In [2]:

    

%run ../common.ipynb
from __future__ import division
image = imread('../MP.tiff')
imshow(image)
image.shape


    

    




Populating the interactive namespace from numpy and matplotlib






    




WARNING: pylab import has clobbered these variables: ['size']
`%matplotlib` prevents importing * from pylab and numpy






    
Out[2]:





(2111, 2198)






    

In [29]:

    

simg = smooth(image, size=40)
imshow(simg)


    

    
Out[29]:





(<matplotlib.figure.Figure at 0x143046690>,
 <matplotlib.axes._subplots.AxesSubplot at 0x149e71150>,
 <matplotlib.image.AxesImage at 0x146775dd0>)






    

In [30]:

    

for i in range(10,15):
    tmp = np.copy(image)
    tmp[simg<i] = 255
    imshow(tmp)


    

In [57]:

    

# make a circle mask
r = 30
size = 2*r
x,y = np.meshgrid(range(size), range(size))
R = np.sqrt((x-r)**2+(y-r)**2)
mask = np.ones((size,size), bool)
mask[R>r] = 0
imshow(mask)
# copy image (values above 30)
img = np.zeros(image.shape, dtype=np.uint8)
img[image>30]=image[image>30]
# dilation
dimg = ndimage.binary_dilation(img, structure=mask)
imshow(dimg)


    

    
Out[57]:





(<matplotlib.figure.Figure at 0x142fc7910>,
 <matplotlib.axes._subplots.AxesSubplot at 0x142fc7150>,
 <matplotlib.image.AxesImage at 0x14300e550>)






    













    

In [59]:

    

eimg = ndimage.binary_erosion(img, structure=mask)
imshow(eimg)
deimg = ndimage.binary_erosion(dimg, structure=mask)
imshow(deimg)


    

    
Out[59]:





(<matplotlib.figure.Figure at 0x1447ad2d0>,
 <matplotlib.axes._subplots.AxesSubplot at 0x1447ad750>,
 <matplotlib.image.AxesImage at 0x1447d4310>)