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annotate binary2label.py @ 5:7f8102bdbfa1 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
author imgteam
date Mon, 12 May 2025 08:15:44 +0000
parents 9bb446db4a1e
children
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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3 import giatools
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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4 import scipy.ndimage as ndi
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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5 import tifffile
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9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
8 # Parse CLI parameters
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9 parser = argparse.ArgumentParser()
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
10 parser.add_argument('input', type=str, help='input file')
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
11 parser.add_argument('output', type=str, help='output file (TIFF)')
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 args = parser.parse_args()
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9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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14 # Read the input image with the original axes
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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15 img = giatools.Image.read(args.input)
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
16 img = img.normalize_axes_like(
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
17 img.original_axes,
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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18 )
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
20 # Make sure the image is truly binary
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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21 img_arr_bin = (img.data > 0)
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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23 # Perform the labeling
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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24 img.data = ndi.label(img_arr_bin)[0]
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
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7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
26 # Write the result image (same axes as input image)
7f8102bdbfa1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents: 3
diff changeset
27 tifffile.imwrite(args.output, img.data, metadata=dict(axes=img.axes))