Revert "Moved 'number_from_name' into a FIB utility module"

This reverts commit 04cfb18.

Author: tieneupin

src/murfey/client/contexts/fib.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import logging
+import re
 import threading
 from datetime import datetime
 from pathlib import Path
@@ -11,7 +12,6 @@
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.util.client import capture_post
-from murfey.util.fib import number_from_name
 
 logger = logging.getLogger("murfey.client.contexts.fib")
 
@@ -29,6 +29,22 @@ class MillingProgress(NamedTuple):
     timestamp: float
 
 
+def _number_from_name(name: str) -> int:
+    """
+    In the AutoTEM and Maps workflows for the FIB, the sites and images are
+    auto-incremented with parenthesised numbers (e.g. "Lamella (2)"), with
+    the first site/image typically not having a number.
+
+    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
+    )
+
+
 def _get_source(file_path: Path, environment: MurfeyInstanceEnvironment) -> Path | None:
     """
     Returns the Path of the file on the client PC.
@@ -89,7 +105,7 @@ def post_transfer(
             parts = transferred_file.parts
             if "DCImages" in parts and transferred_file.suffix == ".png":
                 lamella_name = parts[parts.index("Sites") + 1]
-                lamella_number = number_from_name(lamella_name)
+                lamella_number = _number_from_name(lamella_name)
                 time_from_name = transferred_file.name.split("-")[:6]
                 timestamp = datetime.timestamp(
                     datetime(
@@ -155,7 +171,7 @@ def post_transfer(
                     metadata = xmltodict.parse(for_parsing)
                 sites = metadata["AutoTEM"]["Project"]["Sites"]["Site"]
                 for site in sites:
-                    number = number_from_name(site["Name"])
+                    number = _number_from_name(site["Name"])
                     milling_angle = site["Workflow"]["Recipe"][0]["Activites"][
                         "MillingAngleActivity"
                     ].get("MillingAngle")