In [1]:

    

import os


    

In [2]:

    

import numpy as np


    

In [3]:

    

path='/home/sophie/Desktop/10007ss2/'


    

In [4]:

    

for fn in os.listdir(path):
    fn2=fn.split('-')
    fnnum=fn2[1].split('_')
    i=int(fnnum[0])
    fnnew=fn2[0]+'-'+ str(i).zfill(5) + '_'+fnnum[1]
    os.rename(path+"/"+fn, path+"/"+fnnew)


    

    




---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-4-65d60163e092> in <module>()
----> 1 for fn in os.listdir(path):
      2     fn2=fn.split('-')
      3     fnnum=fn2[1].split('_')
      4     i=int(fnnum[0])
      5     fnnew=fn2[0]+'-'+ str(i).zfill(5) + '_'+fnnum[1]

OSError: [Errno 2] No such file or directory: '/home/sophie/Desktop/10007ss2/'

In [4]:

    

data = tsc.loadImages(path, inputFormat='tif')


    

In [5]:

    

data.dims


    

    
Out[5]:





Dimensions(values=[(0, 0, 0), (159, 209, 41)], n=3)

In [6]:

    

%matplotlib inline
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_context('notebook')
from thunder import Colorize
image = Colorize.image


    

In [7]:

    

N = int(data.nrecords/2)


    

In [8]:

    

N


    

    
Out[8]:





6181

In [9]:

    

imgN = tsc.loadImages(path, inputFormat='tif', startIdx=N, stopIdx=N+1)


    

In [10]:

    

img=thunder.Images.collectValuesAsArray(imgN)


    

In [11]:

    

img.shape


    

    
Out[11]:





(1, 52, 105, 40)

In [13]:

    

image(img[0,:,:,20])


    

In [14]:

    

import Tkinter
import PIL
from PIL import Image, ImageTk, ImageOps
from sys import argv
import numpy as np


    

In [15]:

    

window = Tkinter.Tk(className="bla")


    

In [16]:

    

img2=np.mean(img,3)


    

In [17]:

    

img2=np.squeeze(img2*255/np.max(img2))


    

In [18]:

    

img2.shape


    

    
Out[18]:





(212, 210)

In [19]:

    

imgim=Image.fromarray(img2)


    

In [20]:

    

print imgim.format, imgim.size, imgim.mode


    

    




None (210, 212) F

In [21]:

    

imgim=imgim.convert('L')


    

In [22]:

    

imgim=ImageOps.autocontrast(imgim)


    

In [23]:

    

canvas = Tkinter.Canvas(window, width=img2.shape[1], height=img2.shape[0])


    

In [24]:

    

canvas.pack()


    

In [25]:

    

image_tk = ImageTk.PhotoImage(imgim)


    

In [26]:

    

canvas.create_image(img2.shape[1]/2, img2.shape[0]/2, image=image_tk)


    

    
Out[26]:





1

In [27]:

    

Pcrop=[0,0,0,0]


    

In [28]:

    

def callback(event):
    global Pcrop
    if (Pcrop[1]==0):
        Pcrop[0] = event.x
        Pcrop[1] = event.y
    else:
        Pcrop[2] = event.x
        Pcrop[3] = event.y
        
    print "clicked at: ", event.x, event.y

    
def quit(root):
    root.destroy()

root = Tkinter.Tk()

canvas.bind("<Button-1>", callback)
Tkinter.Button(root, text="Q", command=lambda root=root:quit(root)).pack()
    

root.mainloop()


    

    




clicked at:  16 51
clicked at:  161 153

In [207]:

    

Pcrop


    

    
Out[207]:





[16, 51, 161, 153]

In [238]:

    

S=img.shape


    

In [239]:

    

S


    

    
Out[239]:





(1, 212, 210, 40)

In [8]:

    

datac=data.crop((Pcrop[1],Pcrop[0],0),(Pcrop[3],Pcrop[2],S[3]))


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-8-a84a34ae5cf0> in <module>()
----> 1 datac=data.crop((Pcrop[1],Pcrop[0],0),(Pcrop[3],Pcrop[2],S[3]))

NameError: name 'Pcrop' is not defined

In [241]:

    

datac.dims


    

    
Out[241]:





Dimensions(values=[(0, 0, 0), (101, 144, 39)], n=3)

In [242]:

    

mg = datac[N]


    

In [243]:

    

mg.shape


    

    
Out[243]:





(102, 145, 40)

In [244]:

    

from thunder import Colorize

image = Colorize.image


    

In [245]:

    

image(mg[:,:,20])


    

In [7]:

    

D=thunder.Images.collectValuesAsArray(data)


    

In [8]:

    

S=D.shape


    

In [9]:

    

S


    

    
Out[9]:





(836, 160, 210, 42)

In [10]:

    

M=np.mean(np.mean(np.mean(D,1),1),1)


    

In [11]:

    

plt.plot(np.squeeze(M))
plt.show()


    

In [12]:

    

Mav=M.mean()


    

In [13]:

    

liston=[i for i in range(len(M)) if M[i]>Mav*0.7]


    

In [14]:

    

liston2=[liston[i] for i in range(1,(len(liston)-1))]


    

In [15]:

    

len(liston)


    

    
Out[15]:





811

In [16]:

    

from nifti import NiftiImage


    

In [17]:

    

D2=D[liston2[:],:,:,:]


    

In [18]:

    

D2.shape


    

    
Out[18]:





(809, 160, 210, 42)

In [19]:

    

D3=np.transpose(D2,(0,3,1,2))


    

In [20]:

    

nim = NiftiImage(D3)


    

In [21]:

    

D3.shape


    

    
Out[21]:





(809, 42, 160, 210)

In [22]:

    

print nim.header['dim']


    

    




[4, 210, 160, 42, 809, 1, 1, 1]

In [23]:

    

nim.save('/home/sophie/Desktop/10007ss2.nii.gz')


    

    




/usr/lib/pymodules/python2.7/nifti/image.py:231: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  return (not self._data == None)

In [ ]: