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feat: remove peak limit for optimization and adjust autoPeakPicking parameters #4241

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feat: remove peak limit for optimization and adjust autoPeakPicking parameters #4241

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5debaef
feat: remove peak limit for optimization and adjust autoPeakPicking p…
jobo322 Jun 30, 2026
bab6c97
feat: optimize peak processing by removing peak limit and enhancing p…
jobo322 Jul 1, 2026
a5609bd
chore: update ml-gsd
jobo322 Jul 1, 2026
c209410
chore: update package-lock.json
jobo322 Jul 2, 2026
77518d7
fix: uses the same minMaxRatio for maxAbsoluteRatio option
jobo322 Jul 2, 2026
39b4dbe
fix: uses the same value of minMaxRatio for maxAbsoluteRatio in range…
jobo322 Jul 2, 2026
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8 changes: 4 additions & 4 deletions package-lock.json
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2 changes: 1 addition & 1 deletion package.json
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Expand Up @@ -92,7 +92,7 @@
"ml-array-mean": "^2.0.0",
"ml-array-median": "^2.0.0",
"ml-conrec": "^6.0.0",
"ml-gsd": "^14.2.0",
"ml-gsd": "^14.2.1",
"ml-signal-processing": "^2.2.2",
"ml-spectra-processing": "^14.29.1",
"ml-tree-similarity": "^2.2.0",
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9 changes: 1 addition & 8 deletions src/component/panels/PeaksPanel/PeaksPanel.tsx
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Expand Up @@ -111,14 +111,7 @@ function PeaksPanelInner(props: PeaksPanelInnerProps) {
const filterPeaks = peaks.values.filter((peak) =>
isInRange(peak.x, { from, to }),
);
if (filterPeaks.length <= 15) {
dispatch({ type: 'OPTIMIZE_PEAKS', payload: { peaks: filterPeaks } });
} else {
toaster.show({
message: 'optimization can be done on no more than 15 peaks',
intent: 'danger',
});
}
dispatch({ type: 'OPTIMIZE_PEAKS', payload: { peaks: filterPeaks } });
};

function toggleViewProperty(key: keyof FilterType<PeaksViewState, boolean>) {
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1 change: 1 addition & 0 deletions src/component/reducer/actions/RangesActions.ts
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Expand Up @@ -234,6 +234,7 @@ function handleAutoRangesDetection(
broadWidth: 0.05,
thresholdFactor: 8,
minMaxRatio,
maxAbsoluteRatio: minMaxRatio,
direction: lookNegative ? 'both' : 'positive',
},
};
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1 change: 1 addition & 0 deletions src/data/data1d/Spectrum1D/peaks/autoPeakPicking.ts
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Expand Up @@ -48,6 +48,7 @@ export function autoPeakPicking(
sensitivity: 100,
shape: defaultPeakShape,
noiseLevel: noise * noiseFactor,
maxAbsoluteRatio: minMaxRatio, // Threshold to determine if a given peak should be considered as a noise
minMaxRatio, // Threshold to determine if a given peak should be considered as a noise
realTopDetection: true,
smoothY: false,
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65 changes: 35 additions & 30 deletions src/data/data1d/Spectrum1D/peaks/optimizePeaks.ts
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Expand Up @@ -36,105 +36,110 @@ export function optimizePeaks(
groupingFactor: 10,
stages: [
{
// Stage 1: local stabilization
factorLimits: 2,
maxNumberOfPeaks: 40,
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 1e-3 },
},
parameters: {
fwhm: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 2,
min: (peak: any) => (peak.shape?.fwhm ?? 0) * 0.5,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
},
mu: { optimize: false },
x: { optimize: false },
y: {
optimize: true,
init: (peak: any) => peak.y * 0.8,
init: (peak: any) => peak.y,
},
},
},
{
factorLimits: 2,
maxNumberOfPeaks: 40,
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 5e-4 },
options: { maxIterations: 20, errorTolerance: 1e-3 },
},
parameters: {
fwhm: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 2,
min: (peak: any) => (peak.shape?.fwhm ?? 0) * 0.5,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
},
mu: { optimize: false },
x: { optimize: false },
y: {
optimize: true,
init: (peak: any) => peak.y,
},
},
},
{
// Stage 2: regroup into the real overlapping cluster
factorLimits: 2,
maxNumberOfPeaks: 40,
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 1e-5 },
options: { maxIterations: 25, errorTolerance: 1e-4 },
},
parameters: {
fwhm: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 2,
min: (peak: any) => (peak.shape?.fwhm ?? 0) * 0.5,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
},
mu: { optimize: true },
x: { optimize: false },
y: {
optimize: true,
},
y: { optimize: true },
},
},
{
// Stage 3: final polish
factorLimits: 2,
maxNumberOfPeaks: 40,
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 5e-4 },
options: { maxIterations: 30, errorTolerance: 1e-5 },
},
parameters: {
fwhm: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 3,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 3,
min: (peak: any) => (peak.shape?.fwhm ?? 0) * 0.5,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
},
mu: { optimize: true },
x: { optimize: true },
y: { optimize: true },
},
},
{
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 1e-4 },
},
parameters: {
fwhm: {
x: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 2,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
min: (peak: any) => peak.x - (peak.shape?.fwhm ?? 0) / 4,
max: (peak: any) => peak.x + (peak.shape?.fwhm ?? 0) / 4,
},
mu: { optimize: false },
x: { optimize: true },
y: { optimize: true },
},
},
{
// Stage 3: final polish
factorLimits: 2,
maxNumberOfPeaks: 40,
optimization: {
kind: 'lm',
options: { maxIterations: 20, errorTolerance: 1e-8 },
options: { maxIterations: 30, errorTolerance: 1e-5 },
},
parameters: {
fwhm: {
optimize: true,
min: (peak: any) => (peak.shape?.fwhm ?? 0) / 2,
min: (peak: any) => (peak.shape?.fwhm ?? 0) * 0.5,
max: (peak: any) => (peak.shape?.fwhm ?? 0) * 2,
},
mu: { optimize: true },
x: { optimize: true },
x: {
optimize: true,
min: (peak: any) => peak.x - (peak.shape?.fwhm ?? 0) / 4,
max: (peak: any) => peak.x + (peak.shape?.fwhm ?? 0) / 4,
},
y: { optimize: true },
},
},
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1 change: 1 addition & 0 deletions src/data/data1d/Spectrum1D/ranges/detectSignalsByMultipletAnalysis.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ export function detectSignalsByMultipletAnalysis(
to,
frequency,
minMaxRatio: 0.1,
maxAbsoluteRatio: 0.1,
broadWidth: 0.25,
broadRatio: 0.0025,
optimize: true,
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