Mercurial > repos > imgteam > colocalization_viz

annotate colocalization_viz.py @ 2:c73332d5c3bb draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:01:42 -0500
parents fc85eb253163
children 0f8652663a03
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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
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2 import skimage.color
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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3 from skimage import img_as_uint
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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4 from skimage.exposure import equalize_adapthist
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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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5 import numpy as np
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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6 import argparse
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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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7 import sys
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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9
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c73332d5c3bb "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 1
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10 # TODO make importable by python script
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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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11 def readImg(path):
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 img = skimage.io.imread(path)
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
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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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14 if len(img.shape) > 2:
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 img = skimage.color.rgb2gray(img)
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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16 img = equalize_adapthist(img, clip_limit=0.03)
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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17 img = img_as_uint(img)
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
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18 img = np.reshape(img, [img.shape[0], img.shape[1], 1])
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 return img
9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9ddb11b272ee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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22 parser = argparse.ArgumentParser()
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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23 parser.add_argument('input_file1', type=argparse.FileType('r'), default=sys.stdin, help='input file (red)')
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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24 parser.add_argument('input_file2', type=argparse.FileType('r'), default=sys.stdin, help='input file (green)')
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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25 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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26 args = parser.parse_args()
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
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fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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28 im1 = readImg(args.input_file1.name)
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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29 im2 = readImg(args.input_file2.name)
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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30 res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=-1)
fc85eb253163 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
imgteam
parents: 0
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31 skimage.io.imsave(args.out_file.name, res)