Mercurial > repos > perssond > ashlar

comparison rename_channels.py @ 4:0b8423c7ee3e draft default tip

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planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit d1f9d43d20432cc958e340271ba63c85a17ff338
author goeckslab
date Wed, 26 Feb 2025 18:09:34 +0000
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3:ef68bc2a4dbc 4:0b8423c7ee3e
1 # ------------------------------------------------------------------------------------
2 # Stripped down and modified from:
3 # https://github.com/ohsu-comp-bio/ashlar/blob/master/pyramid_upgrade.py
4 # ------------------------------------------------------------------------------------
5
6 import argparse
7 import csv
8 import xml.etree.ElementTree
9
10 from tifffile import tiffcomment
11
12
13 def fix_attrib_namespace(elt):
14 """Prefix un-namespaced XML attributes with the tag's namespace."""
15 # This fixes ElementTree's inability to round-trip XML with a default
16 # namespace ("cannot use non-qualified names with default_namespace option"
17 # error). 7-year-old BPO issue here: https://bugs.python.org/issue17088
18 # Code inspired by https://gist.github.com/provegard/1381912 .
19 if elt.tag[0] == "{":
20 uri, _ = elt.tag[1:].rsplit("}", 1)
21 new_attrib = {}
22 for name, value in elt.attrib.items():
23 if name[0] != "{":
24 # For un-namespaced attributes, copy namespace from element.
25 name = f"{{{uri}}}{name}"
26 new_attrib[name] = value
27 elt.attrib = new_attrib
28 for child in elt:
29 fix_attrib_namespace(child)
30
31
32 def main(image_fh, marker_file):
33 """
34 Parameters
35 ---------
36 image_fh : str
37 File path to the OME Tiff image.
38 marker_file : str
39 File path to CSV containing marker name information.
40 """
41
42 # parse marker file, create list of new marker names
43 new_channel_names = []
44 with open(marker_file, newline='') as csvfile:
45 reader = csv.DictReader(csvfile)
46 for row in reader:
47 new_channel_names.append(row['marker_name'])
48
49 # read OME-XML metadata and parse down to channels
50 xml_ns = {"ome": "http://www.openmicroscopy.org/Schemas/OME/2016-06"}
51 root = xml.etree.ElementTree.fromstring(tiffcomment(image_fh))
52 image = root.find("ome:Image", xml_ns)
53 pixels = image.find("ome:Pixels", xml_ns)
54 channels = pixels.findall("ome:Channel", xml_ns)
55
56 # name channels
57 for channel, name in zip(channels, new_channel_names):
58 channel.attrib["Name"] = name
59
60 # encode new xml and set image metadata
61 fix_attrib_namespace(root)
62 new_ome_xml = xml.etree.ElementTree.tostring(
63 root,
64 encoding='utf-8',
65 xml_declaration=True,
66 default_namespace=xml_ns["ome"])
67
68 tiffcomment(image_fh, comment=new_ome_xml)
69
70 print("Updated OME-TIFF metadata:")
71 print(tiffcomment(image_fh))
72
73
74 if __name__ == '__main__':
75 aparser = argparse.ArgumentParser()
76 aparser.add_argument("-i", "--image", dest="image", required=True)
77 aparser.add_argument("-m", "--markers", dest="markers", required=True)
78
79 args = aparser.parse_args()
80
81 main(args.image, args.markers)