Rename ome zarr images

scripts/zarr/rename_zarr_images.py

@@ -0,0 +1,124 @@
+
+import argparse
+import os
+import sys
+from omero.cli import cli_login
+from omero.gateway import BlitzGateway
+
+import xml.etree.ElementTree as ET
+
+def rename_images(conn, fileset_id, args):
+
+    fileset = conn.getObject("Fileset", fileset_id)
+
+    if args.report:
+        print("\nFileset:", fileset.id)
+
+    xml_file = None
+    for file in fileset.listFiles():
+        print(file.id, file.path, file.name)
+        if file.name == "METADATA.ome.xml":
+            xml_file = file
+            break
+    if xml_file is None:
+        print("METADATA.ome.xml not found")
+        return
+
+    # serverExceptionClass = ome.conditions.SecurityViolation
+    # message = Download is restricted for ome.model.core.OriginalFile:Id_64567059
+    # xml_chunks = list(xml_file.getFileInChunks())
+    # xml_text = xml_chunks.join(b"").decode("utf-8")
+    # print(xml_text)
+
+    # TODO: Open file directly from "ManagedRepository"
+    # with open("/Users/wmoore/Desktop/IDR/Volkava/METADATA.ome.xml") as f:
+    #     xml_text = f.read()
+    #     print(xml_text)
+
+    #     root = ET.fromstring(xml_text)
+    #     image_names = []
+    #     for child in root:
+    #         # In this case, images have empty names!
+    #         print(child.tag, child.attrib)
+
+
+    # Just use the path/to/image_name.zarr/OME/METADATA.ome.xml to get image_name
+    print("xml_file.path:", xml_file.path)
+    name_path = os.path.join(xml_file.path, xml_file.name)
+    img_name = os.path.basename(name_path.replace("/OME/METADATA.ome.xml", ""))
+    img_name = img_name.replace(".zarr", "")
+    print("img_name:", img_name)
+
+    for image in fileset.copyImages():
+        img_series = image.name.split(" [")[-1]
+        if args.report:
+            print("Image:", image.id, image.name)
+        new_name = f"{img_name} [{img_series}"
+        if args.report:
+            print("  New name:", new_name)
+        if not args.dry_run:
+            image.setName(new_name)
+            image.save()
+
+
+def get_object(conn, obj_string):
+    for dtype in ["Screen", "Plate", "Image", "Fileset", "Dataset"]:
+        if obj_string.startswith(dtype):
+            obj_id = int(obj_string.replace(dtype + ":", ""))
+            obj = conn.getObject(dtype, obj_id)
+            if obj is None:
+                print(obj_string, "not found!")
+            return obj
+
+
+def get_fileset_id(conn, obj_string):
+    """obj_string is Image:123 or Fileset:123 or Plate:123"""
+
+    if obj_string.startswith("Fileset:"):
+        return int(obj_string.replace("Fileset:", ""))
+
+    obj = get_object(conn, obj_string)
+    if obj_string.startswith("Image:"):
+        return obj.fileset.id.val
+    if obj_string.startswith("Plate:"):
+        well = list(obj.listChildren())[0]
+        image = list(well.listChildren())[0].getImage()
+        return image.fileset.id.val
+
+
+def main(argv):
+    """
+    We go through all Filesets under the top-level Object, and load the OME/METADATA.ome.xml
+    for each. This is used to rename the images in the Fileset.
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument('object', help='Object:ID where Object is Screen, Plate, Dataset, Image, Fileset')
+    parser.add_argument("--report", action="store_true", help="Print logs")
+    parser.add_argument("--dry-run", action="store_true", help="Don't save any changes")
+    args = parser.parse_args(argv)
+    object_str = args.object
+
+    processed_filesets = set()
+
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+        assert ":" in object_str
+
+        obj_strings = [object_str]
+        if "Screen" in object_str:
+            screen = get_object(conn, object_str)
+            obj_strings = [f"Plate:{plate.id}" for plate in screen.listChildren()]
+        elif "Dataset" in object_str:
+            dataset = get_object(conn, object_str)
+            obj_strings = [f"Image:{image.id}" for image in dataset.listChildren()]
+
+        for object_str in obj_strings:
+            fileset_id = get_fileset_id(conn, object_str)
+            if fileset_id in processed_filesets:
+                continue
+            rename_images(conn, fileset_id, args)
+            processed_filesets.add(fileset_id)
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])