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Update calculate_adj.py #81

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Update calculate_adj.py #81

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10 changes: 5 additions & 5 deletions SpaGCN_package/SpaGCN/calculate_adj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def calculate_adj_matrix(x, y, x_pixel=None, y_pixel=None, image=None, beta=49,
if histology:
assert (x_pixel is not None) & (x_pixel is not None) & (image is not None)
assert (len(x)==len(x_pixel)) & (len(y)==len(y_pixel))
print("Calculateing adj matrix using histology image...")
print("Calculating adj matrix using histology image...")
#beta to control the range of neighbourhood when calculate grey vale for one spot
#alpha to control the color scale
beta_half=round(beta/2)
Expand All @@ -73,7 +73,7 @@ def calculate_adj_matrix(x, y, x_pixel=None, y_pixel=None, image=None, beta=49,
print("Var of x,y,z = ", np.var(x),np.var(y),np.var(z))
X=np.array([x, y, z]).T.astype(np.float32)
else:
print("Calculateing adj matrix using xy only...")
print("Calculating adj matrix using xy only...")
X=np.array([x, y]).T.astype(np.float32)
return pairwise_distance(X)

Expand All @@ -84,7 +84,7 @@ def calculate_adj_matrix(x, y, x_pixel=None, y_pixel=None, image=None, beta=49,
if histology:
assert (x_pixel is not None) & (x_pixel is not None) & (image is not None)
assert (len(x)==len(x_pixel)) & (len(y)==len(y_pixel))
print("Calculateing adj matrix using histology image...")
print("Calculating adj matrix using histology image...")
#beta to control the range of neighbourhood when calculate grey vale for one spot
#alpha to control the color scale
beta_half=round(beta/2)
Expand Down Expand Up @@ -116,12 +116,12 @@ def calculate_adj_matrix(x, y, x_pixel=None, y_pixel=None, image=None, beta=49,
x1,y1,z1,x2,y2,z2=x[i],y[i],z[i],x[j],y[j],z[j]
adj[i][j]=distance((x1,y1,z1),(x2,y2,z2))
else:
print("Calculateing adj matrix using xy only...")
print("Calculating adj matrix using xy only...")
for i in range(len(x)):
if i%50==0:
print("Calculating spot", i)
for j in range(len(x)):
x1,y1,x2,y2=x[i],y[i],x[j],y[j]
adj[i][j]=distance((x1,y1),(x2,y2))
return adj
"""
"""