Update FIB metadata parsing and registration logic (#825)

* Updated 'number_from_name' so that it can handle the folder naming pattern associated with the FIB waffle method
* Updated milling progress registration logic so that it uses the latest available stage position value present in the metadata

Author: tieneupin

src/murfey/util/fib.py

@@ -2,7 +2,7 @@
 General functinos specific to the FIB workflow
 """
 
-import re
+from pathlib import Path
 
 
 def number_from_name(name: str) -> int:
@@ -11,11 +11,19 @@ def number_from_name(name: str) -> int:
     auto-incremented with parenthesised numbers (e.g. "Lamella (2)"), with
     the first site/image typically not having a number.
 
+    For sites set up and acquired manually, they will be saved in folders
+    labelled "Site #1", "Site #2", etc.
+
     This function extracts the number from the file name, and returns 1 if
     no such number is found.
     """
-    return (
-        int(match.group(1))
-        if (match := re.search(r"^[\w\s]+\((\d+)\)$", name)) is not None
-        else 1
-    )
+    # Ensure only the stem is extracted for parsing
+    stem = Path(name).stem
+    # Handle naming pattern for sites acquired without autoTEM
+    if "#" in stem:
+        return int(stem.rpartition("#")[-1])
+    # Handle naming pattern for sites acquired with autoTEM
+    if "(" in stem and stem.endswith(")"):
+        return int(stem[stem.rfind("(") + 1 : -1])
+    # Names without '()' or '#' should return 1
+    return 1