In [1]:

    

# A demo for segmentation on hcg62 by pycode levelset


    

In [2]:

    

import numpy as np
import os
import time
from astropy.io import fits


    

In [3]:

    

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
%matplotlib inline
from matplotlib import gridspec


    

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import utils
from levelset import LevelSet


    

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# load image and cut
filepath = "../matcode/data/hcg62.fits"
with fits.open(filepath) as h:
    img = h[0].data
    
# cut
img = img[374-100:375+100,374-100:375+100]
plt.imshow(img)


    

    
Out[5]:





<matplotlib.image.AxesImage at 0x7f781f87f518>






    

In [6]:

    

# Preprocessing
img_um = utils.getUnsharpMasking(img,sigma1=5, sigma2=20,kershape=(50,50))
plt.imshow(img_um)


    

    
Out[6]:





<matplotlib.image.AxesImage at 0x7f77dbc67630>






    

In [7]:

    

# Init the levelset function
mu = 0.1
nu = 0.0
lambda1 = 1.0
lambda2 = 1.0
niter = 200
phi_total = 1e-3
dt = 0.5
ls = LevelSet(imgshape=img.shape, mu=mu, nu=nu, 
              lambda1=lambda1, lambda2=lambda2, dt=dt)


    

In [8]:

    

# Do segmentation
ls.calcSegmentation(img_um, niter=niter, phi_total=1e-3,
                    normflag=True, logflag=False)


    

    




[2018-01-15: 17:15:53] Iter: 0	 PhiDiffNorm: 56891.583
[2018-01-15: 17:15:58] Iter: 5	 PhiDiffNorm: 1351.516
[2018-01-15: 17:16:02] Iter: 10	 PhiDiffNorm: 1507.421
[2018-01-15: 17:16:07] Iter: 15	 PhiDiffNorm: 1707.004
[2018-01-15: 17:16:12] Iter: 20	 PhiDiffNorm: 1974.204
[2018-01-15: 17:16:16] Iter: 25	 PhiDiffNorm: 2356.481
[2018-01-15: 17:16:21] Iter: 30	 PhiDiffNorm: 2966.774
[2018-01-15: 17:16:26] Iter: 35	 PhiDiffNorm: 4181.412
[2018-01-15: 17:16:31] Iter: 40	 PhiDiffNorm: 8990.471
[2018-01-15: 17:16:35] Iter: 45	 PhiDiffNorm: 51978.567
[2018-01-15: 17:16:40] Iter: 50	 PhiDiffNorm: 13.801
[2018-01-15: 17:16:45] Iter: 55	 PhiDiffNorm: 11.353
[2018-01-15: 17:16:49] Iter: 60	 PhiDiffNorm: 10.417
[2018-01-15: 17:16:54] Iter: 65	 PhiDiffNorm: 9.973
[2018-01-15: 17:16:59] Iter: 70	 PhiDiffNorm: 9.793
[2018-01-15: 17:17:04] Iter: 75	 PhiDiffNorm: 9.813
[2018-01-15: 17:17:08] Iter: 80	 PhiDiffNorm: 10.054
[2018-01-15: 17:17:13] Iter: 85	 PhiDiffNorm: 10.647
[2018-01-15: 17:17:18] Iter: 90	 PhiDiffNorm: 12.107
[2018-01-15: 17:17:22] Iter: 95	 PhiDiffNorm: 17.953
[2018-01-15: 17:17:27] Iter: 100	 PhiDiffNorm: 1475.629
[2018-01-15: 17:17:32] Iter: 105	 PhiDiffNorm: 1755.340
[2018-01-15: 17:17:36] Iter: 110	 PhiDiffNorm: 43.169
[2018-01-15: 17:17:41] Iter: 115	 PhiDiffNorm: 41.655
[2018-01-15: 17:17:46] Iter: 120	 PhiDiffNorm: 42.155
[2018-01-15: 17:17:51] Iter: 125	 PhiDiffNorm: 43.452
[2018-01-15: 17:17:55] Iter: 130	 PhiDiffNorm: 45.322
[2018-01-15: 17:18:00] Iter: 135	 PhiDiffNorm: 47.739
[2018-01-15: 17:18:05] Iter: 140	 PhiDiffNorm: 50.758
[2018-01-15: 17:18:09] Iter: 145	 PhiDiffNorm: 54.502
[2018-01-15: 17:18:14] Iter: 150	 PhiDiffNorm: 59.175
[2018-01-15: 17:18:19] Iter: 155	 PhiDiffNorm: 65.106
[2018-01-15: 17:18:23] Iter: 160	 PhiDiffNorm: 72.852
[2018-01-15: 17:18:28] Iter: 165	 PhiDiffNorm: 83.431
[2018-01-15: 17:18:33] Iter: 170	 PhiDiffNorm: 99.063
[2018-01-15: 17:18:38] Iter: 175	 PhiDiffNorm: 126.818
[2018-01-15: 17:18:42] Iter: 180	 PhiDiffNorm: 468.146
[2018-01-15: 17:18:47] Iter: 185	 PhiDiffNorm: 121.178
[2018-01-15: 17:18:52] Iter: 190	 PhiDiffNorm: 0.307
[2018-01-15: 17:18:57] Iter: 195	 PhiDiffNorm: 0.008

In [9]:

    

# Display result
ls.drawResult(img_um)


    

    




/home/mzx/.local/lib/python3.5/site-packages/matplotlib/contour.py:967: UserWarning: The following kwargs were not used by contour: 'level'
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