List of usage examples for org.apache.commons.math.optimization.fitting PolynomialFitter PolynomialFitter
public PolynomialFitter(int degree, final DifferentiableMultivariateVectorialOptimizer optimizer)
From source file:net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.RegressionInfo.java
private PolynomialFunction getPolynomialFunction() { Collections.sort(data, new RTs()); PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); }//from w ww.jav a 2 s. c o m try { return fitter.fit(); } catch (Exception ex) { return null; } }
From source file:guineu.modules.filter.Alignment.RANSAC.AlignmentRansacPlot.java
private PolynomialFunction getPolynomialFunction(List<AlignStructMol> list, boolean linear) { List<RTs> data = new ArrayList<RTs>(); for (AlignStructMol m : list) { if (m.Aligned) { data.add(new RTs(m.RT2, m.RT)); }//from w ww .ja v a2 s .com } data = this.smooth(data); Collections.sort(data, new RTs()); double[] xval = new double[data.size()]; double[] yval = new double[data.size()]; int i = 0; for (RTs rt : data) { xval[i] = rt.RT; yval[i++] = rt.RT2; } int degree = 2; if (linear) { degree = 1; } PolynomialFitter fitter = new PolynomialFitter(degree, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } try { return fitter.fit(); } catch (OptimizationException ex) { return null; } }
From source file:net.sf.mzmine.modules.peaklistmethods.alignment.ransac.AlignmentRansacPlot.java
private PolynomialFunction getPolynomialFunction(Vector<AlignStructMol> list, boolean linear) { List<RTs> data = new ArrayList<RTs>(); for (AlignStructMol m : list) { if (m.Aligned) { data.add(new RTs(m.RT2, m.RT)); }/*from www .j a va 2s . c o m*/ } data = this.smooth(data); Collections.sort(data, new RTs()); double[] xval = new double[data.size()]; double[] yval = new double[data.size()]; int i = 0; for (RTs rt : data) { xval[i] = rt.RT; yval[i++] = rt.RT2; } int degree = 2; if (linear) { degree = 1; } PolynomialFitter fitter = new PolynomialFitter(degree, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } try { return fitter.fit(); } catch (Exception ex) { return null; } }
From source file:io.github.msdk.features.ransacaligner.RANSAC.java
private void fittPolinomialFunction(List<AlignStructMol> data, boolean linear) { List<AlignStructMol> points = new ArrayList<AlignStructMol>(); int degree = 3; if (linear) { degree = 1;// w ww . j a va2 s . c o m } PolynomialFitter fitter = new PolynomialFitter(degree, new GaussNewtonOptimizer(true)); for (int i = 0; i < data.size(); i++) { AlignStructMol point = data.get(i); if (point.ransacMaybeInLiers) { points.add(point); fitter.addObservedPoint(1, point.RT, point.RT2); } } try { PolynomialFunction function = fitter.fit(); for (AlignStructMol point : data) { double y = point.RT2; double bestY = function.value(point.RT); if (Math.abs(y - bestY) < t) { point.ransacAlsoInLiers = true; AlsoNumber++; } else { point.ransacAlsoInLiers = false; } } } catch (Exception ex) { } }
From source file:guineu.modules.filter.Alignment.RANSACGCGC.AlignmentGCGCRansacPlot.java
private PolynomialFunction getPolynomialFunction(List<AlignGCGCStructMol> list, boolean linear) { List<GCGCRTs> data = new ArrayList<GCGCRTs>(); for (AlignGCGCStructMol m : list) { if (m.Aligned) { data.add(new GCGCRTs(m.RT2, m.RT)); }//from ww w .ja v a 2s . c om } data = this.smooth(data); Collections.sort(data, new GCGCRTs()); double[] xval = new double[data.size()]; double[] yval = new double[data.size()]; int i = 0; for (GCGCRTs rt : data) { xval[i] = rt.RT; yval[i++] = rt.RT2; } int degree = 2; if (linear) { degree = 1; } PolynomialFitter fitter = new PolynomialFitter(degree, new GaussNewtonOptimizer(true)); for (GCGCRTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } try { return fitter.fit(); } catch (OptimizationException ex) { return null; } }
From source file:guineu.modules.filter.Alignment.RANSAC.RANSAC.java
private void fittPolinomialFunction(List<AlignStructMol> data) { List<AlignStructMol> points = new ArrayList<AlignStructMol>(); PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (int i = 0; i < data.size(); i++) { AlignStructMol point = data.get(i); if (point.ransacMaybeInLiers) { points.add(point);/*from www . j a va 2 s .c o m*/ fitter.addObservedPoint(1, point.RT, point.RT2); } } try { PolynomialFunction function = fitter.fit(); for (AlignStructMol point : data) { double y = point.RT2; double bestY = function.value(point.RT); if (Math.abs(y - bestY) < t) { point.ransacAlsoInLiers = true; AlsoNumber++; } else { point.ransacAlsoInLiers = false; } } } catch (Exception ex) { } }
From source file:guineu.modules.filter.Alignment.RANSACGCGC.RANSACGCGC.java
private void fittPolinomialFunction(List<AlignGCGCStructMol> data) { List<AlignGCGCStructMol> points = new ArrayList<AlignGCGCStructMol>(); PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (int i = 0; i < data.size(); i++) { AlignGCGCStructMol point = data.get(i); if (point.ransacMaybeInLiers) { points.add(point);/*from w w w . j a v a 2s.c om*/ fitter.addObservedPoint(1, point.RT, point.RT2); } } try { PolynomialFunction function = fitter.fit(); for (AlignGCGCStructMol point : data) { double y = point.RT2; double bestY = function.value(point.RT); if (Math.abs(y - bestY) < t) { point.ransacAlsoInLiers = true; AlsoNumber++; } else { point.ransacAlsoInLiers = false; } } } catch (Exception ex) { } }
From source file:guineu.modules.filter.Alignment.RANSAC.RansacAlignerTask.java
/** * Returns the corrected RT of the row/* w ww .j a va 2s . com*/ * * @param row * @param list * @return */ private PolynomialFunction getPolynomialFunction(List<AlignStructMol> list, Range RTrange) { List<RTs> data = new ArrayList<RTs>(); for (AlignStructMol m : list) { if (m.Aligned) { data.add(new RTs(m.RT2, m.RT)); } } data = this.smooth(data, RTrange); Collections.sort(data, new RTs()); try { PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } return fitter.fit(); } catch (Exception ex) { return null; } }
From source file:guineu.modules.filter.Alignment.RANSACGCGC.RansacGCGCAlignerTask.java
/** * Returns the corrected RT of the row/* w w w . ja v a 2s. com*/ * * @param row * @param list * @return */ private PolynomialFunction getPolynomialFunction(List<AlignGCGCStructMol> list, Range RTrange) { List<GCGCRTs> data = new ArrayList<GCGCRTs>(); for (AlignGCGCStructMol m : list) { if (m.Aligned) { data.add(new GCGCRTs(m.RT2, m.RT)); } } data = this.smooth(data, RTrange); Collections.sort(data, new GCGCRTs()); try { PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (GCGCRTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } return fitter.fit(); } catch (Exception ex) { return null; } }
From source file:io.github.msdk.features.ransacaligner.RansacAlignerMethod.java
/** * Return the corrected RT of the row/*from w w w .j av a 2s .co m*/ * * @param row * @param list * @return */ private PolynomialFunction getPolynomialFunction(List<AlignStructMol> list) { List<RTs> data = new ArrayList<RTs>(); for (AlignStructMol m : list) { if (m.Aligned) { data.add(new RTs(m.RT2, m.RT)); } } data = this.smooth(data); Collections.sort(data, new RTs()); double[] xval = new double[data.size()]; double[] yval = new double[data.size()]; int i = 0; for (RTs rt : data) { xval[i] = rt.RT; yval[i++] = rt.RT2; } PolynomialFitter fitter = new PolynomialFitter(3, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } try { return fitter.fit(); } catch (Exception ex) { return null; } }