Moved 'number_from_name' into new module 'murfey.util.fib'

Author: tieneupin

src/murfey/client/contexts/fib.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import re
 import threading
 import xml.etree.ElementTree as ET
 from dataclasses import dataclass, field
@@ -11,6 +10,7 @@
 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
 from murfey.util.models import (
     LamellaSiteInfo,
     MillingStepInfo,
@@ -24,22 +24,6 @@
 lock = threading.Lock()
 
 
-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
-    )
-
-
 T = TypeVar("T")
 
 
@@ -416,7 +400,7 @@ def _parse_autotem_metadata(self, file: Path):
             if (site_name := _parse_xml_text(site, "Name", str)) is None:
                 logger.warning("Current site doesn't have a name")
                 continue
-            site_num = _number_from_name(site_name)
+            site_num = number_from_name(site_name)
             site_info = LamellaSiteInfo(
                 project_name=project_name,
                 site_name=site_name,
@@ -555,7 +539,7 @@ def _make_drift_correction_gif(
         parts = file.parts
         try:
             lamella_name = parts[parts.index("Sites") + 1]
-            lamella_number = _number_from_name(lamella_name)
+            lamella_number = number_from_name(lamella_name)
         except Exception:
             logger.warning(
                 f"Could not extract metadata from file {file}", exc_info=True

src/murfey/util/fib.py

@@ -0,0 +1,21 @@
+"""
+General functinos specific to the FIB workflow
+"""
+
+import re
+
+
+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
+    )