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Update FIB metadata parsing and registration logic #825

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Merged
tieneupin merged 2 commits into from
Jun 16, 2026
Merged

Update FIB metadata parsing and registration logic #825

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a36158d
Updated 'number_from_name' so that it can handle the folder naming pa…
tieneupin Jun 15, 2026
f33e7e9
Updated milling progress registration logic so that it uses the lates…
tieneupin Jun 16, 2026
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20 changes: 14 additions & 6 deletions src/murfey/util/fib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
General functinos specific to the FIB workflow
"""

import re
from pathlib import Path


def number_from_name(name: str) -> int:
Expand All @@ -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
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