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Fix bug when µMUX data has no number of rows stored in LJH file #300

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Fix bug when µMUX data has no number of rows stored in LJH file #300

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9e9fbe3
Ensure positive # of rows and subframe divisions
joefowler Oct 15, 2024
e4899d1
Update VERSIONS.md
joefowler Oct 15, 2024
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2 changes: 2 additions & 0 deletions VERSIONS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@

* Fix problem where numpy 2.0 was failing a regression test. Not a true regression, so we broaden the acceptance criteria (issue 295).
* Add installation instructions to README for https-based installation, in addition to ssh-based.
* Fix Ruff errors.
* Fix bug when no number of rows is stored (for µMUX data) (issue 298).

**0.8.4** June 5, 2024

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12 changes: 6 additions & 6 deletions mass/core/channel.py
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Expand Up @@ -629,12 +629,12 @@ def __init__(self, pulserec_dict, tes_group=None, hdf5_group=None, invert_data=F
self.times = None
self.subframecount = None

self.number_of_rows = None
self.row_number = None
self.number_of_columns = None
self.column_number = None
self.subframe_divisions = None
self.subframe_offset = None
self.number_of_rows = 1
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This set of changes seems totally uneccesary and actually bad. We found this error because mass crashed when something went wrong, by giving default values instead of None values to all these parameters, we increase the likelyhood mass will do something silently wrong instead of crashing. These changes aren't needed to fix the bug at hand.

self.row_number = 0
self.number_of_columns = 1
self.column_number = 0
self.subframe_divisions = 1
self.subframe_offset = 0
self.subframe_timebase = None

self._filter_type = "ats"
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6 changes: 5 additions & 1 deletion mass/core/files.py
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Expand Up @@ -251,14 +251,18 @@ def _parse_header(self):
# Read the new (Feb 2024) subframe information. If missing, assume the old TDM values pertain
# (so # of rows -> subframe divisions, and row # -> subframe offset), unless source is Abaco,
# in which case use 64 subframe divisions and offset of 0.
default_divisions = self.number_of_rows
default_offset = self.row_number
default_divisions = self.number_of_rows
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I believe this is the only place we should have a fix, and it should have a comment explaining why it works the way it does, and probably print a warning about what is wrong that is making it need the fix. Perhaps "warning: malformed ljh filed with number_of_rows = 0 detected, doing x instead".

if default_divisions <= 0:
default_divisions = 1
if "Abaco" in self.source:
# The external trigger file can override this, but assume 64 divisions at first.
default_divisions = 64
default_offset = 0
self.subframe_divisions = int(header_dict.get(b"Subframe divisions", default_divisions))
self.subframe_offset = int(header_dict.get(b"Subframe offset", default_offset))
if self.subframe_divisions <= 0:
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This is a redundant fix, if the above fix works, this isn't necessary. So future readers will have a hard time understanding why this exists and it will make reading the code harder without adding any value.

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The issue title says that the issue happane when no number of rows is stored in the LJH file. But we have a line should make number_of_rows=1 in that case, which should prevent the divide by zero. So I also don't understand from this how the issue ever happens.

self.subframe_divisions = 1

self.version_str = header_dict[b'Save File Format Version']
self.binary_size = os.stat(filename).st_size - self.header_size
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8 changes: 8 additions & 0 deletions tests/core/test_core.py
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Expand Up @@ -585,3 +585,11 @@ def test_ordering_hdf5only(tmp_path):
data = mass.TESGroupHDF5(fname)
for i, ds in enumerate(data):
assert ds.channum == cnums[i]


def test_ljh_norows():
"""Make sure the LJH merge script works."""
src_name = os.path.join('tests', 'regression_test', 'partial_header_chan3.ljh')
data = mass.TESGroup(src_name)
ds = data.channel[3]
assert ds.subframe_divisions > 0
56 changes: 56 additions & 0 deletions tests/regression_test/partial_header_chan3.ljh
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@@ -0,0 +1,56 @@
#LJH Memorial File Format
Save File Format Version: 2.2.0
Software Version: MATTER Client 1.1.2
Software Driver Version: unknown
Server Start Time: 16 Nov 2017, 19:12:14 GMT
Acquisition Mode: 0
Digitized Word Size in Bytes: 2
File First Record Time: 16 Nov 2017, 22:23:34 GMT
Channel: 3
Number of columns: 1
Column number (from 0-0 inclusive): 0
Location: LANL
Cryostat:
Bias level (% Rn): 1.1 V
T set point (mK): 80
"Heater" output (%):
Magnetic field (mg):
Sample:
Photon source: Gd153
Operator(s):
System comment:
#End of description
Number of Digitizers: 1
Number of Active Channels: 1
Timestamp offset (s): 1510859534.658107
Digitizer: 1
Description: n/a
Master: yes
Bits: 16
Effective Bits: unknown
Anti-alias low-pass cutoff frequency (Hz): n/a
Timebase: 1.600000e-05
Number of samples per point: 1
Presamples: 125
Total Samples: 500
Digitizer Channel: 1.0
Dummy: 0
Range: 0.500000
Offset: 0.500000
Coupling: DC
Impedance: n/a
Inverted: No
Preamp gain: 1.0
Discrimination level: n/a
#End of Header
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