Mercurial > repos > thomaswollmann > colocalization_viz
diff colocalization_viz.py @ 0:9174e8eaa1e1 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
| author | thomaswollmann |
|---|---|
| date | Wed, 16 Jan 2019 15:33:42 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/colocalization_viz.py Wed Jan 16 15:33:42 2019 -0500 @@ -0,0 +1,25 @@ +import skimage.io +import skimage.color +import numpy as np +import os +import sys +import warnings + +#TODO make importable by python script + +args = sys.argv + +def readImg(path): + img = skimage.io.imread(path) + if len(img.shape) > 2: + img = skimage.color.rgb2gray(img) + img = np.expand_dims(img > 0, 3) + return img + +im1 = readImg(args[1]) +im2 = readImg(args[2]) +res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=2) * 1.0 + +with warnings.catch_warnings(): + warnings.simplefilter("ignore") + skimage.io.imsave(args[3], res)