Spectroscopy physics review: qPlus setpoint gate, time-axis sanitisation, derivative units#27
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Physics review of the spectroscopy package (probeflow/spectroscopy +
io/spectroscopy.py), pinned by tests/test_spectroscopy_physics.py:
- _createc_setpoint_a read Current[A]/SetPoint unconditionally as amps: for
a constant-delta-f qPlus .VERT (PLL on / FBChannel != 0) SetPoint is a
frequency shift in hertz, so metadata carried e.g. setpoint_a = 3.2 "A"
and setpoint normalization silently divided spectra by a frequency
pretending to be a current (~10 orders of magnitude off, no error). The
same bug was fixed for scan metadata earlier; the spectroscopy path now
shares that gate (_createc_feedback_is_current), so a qPlus file reports
no current setpoint and setpoint normalization blocks honestly.
- SpecFreq=0/negative/non-finite turned the whole time-trace x axis into
inf or negative seconds (x = idx / spec_freq). Sanitised to the
documented 1000 Hz missing-value default, with a log warning.
- Derivative unit propagation now mirrors SpectrumDeltaMeasurement.slope_unit:
A/V for the usual case, 1/V when y is unitless ("A/" .rstrip slicing
previously collapsed mixed cases), bare y unit when x is unitless.
Verified clean: pipeline order (smoothing -> derivative -> normalization ->
outliers -> offset, now pinned numerically), monotonicity-guarded
np.gradient(y, x), all four normalization modes raise on bad denominators,
channel-normalization-with-derivative rejected, forward+backward sweeps
refused. Noted unchanged: per-trace span normalization in
nearest_point_across_traces mildly biases cross-trace snapping; jump-mode
outlier masking excludes finite neighbours of NaN samples (defensible).
Co-Authored-By: Claude Fable 5 <[email protected]>
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Summary
Physics/maths correctness review of
probeflow/spectroscopy+io/spectroscopy.py(first dedicated pass over this package).Findings (physics-check format)
[CRITICAL]
io/spectroscopy.py:341— fixedWhat:
_createc_setpoint_areadSetPointunconditionally as amps.Why: on constant-Δf qPlus VERT files
SetPointis a frequency shift in Hz; the value feeds setpoint normalization, silently dividing displayed spectra by a frequency pretending to be a current (~10 orders of magnitude wrong, no error). Same bug class fixed for scan metadata in an earlier round — the spec path never got the gate.Fix: share
_createc_feedback_is_currentwith the scan path; qPlus files report no current setpoint and setpoint normalization now blocks with a clear error.[WARN]
io/spectroscopy.pytime axis — fixedWhat:
x = idx / spec_freqwithSpecFreq=0/negative/non-finite → inf or negative seconds.Fix: sanitise to the documented 1000 Hz missing-value default with a log warning.
[INFO]
spectroscopy/transforms.py:67— fixedWhat: derivative unit built via
f"{y}/{x}".rstrip("/")collapsed empty-unit cases.Fix: mirror
SpectrumDeltaMeasurement.slope_unit(A/V,1/V, or bare y-unit).Verified clean: pipeline order (smoothing→derivative→normalization→outliers→offset, now pinned numerically), monotonicity-guarded
np.gradient(y, x), forward+backward sweep refusal, all normalization denominator guards, channel-norm-with-derivative rejection, unit propagation to "relative", export round-trips.Noted, unchanged: per-trace span normalization in
nearest_point_across_tracesmildly biases cross-trace click snapping; jump-mode outlier masking drops finite neighbours of NaN samples (defensible — their derivative is unknown).Test plan
tests/test_spectroscopy_physics.py(22 tests) covering the header→setpoint seam end-to-end, time-axis sanitisation, unit propagation, and pipeline-order invariants.🤖 Generated with Claude Code