Skip to content

Don't crash parsing ABF files with an invalid acquisition date #1866

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
h-mayorquin wants to merge 1 commit into
base: master
Choose a base branch
from
+27 −3
Open

Don't crash parsing ABF files with an invalid acquisition date #1866

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 14 additions & 2 deletions neo/rawio/axonrawio.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -673,7 +673,13 @@ def _parse_abf_v1(f, header_description):
ss = header["lFileStartTime"] - hh * 3600 - mm * 60
ms = int(np.mod(ss, 1) * 1e6)
ss = int(ss)
header["rec_datetime"] = datetime.datetime(YY, MM, DD, hh, mm, ss, ms)
try:
header["rec_datetime"] = datetime.datetime(YY, MM, DD, hh, mm, ss, ms)
except (ValueError, OverflowError):
# Date/time header fields hold an out-of-range or "no date" sentinel

@zm711 zm711 Jun 25, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should we warn people? I don't know this system well enough to know if warning a person that they didn't have an acquisition time is a marker of a "poor" acquisition or is something that the user should know they forgot to set up? What do you think? It's not actionable, but it might be valuable for the user to know. I just don't know the reader.

# (e.g. 0xFFFFFFFF). The acquisition date is non-essential annotation,
# so fall back to None rather than blocking the read of the signal.
header["rec_datetime"] = None

return header

Expand Down Expand Up @@ -1025,7 +1031,13 @@ def _parse_abf_v2(f, header_description):
ss = header["uFileStartTimeMS"] / 1000.0 - hh * 3600 - mm * 60
ms = int(np.mod(ss, 1) * 1e6)
ss = int(ss)
header["rec_datetime"] = datetime.datetime(YY, MM, DD, hh, mm, ss, ms)
try:
header["rec_datetime"] = datetime.datetime(YY, MM, DD, hh, mm, ss, ms)
except (ValueError, OverflowError):
# Date/time header fields hold an out-of-range or "no date" sentinel
# (e.g. 0xFFFFFFFF). The acquisition date is non-essential annotation,
# so fall back to None rather than blocking the read of the signal.
header["rec_datetime"] = None

return header

Expand Down
14 changes: 13 additions & 1 deletion neo/test/rawiotest/test_axonrawio.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import unittest

from neo.rawio.axonrawio import AxonRawIO
from neo.rawio.axonrawio import AxonRawIO, parse_axon_soup

from neo.test.rawiotest.common_rawio_test import BaseTestRawIO

Expand Down Expand Up @@ -28,6 +28,18 @@ def test_read_raw_protocol(self):

reader.read_raw_protocol()

def test_invalid_date_falls_back_to_none(self):
# Some ABF files store an out-of-range / "no date" sentinel (e.g. 0xFFFFFFFF)
# in the acquisition date header fields. The date is non-essential annotation,
# so parsing must fall back to rec_datetime=None rather than raising and
# blocking access to the signal.
for fixture in [
"axon/intracellular_data/files_with_errors/invalid_date_abf1.abf", # ABF v1
"axon/intracellular_data/files_with_errors/invalid_date_abf2.abf", # ABF v2
]:
header = parse_axon_soup(self.get_local_path(fixture))
self.assertIsNone(header["rec_datetime"])


if __name__ == "__main__":
unittest.main()
Loading