Reame +pep8

2 files changed, 144 insertions, 144 deletions

diff --git a/examples/plot_barycenter_fgw.py b/examples/plot_barycenter_fgw.py
index f416629..9eea036 100644
--- a/examples/plot_barycenter_fgw.py
+++ b/examples/plot_barycenter_fgw.py
@@ -30,10 +30,11 @@ from matplotlib import cm
 from ot.gromov import fgw_barycenters
 #%% Graph functions
 
-def find_thresh(C,inf=0.5,sup=3,step=10):
+
+def find_thresh(C, inf=0.5, sup=3, step=10):
     """ Trick to find the adequate thresholds from where value of the C matrix are considered close enough to say that nodes are connected
-        Tthe threshold is found by a linesearch between values "inf" and "sup" with "step" thresholds tested. 
-        The optimal threshold is the one which minimizes the reconstruction error between the shortest_path matrix coming from the thresholded adjency matrix 
+        Tthe threshold is found by a linesearch between values "inf" and "sup" with "step" thresholds tested.
+        The optimal threshold is the one which minimizes the reconstruction error between the shortest_path matrix coming from the thresholded adjency matrix
         and the original matrix.
     Parameters
     ----------
@@ -43,21 +44,22 @@ def find_thresh(C,inf=0.5,sup=3,step=10):
           The beginning of the linesearch
     sup : float
           The end of the linesearch
-    step : integer 
-            Number of thresholds tested        
+    step : integer
+            Number of thresholds tested
     """
-    dist=[]
-    search=np.linspace(inf,sup,step)
+    dist = []
+    search = np.linspace(inf, sup, step)
     for thresh in search:
-        Cprime=sp_to_adjency(C,0,thresh)
-        SC=shortest_path(Cprime,method='D')
-        SC[SC==float('inf')]=100
-        dist.append(np.linalg.norm(SC-C))
-    return search[np.argmin(dist)],dist
-
-def sp_to_adjency(C,threshinf=0.2,threshsup=1.8):
-    """ Thresholds the structure matrix in order to compute an adjency matrix. 
-    All values between threshinf and threshsup are considered representing connected nodes and set to 1. Else are set to 0    
+        Cprime = sp_to_adjency(C, 0, thresh)
+        SC = shortest_path(Cprime, method='D')
+        SC[SC == float('inf')] = 100
+        dist.append(np.linalg.norm(SC - C))
+    return search[np.argmin(dist)], dist
+
+
+def sp_to_adjency(C, threshinf=0.2, threshsup=1.8):
+    """ Thresholds the structure matrix in order to compute an adjency matrix.
+    All values between threshinf and threshsup are considered representing connected nodes and set to 1. Else are set to 0
     Parameters
     ----------
     C : ndarray, shape (n_nodes,n_nodes)
@@ -71,102 +73,100 @@ def sp_to_adjency(C,threshinf=0.2,threshsup=1.8):
     C : ndarray, shape (n_nodes,n_nodes)
         The threshold matrix. Each element is in {0,1}
     """
-    H=np.zeros_like(C)
-    np.fill_diagonal(H,np.diagonal(C))
-    C=C-H
-    C=np.minimum(np.maximum(C,threshinf),threshsup)
-    C[C==threshsup]=0
-    C[C!=0]=1   
-    
-    return C 
-
-def build_noisy_circular_graph(N=20,mu=0,sigma=0.3,with_noise=False,structure_noise=False,p=None):
+    H = np.zeros_like(C)
+    np.fill_diagonal(H, np.diagonal(C))
+    C = C - H
+    C = np.minimum(np.maximum(C, threshinf), threshsup)
+    C[C == threshsup] = 0
+    C[C != 0] = 1
+
+    return C
+
+
+def build_noisy_circular_graph(N=20, mu=0, sigma=0.3, with_noise=False, structure_noise=False, p=None):
     """ Create a noisy circular graph
     """
-    g=nx.Graph()
+    g = nx.Graph()
     g.add_nodes_from(list(range(N)))
     for i in range(N):
-        noise=float(np.random.normal(mu,sigma,1))
+        noise = float(np.random.normal(mu, sigma, 1))
         if with_noise:
-            g.add_node(i,attr_name=math.sin((2*i*math.pi/N))+noise)
+            g.add_node(i, attr_name=math.sin((2 * i * math.pi / N)) + noise)
         else:
-            g.add_node(i,attr_name=math.sin(2*i*math.pi/N))
-        g.add_edge(i,i+1)
+            g.add_node(i, attr_name=math.sin(2 * i * math.pi / N))
+        g.add_edge(i, i + 1)
         if structure_noise:
-            randomint=np.random.randint(0,p)
-            if randomint==0:
-                if i<=N-3:
-                    g.add_edge(i,i+2)
-                if i==N-2:
-                    g.add_edge(i,0)
-                if i==N-1:
-                    g.add_edge(i,1)
-    g.add_edge(N,0)
-    noise=float(np.random.normal(mu,sigma,1))
+            randomint = np.random.randint(0, p)
+            if randomint == 0:
+                if i <= N - 3:
+                    g.add_edge(i, i + 2)
+                if i == N - 2:
+                    g.add_edge(i, 0)
+                if i == N - 1:
+                    g.add_edge(i, 1)
+    g.add_edge(N, 0)
+    noise = float(np.random.normal(mu, sigma, 1))
     if with_noise:
-        g.add_node(N,attr_name=math.sin((2*N*math.pi/N))+noise)
+        g.add_node(N, attr_name=math.sin((2 * N * math.pi / N)) + noise)
     else:
-        g.add_node(N,attr_name=math.sin(2*N*math.pi/N))
+        g.add_node(N, attr_name=math.sin(2 * N * math.pi / N))
     return g
 
-def graph_colors(nx_graph,vmin=0,vmax=7):
-    cnorm = mcol.Normalize(vmin=vmin,vmax=vmax)
-    cpick = cm.ScalarMappable(norm=cnorm,cmap='viridis')
+
+def graph_colors(nx_graph, vmin=0, vmax=7):
+    cnorm = mcol.Normalize(vmin=vmin, vmax=vmax)
+    cpick = cm.ScalarMappable(norm=cnorm, cmap='viridis')
     cpick.set_array([])
     val_map = {}
-    for k,v in nx.get_node_attributes(nx_graph,'attr_name').items():
-        val_map[k]=cpick.to_rgba(v)
-    colors=[]
+    for k, v in nx.get_node_attributes(nx_graph, 'attr_name').items():
+        val_map[k] = cpick.to_rgba(v)
+    colors = []
     for node in nx_graph.nodes():
         colors.append(val_map[node])
     return colors
-    
+
 #%% create dataset
 # We build a dataset of noisy circular graphs.
 # Noise is added on the structures by random connections and on the features by gaussian noise.
 
+
 np.random.seed(30)
-X0=[]
+X0 = []
 for k in range(9):
-    X0.append(build_noisy_circular_graph(np.random.randint(15,25),with_noise=True,structure_noise=True,p=3))
-    
+    X0.append(build_noisy_circular_graph(np.random.randint(15, 25), with_noise=True, structure_noise=True, p=3))
+
 #%% Plot dataset
 
-plt.figure(figsize=(8,10))
+plt.figure(figsize=(8, 10))
 for i in range(len(X0)):
-    plt.subplot(3,3,i+1)
-    g=X0[i]
-    pos=nx.kamada_kawai_layout(g)
-    nx.draw(g,pos=pos,node_color = graph_colors(g,vmin=-1,vmax=1),with_labels=False,node_size=100)
-plt.suptitle('Dataset of noisy graphs. Color indicates the label',fontsize=20)
+    plt.subplot(3, 3, i + 1)
+    g = X0[i]
+    pos = nx.kamada_kawai_layout(g)
+    nx.draw(g, pos=pos, node_color=graph_colors(g, vmin=-1, vmax=1), with_labels=False, node_size=100)
+plt.suptitle('Dataset of noisy graphs. Color indicates the label', fontsize=20)
 plt.show()
 
 
-
 #%%
 # We compute the barycenter using FGW. Structure matrices are computed using the shortest_path distance in the graph
 # Features distances are the euclidean distances
-Cs=[shortest_path(nx.adjacency_matrix(x)) for x in X0]
-ps=[np.ones(len(x.nodes()))/len(x.nodes()) for x in X0]
-Ys=[np.array([v for (k,v) in nx.get_node_attributes(x,'attr_name').items()]).reshape(-1,1) for x in X0]
-lambdas=np.array([np.ones(len(Ys))/len(Ys)]).ravel()
-sizebary=15 # we choose a barycenter with 15 nodes
+Cs = [shortest_path(nx.adjacency_matrix(x)) for x in X0]
+ps = [np.ones(len(x.nodes())) / len(x.nodes()) for x in X0]
+Ys = [np.array([v for (k, v) in nx.get_node_attributes(x, 'attr_name').items()]).reshape(-1, 1) for x in X0]
+lambdas = np.array([np.ones(len(Ys)) / len(Ys)]).ravel()
+sizebary = 15  # we choose a barycenter with 15 nodes
 
 #%%
 
-A,C,log=fgw_barycenters(sizebary,Ys,Cs,ps,lambdas,alpha=0.95)
+A, C, log = fgw_barycenters(sizebary, Ys, Cs, ps, lambdas, alpha=0.95)
 
 #%%
-bary=nx.from_numpy_matrix(sp_to_adjency(C,threshinf=0,threshsup=find_thresh(C,sup=100,step=100)[0]))
+bary = nx.from_numpy_matrix(sp_to_adjency(C, threshinf=0, threshsup=find_thresh(C, sup=100, step=100)[0]))
 for i in range(len(A.ravel())):
-    bary.add_node(i,attr_name=float(A.ravel()[i]))
- 
+    bary.add_node(i, attr_name=float(A.ravel()[i]))
+
 #%%
 pos = nx.kamada_kawai_layout(bary)
-nx.draw(bary,pos=pos,node_color = graph_colors(bary,vmin=-1,vmax=1),with_labels=False)
-plt.suptitle('Barycenter',fontsize=20)
+nx.draw(bary, pos=pos, node_color=graph_colors(bary, vmin=-1, vmax=1), with_labels=False)
+plt.suptitle('Barycenter', fontsize=20)
 plt.show()
-
-
-
-
diff --git a/examples/plot_fgw.py b/examples/plot_fgw.py
index bfa7fb4..ae3c487 100644
--- a/examples/plot_fgw.py
+++ b/examples/plot_fgw.py
@@ -20,132 +20,132 @@ This example illustrates the computation of FGW for 1D measures[18].
 import matplotlib.pyplot as pl
 import numpy as np
 import ot
-from ot.gromov import gromov_wasserstein,fused_gromov_wasserstein
+from ot.gromov import gromov_wasserstein, fused_gromov_wasserstein
 
 #%% parameters
-# We create two 1D random measures 
-n=20
-n2=30
-sig=1
-sig2=0.1
+# We create two 1D random measures
+n = 20
+n2 = 30
+sig = 1
+sig2 = 0.1
 
 np.random.seed(0)
 
-phi=np.arange(n)[:,None]
-xs=phi+sig*np.random.randn(n,1)
-ys=np.vstack((np.ones((n//2,1)),0*np.ones((n//2,1))))+sig2*np.random.randn(n,1)
+phi = np.arange(n)[:, None]
+xs = phi + sig * np.random.randn(n, 1)
+ys = np.vstack((np.ones((n // 2, 1)), 0 * np.ones((n // 2, 1)))) + sig2 * np.random.randn(n, 1)
 
-phi2=np.arange(n2)[:,None]
-xt=phi2+sig*np.random.randn(n2,1)
-yt=np.vstack((np.ones((n2//2,1)),0*np.ones((n2//2,1))))+sig2*np.random.randn(n2,1)
-yt= yt[::-1,:]
+phi2 = np.arange(n2)[:, None]
+xt = phi2 + sig * np.random.randn(n2, 1)
+yt = np.vstack((np.ones((n2 // 2, 1)), 0 * np.ones((n2 // 2, 1)))) + sig2 * np.random.randn(n2, 1)
+yt = yt[::-1, :]
 
-p=ot.unif(n)
-q=ot.unif(n2)
+p = ot.unif(n)
+q = ot.unif(n2)
 
 #%% plot the distributions
 
 pl.close(10)
-pl.figure(10,(7,7))
+pl.figure(10, (7, 7))
 
-pl.subplot(2,1,1)
+pl.subplot(2, 1, 1)
 
-pl.scatter(ys,xs,c=phi,s=70)
-pl.ylabel('Feature value a',fontsize=20)
-pl.title('$\mu=\sum_i \delta_{x_i,a_i}$',fontsize=25, usetex=True, y=1)
+pl.scatter(ys, xs, c=phi, s=70)
+pl.ylabel('Feature value a', fontsize=20)
+pl.title('$\mu=\sum_i \delta_{x_i,a_i}$', fontsize=25, usetex=True, y=1)
 pl.xticks(())
 pl.yticks(())
-pl.subplot(2,1,2)
-pl.scatter(yt,xt,c=phi2,s=70)
-pl.xlabel('coordinates x/y',fontsize=25)
-pl.ylabel('Feature value b',fontsize=20)
-pl.title('$\\nu=\sum_j \delta_{y_j,b_j}$',fontsize=25, usetex=True, y=1)
+pl.subplot(2, 1, 2)
+pl.scatter(yt, xt, c=phi2, s=70)
+pl.xlabel('coordinates x/y', fontsize=25)
+pl.ylabel('Feature value b', fontsize=20)
+pl.title('$\\nu=\sum_j \delta_{y_j,b_j}$', fontsize=25, usetex=True, y=1)
 pl.yticks(())
 pl.tight_layout()
 pl.show()
 
 
 #%% Structure matrices and across-features distance matrix
-C1=ot.dist(xs)
-C2=ot.dist(xt).T
-M=ot.dist(ys,yt)
-w1=ot.unif(C1.shape[0])
-w2=ot.unif(C2.shape[0])
-Got=ot.emd([],[],M)
+C1 = ot.dist(xs)
+C2 = ot.dist(xt).T
+M = ot.dist(ys, yt)
+w1 = ot.unif(C1.shape[0])
+w2 = ot.unif(C2.shape[0])
+Got = ot.emd([], [], M)
 
 #%%
-cmap='Reds'
+cmap = 'Reds'
 pl.close(10)
-pl.figure(10,(5,5))
-fs=15
-l_x=[0,5,10,15]
-l_y=[0,5,10,15,20,25]
+pl.figure(10, (5, 5))
+fs = 15
+l_x = [0, 5, 10, 15]
+l_y = [0, 5, 10, 15, 20, 25]
 gs = pl.GridSpec(5, 5)
 
-ax1=pl.subplot(gs[3:,:2])
+ax1 = pl.subplot(gs[3:, :2])
 
-pl.imshow(C1,cmap=cmap,interpolation='nearest')
-pl.title("$C_1$",fontsize=fs)
-pl.xlabel("$k$",fontsize=fs)
-pl.ylabel("$i$",fontsize=fs)
+pl.imshow(C1, cmap=cmap, interpolation='nearest')
+pl.title("$C_1$", fontsize=fs)
+pl.xlabel("$k$", fontsize=fs)
+pl.ylabel("$i$", fontsize=fs)
 pl.xticks(l_x)
 pl.yticks(l_x)
 
-ax2=pl.subplot(gs[:3,2:])
+ax2 = pl.subplot(gs[:3, 2:])
 
-pl.imshow(C2,cmap=cmap,interpolation='nearest')
-pl.title("$C_2$",fontsize=fs)
-pl.ylabel("$l$",fontsize=fs)
+pl.imshow(C2, cmap=cmap, interpolation='nearest')
+pl.title("$C_2$", fontsize=fs)
+pl.ylabel("$l$", fontsize=fs)
 #pl.ylabel("$l$",fontsize=fs)
 pl.xticks(())
 pl.yticks(l_y)
 ax2.set_aspect('auto')
 
-ax3=pl.subplot(gs[3:,2:],sharex=ax2,sharey=ax1)
-pl.imshow(M,cmap=cmap,interpolation='nearest')
+ax3 = pl.subplot(gs[3:, 2:], sharex=ax2, sharey=ax1)
+pl.imshow(M, cmap=cmap, interpolation='nearest')
 pl.yticks(l_x)
 pl.xticks(l_y)
-pl.ylabel("$i$",fontsize=fs)
-pl.title("$M_{AB}$",fontsize=fs)
-pl.xlabel("$j$",fontsize=fs)
+pl.ylabel("$i$", fontsize=fs)
+pl.title("$M_{AB}$", fontsize=fs)
+pl.xlabel("$j$", fontsize=fs)
 pl.tight_layout()
 ax3.set_aspect('auto')
 pl.show()
 
 
 #%% Computing FGW and GW
-alpha=1e-3
-    
+alpha = 1e-3
+
 ot.tic()
-Gwg,logw=fused_gromov_wasserstein(M,C1,C2,p,q,loss_fun='square_loss',alpha=alpha,verbose=True,log=True)
+Gwg, logw = fused_gromov_wasserstein(M, C1, C2, p, q, loss_fun='square_loss', alpha=alpha, verbose=True, log=True)
 ot.toc()
 
-#%reload_ext WGW 
-Gg,log=gromov_wasserstein(C1,C2,p,q,loss_fun='square_loss',verbose=True,log=True)
-    
+#%reload_ext WGW
+Gg, log = gromov_wasserstein(C1, C2, p, q, loss_fun='square_loss', verbose=True, log=True)
+
 #%% visu OT matrix
-cmap='Blues'
-fs=15
-pl.figure(2,(13,5))
+cmap = 'Blues'
+fs = 15
+pl.figure(2, (13, 5))
 pl.clf()
-pl.subplot(1,3,1)    
-pl.imshow(Got,cmap=cmap,interpolation='nearest')
+pl.subplot(1, 3, 1)
+pl.imshow(Got, cmap=cmap, interpolation='nearest')
 #pl.xlabel("$y$",fontsize=fs)
-pl.ylabel("$i$",fontsize=fs)
+pl.ylabel("$i$", fontsize=fs)
 pl.xticks(())
 
 pl.title('Wasserstein ($M$ only)')
 
-pl.subplot(1,3,2)    
-pl.imshow(Gg,cmap=cmap,interpolation='nearest')
+pl.subplot(1, 3, 2)
+pl.imshow(Gg, cmap=cmap, interpolation='nearest')
 pl.title('Gromov ($C_1,C_2$ only)')
 pl.xticks(())
-pl.subplot(1,3,3)    
-pl.imshow(Gwg,cmap=cmap,interpolation='nearest')
+pl.subplot(1, 3, 3)
+pl.imshow(Gwg, cmap=cmap, interpolation='nearest')
 pl.title('FGW  ($M+C_1,C_2$)')
 
-pl.xlabel("$j$",fontsize=fs)
-pl.ylabel("$i$",fontsize=fs)
+pl.xlabel("$j$", fontsize=fs)
+pl.ylabel("$i$", fontsize=fs)
 
 pl.tight_layout()
-pl.show()
\ No newline at end of file
+pl.show()