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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rename_channels.py	Wed Feb 26 18:09:34 2025 +0000
@@ -0,0 +1,81 @@
+# ------------------------------------------------------------------------------------
+# Stripped down and modified from:
+# https://github.com/ohsu-comp-bio/ashlar/blob/master/pyramid_upgrade.py
+# ------------------------------------------------------------------------------------
+
+import argparse
+import csv
+import xml.etree.ElementTree
+
+from tifffile import tiffcomment
+
+
+def fix_attrib_namespace(elt):
+    """Prefix un-namespaced XML attributes with the tag's namespace."""
+    # This fixes ElementTree's inability to round-trip XML with a default
+    # namespace ("cannot use non-qualified names with default_namespace option"
+    # error). 7-year-old BPO issue here: https://bugs.python.org/issue17088
+    # Code inspired by https://gist.github.com/provegard/1381912 .
+    if elt.tag[0] == "{":
+        uri, _ = elt.tag[1:].rsplit("}", 1)
+        new_attrib = {}
+        for name, value in elt.attrib.items():
+            if name[0] != "{":
+                # For un-namespaced attributes, copy namespace from element.
+                name = f"{{{uri}}}{name}"
+            new_attrib[name] = value
+        elt.attrib = new_attrib
+    for child in elt:
+        fix_attrib_namespace(child)
+
+
+def main(image_fh, marker_file):
+    """
+    Parameters
+    ---------
+    image_fh : str
+        File path to the OME Tiff image.
+    marker_file : str
+        File path to CSV containing marker name information.
+    """
+
+    # parse marker file, create list of new marker names
+    new_channel_names = []
+    with open(marker_file, newline='') as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            new_channel_names.append(row['marker_name'])
+
+    # read OME-XML metadata and parse down to channels
+    xml_ns = {"ome": "http://www.openmicroscopy.org/Schemas/OME/2016-06"}
+    root = xml.etree.ElementTree.fromstring(tiffcomment(image_fh))
+    image = root.find("ome:Image", xml_ns)
+    pixels = image.find("ome:Pixels", xml_ns)
+    channels = pixels.findall("ome:Channel", xml_ns)
+
+    # name channels
+    for channel, name in zip(channels, new_channel_names):
+        channel.attrib["Name"] = name
+
+    # encode new xml and set image metadata
+    fix_attrib_namespace(root)
+    new_ome_xml = xml.etree.ElementTree.tostring(
+        root,
+        encoding='utf-8',
+        xml_declaration=True,
+        default_namespace=xml_ns["ome"])
+
+    tiffcomment(image_fh, comment=new_ome_xml)
+
+    print("Updated OME-TIFF metadata:")
+    print(tiffcomment(image_fh))
+
+
+if __name__ == '__main__':
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--image", dest="image", required=True)
+    aparser.add_argument("-m", "--markers", dest="markers", required=True)
+
+    args = aparser.parse_args()
+
+    main(args.image, args.markers)