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Adjust local min edges #1977

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Merged
robinschmid merged 4 commits into from
Jul 29, 2024
Merged

Adjust local min edges #1977

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SteffenHeu Jul 2, 2024
145530f
Merge branch 'refs/heads/master' into adjust-local-min-edges
SteffenHeu Jul 18, 2024
1cde9e0
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SteffenHeu Jul 29, 2024
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SteffenHeu Jul 29, 2024
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30 changes: 24 additions & 6 deletions ...cessing/featdet_chromatogramdeconvolution/minimumsearch/MinimumSearchFeatureResolver.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2004-2022 The MZmine Development Team
* Copyright (c) 2004-2024 The mzmine Development Team
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
Expand Down Expand Up @@ -143,10 +143,28 @@ public List<Range<Double>> resolve(double[] x, double[] y) {
// Check the shape of the peak.
if (numberOfDataPoints >= minDataPoints && currentRegionHeight >= minHeight
&& currentRegionHeight >= peakMinLeft * minRatio
&& currentRegionHeight >= peakMinRight * minRatio && xRange
.contains(x[currentRegionEnd] - x[currentRegionStart])) {
&& currentRegionHeight >= peakMinRight * minRatio && xRange.contains(
x[currentRegionEnd] - x[currentRegionStart])) {

// adjust start and end points of signals to produce better peak shapes
// (e.g. include 0 intensity points on the edges.), as start and end points of this
// resolver will never be 0.
int start;
if (y[currentRegionStart] != 0 && y[Math.max(currentRegionStart - 1, 0)] == 0.0) {
start = currentRegionStart - 1;
} else {
start = currentRegionStart;
}

int end;
if (y[currentRegionEnd] != 0
&& y[Math.min(currentRegionEnd + 1, y.length - 1)] == 0.0) {
end = currentRegionEnd + 1;
} else {
end = currentRegionEnd;
}

resolved.add(Range.closed(x[currentRegionStart], x[currentRegionEnd]));
resolved.add(Range.closed(x[start], x[end]));
}

// Set the next region start to current region end - 1
Expand Down Expand Up @@ -203,8 +221,8 @@ public List<Range<Double>> resolve(double[] x, double[] y) {
// Check the shape of the peak.
if (numberOfDataPoints >= minDataPoints && currentRegionHeight >= minHeight
&& currentRegionHeight >= peakMinLeft * minRatio
&& currentRegionHeight >= peakMinRight * minRatio && xRange
.contains(x[currentRegionEnd] - x[currentRegionStart])) {
&& currentRegionHeight >= peakMinRight * minRatio && xRange.contains(
x[currentRegionEnd] - x[currentRegionStart])) {

resolved.add(Range.closed(x[currentRegionStart], x[currentRegionEnd]));
}
Expand Down