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build: replace org.jlab.plugins:trackfitter (#1501)
1 parent 09ef81a commit 14510e6

14 files changed

Lines changed: 131 additions & 139 deletions

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‎common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/utilities/ProbChi2perNDF.java‎

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@@ -0,0 +1,23 @@
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package org.jlab.clas.tracking.utilities;
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import org.apache.commons.math3.special.Gamma;
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/** Chi-square probability utilities */
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public class ProbChi2perNDF {
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/**
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* Returns the upper-tail probability (survival function, or p-value) of the
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* chi-square distribution: P(X >= chi2) for X ~ χ²(ndf).
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* @param chi2 the chi-square statistic
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* @param ndf the number of degrees of freedom
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* @return the probability of observing a chi-square value at least as large as {@code chi2}, in the range [0, 1]
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*/
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public static double prob(double chi2, int ndf) {
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if(ndf <= 0)
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return 0.0;
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if(chi2 <= 0.0) { // edge cases follow ROOT's `TMath::Prob` conventions
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return chi2 < 0.0 ? 0.0 : 1.0;
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}
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return Gamma.regularizedGammaQ(0.5 * ndf, 0.5 * chi2);
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}
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}

‎common-tools/coat-libs/pom.xml‎

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@@ -36,12 +36,6 @@
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<artifactId>j4ml-clas12</artifactId>
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</dependency>
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<dependency>
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<groupId>org.jlab.plugins</groupId>
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<artifactId>trackfitter</artifactId>
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<version>1.0</version>
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</dependency>
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<dependency>
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<groupId>org.jlab.clas</groupId>
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<artifactId>clas-io</artifactId>

‎reconstruction/cvt/pom.xml‎

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@@ -85,11 +85,6 @@
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<scope>test</scope>
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<type>jar</type>
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</dependency>
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<dependency>
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<groupId>org.jlab.plugins</groupId>
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<artifactId>trackfitter</artifactId>
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<version>1.0</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>

‎reconstruction/cvt/src/main/java/org/jlab/rec/cvt/Constants.java‎

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@@ -269,7 +269,7 @@ public static double getRCUT() {
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return RCUT;
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}
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public static void setRCUT(double r) {
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private static void setRCUT(double r) {
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RCUT = r;
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}
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@@ -281,7 +281,7 @@ public static double getZRANGE() {
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return ZRANGE;
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}
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public static void setZRANGE(double zr) {
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private static void setZRANGE(double zr) {
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ZRANGE = zr;
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}
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‎reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CosmicFitter.java‎

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@@ -6,7 +6,7 @@
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import org.jlab.geom.prim.Point3D;
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import org.jlab.geom.prim.Vector3D;
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import org.jlab.rec.cvt.trajectory.Ray;
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import trackfitter.fitter.utilities.ProbChi2perNDF;
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import org.jlab.clas.tracking.utilities.ProbChi2perNDF;
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/**
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* A fitter which does sequential fit (for x, y coordinates) and then (for r, z
@@ -21,7 +21,6 @@ public class CosmicFitter {
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private CosmicFitPars _rayfitoutput;
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private LineFitPars _linefitparsRhoZ;
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private LineFitPars _linefitparsYX;
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/**
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* Status of the HelicalTrackFit
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*/
@@ -164,7 +163,7 @@ public FitStatus fit2(List<Double> X, List<Double> Y, List<Double> Z, List<Doubl
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//Line fits
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_linefitYX = new LineFitter();
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boolean linefitstatusXYOK = _linefitYX.fitStatus(Y, X, errRt, new ArrayList<>(X.size()), X.size());
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_linefitYX.fitStatus(Y, X, errRt, new ArrayList<>(X.size()), X.size());
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_linefitRhoZ = new LineFitter();
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boolean linefitstatusOK = _linefitRhoZ.fitStatus(Rho, Z, errRho, ErrZ, Z.size());
@@ -174,7 +173,6 @@ public FitStatus fit2(List<Double> X, List<Double> Y, List<Double> Z, List<Doubl
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}
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// Get the results of the fits
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_linefitparsRhoZ = _linefitRhoZ.getFit();
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_linefitparsYX = _linefitYX.getFit();
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double fit_tandip = _linefitparsRhoZ.slope();
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double fit_Z0 = _linefitparsRhoZ.intercept();

‎reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/LineFitPars.java‎

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package org.jlab.rec.cvt.fit;
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import org.jlab.rec.cvt.trajectory.Ray;
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import trackfitter.fitter.utilities.ProbChi2perNDF;
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import org.jlab.clas.tracking.utilities.ProbChi2perNDF;
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/**
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* The fit parameters of a line fit returned by LineFitter

‎reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Track.java‎

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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.jlab.rec.cvt.trajectory.Helix;
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import org.jlab.rec.cvt.trajectory.StateVec;
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import org.jlab.rec.cvt.trajectory.Trajectory;
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import trackfitter.fitter.utilities.ProbChi2perNDF;
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import org.jlab.clas.tracking.utilities.ProbChi2perNDF;
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/**
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* A class representing track candidates in the CVT. A track has a trajectory
@@ -328,9 +327,9 @@ else if(this.getChi2() > Constants.CHI2CUT * (this.getNDF() + 5))
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return false;
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if(this.getNDF() < Constants.NDFCUT)
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return false;
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if(this.getHelix().radius() < Constants.getInstance().getRCUT())
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if(this.getHelix().radius() < Constants.getRCUT())
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return false;
333-
if(Math.abs(Geometry.getInstance().getTargetZOffset()-this.getHelix().getZ0()) > Geometry.getInstance().getTargetHalfLength()+Constants.getInstance().getZRANGE())
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if(Math.abs(Geometry.getInstance().getTargetZOffset()-this.getHelix().getZ0()) > Geometry.getInstance().getTargetHalfLength()+Constants.getZRANGE())
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return false;
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else
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return true;

‎reconstruction/dc/pom.xml‎

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<artifactId>snr</artifactId>
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<version>14.2.1-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.jlab.plugins</groupId>
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<artifactId>trackfitter</artifactId>
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<version>1.0</version>
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</dependency>
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<dependency>
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<groupId>org.jlab.clas</groupId>
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<artifactId>swim-tools</artifactId>

‎reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/RecoBankWriter.java‎

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import org.jlab.rec.dc.segment.Segment;
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import org.jlab.rec.dc.track.Track;
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16-
import trackfitter.fitter.utilities.*;
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import org.jlab.clas.tracking.utilities.ProbChi2perNDF;
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/**
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* A class to fill the reconstructed DC banks
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3737
public void updateListsWithClusterInfo(List<FittedHit> fhits,
3838
List<FittedCluster> clusters) {
39-
ArrayList rmHits = new ArrayList<FittedHit>();
40-
ArrayList addHits = new ArrayList<FittedHit>();
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List<FittedHit> rmHits = new ArrayList<>();
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List<FittedHit> addHits = new ArrayList<>();
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for (int i = 0; i < clusters.size(); i++) {
4242
clusters.get(i).set_Id(i + 1);
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for (int j = 0; j < clusters.get(i).size(); j++) {
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DataBank bank = event.createBank(name, cluslist.size());
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int[] hitIdxArray = new int[12];
207-
if(cluslist==null)
208-
return bank;
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for (int i = 0; i < cluslist.size(); i++) {
210208
if (cluslist.get(i) == null || cluslist.get(i).get_Id() == -1) {
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continue;

‎reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossListFinder.java‎

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import org.jlab.rec.dc.segment.Segment;
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import org.jlab.rec.dc.timetodistance.TimeToDistanceEstimator;
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import org.jlab.utils.groups.IndexedTable;
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import trackfitter.fitter.LineFitter;
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import org.jlab.rec.dc.track.fit.basefit.LineFitter;
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/**
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* A class with methods used to find lists of crosses. This is the Pattern Recognition step used in track seeding, to

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