Mercurial > repos > imgteam > colocalization_viz

annotate colocalization_viz.py @ 0:9ddb11b272ee draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:32:01 -0500
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children fc85eb253163
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import skimage.io
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import skimage.color
9ddb11b272ee 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
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
4 import os
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import sys
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9ddb11b272ee 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
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 args = sys.argv
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 def readImg(path):
9ddb11b272ee 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)
9ddb11b272ee 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:
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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15 img = skimage.color.rgb2gray(img)
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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16 img = np.expand_dims(img > 0, 3)
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 return img
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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19 im1 = readImg(args[1])
9ddb11b272ee 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])
9ddb11b272ee 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
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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23 with warnings.catch_warnings():
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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24 warnings.simplefilter("ignore")
9ddb11b272ee 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)