Alert engine for combined ATOF/AHDC reconstruction

.gitlab-ci.yml

@@ -72,6 +72,7 @@ shared_for_alert_tests:
 
 coatjava:singularity:
   image: eicweb.phy.anl.gov:4567/containers/image_recipes/ubuntu_dind:latest
+  needs: ["coatjava_build"]
   tags:
      - silicon
   allow_failure: true
@@ -82,4 +83,21 @@ coatjava:singularity:
       paths:
         - coatjava.sif
 
+create-pages:
+  image: codecr.jlab.org/hallb/alert/coatjava/coatjava:development
+  script:
+    - export MAVEN_OPTS=" -Dfile.encoding=UTF-8"
+    - echo "${CI_COMMIT_REF_NAME}"
+    - ls -lrth
+    - mvn --version
+    - java --version 
+    - ls -lrth
+    - pwd
+    - ls -lrth docs/javadoc
+    - ./build-javadocs.sh 
+    - ls -lrth
+    - ls -lrth docs/
+    - ls -lrth docs/javadoc
+    - mv docs/javadoc public
+  pages: true  # specifies that this is a Pages job and publishes the default public directory
 

build-javadocs.sh

@@ -5,8 +5,10 @@
 
 set -e
 
+export MAVEN_OPTS=" -Dfile.encoding=UTF-8"
+
 ##### generate documentation
-mvn javadoc:javadoc -Ddoclint=none
+mvn javadoc:javadoc -Ddoclint=none 
 
 
 ##### collect documentation

pom.xml

@@ -1,10 +1,16 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+  </properties>
+
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas12</artifactId>
   <version>12.0.1t-SNAPSHOT</version>
   <packaging>pom</packaging>
 
+
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/Model.java

@@ -16,6 +16,11 @@
 import java.io.IOException;
 import java.nio.file.Paths;
 
+/** Model of What.
+ * 
+ *
+ * \todo fix class name 
+ */
 public class Model {
     private ZooModel<float[], Float> model;
 

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Cluster/ClusterFinder.java

@@ -5,6 +5,11 @@
 import java.util.ArrayList;
 import java.util.List;
 
+/** ClusterFinder
+ *
+ * \todo description of what it does and how it works
+ *
+ */
 public class ClusterFinder {
 
 	private final ArrayList<Cluster> _AHDCClusters                 = new ArrayList<>();
@@ -55,6 +60,7 @@ private void find_associate_cluster(PreCluster precluster, List<PreCluster> AHDC
 	}
 
 	public void findCluster(List<PreCluster> AHDC_precluster_list) {
+            /// \todo parameters should be exposed 
 		int window           = 30;
 		int minimal_distance = 10;
 

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/Distance.java

@@ -7,6 +7,11 @@
 import java.util.Arrays;
 import java.util.List;
 
+/**  Distance.
+ *
+ * \todo What is this class and what does it do?
+ *
+ */ 
 public class Distance {
 
     private ArrayList<Track> _AHDCTracks;

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitJava.java

@@ -1,8 +1,14 @@
 package org.jlab.rec.ahdc.HelixFit;
 
-
+/** Helix Fit.
+ *
+ * This appears to be some code translation.
+ */
 public class HelixFitJava {
 
+    /** \todo What does this method do
+     *  \what does its name even mean?
+     */
 	void rwsmav(double r[], double a[], double v[], int n)
 	{
 	    //  Author: Martin Poppe. r[n] = a[n,n]*v[n]

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitObject.java

@@ -1,6 +1,6 @@
 package org.jlab.rec.ahdc.HelixFit;
 
-/**
+/** Helix track model.
  *
  * @author davidpayette
  */

reconstruction/alert/src/main/java/org/jlab/rec/ahdc/PreCluster/PreCluster.java

@@ -4,6 +4,11 @@
 
 import java.util.ArrayList;
 
+/** PreCluster.
+ *
+ *  \todo What is a pre cluster?
+ *
+ */
 public class PreCluster implements Comparable<PreCluster> {
 
 	private int            _Id;

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

@@ -0,0 +1,81 @@
+package org.jlab.rec.alert.banks;
+
+import java.util.ArrayList;
+import org.jlab.io.base.DataBank;
+import org.jlab.io.base.DataEvent;
+import org.jlab.rec.alert.projections.TrackProjection;
+
+/**
+ * The ALERT {@code RecoBankWriter} writes the banks needed for the ALERT
+ * reconstruction: track projections.
+ *
+ * @author Noemie Pilleux
+ * @author Whit Armstrong
+ */
+public class RecoBankWriter {
+
+    /**
+     * Writes the bank of track projections.
+     *
+     * @param event the {@link DataEvent} in which to add the bank
+     * @param projections the {@link ArrayList} of {@link TrackProjection}
+     * containing the track projection info to be added to the bank
+     *
+     * @return {@link DataBank} the bank with all the projected tracks in the
+     * event.
+     *
+     */
+    public static DataBank fillProjectionsBank(DataEvent event, ArrayList<TrackProjection> projections) {
+
+        DataBank bank = event.createBank("ALERT::Projections", projections.size());
+
+        if (bank == null) {
+            System.err.println("COULD NOT CREATE A ALERT::Projections BANK!!!!!!");
+            return null;
+        }
+        for (int i = 0; i < projections.size(); i++) {
+            TrackProjection projection = projections.get(i);
+            bank.setShort("id", i, (short) (i + 1));
+            bank.setShort("trackID", i, (short) projection.getTrackID());
+            bank.setFloat("x_at_bar", i, (float) projection.getBarIntersect().x());
+            bank.setFloat("y_at_bar", i, (float) projection.getBarIntersect().y());
+            bank.setFloat("z_at_bar", i, (float) projection.getBarIntersect().z());
+            bank.setFloat("L_at_bar", i, (float) projection.getBarPathLength());
+            bank.setFloat("L_in_bar", i, (float) projection.getBarInPathLength());
+            bank.setFloat("x_at_wedge", i, (float) projection.getWedgeIntersect().x());
+            bank.setFloat("y_at_wedge", i, (float) projection.getWedgeIntersect().y());
+            bank.setFloat("z_at_wedge", i, (float) projection.getWedgeIntersect().z());
+            bank.setFloat("L_at_wedge", i, (float) projection.getWedgePathLength());
+            bank.setFloat("L_in_wedge", i, (float) projection.getWedgeInPathLength());
+        }
+        return bank;
+    }
+
+    /**
+     * Appends the alert match banks to an event.
+     *
+     * @param event the {@link DataEvent} in which to append the banks
+     * @param projections the {@link ArrayList} of {@link TrackProjection} containing the 
+     * track projections info to be added
+     *
+     * @return 0 if it worked, 1 if it failed
+     *
+     */
+    public int appendMatchBanks(DataEvent event, ArrayList<TrackProjection> projections) {
+
+        DataBank projbank = this.fillProjectionsBank(event, projections);
+        if (projbank != null) {
+            event.appendBank(projbank);
+        } else {
+            return 1;
+        }
+        return 0;
+    }
+
+    /**
+     * @param args the command line arguments
+     */
+    public static void main(String[] args) {
+    }
+
+}