In [1]:

    

import h5py
import numpy as np
import skimage as sk
#print sk.__version__
from skimage import io
from matplotlib import pyplot as plt


    

In [2]:

    

from skimage import filters
from skimage import feature
from skimage import io
from scipy import ndimage as nd
from scipy import misc


    

In [3]:

    

from subprocess import check_output
print(check_output(["ls", "../dataset"]).decode("utf8"))


    

    




Cy3.tif
DAPI.tif
LowRes_13434_overlapping_pairs.h5
overlapping_chromosomes_examples.h5

In [3]:

    

h5f = h5py.File('overlapping_pairs.h5','r')
pairs = h5f['dataset_1'][:]
h5f.close()


    

In [4]:

    

pairs.shape
pairs[0,:,:,0].dtype
pairs[0,:,:,0].max()


    

    
Out[4]:





3040

In [5]:

    

subset = pairs[::2,:,:,:]
subset.shape


    

    
Out[5]:





(1427, 190, 189, 2)

In [ ]:

    




    

In [11]:

    

h5f = h5py.File('overlapping_subset_pairs.h5', 'w')
h5f.create_dataset('dataset_1', data= subset)
h5f.close()


    

In [6]:

    

h5f = h5py.File('overlapping_subset_pairs.h5','r')
subset = h5f['dataset_1'][:]
h5f.close()
grey = subset[10,:,:,0]
mask = subset[10,:,:,1]
%matplotlib inline
plt.subplot(121)
plt.imshow(grey)
plt.subplot(122)
plt.imshow(mask)


    

    
Out[6]:





<matplotlib.image.AxesImage at 0x7f7cf035fb90>






    

In [ ]:

    

def toUint8(array4):
    a = array4/16
    a.astype(np.int8)


    

In [10]:

    

sub25 = np.copy(subset[0:24,:,:,:])
print sub25.shape, sub25.dtype


    

    




(24, 190, 189, 2) int64

In [14]:

    

greys = pairs[:,:,:,0]
masks = pairs[:,:,:,1]
g_ex1 = greys[200,:,:]
m_ex1 = masks[200,:,:]


    

In [15]:

    

%matplotlib inline
plt.subplot(121)
plt.imshow(grey)
plt.subplot(122)
plt.imshow(mask)


    

    
Out[15]:





<matplotlib.image.AxesImage at 0x7fb599bfbd90>






    

In [17]:

    

np.apply_along_axis(
    func1d=lambda x: subset[:,:,:,0]/16,
    axis=1,
    arr=dat[:2,0])


    

    




---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-17-2ca8953dc5d4> in <module>()
----> 1 import mahotas as mh

ImportError: No module named mahotas

In [96]:

    

gabs = filters.gabor(g_ex1, 0.2)
images = []
factors = [2.0, 1.5, 1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1]
for i,k in enumerate(factors):
    images.append(misc.imresize(g_ex1, k))


    

In [101]:

    

filters.gaussian(im, sigma=3)
from generator_tools import ResizeImages
plt.figure(figsize=(10,10))
for i,im in enumerate(images):
    plt.subplot(3,4,1+i, xticks=[],yticks=[])
    #plt.imshow(im, interpolation = 'nearest')
    plt.title(str(factors[i]))
    plt.imshow(filters.edges.laplace(im, ksize=3))


    

In [ ]: