sorting points to form a continuous line

Question

I have a list of (x,y)-coordinates that represent a line skeleton. The list is obtained directly from a binary image:

import numpy as np    
list=np.where(im         


        

Answer 1

I had the exact same problem. If you have two arrays of scattered x and y values that are not too curvy, then you can transform the points into PCA space, sort them in PCA space, and then transform them back. (I've also added in some bonus smoothing functionality).

import numpy as np
from scipy.signal import savgol_filter
from sklearn.decomposition import PCA

def XYclean(x,y): 

    xy = np.concatenate((x.reshape(-1,1), y.reshape(-1,1)), axis=1)     

    # make PCA object
    pca = PCA(2)
    # fit on data
    pca.fit(xy)
    
    #transform into pca space   
    xypca = pca.transform(xy) 
    newx = xypca[:,0]
    newy = xypca[:,1]

    #sort
    indexSort = np.argsort(x)
    newx = newx[indexSort]
    newy = newy[indexSort]

    #add some more points (optional)
    f = interpolate.interp1d(newx, newy, kind='linear')        
    newX=np.linspace(np.min(newx), np.max(newx), 100)
    newY = f(newX)            

    #smooth with a filter (optional)
    window = 43
    newY = savgol_filter(newY, window, 2)

    #return back to old coordinates
    xyclean = pca.inverse_transform(np.concatenate((newX.reshape(-1,1), newY.reshape(-1,1)), axis=1) )
    xc=xyclean[:,0]
    yc = xyclean[:,1]

    return xc, yc