pep8 fixes

src/porespy/metrics/_meshtools.py

@@ -60,7 +60,7 @@ def region_volumes(regions, mode='marching_cubes', voxel_size=(1, 1, 1)):
     msg = "Computing region volumes".ljust(60)
     voxel_size = np.array(voxel_size, dtype=float, ndmin=1)
     if np.size(voxel_size) == 1:
-        voxel_size = np.array([voxel_size for i in range(im.ndim)]).flatten()
+        voxel_size = np.array([voxel_size for i in range(regions.ndim)]).flatten()
     for i, s in enumerate(tqdm(slices, desc=msg, **settings.tqdm)):
         region = regions[s] == (i + 1)
         if mode == 'marching_cubes':

src/porespy/networks/_getnet_para.py

@@ -58,20 +58,20 @@ def wait():
 
 def calculate_throat_perimeter(vx, sub_dt, voxel_size):
     # Directions used to evaluate geom properties
-    dirs = [
-        (1, 0, 0),
-        (0, 1, 0),
-        (0, 0, 1),
-        (-1, 0, 0),
-        (0, -1, 0),
-        (0, 0, -1),
-    ]
-    voxel_size = np.array(voxel_size)
-    voxel_areas = np.array([
-        voxel_size[1] * voxel_size[2],
-        voxel_size[2] * voxel_size[0],
-        voxel_size[0] * voxel_size[1],
-    ])
+    # dirs = [
+    #     (1, 0, 0),
+    #     (0, 1, 0),
+    #     (0, 0, 1),
+    #     (-1, 0, 0),
+    #     (0, -1, 0),
+    #     (0, 0, -1),
+    # ]
+    # voxel_size = np.array(voxel_size)
+    # voxel_areas = np.array([
+    #     voxel_size[1] * voxel_size[2],
+    #     voxel_size[2] * voxel_size[0],
+    #     voxel_size[0] * voxel_size[1],
+    # ])
 
     dx = voxel_size[0]*(max(vx[0]) - min(vx[0]))
     dy = voxel_size[1]*(max(vx[1]) - min(vx[1]))
@@ -552,14 +552,10 @@ def _jit_regions_to_network_parallel(
     worker_target = np.zeros((threads-1,), dtype=np.uint32)
 
     for self_id in prange(threads):
-
         if (self_id == (threads - 1)):
-
             current_pore = 1
-
             while True:
                 wait()
-
                 for worker_id in range(len(worker_status)):
                     if worker_status[worker_id] == IDLE:
                         if current_pore <= Np:
@@ -569,17 +565,23 @@ def _jit_regions_to_network_parallel(
                         else:
                             worker_status[worker_id] = FINISHED
                     if worker_status[worker_id] == DONE:
-
                         for throat_i in range(len(partial_t_conns_0[worker_id])):
-                            t_conns_0.append(partial_t_conns_0[worker_id][throat_i])
-                            t_conns_1.append(partial_t_conns_1[worker_id][throat_i])
-                            t_dia_inscribed.append(partial_t_dia_inscribed[worker_id][throat_i])
-                            t_perimeter.append(partial_t_perimeter[worker_id][throat_i])
-                            t_area.append(partial_t_area[worker_id][throat_i])
-                            t_coords_0.append(partial_t_coords_0[worker_id][throat_i])
-                            t_coords_1.append(partial_t_coords_1[worker_id][throat_i])
-                            t_coords_2.append(partial_t_coords_2[worker_id][throat_i])
-
+                            t_conns_0.append(
+                                partial_t_conns_0[worker_id][throat_i])
+                            t_conns_1.append(
+                                partial_t_conns_1[worker_id][throat_i])
+                            t_dia_inscribed.append(
+                                partial_t_dia_inscribed[worker_id][throat_i])
+                            t_perimeter.append(
+                                partial_t_perimeter[worker_id][throat_i])
+                            t_area.append(
+                                partial_t_area[worker_id][throat_i])
+                            t_coords_0.append(
+                                partial_t_coords_0[worker_id][throat_i])
+                            t_coords_1.append(
+                                partial_t_coords_1[worker_id][throat_i])
+                            t_coords_2.append(
+                                partial_t_coords_2[worker_id][throat_i])
                         if current_pore <= Np:
                             worker_target[worker_id] = current_pore
                             current_pore += 1
@@ -588,16 +590,11 @@ def _jit_regions_to_network_parallel(
                             worker_status[worker_id] = FINISHED
                 if (np.equal(worker_status, FINISHED).all()):
                     break
-
         else:
-
             while True:
-
                 wait()
                 status = worker_status[self_id]
-
                 if status == ASSIGNED:
-
                     partial_t_conns_0[self_id] = List.empty_list(np.uint64)
                     partial_t_conns_1[self_id] = List.empty_list(np.uint64)
                     partial_t_dia_inscribed[self_id] = List.empty_list(np.float64)
@@ -654,20 +651,24 @@ def _jit_regions_to_network_parallel(
                         if j > pore:
                             partial_t_conns_0[self_id].append(pore)
                             partial_t_conns_1[self_id].append(j)
-                            partial_t_dia_inscribed[self_id].append(inscribed_diameter[j])
+                            partial_t_dia_inscribed[self_id].append(
+                                inscribed_diameter[j])
                             partial_t_perimeter[self_id].append(perimeters[j])
                             partial_t_area[self_id].append(areas[j])
-                            partial_t_coords_0[self_id].append(centers[j][0] + s_offset[0])
-                            partial_t_coords_1[self_id].append(centers[j][1] + s_offset[1])
-                            partial_t_coords_2[self_id].append(centers[j][2] + s_offset[2])
+                            partial_t_coords_0[self_id].append(centers[j][0] +
+                                                               s_offset[0])
+                            partial_t_coords_1[self_id].append(centers[j][1] +
+                                                               s_offset[1])
+                            partial_t_coords_2[self_id].append(centers[j][2] +
+                                                               s_offset[2])
 
                     worker_status[self_id] = DONE
 
                 elif status == FINISHED:
                     break
 
     # Clean up values
-    Nt = len(t_conns_0)  # Get number of throats
+    # Nt = len(t_conns_0)  # Get number of throats
 
     if len(t_conns_0) == 0:
         return None

src/porespy/tools/_marching_cubes.py

@@ -2,16 +2,17 @@
 import math
 import itertools
 from pathlib import Path
-
 from numba import njit
 import numpy as np
 from skimage import measure
 from scipy import spatial
 
+
 MC_TEMPLATES_FILENAME = 'marching_cubes_templates.dat'
 THIS_FOLDER = Path(__file__).absolute().parent
 MC_TEMPLATES_PATH = os.path.join(THIS_FOLDER, MC_TEMPLATES_FILENAME)
 
+
 def face_orientation(v0, v1, v2):
     '''
     Return outward perpendicular vector distance of face along the z axis
@@ -28,36 +29,37 @@ def face_orientation(v0, v1, v2):
     else:
         return 0
 
+
 def area_of_triangle(p0, p1, p2):
     '''
     As per Herons formula
     '''
-    lines = list(itertools.combinations((p0,p1,p2),2))
-    distances = [(spatial.distance.euclidean(i[0],i[1])) for i in lines]
+    lines = list(itertools.combinations((p0, p1, p2), 2))
+    distances = [(spatial.distance.euclidean(i[0], i[1])) for i in lines]
     s = sum(distances)/2
     product_of_diferences = np.prod([(s-i) for i in distances])
     area = math.sqrt(s*product_of_diferences)
     return area
 
 
-def mc_templates_generator(override = False):
+def mc_templates_generator(override=False):
     '''
     Generates a marching cubes template list file, if one is not available
     '''
     if os.path.isfile(MC_TEMPLATES_PATH) and not override:
         return
     summation_to_coordinate = {}
-    for i in [(x,y,z) for x in range(2) for y in range(2) for z in range(2)]:
+    for i in [(x, y, z) for x in range(2) for y in range(2) for z in range(2)]:
         summation_to_coordinate[2 ** (i[0] + 2*i[1] + 4*i[2])] = i
 
     templates_triangles = []
     for _ in range(256):
-        templates_triangles.append( [[],[]] )
+        templates_triangles.append([[], []])
 
-    for i in range(1,255):
-        array = np.zeros((2,2,2))
+    for i in range(1, 255):
+        array = np.zeros((2, 2, 2))
         index = i
-        for j in range(7,-1,-1):
+        for j in range(7, -1, -1):
             e = 2**j
             if index >= e:
                 index -= e
@@ -66,7 +68,7 @@ def mc_templates_generator(override = False):
         templates_triangles[i][0] = verts
         templates_triangles[i][1] = faces
 
-    with open(MC_TEMPLATES_PATH, mode = 'w') as file:
+    with open(MC_TEMPLATES_PATH, mode='w') as file:
         for i in range(256):
             verts, faces = templates_triangles[i]
             file.write(f'{i};')
@@ -78,7 +80,7 @@ def mc_templates_generator(override = False):
             file.write('\n')
 
 
-def create_mc_template_list(spacing = (1,1,1)):
+def create_mc_template_list(spacing=(1, 1, 1)):
     '''
     Return area and volume lists for the marching cubes templates
     Reads the templates file
@@ -90,8 +92,8 @@ def create_mc_template_list(spacing = (1,1,1)):
     areas = {}
     volumes = {}
     triangles = {}
-    vertices_on_top = set((16,32,64,128))
-    with open(MC_TEMPLATES_PATH, mode = 'r') as file:
+    vertices_on_top = set((16, 32, 64, 128))
+    with open(MC_TEMPLATES_PATH, mode='r') as file:
         for line in file:
             index, verts, faces = line.split(';')
             index = int(index)
@@ -108,7 +110,7 @@ def create_mc_template_list(spacing = (1,1,1)):
 
             occupied_vertices = set()
             sub_index = index
-            for i in range(7,-1,-1):
+            for i in range(7, -1, -1):
                 e = 2 ** i
                 if sub_index >= e:
                     occupied_vertices.add(e)
@@ -120,7 +122,7 @@ def create_mc_template_list(spacing = (1,1,1)):
                 basic_volume = 1/8
             elif total_vertices_on_top == 2:
                 if ((16 in occupied_vertices and 128 in occupied_vertices) or
-                    (32 in occupied_vertices and 64 in occupied_vertices)):
+                        (32 in occupied_vertices and 64 in occupied_vertices)):
                     basic_volume = 1/4
                 else:
                     basic_volume = 1/2
@@ -131,10 +133,10 @@ def create_mc_template_list(spacing = (1,1,1)):
 
             for f in faces:
                 v0, v1, v2 = [verts[i] for i in f]
-                v0_proj, v1_proj, v2_proj = [(i[0],i[1],0) for i in (v0,v1,v2)]
-                mean_z = sum([i[2] for i in (v0,v1,v2)])/3
+                v0_proj, v1_proj, v2_proj = [(i[0], i[1], 0) for i in (v0, v1, v2)]
+                mean_z = sum([i[2] for i in (v0, v1, v2)])/3
                 proj_area = area_of_triangle(v0_proj, v1_proj, v2_proj)
-                direction = face_orientation(v0,v1,v2)
+                direction = face_orientation(v0, v1, v2)
                 basic_volume += mean_z * proj_area * direction
 
             for i in range(len(verts)):
@@ -175,14 +177,15 @@ def calculate_area_and_volume(
     area = 0.0
     volume = 0.0
 
-    if debug: print("Shape: ", w, h, d)
+    if debug:
+        print("Shape: ", w, h, d)
 
     for x in range(w - 1):
         for y in range(h - 1):
             for z in range(d - 1):
-                if debug: print(x, y, z)
-                sub_array = img[x : x + 2, y : y + 2, z : z + 2]
-
+                if debug:
+                    print(x, y, z)
+                sub_array = img[x:x + 2, y:y + 2, z:z + 2]
                 if target_label not in sub_array:
                     continue
 
@@ -221,6 +224,7 @@ def marching_cubes_area_and_volume(
 
     return area, volume
 
+
 @njit
 def jit_marching_cubes_area_and_volume(
     img,
@@ -232,10 +236,10 @@ def jit_marching_cubes_area_and_volume(
 ):
 
     vertex_index_array = np.array(
-        [[[  1,  16],
-        [  4,  64]],
-        [[  2,  32],
-        [  8, 128]]], 
+        [[[1, 16],
+          [4, 64]],
+         [[2, 32],
+          [8, 128]]],
         dtype=np.int32
     )
 

src/porespy/tools/_marching_squares.py

@@ -59,6 +59,7 @@
     1/4,
 )
 
+
 @njit
 def jit_marching_squares_perimeter_and_area(
     img,
@@ -82,17 +83,21 @@ def jit_marching_squares_perimeter_and_area(
     for x in range(max_x - 1):
         for y in range(max_y - 1):
             template = 0
-            if img[x    , y    ] == target_label: template += 1
-            if img[x + 1, y    ] == target_label: template += 2
-            if img[x    , y + 1] == target_label: template += 4
-            if img[x + 1, y + 1] == target_label: template += 8
+            if img[x, y] == target_label:
+                template += 1
+            if img[x + 1, y] == target_label:
+                template += 2
+            if img[x, y + 1] == target_label:
+                template += 4
+            if img[x + 1, y + 1] == target_label:
+                template += 8
             if overlap:
-                total_perimeter += perimeters[TEMPLATE_PERIMETER[template]] * TEMPLATE_REPETITION[template]
-                total_area += complete_area * TEMPLATE_AREA[template] * TEMPLATE_REPETITION[template]
+                total_perimeter += perimeters[TEMPLATE_PERIMETER[template]] \
+                    * TEMPLATE_REPETITION[template]
+                total_area += complete_area * TEMPLATE_AREA[template] \
+                    * TEMPLATE_REPETITION[template]
             else:
                 total_perimeter += perimeters[TEMPLATE_PERIMETER[template]]
                 total_area += complete_area * TEMPLATE_AREA[template]
 
     return total_perimeter/2, total_area
-
-