Implement generic date tag resetting

bin/reset_datetime.py

@@ -8,15 +8,30 @@
 import tiffsurgeon
 
 
+# Define a custom argument type for a list of integers
+def list_of_ints(arg):
+    return list(map(int, arg.split(",")))
+
+
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="Set all DateTime tags in a TIFF to one value (in place).",
+        description="Set all specified date tags in a TIFF to one value (in place).",
     )
     parser.add_argument("image_path", help="TIFF file to process")
     parser.add_argument(
-        "datetime",
+        "--datetags",
+        help="Space-separated list of tags (integer ids) with dates to replace (default: 306)",
+        nargs="+",
+        type=int,
+        default=[306],
+    )
+    parser.add_argument(
+        "--datetime",
         help="YYYY:MM:DD HH:MM:SS string to replace all DateTime values."
-        "Note the use of colons in the date, as required by the TIFF standard.",
+        " Note the use of colons in the date, as required by the TIFF standard."
+        " Default: 1970:01:01 00:00:00 (start of Unix epoch).",
+        type=str,
+        default="1970:01:01 00:00:00",
     )
     argv = sys.argv[1:]
     # Allow date and time to be passed as separate args for convenience.
@@ -35,6 +50,17 @@ def main():
         tiff = tiffsurgeon.TiffSurgeon(
             args.image_path, encoding="utf-8", writeable=True
         )
+        tiff.read_ifds()
+    except (tiffsurgeon.FormatError, UnicodeDecodeError) as e:
+        print(f"TIFF format or encoding error: {e}. Trying with Latin-1 encoding.")
+        try:
+            tiff = tiffsurgeon.TiffSurgeon(
+                args.image_path, encoding="latin-1", writeable=True
+            )
+            tiff.read_ifds()
+        except tiffsurgeon.FormatError as e:
+            print(f"Error reading IFDs: {e}")
+            sys.exit(1)
     except tiffsurgeon.FormatError as e:
         print(f"TIFF format error: {e}")
         sys.exit(1)
@@ -48,22 +74,33 @@ def main():
 
     tiff.read_ifds()
 
-    subifds = [
-        tiff.read_ifd(v) for i in tiff.ifds if 330 in i.tags for v in i.tags[330].value
-    ]
-    offsets = [
-        i.tags[306].offset_range.start for i in tiff.ifds + subifds if 306 in i.tags
-    ]
-    if offsets:
-        for x in offsets:
-            tiff.file.seek(x)
-            tiff.file.write(new_datetime)
-        print(
-            f"Successfully replaced {len(offsets)} DateTime values in"
-            f" {args.image_path}"
-        )
-    else:
-        print(f"No DateTime tags found in {args.image_path} -- file not modified")
+    for tag in args.datetags:
+        if not any(tag in i.tags for i in tiff.ifds):
+            print(f"Tag {tag} not found in {args.image_path} -- file not modified")
+            sys.exit(1)
+
+        subifds = [
+            tiff.read_ifd(v)
+            for i in tiff.ifds
+            if 330 in i.tags
+            for v in i.tags[330].value
+        ]
+        offsets = [
+            i.tags[tag].offset_range.start for i in tiff.ifds + subifds if tag in i.tags
+        ]
+
+        if offsets:
+            for x in offsets:
+                tiff.file.seek(x)
+                tiff.file.write(new_datetime)
+            print(
+                f"Successfully replaced {len(offsets)} values of tag {tag} in"
+                f" {args.image_path}"
+            )
+        else:
+            print(
+                f"No tags with number {tag} found in {args.image_path} -- file not modified"
+            )
 
     tiff.close()
 

main.nf

@@ -21,6 +21,10 @@ params.rm_svs_macro = false         // Remove macro image in SVS files
 params.rm_svs_label = true          // Remove label image in SVS files
 params.rm_ome_sa    = true          // Remove structural annotations in OME-XML files
 
+// Tags that contain a DateTime to be reset
+// Ideally we would parse as a list but this works for now
+params.datetags     = "306 45278 45279 45494"
+
 if (params.input) {
   params.input = file(params.input)
   } else {

modules/reset_datetime.nf

@@ -10,6 +10,6 @@ process reset_datetime {
   """
   script:
   """
-  reset_datetime.py $image "1970:01:01 00:00:00"
+  reset_datetime.py $image --datetags $params.datetags
   """
 }