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

planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit d1f9d43d20432cc958e340271ba63c85a17ff338

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)