From 842dc1c791d1cfb2627eeee57c330e56dcce0c9c Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@jlab.org>
Date: Wed, 6 May 2026 17:16:05 -0400
Subject: [PATCH 1/7] switch to indexed loops

---
 .../jlab/rec/dc/cluster/ClusterFitter.java    | 76 ++++++++-----------
 1 file changed, 33 insertions(+), 43 deletions(-)

diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
index 3744a3ff65..eb5b9aea29 100644
--- a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
+++ b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
@@ -3,36 +3,33 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import org.jlab.clas.clas.math.FastMath;
 import org.jlab.detector.geant4.v2.DCGeant4Factory;
 
 import org.jlab.geom.prim.Line3D;
 import org.jlab.geom.prim.Point3D;
 import org.jlab.geom.prim.Vector3D;
-import org.jlab.rec.dc.hit.FittedHit;
 import org.jlab.rec.dc.track.fit.basefit.LineFitPars;
 import org.jlab.rec.dc.track.fit.basefit.LineFitter;
 import org.jlab.rec.dc.Constants; 
 
 public class ClusterFitter {
 
-
     /**
      * Fits a cluster to a line
      *
      */
     private LineFitPars FitPars;
-    private final List<ArrayList<Double>> FitArray = new ArrayList<ArrayList<Double>>(); 
-    private final List<Double> x = new ArrayList<Double>();
-    private final List<Double> y = new ArrayList<Double>();
-    private final List<Double> ex = new ArrayList<Double>();
-    private final List<Double> ey = new ArrayList<Double>();
+    private final List<ArrayList<Double>> FitArray = new ArrayList<>(); 
+    private final List<Double> x = new ArrayList<>();
+    private final List<Double> y = new ArrayList<>();
+    private final List<Double> ex = new ArrayList<>();
+    private final List<Double> ey = new ArrayList<>();
     private final double stereo = Constants.COS6;
     
     private String CoordinateSystem; // LC= local, TSC = tilted Sector
-    public ClusterFitter() {
-        // TODO Auto-generated constructor stub
-    }
+
+    public ClusterFitter() {}
+
     public void reset() {
         for(int i =0; i<FitArray.size(); i++)
             FitArray.get(i).clear();
@@ -42,18 +39,11 @@ public void reset() {
         ex.clear();
         ey.clear();
     }
+
     public void SetFitArray(FittedCluster clus, String system) {
 
         Collections.sort(clus);
-        //for(int i =0; i<FitArray.size(); i++)
-        //    FitArray.get(i).clear();
         reset();
-        //double[][] fitArray = new double[4][clus.size()];
-        //double[] x = new double[clus.size()];
-        //double[] y = new double[clus.size()];
-        //double[] ex = new double[clus.size()];
-        //double[] ey = new double[clus.size()];
-        
         
         for (int i = 0; i < clus.size(); i++) {
             if (system.equals("LC")) {
@@ -77,8 +67,8 @@ public void SetFitArray(FittedCluster clus, String system) {
         FitArray.add((ArrayList<Double>) ex);
         FitArray.add((ArrayList<Double>) y);
         FitArray.add((ArrayList<Double>) ey);
-        
     }
+
     /**
      * 
      * @param clus fitted cluster
@@ -242,23 +232,23 @@ public void SetResidualDerivedParams(FittedCluster clus, boolean calcTimeResidua
      * @return the fitted cluster with the best fit chi2
      */
     public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String system) {
-        //init
+
         FittedCluster BestCluster = null;
         double bestChisq = 999999999.;
-        //	double bestClusx0=0;
 
-        for (FittedCluster clusCand : clusters) {
-            if(isBrickWall(clusCand)) {
+        for (int i=0; i<clusters.size(); i++) {
+            if (isBrickWall(clusters.get(i))) {
                 int LRSum=0;
-                for(FittedHit hit : clusCand) {
-                    LRSum+=hit.get_LeftRightAmb();
+                for(int j=0; j<clusters.get(i).size(); j++) {
+                    LRSum += clusters.get(i).get(j).get_LeftRightAmb();
                 }
                 if(LRSum!=0)
                     continue;
             }
-            SetFitArray(clusCand, system); // set the array of measurements according to the system used in the analysis
+            // set the array of measurements according to the system used in the analysis
+            SetFitArray(clusters.get(i), system);
             // do the fit and get the chisq
-            Fit(clusCand, true);
+            Fit(clusters.get(i), true);
             if (FitPars == null) {
                 continue;
             }
@@ -266,14 +256,11 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
 
             if (chisq < bestChisq) {
                 bestChisq = chisq;
-                BestCluster = clusCand;
-                //		bestClusx0 = FitArray[0][0];
+                BestCluster = clusters.get(i);
             }
         }
-        //SetSegmentLineParameters(bestClusx0, BestCluster) ;
         
         return BestCluster;
-
     }
 
     /**
@@ -306,19 +293,22 @@ private Point3D get_PointOnLine(double d, double the_slope,
      */
     private boolean isBrickWall(FittedCluster clusCand) {
         boolean isBW = true;
-        int sumWireNum = 0;
-        if(clusCand.size()!=6)
-            isBW=false;
-        
-        for(FittedHit hit : clusCand) {
-            sumWireNum+=hit.get_Wire();
+        if (clusCand.size() != 6) {
+            isBW = false;
+        }
+        else {
+            int sumWireNum = 0;
+            for (int i=0; i<clusCand.size(); i++) {
+                sumWireNum += clusCand.get(i).get_Wire();
+            }
+            for (int i=0; i<clusCand.size(); i++) {
+                if (clusCand.get(i).get_Wire()*clusCand.size()!=sumWireNum) {
+                    isBW = false;
+                    break;
+                }
+            }
         }
-        for(FittedHit hit : clusCand) {
-            if(hit.get_Wire()*clusCand.size()!=sumWireNum)
-                isBW = false;
-        }    
         return isBW;
     }
-
     
 }

From a80ff2ee47344b5020368eff3b22528de548bdc4 Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@jlab.org>
Date: Wed, 6 May 2026 17:23:41 -0400
Subject: [PATCH 2/7] switch to indexed loops

---
 .../java/cnuphys/magfield/CompositeField.java | 29 +++++++++----------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java b/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
index f80a8560db..e8118b77db 100644
--- a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
+++ b/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
@@ -99,8 +99,8 @@ public boolean hasSolenoid() {
 	 * @return <code>true</code> if we have a transverse solenoid
 	 */
 	public boolean hasTransverseSolenoid() {
-		for (IMagField field : this) {
-			if (field instanceof TransverseSolenoid) {
+		for (int i=0; i<this.size(); i++) {
+			if (this.get(i) instanceof TransverseSolenoid) {
 				return true;
 			}
 		}
@@ -111,8 +111,8 @@ public boolean hasTransverseSolenoid() {
 	@Override
 	public float getB1(int index) {
 		float b = 0f;
-		for (IMagField field : this) {
-			b += field.getB1(index);
+		for (int i=0; i<this.size(); i++) {
+			b += this.get(i).getB1(index);
 		}
 		return b;
 	}
@@ -120,8 +120,8 @@ public float getB1(int index) {
 	@Override
 	public float getB2(int index) {
 		float b = 0f;
-		for (IMagField field : this) {
-			b += field.getB2(index);
+		for (int i=0; i<this.size(); i++) {
+			b += this.get(i).getB2(index);
 		}
 		return b;
 	}
@@ -129,8 +129,8 @@ public float getB2(int index) {
 	@Override
 	public float getB3(int index) {
 		float b = 0f;
-		for (IMagField field : this) {
-			b += field.getB3(index);
+		for (int i=0; i<this.size(); i++) {
+			b += this.get(i).getB3(index);
 		}
 		return b;
 	}
@@ -138,8 +138,8 @@ public float getB3(int index) {
 	@Override
 	public float getMaxFieldMagnitude() {
 		float max = 0;
-		for (IMagField field : this) {
-			max = Math.max(max, field.getMaxFieldMagnitude());
+		for (int i=0; i<this.size(); i++) {
+			max = Math.max(max, this.get(i).getMaxFieldMagnitude());
 		}
 		return max;
 	}
@@ -157,16 +157,15 @@ public double getScaleFactor() {
 	@Override
 	public void printConfiguration(PrintStream ps) {
 		ps.println("COMPOSITE FIELD");
-		for (IMagField field : this) {
-			field.printConfiguration(ps);
-
+		for (int i=0; i<this.size(); i++) {
+			this.get(i).printConfiguration(ps);
 		}
 	}
 
 	@Override
 	public boolean contains(double x, double y, double z) {
-		for (IMagField field : this) {
-			if (field.contains(x, y, z)) {
+		for (int i=0; i<this.size(); i++) {
+			if (this.get(i).contains(x, y, z)) {
 				return true;
 			}
 		}

From 77aa3a8fddcb39794221e766ee24e21ada464ab1 Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@jlab.org>
Date: Sun, 10 May 2026 17:54:26 -0400
Subject: [PATCH 3/7] revert changes to CompositeField

---
 .../java/cnuphys/magfield/CompositeField.java | 29 ++++++++++---------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java b/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
index e8118b77db..f80a8560db 100644
--- a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
+++ b/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java
@@ -99,8 +99,8 @@ public boolean hasSolenoid() {
 	 * @return <code>true</code> if we have a transverse solenoid
 	 */
 	public boolean hasTransverseSolenoid() {
-		for (int i=0; i<this.size(); i++) {
-			if (this.get(i) instanceof TransverseSolenoid) {
+		for (IMagField field : this) {
+			if (field instanceof TransverseSolenoid) {
 				return true;
 			}
 		}
@@ -111,8 +111,8 @@ public boolean hasTransverseSolenoid() {
 	@Override
 	public float getB1(int index) {
 		float b = 0f;
-		for (int i=0; i<this.size(); i++) {
-			b += this.get(i).getB1(index);
+		for (IMagField field : this) {
+			b += field.getB1(index);
 		}
 		return b;
 	}
@@ -120,8 +120,8 @@ public float getB1(int index) {
 	@Override
 	public float getB2(int index) {
 		float b = 0f;
-		for (int i=0; i<this.size(); i++) {
-			b += this.get(i).getB2(index);
+		for (IMagField field : this) {
+			b += field.getB2(index);
 		}
 		return b;
 	}
@@ -129,8 +129,8 @@ public float getB2(int index) {
 	@Override
 	public float getB3(int index) {
 		float b = 0f;
-		for (int i=0; i<this.size(); i++) {
-			b += this.get(i).getB3(index);
+		for (IMagField field : this) {
+			b += field.getB3(index);
 		}
 		return b;
 	}
@@ -138,8 +138,8 @@ public float getB3(int index) {
 	@Override
 	public float getMaxFieldMagnitude() {
 		float max = 0;
-		for (int i=0; i<this.size(); i++) {
-			max = Math.max(max, this.get(i).getMaxFieldMagnitude());
+		for (IMagField field : this) {
+			max = Math.max(max, field.getMaxFieldMagnitude());
 		}
 		return max;
 	}
@@ -157,15 +157,16 @@ public double getScaleFactor() {
 	@Override
 	public void printConfiguration(PrintStream ps) {
 		ps.println("COMPOSITE FIELD");
-		for (int i=0; i<this.size(); i++) {
-			this.get(i).printConfiguration(ps);
+		for (IMagField field : this) {
+			field.printConfiguration(ps);
+
 		}
 	}
 
 	@Override
 	public boolean contains(double x, double y, double z) {
-		for (int i=0; i<this.size(); i++) {
-			if (this.get(i).contains(x, y, z)) {
+		for (IMagField field : this) {
+			if (field.contains(x, y, z)) {
 				return true;
 			}
 		}

From 8c5ab8e5f417715316505671d7467096b3f100be Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@gmx.com>
Date: Sun, 10 May 2026 20:41:08 -0400
Subject: [PATCH 4/7] Optimize for loop by storing size in a variable

---
 .../main/java/org/jlab/rec/dc/cluster/ClusterFitter.java  | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
index eb5b9aea29..52fd0fbaa6 100644
--- a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
+++ b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
@@ -236,7 +236,8 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
         FittedCluster BestCluster = null;
         double bestChisq = 999999999.;
 
-        for (int i=0; i<clusters.size(); i++) {
+        int size = clusters.size();
+        for (int i=0; i<size; i++) {
             if (isBrickWall(clusters.get(i))) {
                 int LRSum=0;
                 for(int j=0; j<clusters.get(i).size(); j++) {
@@ -298,10 +299,11 @@ private boolean isBrickWall(FittedCluster clusCand) {
         }
         else {
             int sumWireNum = 0;
-            for (int i=0; i<clusCand.size(); i++) {
+            int size = clusCand.size();
+            for (int i=0; i<size; i++) {
                 sumWireNum += clusCand.get(i).get_Wire();
             }
-            for (int i=0; i<clusCand.size(); i++) {
+            for (int i=0; i<size; i++) {
                 if (clusCand.get(i).get_Wire()*clusCand.size()!=sumWireNum) {
                     isBW = false;
                     break;

From 43f6506a97ba5020725fa22da6989c7d0f1c178d Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@gmx.com>
Date: Sun, 10 May 2026 20:42:56 -0400
Subject: [PATCH 5/7] Refactor loop for cluster size calculation

---
 .../main/java/org/jlab/rec/dc/cluster/ClusterFitter.java    | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
index 52fd0fbaa6..e259025272 100644
--- a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
+++ b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
@@ -240,11 +240,13 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
         for (int i=0; i<size; i++) {
             if (isBrickWall(clusters.get(i))) {
                 int LRSum=0;
-                for(int j=0; j<clusters.get(i).size(); j++) {
+                int size2 = clusters.get(i).size();
+                for (int j=0; j<size2; j++) {
                     LRSum += clusters.get(i).get(j).get_LeftRightAmb();
                 }
-                if(LRSum!=0)
+                if (LRSum != 0) {
                     continue;
+                }
             }
             // set the array of measurements according to the system used in the analysis
             SetFitArray(clusters.get(i), system);

From ae5e2ab0299e97507b686f84c2cf2d0b39772ff9 Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@jlab.org>
Date: Tue, 12 May 2026 17:00:29 -0400
Subject: [PATCH 6/7] reduce getter calls

---
 .../org/jlab/rec/dc/cluster/ClusterFitter.java    | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
index e259025272..b93d264e73 100644
--- a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
+++ b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
@@ -238,20 +238,21 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
 
         int size = clusters.size();
         for (int i=0; i<size; i++) {
-            if (isBrickWall(clusters.get(i))) {
+            FittedClusters cluster = clusters.get(i);
+            if (isBrickWall(cluster)) {
                 int LRSum=0;
-                int size2 = clusters.get(i).size();
+                int size2 = cluster.size();
                 for (int j=0; j<size2; j++) {
-                    LRSum += clusters.get(i).get(j).get_LeftRightAmb();
+                    LRSum += cluster.get(j).get_LeftRightAmb();
                 }
                 if (LRSum != 0) {
                     continue;
                 }
             }
             // set the array of measurements according to the system used in the analysis
-            SetFitArray(clusters.get(i), system);
+            SetFitArray(cluster, system);
             // do the fit and get the chisq
-            Fit(clusters.get(i), true);
+            Fit(cluster, true);
             if (FitPars == null) {
                 continue;
             }
@@ -259,7 +260,7 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
 
             if (chisq < bestChisq) {
                 bestChisq = chisq;
-                BestCluster = clusters.get(i);
+                BestCluster = cluster;
             }
         }
         
@@ -306,7 +307,7 @@ private boolean isBrickWall(FittedCluster clusCand) {
                 sumWireNum += clusCand.get(i).get_Wire();
             }
             for (int i=0; i<size; i++) {
-                if (clusCand.get(i).get_Wire()*clusCand.size()!=sumWireNum) {
+                if (clusCand.get(i).get_Wire()*size != sumWireNum) {
                     isBW = false;
                     break;
                 }

From 47d7a06a66071f06fddcbd301eeac88d0386c1a8 Mon Sep 17 00:00:00 2001
From: Nathan Baltzell <baltzell@jlab.org>
Date: Tue, 12 May 2026 17:05:09 -0400
Subject: [PATCH 7/7] fix oops

---
 .../dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
index b93d264e73..40a5b39d81 100644
--- a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
+++ b/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFitter.java
@@ -238,7 +238,7 @@ public FittedCluster BestClusterSelector(List<FittedCluster> clusters, String sy
 
         int size = clusters.size();
         for (int i=0; i<size; i++) {
-            FittedClusters cluster = clusters.get(i);
+            FittedCluster cluster = clusters.get(i);
             if (isBrickWall(cluster)) {
                 int LRSum=0;
                 int size2 = cluster.size();