mask = np.ones(X.shape[0], dtype=bool)
X[mask].shape
mask.shape
mask[indices[0]] = False
mask.shape
X[mask].shape
X[~mask].shape
(678, 2)
(678,)
(678,)
(675, 2)
(3, 2)

from sklearn.neighbors import NearestNeighbors
nbrs = NearestNeighbors(10).fit(X)
_,indices = nbrs.kneighbors(X)
mask = np.ones(X.shape[0], dtype=bool)
mask[indices[0]] = False
plt.scatter(X[mask][:,0],X[mask][:,1],c='g')
plt.scatter(X[~mask][:,0],X[~mask][:,1],c='r')

mask = np.ones(a.shape,dtype=bool) #np.ones_like(a,dtype=bool)
mask[indices] = False
a[~mask] = 999
a[mask] = 888
#############
np.where(mask, 888, 999)