Mercurial > repos > imgteam > colocalization_viz

annotate colocalization_viz.py @ 0:dd3ffe3141ae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:14:27 -0500
parents
children 9d740d639013
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import skimage.io
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import skimage.color
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
3 import numpy as np
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
4 import os
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import sys
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
7
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8 #TODO make importable by python script
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 args = sys.argv
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 def readImg(path):
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13 img = skimage.io.imread(path)
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 if len(img.shape) > 2:
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
15 img = skimage.color.rgb2gray(img)
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16 img = np.expand_dims(img > 0, 3)
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 return img
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 im1 = readImg(args[1])
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
20 im2 = readImg(args[2])
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
21 res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=2) * 1.0
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
22
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
23 with warnings.catch_warnings():
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 warnings.simplefilter("ignore")
dd3ffe3141ae planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
25 skimage.io.imsave(args[3], res)