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Fix min and max mz filtering in cut_mz_domain_noise #13

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Fix min and max mz filtering in cut_mz_domain_noise #13

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9a22b35
Fix min and max mz filtering in cut_mz_domain_noise
Kzra Mar 6, 2023
0164831
updated indexing
Kzra Mar 7, 2023
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16 changes: 8 additions & 8 deletions corems/mass_spectrum/calc/NoiseCalc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,20 +120,20 @@ def cut_mz_domain_noise(self):

if max_mz_noise > max_mz_whole_ms:
max_mz_noise = max_mz_whole_ms

#print(min_mz_noise, max_mz_noise)
low_mz_index = (where(self.mz_exp_profile >= min_mz_noise)[0][0])
#print(self.mz_exp_profile[low_mz_index])
# low_mz_index = (argmax(self.mz_exp_profile <= min_mz_noise))

high_mz_index = (where(self.mz_exp_profile <= max_mz_noise)[-1][-1])

#the following indexing relies on mz_exp_profile being ordered high mz to low mz
low_mz_index = (where(self.mz_exp_profile >= min_mz_noise)[-1][-1])
#print(self.mz_exp_profile[low_mz_index])
#low_mz_index = (argmax(self.mz_exp_profile <= min_mz_noise))

high_mz_index = (where(self.mz_exp_profile <= max_mz_noise)[0][0])
#print(self.mz_exp_profile[high_mz_index])
Comment on lines +124 to +130
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Copilot AI Mar 9, 2026

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The new where(...)[-1][-1] / [0][0] selection assumes mz_exp_profile is sorted high→low. If mz_exp_profile is low→high (which the if high_mz_index > low_mz_index branch suggests is possible, and can happen for array-based inputs), low_mz_index becomes the last element and the slice includes values outside [min_mz_noise, max_mz_noise], so min/max filtering breaks again. Consider making the index selection order-independent, e.g., build a boolean mask for (mz>=min)&(mz<=max) and slice using min(idx):max(idx)+1, which also lets you drop the order-dependent comment and the if/else.

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#high_mz_index = (argmax(self.mz_exp_profile <= max_mz_noise))

if high_mz_index > low_mz_index:
# pyplot.plot(self.mz_exp_profile[low_mz_index:high_mz_index], self.abundance_profile[low_mz_index:high_mz_index])
# pyplot.show()
return self.mz_exp_profile[high_mz_index:low_mz_index], self.abundance_profile[low_mz_index:high_mz_index]
return self.mz_exp_profile[low_mz_index:high_mz_index], self.abundance_profile[low_mz_index:high_mz_index]
Comment on lines 133 to +136
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Copilot AI Mar 9, 2026

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This change affects how noise ROI is selected for all non-'minima' threshold methods, but there doesn’t appear to be a unit test that asserts min_noise_mz/max_noise_mz actually change the computed noise baseline/STD (especially for both ascending and descending mz_exp_profile). Adding a focused test around cut_mz_domain_noise() (or run_noise_threshold_calc() with threshold_method='signal_noise') would prevent regressions like the original bug and the ordering edge case.

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else:
# pyplot.plot(self.mz_exp_profile[high_mz_index:low_mz_index], self.abundance_profile[high_mz_index:low_mz_index])
# pyplot.show()
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