codebase / stimlib

Commit 2119be83b31be62fb4ff0d32cbd5c2d019bec689

Authored by David Mayerich
1 parent a296b833

updated libraries for imagestack and the muve alignment script

Showing 2 changed files with 13 additions and 16 deletions   Show diff stats
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python/imagestack.py
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1 1 import glob
2   -import imageio
3 2 import numpy
4 3 import progressbar
  4 +import skimage.io
5 5 import skimage.transform
6 6 import os
7 7  
... ... @@ -13,7 +13,7 @@ def load(fmask, dtype=numpy.float32):
13 13 return
14 14  
15 15 #load the first file
16   - I = imageio.imread(F[0])
  16 + I = skimage.io.imread(F[0])
17 17  
18 18 #generate the image stack
19 19 if I.ndim == 3:
... ... @@ -24,7 +24,7 @@ def load(fmask, dtype=numpy.float32):
24 24 bar = progressbar.ProgressBar(max_value=len(F))
25 25  
26 26 for i in range(0, len(F)):
27   - I = imageio.imread(F[i])
  27 + I = skimage.io.imread(F[i])
28 28 S[i, ...] = I
29 29 bar.update(i+1)
30 30  
... ... @@ -41,7 +41,7 @@ def save(I, fname, extension = "bmp"):
41 41 bar = progressbar.ProgressBar(max_value=I.shape[0])
42 42 #save the output files
43 43 for i in range(0, I.shape[0]):
44   - imageio.imwrite(fname + "%03d" % i + "." + extension, I[i, ...])
  44 + skimage.io.imsave(fname + "%03d" % i + "." + extension, I[i, ...])
45 45 bar.update(i+1)
46 46  
47 47 #rescale a stack of images along X and Y by an integer value n and save to directory dest
... ... @@ -59,12 +59,12 @@ def resize(fmask, dest, n, outformat=None):
59 59 for i in range(0, len(F)):
60 60  
61 61 #load the file to memory
62   - I = imageio.imread(F[i])
  62 + I = skimage.io.imread(F[i])
63 63 R = skimage.transform.downscale_local_mean(I, (n, n))
64 64 if outformat is None:
65   - imageio.imwrite(dest+"/"+os.path.basename(F[i]), R)
  65 + skimage.io.imwrite(dest+"/"+os.path.basename(F[i]), R)
66 66 else:
67   - imageio.imwrite(dest+"/"+os.path.basename(F[i]).split('.')[0] + "." + outformat, R)
  67 + skimage.io.imwrite(dest+"/"+os.path.basename(F[i]).split('.')[0] + "." + outformat, R)
68 68 bar.update(i+1)
69 69  
70 70  
71 71 \ No newline at end of file
... ...
python/muve-align.py
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... ... @@ -12,6 +12,7 @@ import cv2
12 12 import progressbar
13 13 import scipy.ndimage
14 14 import sys
  15 +import os
15 16  
16 17  
17 18 def press(event):
... ... @@ -95,22 +96,18 @@ def align(A, B, max_power=5):
95 96 #warp_matrix[0, 2] = 0
96 97 # return warp_matrix
97 98  
98   -if len(sys.argv) < 3:
99   - print("usage: muve-align input_mask output_directory")
100   - print("ex: muve-align *.bmp ./aligned")
101   - return
102   -
103   -fmask = sys.argv[1]
104   -out_dir = sys.argv[2]
  99 +fmask = "Z:/jack/TinkParaffinLung0.005S/*.png"
  100 +out_dir = "Z:/jack/TinkParaffinLung0.005S/aligned"
105 101  
106 102 if not os.path.isdir(out_dir):
107 103 os.mkdir(out_dir)
108 104  
109 105 #read the image stack for alignment
110 106 print("Loading image stack...")
111   -S = imagestack.load(fmask, dtype=numpy.float32)
  107 +S = imagestack.load(fmask, dtype=numpy.uint8)
  108 +
112 109 #convert to grayscale
113   -G = imagestack.rgb2gray(S)
  110 +G = imagestack.rgb2gray(S.astype(numpy.float32))
114 111  
115 112 # Define the motion model
116 113 warp_mode = cv2.MOTION_TRANSLATION
... ...