Mercurial > repos > imgteam > imagej2_bunwarpj_compose_elastic

annotate imagej2_create_image_jython_script.py @ 1:423400b3c47f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:47:44 +0000
parents 6840ce593a91
children 7121957d0bbf
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6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
1 import sys
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423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
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6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
3 from ij import IJ
6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
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6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
5 # Fiji Jython interpreter implements Python 2.5 which does not
6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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6 # provide support for argparse.
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423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
7 title = sys.argv[-6]
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
8 width = int(sys.argv[-5])
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
9 height = int(sys.argv[-4])
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
10 depth = int(sys.argv[-3])
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
11 type = sys.argv[-2].replace('_', ' ')
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
12 tmp_image_path = sys.argv[-1]
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6840ce593a91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
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diff changeset
13
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423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
14 imp = IJ.newImage(title, type, width, height, depth)
423400b3c47f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
imgteam
parents: 0
diff changeset
15 IJ.save(imp, "%s" % tmp_image_path)