a69fee9d
 David Mayerich
added python scri...
|
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
|
# -*- coding: utf-8 -*-
"""
Created on Thu May 18 15:56:20 2017
@author: david
"""
import numpy as np
import scipy as sp
import scipy.misc
import scipy.ndimage
import matplotlib.pyplot as plt
import os
#calculate a 3D image from a 2D binary mask
def binary(infile, sigma=2):
I = sp.misc.imread(infile).astype(np.bool)
#if the image has more than one channel, just keep the first one
if(I.ndim == 3):
I = I[:, :, 0]
L = []
while np.count_nonzero(I) != 0:
L.append(I)
I = sp.ndimage.binary_erosion(I)
#create a 3D image representing the new stack
S = np.zeros( (I.shape[0], I.shape[1], len(L) * 2 - 1) )
#for each image in the list
for i in range(0, len(L)):
if(i == 0):
S[:, :, len(L) - 1] = L[0]
else:
S[:, :, len(L) - 1 + i] = L[i]
S[:, :, len(L) - 1 - i] = L[i]
S = sp.ndimage.filters.gaussian_filter(S, sigma)
return S
#generate a 3D image stack from a 2D binary mask
def binary_stack(infile, outdir, sigma=2):
outfile_base = os.path.basename(infile)
outfile_prefix, outfile_ext = os.path.splitext(outfile_base)
S = binary(infile, sigma)
zcount = len(str(S.shape[2]))
for f in range(0, S.shape[2]):
fname = outdir + "/" + outfile_prefix + str(f).zfill(zcount) + outfile_ext
sp.misc.imsave(fname, S[:, :, f])
|
