - 0.2 * xx +   0.9 * yy
+    xx, yy = np.meshgrid(*[np.arange(n) for n in logo_im.shape])
+    zz = - 0.2 * xx + 0.9 * yy
     ss = (zz - zz.min()) / (zz.max() - zz.min())
 
     c1 = [67, 206, 162]
     c2 = [24, 90, 157]
 
-
     logo_im[mask, -1] = 0  # transparent background
 
     # gradient
@@ -124,9 +123,9 @@ def main(n_seeds, size_rng, pos_rng, k_lw):
     logo_im = logo_im[inds]
     logo_im = logo_im[:, inds]
 
-    pad_width =  logo_im.shape[0]
-    pad_height = 0.5 * logo_im.shape[1]
-    pad_shape = np.array([pad_width, pad_height, logo_im.shape[2]]).astype('int')
+    pad_w = logo_im.shape[0]
+    pad_h = 0.5 * logo_im.shape[1]
+    pad_shape = np.array([pad_w, pad_h, logo_im.shape[2]]).astype('int')
     logo_pad = np.zeros(pad_shape, dtype=logo_im.dtype)
     pad_im = np.concatenate((logo_pad, logo_im, logo_pad), axis=1)
     doc_im = np.concatenate((logo_pad, pad_im, logo_pad), axis=1)
@@ -141,7 +140,7 @@ def main(n_seeds, size_rng, pos_rng, k_lw):
     inds = np.linspace(0, fav_im.shape[0] - 1, favicon_size).astype('int')
     fav_im = fav_im[inds]
     fav_im = fav_im[:, inds]
-    
+
     plt.imsave(favicon_filename, fav_im, dpi=dpi, format='png')
 
     # Create the Social Banner
@@ -172,7 +171,6 @@ def main(n_seeds, size_rng, pos_rng, k_lw):
     plt.close('all')
 
 
-
 if __name__ == '__main__':
     n_seeds = 14
     size_rng = 4

src/microstructpy/examples/standard_voronoi.py

@@ -1,8 +1,8 @@
 import os
 
 import matplotlib.pyplot as plt
-import microstructpy as msp
 
+import microstructpy as msp
 
 # Create domain
 domain = msp.geometry.Square()

src/microstructpy/examples/uniform_seeding.py

@@ -4,13 +4,13 @@
 
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-import microstructpy as msp
 import numpy as np
 from scipy.spatial import distance
 
+import microstructpy as msp
 
 # Create domain
-domain = msp.geometry.Square(corner=(0,0))
+domain = msp.geometry.Square(corner=(0, 0))
 
 # Create list of seed points
 factory = msp.seeding.Seed.factory

src/microstructpy/verification.py

@@ -309,7 +309,7 @@ def seeds_of_best_fit(seeds, phases, pmesh, tmesh):
                 seed_facets = [f for f, m in zip(pmesh.facets, mask) if m]
                 kps = np.unique([kp for f in seed_facets for kp in f])
             seed_pts = poly_pts[kps.astype('int')]
-        
+
         try:
             fit_geom = seed.geometry.best_fit(seed_pts)
         except ValueError: