fix: xNoiseSanPlot refined negative noise read from wrong array

[lpatiny]

Bug

In the refine branch of xNoiseSanPlot, the refined negative noise level was read from cloneSignPositive (the positive signal) while indexing with cloneSignNegative.length — a copy-paste error from the positive branch just above. With refine: true (the default), the reported negative level did not reflect the negative signal at all.

The fix reads from cloneSignNegative and negates it, mirroring the initial negative-noise formula (-1 * signNegative[...]). Added a regression assertion: the refined negative level is now positive and of the same order as the positive one.

All 2230 tests pass.

For your review, @jobo322 — a second, separate issue I did not touch

determineCutOff accumulates averageValue as a plain sum and then uses it as a mean in (element[1] - averageValue)², so kiSqrt isn't the intended dispersion measure and the chosen cut-off is likely skewed. Dividing averageValue by elementsOfCutOff.length looks correct, but it changes the magnitude-mode SNR on the test spectrum from ~40.2 to ~63.5 — a real behavioral change to the published-method output. I left it as-is since that needs your domain judgment on what the reference value should be. Happy to open a follow-up if you confirm the intended behavior.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.15%. Comparing base (9fed281) to head (2c12305).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #386      +/-   ##
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+ Coverage   97.13%   97.15%   +0.02%     
==========================================
  Files         207      209       +2     
  Lines        4147     4148       +1     
  Branches     1036     1030       -6     
==========================================
+ Hits         4028     4030       +2     
+ Misses        115      114       -1     
  Partials        4        4              

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[jobo322]

seems to me that cutOffSignalsIndexNeg would be always zero. because cutOffSignals defined positive. So there is not a refinning for noiseLevelNegative.

[jobo322]

Correct sign handling for negative noise in xNoiseSanPlot and uses cutoff for negative using negative data

Experiment	Refactored	Current state
DEPT
1H

[jobo322]

@lpatiny could you have a look, I propose use negative data to find the negative noise level

[jobo322]

It is true than there is a bug in the determineCutOff function with the missing division for the number of elements in the window, but I would like to keep it out of this PR, to open a new one that would refactor the xFindClosestIndex to accept descending order arrays. @lpatiny what do you think?

[jobo322]

In the case of ibuprofen, the result of the strange sanplot line is due to NUS processing, where most of the points are zero, so there is not a real distribution of noise. When I deactivate the NUS reconstruction we got the expected sanplot line

with NUS activated the number of positive points are 9631 and negative 2144. it make sense because NUS by IST take only the signal points.

[jobo322]

[jobo322]

The value of negative noise is bigger in absolute value. Is not particularly symmetric, I try to fix the baseline and the phase of the spectrum