From 3cfbb4c9162354ca9274a7397a7b04f821b02ca8 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 29 May 2024 18:12:34 -0500
Subject: [PATCH 01/35] create initial types of collections defined in gsoc

---
 js/types/Cluster.js      | 17 +++++++++++++++++
 js/types/ParticleID.js   | 10 ++++++++++
 js/types/RecoParticle.js | 17 +++++++++++++++++
 js/types/Track.js        | 15 +++++++++++++++
 js/types/Vertex.js       | 13 +++++++++++++
 5 files changed, 72 insertions(+)
 create mode 100644 js/types/Cluster.js
 create mode 100644 js/types/ParticleID.js
 create mode 100644 js/types/RecoParticle.js
 create mode 100644 js/types/Track.js
 create mode 100644 js/types/Vertex.js

diff --git a/js/types/Cluster.js b/js/types/Cluster.js
new file mode 100644
index 00000000..a1d842aa
--- /dev/null
+++ b/js/types/Cluster.js
@@ -0,0 +1,17 @@
+export class Cluster {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.energy = 0; // GeV
+    this.energyError = 0; // GeV
+    this.position = []; // mm
+    this.positionError = [];
+    this.iTheta = 0;
+    this.phi = 0;
+    this.directionError; // mm^2
+    this.shapeParameters = [];
+    this.subdetectorEnergies = [];
+    this.clusters = [];
+    this.hits = [];
+  }
+}
diff --git a/js/types/ParticleID.js b/js/types/ParticleID.js
new file mode 100644
index 00000000..69f5e890
--- /dev/null
+++ b/js/types/ParticleID.js
@@ -0,0 +1,10 @@
+export class ParticleID {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.pdg = 0;
+    this.algorithmType = 0;
+    this.likelihood = 0;
+    this.parameters = [];
+  }
+}
diff --git a/js/types/RecoParticle.js b/js/types/RecoParticle.js
new file mode 100644
index 00000000..4f68b320
--- /dev/null
+++ b/js/types/RecoParticle.js
@@ -0,0 +1,17 @@
+export class ReconstructedParticle {
+  constructor() {
+    // Physics properties
+    this.pdg = 0;
+    this.energy = 0; // GeV
+    this.momentum = 0; // GeV
+    this.referencePoint = 0; // mm
+    this.charge = 0;
+    this.mass = 0; // GeV
+    this.goodnessOfPID = 0;
+    this.covMatrix = [];
+    this.startVertex = [];
+    this.clusters = [];
+    this.tracks = [];
+    this.particles = [];
+  }
+}
diff --git a/js/types/Track.js b/js/types/Track.js
new file mode 100644
index 00000000..5a910826
--- /dev/null
+++ b/js/types/Track.js
@@ -0,0 +1,15 @@
+export class Track {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.chi2 = 0;
+    this.ndf = 0;
+    this.dEdx = 0;
+    this.dEdxError = 0;
+    this.radiusOfInnermostHit = 0;
+    this.subdetectorHitNumbers = [];
+    this.dxQuantities = [];
+    this.trackerHits = [];
+    this.tracks = [];
+  }
+}
diff --git a/js/types/Vertex.js b/js/types/Vertex.js
new file mode 100644
index 00000000..d954723c
--- /dev/null
+++ b/js/types/Vertex.js
@@ -0,0 +1,13 @@
+export class Vertex {
+  constructor() {
+    // Physics properties
+    this.primary = 0;
+    this.chi2 = 0;
+    this.probability = 0;
+    this.position = 0; // mm
+    this.covMatrix = [];
+    this.algorithmType = 0;
+    this.parameters = 0;
+    this.associatedParticles = [];
+  }
+}

From 186024e23eef19fd182a158b06a535daf26c4081 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 30 May 2024 20:38:12 -0500
Subject: [PATCH 02/35] loading function to check if types are correctly
 working

---
 js/types/Cluster.js        |  17 ----
 js/types/ParticleID.js     |  10 ---
 js/types/RecoParticle.js   |  17 ----
 js/types/Track.js          |  15 ----
 js/types/Vertex.js         |  13 ---
 js/types/load.js           |  62 +++++++++++++
 js/types/reconstruction.js | 175 +++++++++++++++++++++++++++++++++++++
 7 files changed, 237 insertions(+), 72 deletions(-)
 delete mode 100644 js/types/Cluster.js
 delete mode 100644 js/types/ParticleID.js
 delete mode 100644 js/types/RecoParticle.js
 delete mode 100644 js/types/Track.js
 delete mode 100644 js/types/Vertex.js
 create mode 100644 js/types/load.js
 create mode 100644 js/types/reconstruction.js

diff --git a/js/types/Cluster.js b/js/types/Cluster.js
deleted file mode 100644
index a1d842aa..00000000
--- a/js/types/Cluster.js
+++ /dev/null
@@ -1,17 +0,0 @@
-export class Cluster {
-  constructor() {
-    // Physics properties
-    this.type = 0;
-    this.energy = 0; // GeV
-    this.energyError = 0; // GeV
-    this.position = []; // mm
-    this.positionError = [];
-    this.iTheta = 0;
-    this.phi = 0;
-    this.directionError; // mm^2
-    this.shapeParameters = [];
-    this.subdetectorEnergies = [];
-    this.clusters = [];
-    this.hits = [];
-  }
-}
diff --git a/js/types/ParticleID.js b/js/types/ParticleID.js
deleted file mode 100644
index 69f5e890..00000000
--- a/js/types/ParticleID.js
+++ /dev/null
@@ -1,10 +0,0 @@
-export class ParticleID {
-  constructor() {
-    // Physics properties
-    this.type = 0;
-    this.pdg = 0;
-    this.algorithmType = 0;
-    this.likelihood = 0;
-    this.parameters = [];
-  }
-}
diff --git a/js/types/RecoParticle.js b/js/types/RecoParticle.js
deleted file mode 100644
index 4f68b320..00000000
--- a/js/types/RecoParticle.js
+++ /dev/null
@@ -1,17 +0,0 @@
-export class ReconstructedParticle {
-  constructor() {
-    // Physics properties
-    this.pdg = 0;
-    this.energy = 0; // GeV
-    this.momentum = 0; // GeV
-    this.referencePoint = 0; // mm
-    this.charge = 0;
-    this.mass = 0; // GeV
-    this.goodnessOfPID = 0;
-    this.covMatrix = [];
-    this.startVertex = [];
-    this.clusters = [];
-    this.tracks = [];
-    this.particles = [];
-  }
-}
diff --git a/js/types/Track.js b/js/types/Track.js
deleted file mode 100644
index 5a910826..00000000
--- a/js/types/Track.js
+++ /dev/null
@@ -1,15 +0,0 @@
-export class Track {
-  constructor() {
-    // Physics properties
-    this.type = 0;
-    this.chi2 = 0;
-    this.ndf = 0;
-    this.dEdx = 0;
-    this.dEdxError = 0;
-    this.radiusOfInnermostHit = 0;
-    this.subdetectorHitNumbers = [];
-    this.dxQuantities = [];
-    this.trackerHits = [];
-    this.tracks = [];
-  }
-}
diff --git a/js/types/Vertex.js b/js/types/Vertex.js
deleted file mode 100644
index d954723c..00000000
--- a/js/types/Vertex.js
+++ /dev/null
@@ -1,13 +0,0 @@
-export class Vertex {
-  constructor() {
-    // Physics properties
-    this.primary = 0;
-    this.chi2 = 0;
-    this.probability = 0;
-    this.position = 0; // mm
-    this.covMatrix = [];
-    this.algorithmType = 0;
-    this.parameters = 0;
-    this.associatedParticles = [];
-  }
-}
diff --git a/js/types/load.js b/js/types/load.js
new file mode 100644
index 00000000..7c88b530
--- /dev/null
+++ b/js/types/load.js
@@ -0,0 +1,62 @@
+import jsonData from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" }; // node 20
+import {
+  Cluster,
+  ParticleID,
+  ReconstructedParticle,
+  Vertex,
+  Track,
+} from "./reconstruction.js";
+
+const loaders = {
+  ReconstructedParticle: ReconstructedParticle.load,
+  ParticleID: ParticleID.load,
+  Vertex: Vertex.load,
+  Track: Track.load,
+  Cluster: Cluster.load,
+};
+
+const loadersConfig = [
+  "ReconstructedParticle",
+  "ParticleID",
+  "Vertex",
+  "Track",
+  "Cluster",
+];
+
+function selectedParticles(loaders, particles) {
+  let newLoader = {};
+
+  for (const particle of particles) {
+    if (loaders.hasOwnProperty(particle)) {
+      newLoader[particle] = loaders[particle];
+    }
+  }
+
+  return newLoader;
+}
+
+export function loadParticles(event, loadersConfig) {
+  const eventData = Object.values(jsonData["Event " + event]);
+
+  const particles = [];
+
+  const loader = selectedParticles(loaders, loadersConfig);
+
+  for (const [type, loadFunction] of Object.entries(loader)) {
+    const particlesType = eventData.filter(
+      (element) => element.collType === `edm4hep::${type}Collection`
+    );
+
+    particlesType.forEach((collection) => {
+      const loadedParticles = loadFunction(collection.collection);
+    });
+  }
+  try {
+  } catch (error) {
+    console.error(error);
+  }
+
+  return particles;
+}
+
+loadParticles(4, loadersConfig);
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
new file mode 100644
index 00000000..f072440f
--- /dev/null
+++ b/js/types/reconstruction.js
@@ -0,0 +1,175 @@
+export class Cluster {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.energy = 0; // GeV
+    this.energyError = 0; // GeV
+    this.position = []; // mm
+    this.positionError = [];
+    this.iTheta = 0;
+    this.phi = 0;
+    this.directionError = {}; // mm^2
+    this.shapeParameters = [];
+    this.subdetectorEnergies = [];
+    this.clusters = [];
+    this.hits = [];
+  }
+
+  static load(collection) {
+    const particles = [];
+
+    for (const [index, particle] of collection.entries()) {
+      const cluster = new Cluster();
+      cluster.index = index;
+
+      cluster.type = particle.type;
+      cluster.energy = particle.energy;
+      cluster.energyError = particle.energyError;
+      cluster.position = particle.position;
+      cluster.positionError = particle.positionError;
+      cluster.iTheta = particle.iTheta;
+      cluster.phi = particle.phi;
+      cluster.directionError = particle.directionError;
+      cluster.shapeParameters = particle.shapeParameters;
+      cluster.subdetectorEnergies = particle.subdetectorEnergies;
+      cluster.clusters = particle.clusters;
+      cluster.hits = particle.hits;
+
+      particles.push(cluster);
+    }
+
+    return particles;
+  }
+}
+
+export class ParticleID {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.pdg = 0;
+    this.algorithmType = 0;
+    this.likelihood = 0;
+    this.parameters = [];
+    this.particle = [];
+  }
+
+  static load(collection) {
+    const particles = [];
+
+    for (const [index, particle] of collection.entries()) {
+      const particleID = new ParticleID();
+      particleID.index = index;
+
+      particleID.type = particle.type;
+      particleID.pdg = particle.pdg;
+      particleID.algorithmType = particle.algorithmType;
+      particleID.likelihood = particle.likelihood;
+      particleID.parameters = particle.parameters;
+
+      particles.push(particleID);
+    }
+
+    return particles;
+  }
+}
+
+export class ReconstructedParticle {
+  constructor() {
+    // Physics properties
+    this.pdg = 0;
+    this.energy = 0; // GeV
+    this.momentum = {}; // GeV
+    this.referencePoint = {}; // mm
+    this.charge = 0;
+    this.mass = 0; // GeV
+    this.goodnessOfPID = 0;
+    this.covMatrix = [];
+    this.startVertex = {};
+    this.clusters = [];
+    this.tracks = [];
+    this.particles = [];
+  }
+
+  static load(collection) {
+    const particles = [];
+
+    for (const [index, particle] of collection.entries()) {
+      const reconstructedParticle = new ReconstructedParticle();
+      reconstructedParticle.index = index;
+
+      reconstructedParticle.energy = particle.energy;
+      reconstructedParticle.momentum = particle.momentum;
+      reconstructedParticle.referencePoint = particle.referencePoint;
+      reconstructedParticle.charge = particle.charge;
+      reconstructedParticle.mass = particle.mass;
+      reconstructedParticle.goodnessOfPID = particle.goodnessOfPID;
+      reconstructedParticle.covMatrix = particle.covMatrix;
+      reconstructedParticle.startVertex = particle.startVertex;
+      reconstructedParticle.clusters = particle.clusters;
+      reconstructedParticle.tracks = particle.tracks;
+      reconstructedParticle.particles = particle.particles;
+
+      particles.push(reconstructedParticle);
+    }
+
+    return particles;
+  }
+}
+
+export class Vertex {
+  constructor() {
+    // Physics properties
+    this.primary = 0;
+    this.chi2 = 0;
+    this.probability = 0;
+    this.position = 0; // mm
+    this.covMatrix = [];
+    this.algorithmType = 0;
+    this.parameters = 0;
+    this.associatedParticles = [];
+  }
+
+  static load() {}
+}
+
+export class Track {
+  constructor() {
+    // Physics properties
+    this.type = 0;
+    this.chi2 = 0;
+    this.ndf = 0;
+    this.dEdx = 0;
+    this.dEdxError = 0;
+    this.radiusOfInnermostHit = 0;
+    this.subdetectorHitNumbers = [];
+    this.trackStates = [];
+    this.dxQuantities = [];
+    this.trackerHits = [];
+    this.tracks = [];
+  }
+
+  static load(collection) {
+    const particles = [];
+
+    for (const [index, particle] of collection.entries()) {
+      const track = new Track();
+      track.index = index;
+
+      track.type = particle.type;
+      track.chi2 = particle.chi2;
+      track.ndf = particle.ndf;
+      track.dEdx = particle.dEdx;
+      track.dEdxError = particle.dEdxError;
+      track.radiusOfInnermostHit = particle.radiusOfInnermostHit;
+      track.subdetectorHitNumbers = particle.subdetectorHitNumbers;
+      track.trackStates = particle.trackStates;
+      track.dxQuantities = particle.dxQuantities;
+      track.trackerHits = particle.trackerHits;
+      track.tracks = particle.tracks;
+
+      particles.push(track);
+    }
+
+    return particles;
+  }
+}

From fbfb0eaa80b4af4b04ef24fad8d3e60c3f49c93e Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 30 May 2024 21:58:12 -0500
Subject: [PATCH 03/35] test suite for loadParticles and buildLoader

---
 js/types/load.js  | 33 ++++++++++++++------
 test/load.test.js | 77 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 101 insertions(+), 9 deletions(-)
 create mode 100644 test/load.test.js

diff --git a/js/types/load.js b/js/types/load.js
index 7c88b530..90abdda7 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -23,32 +23,47 @@ const loadersConfig = [
   "Cluster",
 ];
 
-function selectedParticles(loaders, particles) {
-  let newLoader = {};
+export function buildLoader(config) {
+  let newLoader = {
+    types: {},
+    getLoader: (name) => {
+      if (newLoader.types.hasOwnProperty(name)) {
+        return newLoader.types[name];
+      }
+      return false;
+    },
+    getAllLoaders: () => {
+      return newLoader.types;
+    },
+  };
 
-  for (const particle of particles) {
+  for (const particle of config) {
     if (loaders.hasOwnProperty(particle)) {
-      newLoader[particle] = loaders[particle];
+      newLoader.types[particle] = loaders[particle];
     }
   }
 
   return newLoader;
 }
 
-export function loadParticles(event, loadersConfig) {
+export function loadParticles(jsonData, event, loadersConfig) {
   const eventData = Object.values(jsonData["Event " + event]);
 
-  const particles = [];
+  const particles = {};
 
-  const loader = selectedParticles(loaders, loadersConfig);
+  if (typeof loadersConfig === "string") loadersConfig = [loadersConfig];
+  const loader = buildLoader(loadersConfig);
 
-  for (const [type, loadFunction] of Object.entries(loader)) {
+  Object.keys(loader.getAllLoaders()).forEach((key) => (particles[key] = []));
+
+  for (const [type, loadFunction] of Object.entries(loader.getAllLoaders())) {
     const particlesType = eventData.filter(
       (element) => element.collType === `edm4hep::${type}Collection`
     );
 
     particlesType.forEach((collection) => {
       const loadedParticles = loadFunction(collection.collection);
+      particles[type] = loadedParticles;
     });
   }
   try {
@@ -59,4 +74,4 @@ export function loadParticles(event, loadersConfig) {
   return particles;
 }
 
-loadParticles(4, loadersConfig);
+loadParticles(jsonData, 4, loadersConfig);
diff --git a/test/load.test.js b/test/load.test.js
new file mode 100644
index 00000000..8dc5e19f
--- /dev/null
+++ b/test/load.test.js
@@ -0,0 +1,77 @@
+import { buildLoader, loadParticles } from "../js/types/load";
+
+const data = {
+  "Event 0": {
+    "AllMuon": {
+      "collID": 12,
+      "collType": "edm4hep::ReconstructedParticleCollection",
+      "collection": [],
+    },
+    "EFlowPhoton": {
+      "collID": 7,
+      "collType": "edm4hep::ClusterCollection",
+      "collection": [
+        {
+          "clusters": [],
+          "directionError": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "energy": 6.2020978927612305,
+          "energyError": 0.0,
+          "hits": [],
+          "iTheta": 0.0,
+          "particleIDs": [],
+          "phi": 0.0,
+          "position": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "positionError": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+          "shapeParameters": [],
+          "subdetectorEnergies": [],
+          "type": 0,
+        },
+      ],
+    },
+  },
+};
+
+describe("build loader", () => {
+  it("should create a loader with a set of types", () => {
+    const loadersConfig = ["ReconstructedParticle", "ParticleID"];
+    const loader = buildLoader(loadersConfig);
+    const loaderFunctions = loadersConfig.map((type) => loader.getLoader(type));
+
+    expect(loaderFunctions.every((f) => typeof f === "function")).toBe(true);
+  });
+
+  it("should fail when requesting a loader that doesn't exist", () => {
+    const loadersConfig = ["ReconstructedParticle", "ParticleID"];
+    const loader = buildLoader(loadersConfig);
+
+    expect(loader.getLoader("Vertex")).toBe(false);
+  });
+});
+
+describe("load different types of particles", () => {
+  it("should only load particles of one type", () => {
+    const loadersConfig = "ReconstructedParticle";
+
+    const particles = loadParticles(data, "0", loadersConfig);
+
+    expect(particles.hasOwnProperty(loadersConfig)).toBe(true);
+  });
+
+  it("should load particles of multiple types", () => {
+    const loadersConfig = ["ReconstructedParticle", "Cluster"];
+
+    const particles = loadParticles(data, "0", loadersConfig);
+
+    expect(loadersConfig.every((type) => particles.hasOwnProperty(type))).toBe(
+      true
+    );
+  });
+});

From c7b270cd9ee21dc9fd41e1580fc0bc8624f1d559 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Fri, 31 May 2024 08:46:39 -0500
Subject: [PATCH 04/35] change example data for RecoParticle test

---
 test/load.test.js | 71 +++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 66 insertions(+), 5 deletions(-)

diff --git a/test/load.test.js b/test/load.test.js
index 8dc5e19f..d6183b19 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -2,11 +2,6 @@ import { buildLoader, loadParticles } from "../js/types/load";
 
 const data = {
   "Event 0": {
-    "AllMuon": {
-      "collID": 12,
-      "collType": "edm4hep::ReconstructedParticleCollection",
-      "collection": [],
-    },
     "EFlowPhoton": {
       "collID": 7,
       "collType": "edm4hep::ClusterCollection",
@@ -36,6 +31,72 @@ const data = {
         },
       ],
     },
+    "Jet": {
+      "collID": 13,
+      "collType": "edm4hep::ReconstructedParticleCollection",
+      "collection": [
+        {
+          "charge": 1.0,
+          "clusters": [],
+          "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+          "energy": 12.062528610229492,
+          "goodnessOfPID": 0.0,
+          "mass": 2.315242290496826,
+          "momentum": {
+            "x": 11.738886833190918,
+            "y": 1.2114704847335815,
+            "z": 0.9354811906814575,
+          },
+          "particleIDUsed": {
+            "collectionID": -2,
+            "index": -2,
+          },
+          "particleIDs": [
+            {
+              "collectionID": 4,
+              "index": 45,
+            },
+          ],
+          "particles": [
+            {
+              "collectionID": 14,
+              "index": 24,
+            },
+            {
+              "collectionID": 14,
+              "index": 22,
+            },
+            {
+              "collectionID": 14,
+              "index": 74,
+            },
+            {
+              "collectionID": 14,
+              "index": 23,
+            },
+            {
+              "collectionID": 14,
+              "index": 25,
+            },
+            {
+              "collectionID": 14,
+              "index": 26,
+            },
+          ],
+          "referencePoint": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "startVertex": {
+            "collectionID": -2,
+            "index": -2,
+          },
+          "tracks": [],
+          "type": 0,
+        },
+      ],
+    },
   },
 };
 

From 27d03eca6e1cb7f16d90fc90eab84f0559f9685c Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Fri, 31 May 2024 10:35:03 -0500
Subject: [PATCH 05/35] check if previews work

---
 index.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/index.html b/index.html
index 450c5126..b320acd8 100644
--- a/index.html
+++ b/index.html
@@ -17,9 +17,9 @@
   <div id="input-modal" class="modal-background">
     <div class="modal-content">
 
-      <p>¡Welcome to <span id="logo">
+      <p>Welcome to <span id="logo">
           <span id="logo-d">d</span><span id="logo-m">m</span><span id="logo-x">X</span>
-        </span>!</p>
+        </span></p>
 
       <div id="input-message">
       </div>

From 0a52737abd96a637173a1fa80e290e0bef15ecc6 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Fri, 31 May 2024 10:39:34 -0500
Subject: [PATCH 06/35] small change

---
 index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.html b/index.html
index b320acd8..55d74dda 100644
--- a/index.html
+++ b/index.html
@@ -17,7 +17,7 @@
   <div id="input-modal" class="modal-background">
     <div class="modal-content">
 
-      <p>Welcome to <span id="logo">
+      <p>¡Welcome to <span id="logo">
           <span id="logo-d">d</span><span id="logo-m">m</span><span id="logo-x">X</span>
         </span></p>
 

From 02392eb623d7542f2ed645753832fd5c913393fa Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Fri, 31 May 2024 11:08:36 -0500
Subject: [PATCH 07/35] another small change

---
 index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.html b/index.html
index 55d74dda..a1b96a88 100644
--- a/index.html
+++ b/index.html
@@ -17,7 +17,7 @@
   <div id="input-modal" class="modal-background">
     <div class="modal-content">
 
-      <p>¡Welcome to <span id="logo">
+      <p>¡¡¡Welcome to <span id="logo">
           <span id="logo-d">d</span><span id="logo-m">m</span><span id="logo-x">X</span>
         </span></p>
 

From 13978a4fb60d27c08e11b7e9f9a39a128c9f145b Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Sun, 2 Jun 2024 16:24:52 -0500
Subject: [PATCH 08/35] remove unnecessary exclamation mark

---
 index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.html b/index.html
index a1b96a88..b320acd8 100644
--- a/index.html
+++ b/index.html
@@ -17,7 +17,7 @@
   <div id="input-modal" class="modal-background">
     <div class="modal-content">
 
-      <p>¡¡¡Welcome to <span id="logo">
+      <p>Welcome to <span id="logo">
           <span id="logo-d">d</span><span id="logo-m">m</span><span id="logo-x">X</span>
         </span></p>
 

From 5f48b1dc2d0c7e85f7f57d5d278d9d017d3560d3 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 3 Jun 2024 14:49:09 -0500
Subject: [PATCH 09/35] eliminate try catch

---
 js/types/load.js | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/js/types/load.js b/js/types/load.js
index 90abdda7..2e27311f 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -66,10 +66,6 @@ export function loadParticles(jsonData, event, loadersConfig) {
       particles[type] = loadedParticles;
     });
   }
-  try {
-  } catch (error) {
-    console.error(error);
-  }
 
   return particles;
 }

From 00bb203c5e3d5537657e3bda49c69d386bda32e7 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 3 Jun 2024 17:50:40 -0500
Subject: [PATCH 10/35] add version check + dynamic load of object

---
 js/types/load.js           | 63 +++++++++++++++++-----------------
 js/types/reconstruction.js | 70 +++++++++++++++++---------------------
 js/types/version.js        | 43 +++++++++++++++++++++++
 3 files changed, 105 insertions(+), 71 deletions(-)
 create mode 100644 js/types/version.js

diff --git a/js/types/load.js b/js/types/load.js
index 2e27311f..0122e42c 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -6,13 +6,14 @@ import {
   Vertex,
   Track,
 } from "./reconstruction.js";
+import { compatible } from "./version.js";
 
-const loaders = {
-  ReconstructedParticle: ReconstructedParticle.load,
-  ParticleID: ParticleID.load,
-  Vertex: Vertex.load,
-  Track: Track.load,
-  Cluster: Cluster.load,
+const types = {
+  "Cluster": Cluster,
+  "ParticleID": ParticleID,
+  "ReconstructedParticle": ReconstructedParticle,
+  "Vertex": Vertex,
+  "Track": Track,
 };
 
 const loadersConfig = [
@@ -23,23 +24,22 @@ const loadersConfig = [
   "Cluster",
 ];
 
-export function buildLoader(config) {
-  let newLoader = {
-    types: {},
-    getLoader: (name) => {
-      if (newLoader.types.hasOwnProperty(name)) {
-        return newLoader.types[name];
-      }
-      return false;
-    },
-    getAllLoaders: () => {
-      return newLoader.types;
-    },
-  };
+export function buildLoader(config, version) {
+  const newLoader = {};
+
+  if (typeof config === "string") config = [config];
 
   for (const particle of config) {
-    if (loaders.hasOwnProperty(particle)) {
-      newLoader.types[particle] = loaders[particle];
+    if (types.hasOwnProperty(particle)) {
+      const isCompatible = compatible(types[particle], version);
+
+      if (isCompatible) {
+        newLoader[particle] = types[particle].load;
+      } else {
+        newLoader[particle] = () => {
+          return [];
+        };
+      }
     }
   }
 
@@ -47,23 +47,22 @@ export function buildLoader(config) {
 }
 
 export function loadParticles(jsonData, event, loadersConfig) {
-  const eventData = Object.values(jsonData["Event " + event]);
+  const eventData = jsonData["Event " + event];
+  const version = eventData.edm4hepVersion;
+  delete eventData["edm4hepVersion"];
 
-  const particles = {};
-
-  if (typeof loadersConfig === "string") loadersConfig = [loadersConfig];
-  const loader = buildLoader(loadersConfig);
+  const loader = buildLoader(loadersConfig, version);
 
-  Object.keys(loader.getAllLoaders()).forEach((key) => (particles[key] = []));
+  const particles = {};
+  Object.keys(loader).forEach((key) => (particles[key] = []));
 
-  for (const [type, loadFunction] of Object.entries(loader.getAllLoaders())) {
-    const particlesType = eventData.filter(
+  for (const [type, loadFunction] of Object.entries(loader)) {
+    const particlesType = Object.values(eventData).filter(
       (element) => element.collType === `edm4hep::${type}Collection`
     );
 
-    particlesType.forEach((collection) => {
-      const loadedParticles = loadFunction(collection.collection);
-      particles[type] = loadedParticles;
+    particlesType.forEach(({ collection }) => {
+      const loadedParticles = loadFunction(collection);
     });
   }
 
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index f072440f..d40d5321 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -1,4 +1,19 @@
+function dynamicLoad(object, data, ignore = null) {
+  if (ignore !== null) {
+    for (const key of ignore) {
+      delete data[key];
+    }
+  }
+
+  for (const [key, value] of Object.entries(data)) {
+    object[key] = value;
+  }
+}
+
 export class Cluster {
+  static MIN_VERSION = "0.7.0"; // may vary per type of particle
+  static MAX_VERSION = "1.0.0";
+
   constructor() {
     // Physics properties
     this.type = 0;
@@ -22,18 +37,7 @@ export class Cluster {
       const cluster = new Cluster();
       cluster.index = index;
 
-      cluster.type = particle.type;
-      cluster.energy = particle.energy;
-      cluster.energyError = particle.energyError;
-      cluster.position = particle.position;
-      cluster.positionError = particle.positionError;
-      cluster.iTheta = particle.iTheta;
-      cluster.phi = particle.phi;
-      cluster.directionError = particle.directionError;
-      cluster.shapeParameters = particle.shapeParameters;
-      cluster.subdetectorEnergies = particle.subdetectorEnergies;
-      cluster.clusters = particle.clusters;
-      cluster.hits = particle.hits;
+      dynamicLoad(cluster, particle);
 
       particles.push(cluster);
     }
@@ -43,6 +47,9 @@ export class Cluster {
 }
 
 export class ParticleID {
+  static MIN_VERSION = "0.7.0";
+  static MAX_VERSION = "1.0.0";
+
   constructor() {
     // Physics properties
     this.type = 0;
@@ -60,11 +67,7 @@ export class ParticleID {
       const particleID = new ParticleID();
       particleID.index = index;
 
-      particleID.type = particle.type;
-      particleID.pdg = particle.pdg;
-      particleID.algorithmType = particle.algorithmType;
-      particleID.likelihood = particle.likelihood;
-      particleID.parameters = particle.parameters;
+      dynamicLoad(particleID, particle);
 
       particles.push(particleID);
     }
@@ -74,6 +77,9 @@ export class ParticleID {
 }
 
 export class ReconstructedParticle {
+  static MIN_VERSION = "0.7.0";
+  static MAX_VERSION = "1.0.0";
+
   constructor() {
     // Physics properties
     this.pdg = 0;
@@ -97,17 +103,7 @@ export class ReconstructedParticle {
       const reconstructedParticle = new ReconstructedParticle();
       reconstructedParticle.index = index;
 
-      reconstructedParticle.energy = particle.energy;
-      reconstructedParticle.momentum = particle.momentum;
-      reconstructedParticle.referencePoint = particle.referencePoint;
-      reconstructedParticle.charge = particle.charge;
-      reconstructedParticle.mass = particle.mass;
-      reconstructedParticle.goodnessOfPID = particle.goodnessOfPID;
-      reconstructedParticle.covMatrix = particle.covMatrix;
-      reconstructedParticle.startVertex = particle.startVertex;
-      reconstructedParticle.clusters = particle.clusters;
-      reconstructedParticle.tracks = particle.tracks;
-      reconstructedParticle.particles = particle.particles;
+      dynamicLoad(reconstructedParticle, particle);
 
       particles.push(reconstructedParticle);
     }
@@ -117,6 +113,9 @@ export class ReconstructedParticle {
 }
 
 export class Vertex {
+  static MIN_VERSION = "0.7.0";
+  static MAX_VERSION = "1.0.0";
+
   constructor() {
     // Physics properties
     this.primary = 0;
@@ -133,6 +132,9 @@ export class Vertex {
 }
 
 export class Track {
+  static MIN_VERSION = "0.7.0";
+  static MAX_VERSION = "1.0.0";
+
   constructor() {
     // Physics properties
     this.type = 0;
@@ -155,17 +157,7 @@ export class Track {
       const track = new Track();
       track.index = index;
 
-      track.type = particle.type;
-      track.chi2 = particle.chi2;
-      track.ndf = particle.ndf;
-      track.dEdx = particle.dEdx;
-      track.dEdxError = particle.dEdxError;
-      track.radiusOfInnermostHit = particle.radiusOfInnermostHit;
-      track.subdetectorHitNumbers = particle.subdetectorHitNumbers;
-      track.trackStates = particle.trackStates;
-      track.dxQuantities = particle.dxQuantities;
-      track.trackerHits = particle.trackerHits;
-      track.tracks = particle.tracks;
+      dynamicLoad(track, particle);
 
       particles.push(track);
     }
diff --git a/js/types/version.js b/js/types/version.js
new file mode 100644
index 00000000..dd710ca4
--- /dev/null
+++ b/js/types/version.js
@@ -0,0 +1,43 @@
+export class Version {
+  constructor(string) {
+    const [major, minor, patch] = string.split(".");
+    this.major = parseInt(major);
+    this.minor = parseInt(minor);
+    this.patch = parseInt(patch);
+  }
+
+  toString() {
+    return `${this.major}.${this.minor}.${this.patch}`;
+  }
+
+  greaterOrEqualThan(version) {
+    return (
+      this.major >= version.major ||
+      (this.major === version.major &&
+        (this.minor >= version.minor ||
+          (this.minor === version.minor && this.patch >= version.patch)))
+    );
+  }
+
+  lessOrEqualThan(version) {
+    return (
+      this.major <= version.major ||
+      (this.major === version.major &&
+        (this.minor <= version.minor ||
+          (this.minor === version.minor && this.patch <= version.patch)))
+    );
+  }
+
+  isBetween(version1, version2) {
+    return this.greaterOrEqualThan(version1) && this.lessOrEqualThan(version2);
+  }
+}
+
+export function compatible(type, version) {
+  const minV = new Version(type.MIN_VERSION);
+  const maxV = new Version(type.MAX_VERSION);
+
+  const v = new Version(version);
+
+  return v.isBetween(minV, maxV);
+}

From 83a9bbde1135d7cf24a3f2609260aa4253060503 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 3 Jun 2024 18:21:45 -0500
Subject: [PATCH 11/35] update tests

---
 js/types/load.js  |  1 -
 test/load.test.js | 15 +++++----------
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/js/types/load.js b/js/types/load.js
index 0122e42c..667ec292 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -49,7 +49,6 @@ export function buildLoader(config, version) {
 export function loadParticles(jsonData, event, loadersConfig) {
   const eventData = jsonData["Event " + event];
   const version = eventData.edm4hepVersion;
-  delete eventData["edm4hepVersion"];
 
   const loader = buildLoader(loadersConfig, version);
 
diff --git a/test/load.test.js b/test/load.test.js
index d6183b19..c93c79ab 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -97,23 +97,18 @@ const data = {
         },
       ],
     },
+    "edm4hepVersion": "0.7.0",
   },
 };
 
 describe("build loader", () => {
   it("should create a loader with a set of types", () => {
     const loadersConfig = ["ReconstructedParticle", "ParticleID"];
-    const loader = buildLoader(loadersConfig);
-    const loaderFunctions = loadersConfig.map((type) => loader.getLoader(type));
+    const loader = buildLoader(loadersConfig, "0.7.0");
 
-    expect(loaderFunctions.every((f) => typeof f === "function")).toBe(true);
-  });
-
-  it("should fail when requesting a loader that doesn't exist", () => {
-    const loadersConfig = ["ReconstructedParticle", "ParticleID"];
-    const loader = buildLoader(loadersConfig);
-
-    expect(loader.getLoader("Vertex")).toBe(false);
+    expect(Object.values(loader).every((f) => typeof f === "function")).toBe(
+      true
+    );
   });
 });
 

From 3e64c411d075dbdbf83f07a04eab508f8243bf53 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 3 Jun 2024 20:41:44 -0500
Subject: [PATCH 12/35] types for RecoParticle relations including 1:1 and
 1:many

---
 js/types/load.js           | 28 +++++++++++---
 js/types/reconstruction.js | 78 +++++++++++++++++++++++++++++++-------
 test/load.test.js          | 50 ++++++++----------------
 3 files changed, 102 insertions(+), 54 deletions(-)

diff --git a/js/types/load.js b/js/types/load.js
index 667ec292..e02748c5 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -18,10 +18,10 @@ const types = {
 
 const loadersConfig = [
   "ReconstructedParticle",
-  "ParticleID",
-  "Vertex",
-  "Track",
-  "Cluster",
+  // "ParticleID",
+  // "Vertex",
+  // "Track",
+  // "Cluster",
 ];
 
 export function buildLoader(config, version) {
@@ -61,11 +61,27 @@ export function loadParticles(jsonData, event, loadersConfig) {
     );
 
     particlesType.forEach(({ collection }) => {
-      const loadedParticles = loadFunction(collection);
+      const [particles, links] = loadFunction(collection);
     });
   }
 
   return particles;
 }
 
-loadParticles(jsonData, 4, loadersConfig);
+export function dynamicLoad(object, data, ignore = null) {
+  let filteredData = {};
+
+  if (ignore !== null) {
+    for (const key in data) {
+      if (!ignore.has(key)) filteredData[key] = data[key];
+    }
+  } else {
+    filteredData = data;
+  }
+
+  for (const [key, value] of Object.entries(data)) {
+    object[key] = value;
+  }
+}
+
+loadParticles(jsonData, 0, loadersConfig);
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index d40d5321..c34a0be5 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -1,14 +1,4 @@
-function dynamicLoad(object, data, ignore = null) {
-  if (ignore !== null) {
-    for (const key of ignore) {
-      delete data[key];
-    }
-  }
-
-  for (const [key, value] of Object.entries(data)) {
-    object[key] = value;
-  }
-}
+import { dynamicLoad } from "./load.js";
 
 export class Cluster {
   static MIN_VERSION = "0.7.0"; // may vary per type of particle
@@ -98,17 +88,34 @@ export class ReconstructedParticle {
 
   static load(collection) {
     const particles = [];
+    const links = createLinksManager([
+      "tracks",
+      "clusters",
+      "particles",
+      "startVertex",
+    ]);
 
     for (const [index, particle] of collection.entries()) {
       const reconstructedParticle = new ReconstructedParticle();
       reconstructedParticle.index = index;
 
-      dynamicLoad(reconstructedParticle, particle);
+      extractOneToManyLinks(
+        links,
+        ["tracks", "clusters", "particles"],
+        particle
+      );
+      extractOneToOneLinks(links, "startVertex", particle);
+
+      dynamicLoad(
+        reconstructedParticle,
+        particle,
+        new Set(["tracks", "clusters", "particles", "startVertex"])
+      );
 
       particles.push(reconstructedParticle);
     }
 
-    return particles;
+    return [particles, links];
   }
 }
 
@@ -165,3 +172,48 @@ export class Track {
     return particles;
   }
 }
+
+export class GenericLink {
+  // we may create a specific class for each type if needed
+  constructor(id, from, to) {
+    this.id = id;
+    this.from = from;
+    this.to = to;
+  }
+}
+
+function createLinksManager(types) {
+  const links = {};
+  types.forEach((type) => (links[type] = []));
+  return links;
+}
+
+export function createGenericLink(id, from, { collectionID, index }) {
+  const genericLink = new GenericLink(id, from, index);
+  genericLink.collectionID = collectionID;
+  return genericLink;
+}
+
+function extractOneToManyLinks(linksManager, keys, particle) {
+  for (const key of keys) {
+    particle[key].map((val) => {
+      const link = createGenericLink(
+        linksManager[key].length,
+        particle.index,
+        val
+      );
+      linksManager[key].push(link);
+      particle[key].push(link.id);
+    });
+  }
+}
+
+function extractOneToOneLinks(linksManager, key, particle) {
+  const link = createGenericLink(
+    linksManager[key].length,
+    particle.index,
+    particle[key]
+  );
+  linksManager[key].push(link);
+  particle[key] = link.id;
+}
diff --git a/test/load.test.js b/test/load.test.js
index c93c79ab..1f35effe 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -31,21 +31,21 @@ const data = {
         },
       ],
     },
-    "Jet": {
-      "collID": 13,
+    "ReconstructedParticles": {
+      "collID": 14,
       "collType": "edm4hep::ReconstructedParticleCollection",
       "collection": [
         {
           "charge": 1.0,
           "clusters": [],
           "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-          "energy": 12.062528610229492,
+          "energy": 0.358455091714859,
           "goodnessOfPID": 0.0,
-          "mass": 2.315242290496826,
+          "mass": 0.13957038521766663,
           "momentum": {
-            "x": 11.738886833190918,
-            "y": 1.2114704847335815,
-            "z": 0.9354811906814575,
+            "x": 0.09558331221342087,
+            "y": -0.11288221180438995,
+            "z": -0.2951807975769043,
           },
           "particleIDUsed": {
             "collectionID": -2,
@@ -54,35 +54,10 @@ const data = {
           "particleIDs": [
             {
               "collectionID": 4,
-              "index": 45,
-            },
-          ],
-          "particles": [
-            {
-              "collectionID": 14,
-              "index": 24,
-            },
-            {
-              "collectionID": 14,
-              "index": 22,
-            },
-            {
-              "collectionID": 14,
-              "index": 74,
-            },
-            {
-              "collectionID": 14,
-              "index": 23,
-            },
-            {
-              "collectionID": 14,
-              "index": 25,
-            },
-            {
-              "collectionID": 14,
-              "index": 26,
+              "index": 0,
             },
           ],
+          "particles": [],
           "referencePoint": {
             "x": 0.0,
             "y": 0.0,
@@ -92,7 +67,12 @@ const data = {
             "collectionID": -2,
             "index": -2,
           },
-          "tracks": [],
+          "tracks": [
+            {
+              "collectionID": 3,
+              "index": 0,
+            },
+          ],
           "type": 0,
         },
       ],

From f7a14c5cdca86e364bd80c77a7f839d8844dcddc Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 5 Jun 2024 18:21:00 -0500
Subject: [PATCH 13/35] add links for types

---
 js/types/load.js           | 12 +++----
 js/types/reconstruction.js | 73 +++++++++++++++++++++++++++-----------
 2 files changed, 58 insertions(+), 27 deletions(-)

diff --git a/js/types/load.js b/js/types/load.js
index e02748c5..289c7efe 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -1,4 +1,4 @@
-import jsonData from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" }; // node 20
+import jsonData from "../../input/wzp6_ee_mumuH_ecm240_CLD_RECO.edm4hep.json" assert { type: "json" }; // node 20
 import {
   Cluster,
   ParticleID,
@@ -18,10 +18,10 @@ const types = {
 
 const loadersConfig = [
   "ReconstructedParticle",
-  // "ParticleID",
-  // "Vertex",
-  // "Track",
-  // "Cluster",
+  "ParticleID",
+  "Vertex",
+  "Track",
+  "Cluster",
 ];
 
 export function buildLoader(config, version) {
@@ -79,7 +79,7 @@ export function dynamicLoad(object, data, ignore = null) {
     filteredData = data;
   }
 
-  for (const [key, value] of Object.entries(data)) {
+  for (const [key, value] of Object.entries(filteredData)) {
     object[key] = value;
   }
 }
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index c34a0be5..ae292903 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -9,8 +9,8 @@ export class Cluster {
     this.type = 0;
     this.energy = 0; // GeV
     this.energyError = 0; // GeV
-    this.position = []; // mm
-    this.positionError = [];
+    this.position = {}; // mm
+    this.positionError = {};
     this.iTheta = 0;
     this.phi = 0;
     this.directionError = {}; // mm^2
@@ -22,17 +22,20 @@ export class Cluster {
 
   static load(collection) {
     const particles = [];
+    const links = createLinksManager(["clusters", "hits"]);
 
     for (const [index, particle] of collection.entries()) {
       const cluster = new Cluster();
       cluster.index = index;
 
+      extractOneToManyLinks(links, ["clusters", "hits"], cluster, particle);
+
       dynamicLoad(cluster, particle);
 
       particles.push(cluster);
     }
 
-    return particles;
+    return [particles, links];
   }
 }
 
@@ -47,22 +50,25 @@ export class ParticleID {
     this.algorithmType = 0;
     this.likelihood = 0;
     this.parameters = [];
-    this.particle = [];
+    this.particle = null;
   }
 
   static load(collection) {
     const particles = [];
+    const links = createLinksManager(["particle"]);
 
     for (const [index, particle] of collection.entries()) {
       const particleID = new ParticleID();
       particleID.index = index;
 
+      extractOneToOneLink(links, "particle", particleID, particle);
+
       dynamicLoad(particleID, particle);
 
       particles.push(particleID);
     }
 
-    return particles;
+    return [particles, links];
   }
 }
 
@@ -79,8 +85,8 @@ export class ReconstructedParticle {
     this.charge = 0;
     this.mass = 0; // GeV
     this.goodnessOfPID = 0;
-    this.covMatrix = [];
-    this.startVertex = {};
+    this.covMatrix = {};
+    this.startVertex = null;
     this.clusters = [];
     this.tracks = [];
     this.particles = [];
@@ -102,9 +108,15 @@ export class ReconstructedParticle {
       extractOneToManyLinks(
         links,
         ["tracks", "clusters", "particles"],
+        reconstructedParticle,
+        particle
+      );
+      extractOneToOneLink(
+        links,
+        "startVertex",
+        reconstructedParticle,
         particle
       );
-      extractOneToOneLinks(links, "startVertex", particle);
 
       dynamicLoad(
         reconstructedParticle,
@@ -128,14 +140,30 @@ export class Vertex {
     this.primary = 0;
     this.chi2 = 0;
     this.probability = 0;
-    this.position = 0; // mm
-    this.covMatrix = [];
+    this.position = {}; // mm
+    this.covMatrix = {};
     this.algorithmType = 0;
     this.parameters = 0;
-    this.associatedParticles = [];
+    this.associatedParticle = null;
   }
 
-  static load() {}
+  static load(collection) {
+    const particles = [];
+    const links = createLinksManager(["associatedParticle"]);
+
+    for (const [index, particle] of collection.entries()) {
+      const vertex = new Vertex();
+      vertex.index = index;
+
+      extractOneToOneLink(links, "associatedParticle", vertex, particle);
+
+      dynamicLoad(vertex, particle, new Set(["associatedParticle"]));
+
+      particles.push(vertex);
+    }
+
+    return [particles, links];
+  }
 }
 
 export class Track {
@@ -159,17 +187,20 @@ export class Track {
 
   static load(collection) {
     const particles = [];
+    const links = createLinksManager(["trackerHits", "tracks"]);
 
     for (const [index, particle] of collection.entries()) {
       const track = new Track();
       track.index = index;
 
+      extractOneToManyLinks(links, ["trackerHits", "tracks"], track, particle);
+
       dynamicLoad(track, particle);
 
       particles.push(track);
     }
 
-    return particles;
+    return [particles, links];
   }
 }
 
@@ -194,26 +225,26 @@ export function createGenericLink(id, from, { collectionID, index }) {
   return genericLink;
 }
 
-function extractOneToManyLinks(linksManager, keys, particle) {
+function extractOneToManyLinks(linksManager, keys, newParticle, particleData) {
   for (const key of keys) {
-    particle[key].map((val) => {
+    particleData[key].map((val) => {
       const link = createGenericLink(
         linksManager[key].length,
-        particle.index,
+        newParticle.index,
         val
       );
       linksManager[key].push(link);
-      particle[key].push(link.id);
+      newParticle[key].push(link.id);
     });
   }
 }
 
-function extractOneToOneLinks(linksManager, key, particle) {
+function extractOneToOneLink(linksManager, key, newParticle, particleData) {
   const link = createGenericLink(
     linksManager[key].length,
-    particle.index,
-    particle[key]
+    newParticle.index,
+    particleData[key]
   );
   linksManager[key].push(link);
-  particle[key] = link.id;
+  newParticle[key] = link.id;
 }

From 904cd514a3d8a994a2f8ab68b7f45022f2aecc60 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 5 Jun 2024 19:04:51 -0500
Subject: [PATCH 14/35] test for loading functions

---
 js/types/reconstruction.js |   4 +-
 test/load.test.js          | 236 ++++++++++++++++++++++++-------------
 2 files changed, 156 insertions(+), 84 deletions(-)

diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index ae292903..d9148caf 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -46,7 +46,7 @@ export class ParticleID {
   constructor() {
     // Physics properties
     this.type = 0;
-    this.pdg = 0;
+    this.PDG = 0;
     this.algorithmType = 0;
     this.likelihood = 0;
     this.parameters = [];
@@ -78,7 +78,7 @@ export class ReconstructedParticle {
 
   constructor() {
     // Physics properties
-    this.pdg = 0;
+    this.PDG = 0;
     this.energy = 0; // GeV
     this.momentum = {}; // GeV
     this.referencePoint = {}; // mm
diff --git a/test/load.test.js b/test/load.test.js
index 1f35effe..b131248b 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,85 +1,5 @@
-import { buildLoader, loadParticles } from "../js/types/load";
-
-const data = {
-  "Event 0": {
-    "EFlowPhoton": {
-      "collID": 7,
-      "collType": "edm4hep::ClusterCollection",
-      "collection": [
-        {
-          "clusters": [],
-          "directionError": {
-            "x": 0.0,
-            "y": 0.0,
-            "z": 0.0,
-          },
-          "energy": 6.2020978927612305,
-          "energyError": 0.0,
-          "hits": [],
-          "iTheta": 0.0,
-          "particleIDs": [],
-          "phi": 0.0,
-          "position": {
-            "x": 0.0,
-            "y": 0.0,
-            "z": 0.0,
-          },
-          "positionError": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-          "shapeParameters": [],
-          "subdetectorEnergies": [],
-          "type": 0,
-        },
-      ],
-    },
-    "ReconstructedParticles": {
-      "collID": 14,
-      "collType": "edm4hep::ReconstructedParticleCollection",
-      "collection": [
-        {
-          "charge": 1.0,
-          "clusters": [],
-          "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-          "energy": 0.358455091714859,
-          "goodnessOfPID": 0.0,
-          "mass": 0.13957038521766663,
-          "momentum": {
-            "x": 0.09558331221342087,
-            "y": -0.11288221180438995,
-            "z": -0.2951807975769043,
-          },
-          "particleIDUsed": {
-            "collectionID": -2,
-            "index": -2,
-          },
-          "particleIDs": [
-            {
-              "collectionID": 4,
-              "index": 0,
-            },
-          ],
-          "particles": [],
-          "referencePoint": {
-            "x": 0.0,
-            "y": 0.0,
-            "z": 0.0,
-          },
-          "startVertex": {
-            "collectionID": -2,
-            "index": -2,
-          },
-          "tracks": [
-            {
-              "collectionID": 3,
-              "index": 0,
-            },
-          ],
-          "type": 0,
-        },
-      ],
-    },
-    "edm4hepVersion": "0.7.0",
-  },
-};
+import { buildLoader, loadParticles, dynamicLoad } from "../js/types/load";
+import { ReconstructedParticle } from "../js/types/reconstruction";
 
 describe("build loader", () => {
   it("should create a loader with a set of types", () => {
@@ -93,6 +13,91 @@ describe("build loader", () => {
 });
 
 describe("load different types of particles", () => {
+  let data = {};
+
+  beforeAll(() => {
+    data = {
+      "Event 0": {
+        "EFlowPhoton": {
+          "collID": 7,
+          "collType": "edm4hep::ClusterCollection",
+          "collection": [
+            {
+              "clusters": [],
+              "directionError": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+              },
+              "energy": 6.2020978927612305,
+              "energyError": 0.0,
+              "hits": [],
+              "iTheta": 0.0,
+              "particleIDs": [],
+              "phi": 0.0,
+              "position": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+              },
+              "positionError": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+              "shapeParameters": [],
+              "subdetectorEnergies": [],
+              "type": 0,
+            },
+          ],
+        },
+        "ReconstructedParticles": {
+          "collID": 14,
+          "collType": "edm4hep::ReconstructedParticleCollection",
+          "collection": [
+            {
+              "charge": 1.0,
+              "clusters": [],
+              "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+              "energy": 0.358455091714859,
+              "goodnessOfPID": 0.0,
+              "mass": 0.13957038521766663,
+              "momentum": {
+                "x": 0.09558331221342087,
+                "y": -0.11288221180438995,
+                "z": -0.2951807975769043,
+              },
+              "particleIDUsed": {
+                "collectionID": -2,
+                "index": -2,
+              },
+              "particleIDs": [
+                {
+                  "collectionID": 4,
+                  "index": 0,
+                },
+              ],
+              "particles": [],
+              "referencePoint": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+              },
+              "startVertex": {
+                "collectionID": -2,
+                "index": -2,
+              },
+              "tracks": [
+                {
+                  "collectionID": 3,
+                  "index": 0,
+                },
+              ],
+              "type": 0,
+            },
+          ],
+        },
+        "edm4hepVersion": "0.7.0",
+      },
+    };
+  });
+
   it("should only load particles of one type", () => {
     const loadersConfig = "ReconstructedParticle";
 
@@ -111,3 +116,70 @@ describe("load different types of particles", () => {
     );
   });
 });
+
+describe("dynamically load an object", () => {
+  let particleData = {};
+  let reconstructedParticle;
+
+  beforeAll(() => {
+    particleData = {
+      "PDG": 3,
+      "charge": 0.0,
+      "clusters": [],
+      "covMatrix": {
+        "values": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+      },
+      "energy": 9.644623756408691,
+      "goodnessOfPID": 0.0,
+      "mass": 0.45484575629234314,
+      "momentum": {
+        "x": -4.557793617248535,
+        "y": -6.684719085693359,
+        "z": 5.230002403259277,
+      },
+      "particles": [
+        {
+          "collectionID": 4196981182,
+          "index": 20,
+        },
+        {
+          "collectionID": 4196981182,
+          "index": 19,
+        },
+      ],
+      "referencePoint": {
+        "x": -1.2017582654953003,
+        "y": -2.118278741836548,
+        "z": 1.424477458000183,
+      },
+      "startVertex": {
+        "collectionID": 4294967295,
+        "index": -1,
+      },
+      "tracks": [],
+    };
+  });
+
+  beforeEach(() => {
+    reconstructedParticle = new ReconstructedParticle();
+    reconstructedParticle.index = 0;
+  });
+
+  it("should load all the properties of an object", () => {
+    dynamicLoad(reconstructedParticle, particleData);
+
+    expect(reconstructedParticle).toMatchObject(particleData);
+  });
+
+  it("should ignore some properties of an object", () => {
+    const ignore = new Set(["PDG", "charge", "particles"]);
+
+    dynamicLoad(reconstructedParticle, particleData, ignore);
+    expect(reconstructedParticle).toMatchObject({
+      ...particleData,
+      PDG: 0,
+      charge: 0,
+      particles: [],
+    });
+  });
+});

From ba9630c02d087f3961b4729f4ac557311c4d2681 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 5 Jun 2024 19:55:21 -0500
Subject: [PATCH 15/35] test reconstruction

---
 js/types/dynamic.js         | 15 +++++++
 js/types/load.js            | 32 +--------------
 js/types/reconstruction.js  | 26 +++++++++++--
 js/types/version.js         |  8 ++--
 test/load.test.js           |  3 +-
 test/reconstruction.test.js | 49 +++++++++++++++++++++++
 test/version.test.js        | 78 +++++++++++++++++++++++++++++++++++++
 7 files changed, 171 insertions(+), 40 deletions(-)
 create mode 100644 js/types/dynamic.js
 create mode 100644 test/reconstruction.test.js
 create mode 100644 test/version.test.js

diff --git a/js/types/dynamic.js b/js/types/dynamic.js
new file mode 100644
index 00000000..d06ebace
--- /dev/null
+++ b/js/types/dynamic.js
@@ -0,0 +1,15 @@
+export function dynamicLoad(object, data, ignore = null) {
+  let filteredData = {};
+
+  if (ignore !== null) {
+    for (const key in data) {
+      if (!ignore.has(key)) filteredData[key] = data[key];
+    }
+  } else {
+    filteredData = data;
+  }
+
+  for (const [key, value] of Object.entries(filteredData)) {
+    object[key] = value;
+  }
+}
diff --git a/js/types/load.js b/js/types/load.js
index 289c7efe..2ac27473 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -1,21 +1,7 @@
 import jsonData from "../../input/wzp6_ee_mumuH_ecm240_CLD_RECO.edm4hep.json" assert { type: "json" }; // node 20
-import {
-  Cluster,
-  ParticleID,
-  ReconstructedParticle,
-  Vertex,
-  Track,
-} from "./reconstruction.js";
+import { types } from "./reconstruction.js";
 import { compatible } from "./version.js";
 
-const types = {
-  "Cluster": Cluster,
-  "ParticleID": ParticleID,
-  "ReconstructedParticle": ReconstructedParticle,
-  "Vertex": Vertex,
-  "Track": Track,
-};
-
 const loadersConfig = [
   "ReconstructedParticle",
   "ParticleID",
@@ -68,20 +54,4 @@ export function loadParticles(jsonData, event, loadersConfig) {
   return particles;
 }
 
-export function dynamicLoad(object, data, ignore = null) {
-  let filteredData = {};
-
-  if (ignore !== null) {
-    for (const key in data) {
-      if (!ignore.has(key)) filteredData[key] = data[key];
-    }
-  } else {
-    filteredData = data;
-  }
-
-  for (const [key, value] of Object.entries(filteredData)) {
-    object[key] = value;
-  }
-}
-
 loadParticles(jsonData, 0, loadersConfig);
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index d9148caf..efc3b5cc 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -1,4 +1,4 @@
-import { dynamicLoad } from "./load.js";
+import { dynamicLoad } from "./dynamic.js";
 
 export class Cluster {
   static MIN_VERSION = "0.7.0"; // may vary per type of particle
@@ -213,7 +213,7 @@ export class GenericLink {
   }
 }
 
-function createLinksManager(types) {
+export function createLinksManager(types) {
   const links = {};
   types.forEach((type) => (links[type] = []));
   return links;
@@ -225,7 +225,12 @@ export function createGenericLink(id, from, { collectionID, index }) {
   return genericLink;
 }
 
-function extractOneToManyLinks(linksManager, keys, newParticle, particleData) {
+export function extractOneToManyLinks(
+  linksManager,
+  keys,
+  newParticle,
+  particleData
+) {
   for (const key of keys) {
     particleData[key].map((val) => {
       const link = createGenericLink(
@@ -239,7 +244,12 @@ function extractOneToManyLinks(linksManager, keys, newParticle, particleData) {
   }
 }
 
-function extractOneToOneLink(linksManager, key, newParticle, particleData) {
+export function extractOneToOneLink(
+  linksManager,
+  key,
+  newParticle,
+  particleData
+) {
   const link = createGenericLink(
     linksManager[key].length,
     newParticle.index,
@@ -248,3 +258,11 @@ function extractOneToOneLink(linksManager, key, newParticle, particleData) {
   linksManager[key].push(link);
   newParticle[key] = link.id;
 }
+
+export const types = {
+  "Cluster": Cluster,
+  "ParticleID": ParticleID,
+  "ReconstructedParticle": ReconstructedParticle,
+  "Vertex": Vertex,
+  "Track": Track,
+};
diff --git a/js/types/version.js b/js/types/version.js
index dd710ca4..2d1efad8 100644
--- a/js/types/version.js
+++ b/js/types/version.js
@@ -12,18 +12,18 @@ export class Version {
 
   greaterOrEqualThan(version) {
     return (
-      this.major >= version.major ||
+      this.major > version.major ||
       (this.major === version.major &&
-        (this.minor >= version.minor ||
+        (this.minor > version.minor ||
           (this.minor === version.minor && this.patch >= version.patch)))
     );
   }
 
   lessOrEqualThan(version) {
     return (
-      this.major <= version.major ||
+      this.major < version.major ||
       (this.major === version.major &&
-        (this.minor <= version.minor ||
+        (this.minor < version.minor ||
           (this.minor === version.minor && this.patch <= version.patch)))
     );
   }
diff --git a/test/load.test.js b/test/load.test.js
index b131248b..38f42d24 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,4 +1,5 @@
-import { buildLoader, loadParticles, dynamicLoad } from "../js/types/load";
+import { buildLoader, loadParticles } from "../js/types/load";
+import { dynamicLoad } from "../js/types/dynamic.js";
 import { ReconstructedParticle } from "../js/types/reconstruction";
 
 describe("build loader", () => {
diff --git a/test/reconstruction.test.js b/test/reconstruction.test.js
new file mode 100644
index 00000000..90278d6f
--- /dev/null
+++ b/test/reconstruction.test.js
@@ -0,0 +1,49 @@
+import {
+  extractOneToManyLinks,
+  extractOneToOneLink,
+  createLinksManager,
+  createGenericLink,
+  GenericLink,
+} from "../js/types/reconstruction.js";
+
+test("it should create a generic link", () => {
+  const link = createGenericLink(1, 2, { collectionID: 3, index: 4 });
+  expect(link.id).toBe(1);
+  expect(link.from).toBe(2);
+  expect(link.to).toBe(4);
+  expect(link.collectionID).toBe(3);
+});
+
+test("it should create a links manager", () => {
+  const linksManager = createLinksManager(["a", "b"]);
+  expect(linksManager).toEqual({ a: [], b: [] });
+});
+
+test("it should extract one-to-many links", () => {
+  const linksManager = { a: [], b: [] };
+  const keys = ["a", "b"];
+  const newParticle = { index: 0, a: [], b: [] };
+  const particleData = {
+    a: [{ collectionID: 1, index: 2 }],
+    b: [{ collectionID: 3, index: 4 }],
+  };
+  const firstLink = createGenericLink(0, 0, { collectionID: 1, index: 2 });
+  const secondLink = createGenericLink(0, 0, { collectionID: 3, index: 4 });
+
+  extractOneToManyLinks(linksManager, keys, newParticle, particleData);
+  expect(linksManager).toEqual({ a: [firstLink], b: [secondLink] });
+  expect(newParticle.a).toEqual([0]);
+  expect(newParticle.b).toEqual([0]);
+});
+
+test("it should extract one-to-one link", () => {
+  const linksManager = { a: [] };
+  const key = "a";
+  const newParticle = { index: 0, a: [] };
+  const particleData = { a: { collectionID: 1, index: 2 } };
+  const link = createGenericLink(0, 0, { collectionID: 1, index: 2 });
+
+  extractOneToOneLink(linksManager, key, newParticle, particleData);
+  expect(linksManager).toEqual({ a: [link] });
+  expect(newParticle.a).toEqual(0);
+});
diff --git a/test/version.test.js b/test/version.test.js
new file mode 100644
index 00000000..dd4063bb
--- /dev/null
+++ b/test/version.test.js
@@ -0,0 +1,78 @@
+import { Version, compatible } from "../js/types/version.js";
+
+describe("version class methods", () => {
+  let version;
+
+  beforeAll(() => {
+    version = new Version("1.12.4");
+  });
+
+  it("should return a string", () => {
+    expect(version.toString()).toBe("1.12.4");
+  });
+
+  describe("greater version than current", () => {
+    let greaterVersion;
+
+    beforeAll(() => {
+      greaterVersion = new Version("1.12.5");
+    });
+
+    it("should return false", () => {
+      expect(version.greaterOrEqualThan(greaterVersion)).toBe(false);
+    });
+
+    it("should return true", () => {
+      expect(version.lessOrEqualThan(version)).toBe(true);
+    });
+  });
+
+  describe("smaller version than current", () => {
+    let lessVersion;
+
+    beforeAll(() => {
+      lessVersion = new Version("1.5.4");
+    });
+
+    it("should return false", () => {
+      expect(version.lessOrEqualThan(lessVersion)).toBe(false);
+    });
+
+    it("should return true", () => {
+      expect(version.greaterOrEqualThan(version)).toBe(true);
+    });
+  });
+
+  it("should return true if version is between", () => {
+    const version1 = new Version("1.0.0");
+    const version2 = new Version("2.0.0");
+
+    expect(version.isBetween(version1, version2)).toBe(true);
+  });
+
+  it("should return false if version is not between", () => {
+    const version1 = new Version("0.7.0");
+    const version2 = new Version("1.12.3");
+
+    expect(version.isBetween(version1, version2)).toBe(false);
+  });
+});
+
+describe("compatible function", () => {
+  let type;
+
+  beforeAll(() => {
+    type = {
+      MIN_VERSION: "0.7.0",
+      MAX_VERSION: "1.0.0",
+    };
+  });
+
+  it("should be compatible", () => {
+    expect(compatible(type, "0.7.0")).toBe(true);
+  });
+
+  it("should not be compatible with a greater version", () => {
+    expect(compatible(type, "1.0.1")).toBe(false);
+  });
+});

From 69f3fd672a6acf40252e26246a907831afcedf22 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 6 Jun 2024 21:03:24 -0500
Subject: [PATCH 16/35] remove a few things

---
 js/types/load.js            | 11 -----------
 test/reconstruction.test.js |  1 -
 2 files changed, 12 deletions(-)

diff --git a/js/types/load.js b/js/types/load.js
index 2ac27473..2ce5e375 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -1,15 +1,6 @@
-import jsonData from "../../input/wzp6_ee_mumuH_ecm240_CLD_RECO.edm4hep.json" assert { type: "json" }; // node 20
 import { types } from "./reconstruction.js";
 import { compatible } from "./version.js";
 
-const loadersConfig = [
-  "ReconstructedParticle",
-  "ParticleID",
-  "Vertex",
-  "Track",
-  "Cluster",
-];
-
 export function buildLoader(config, version) {
   const newLoader = {};
 
@@ -53,5 +44,3 @@ export function loadParticles(jsonData, event, loadersConfig) {
 
   return particles;
 }
-
-loadParticles(jsonData, 0, loadersConfig);
diff --git a/test/reconstruction.test.js b/test/reconstruction.test.js
index 90278d6f..06713735 100644
--- a/test/reconstruction.test.js
+++ b/test/reconstruction.test.js
@@ -3,7 +3,6 @@ import {
   extractOneToOneLink,
   createLinksManager,
   createGenericLink,
-  GenericLink,
 } from "../js/types/reconstruction.js";
 
 test("it should create a generic link", () => {

From a1afbfe39ccb8053e7887c8c04924daeb775f879 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Sun, 9 Jun 2024 11:29:05 -0500
Subject: [PATCH 17/35] extract up-to-date types from edm4hep

---
 build/build.js      |    1 +
 model/.gitignore    |    2 +
 model/download.js   |   17 +
 model/index.js      |   97 +
 output/datatypes.js |  302 ++
 package-lock.json   | 8153 ++++++++++++++++++++++---------------------
 package.json        |   13 +-
 pnpm-lock.yaml      |   16 +
 8 files changed, 4530 insertions(+), 4071 deletions(-)
 create mode 100644 build/build.js
 create mode 100644 model/.gitignore
 create mode 100644 model/download.js
 create mode 100644 model/index.js
 create mode 100644 output/datatypes.js

diff --git a/build/build.js b/build/build.js
new file mode 100644
index 00000000..d78a52eb
--- /dev/null
+++ b/build/build.js
@@ -0,0 +1 @@
+import { datatypes } from "../output/datatypes";
diff --git a/model/.gitignore b/model/.gitignore
new file mode 100644
index 00000000..4102c031
--- /dev/null
+++ b/model/.gitignore
@@ -0,0 +1,2 @@
+*.yaml
+*.yml
\ No newline at end of file
diff --git a/model/download.js b/model/download.js
new file mode 100644
index 00000000..125412c1
--- /dev/null
+++ b/model/download.js
@@ -0,0 +1,17 @@
+import https from "https";
+import fs from "fs";
+
+const URL =
+  "https://raw.githubusercontent.com/key4hep/EDM4hep/main/edm4hep.yaml";
+
+const folder = process.argv[2] ?? "model";
+
+const file = fs.createWriteStream(`${folder}/edm4hep.yaml`);
+https.get(URL, (res) => {
+  res.pipe(file);
+
+  file.on("finish", () => {
+    file.close();
+    console.log("Download completed");
+  });
+});
diff --git a/model/index.js b/model/index.js
new file mode 100644
index 00000000..a93f77f8
--- /dev/null
+++ b/model/index.js
@@ -0,0 +1,97 @@
+import jsYaml from "js-yaml";
+import fs from "fs/promises";
+
+const fileRoute = process.argv[2] ?? "model/edm4hep.yaml";
+const folderOutput = process.argv[3] ?? "output";
+
+const definitionFile = await fs.readFile(fileRoute, "utf-8");
+const definitionObject = jsYaml.load(definitionFile);
+
+const components = definitionObject.components;
+const datatypes = definitionObject.datatypes;
+
+const configTypes = new Set([
+  "edm4hep::Cluster",
+  "edm4hep::ParticleID",
+  "edm4hep::MCParticle",
+  "edm4hep::Vertex",
+  "edm4hep::ReconstructedParticle",
+  "edm4hep::Track",
+]);
+
+const selectedTypes = Object.entries(datatypes).filter(([key, _]) =>
+  configTypes.has(key)
+);
+
+const componentsDefinition = {};
+const datatypesDefinition = {};
+
+class Component {}
+
+class DataTypeMember {
+  constructor(type, name, unit = null) {
+    this.type = type;
+    this.name = name;
+    if (unit) this.unit = unit;
+  }
+}
+
+class Relation {
+  constructor(type, name) {
+    this.type = type;
+    this.name = name;
+  }
+}
+
+const parseString = (string) => {
+  return string
+    .split("//")[0]
+    .trim()
+    .split(" ")
+    .filter((substring) => substring !== "");
+};
+
+const parseDatatypesMembers = (members) => {
+  const newMembers = [];
+
+  for (const member of members) {
+    let [type, name, unit] = parseString(member);
+    if (unit) unit = unit.replace("[", "").replace("]", "");
+    const newMember = new DataTypeMember(type, name, unit);
+    newMembers.push(newMember);
+  }
+
+  return newMembers;
+};
+
+const parseRelation = (relations) => {
+  return relations.map((relation) => new Relation(parseString(relation)));
+};
+
+selectedTypes.forEach(([name, values]) => {
+  const members = values["Members"] ?? false;
+  let parsedMembers;
+  if (members) parsedMembers = parseDatatypesMembers(members);
+  const oneToManyRelations = values["OneToManyRelations"] ?? false;
+  let parsedOneToManyRelations;
+  if (oneToManyRelations)
+    parsedOneToManyRelations = parseRelation(oneToManyRelations);
+  const oneToOneRelations = values["OneToOneRelations"] ?? false;
+  let parsedOneToOneRelations;
+  if (oneToOneRelations)
+    parsedOneToOneRelations = parseRelation(oneToOneRelations);
+
+  datatypesDefinition[name] = {
+    members: parsedMembers,
+    oneToManyRelations: parsedOneToManyRelations,
+    oneToOneRelations: parsedOneToOneRelations,
+  };
+});
+
+const output = `export const datatypes = ${JSON.stringify(
+  datatypesDefinition,
+  null,
+  2
+)}`;
+
+await fs.writeFile(`${folderOutput}/datatypes.js`, output);
diff --git a/output/datatypes.js b/output/datatypes.js
new file mode 100644
index 00000000..31b015ff
--- /dev/null
+++ b/output/datatypes.js
@@ -0,0 +1,302 @@
+export const datatypes = {
+  "edm4hep::MCParticle": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "PDG"
+      },
+      {
+        "type": "int32_t",
+        "name": "generatorStatus"
+      },
+      {
+        "type": "int32_t",
+        "name": "simulatorStatus"
+      },
+      {
+        "type": "float",
+        "name": "charge"
+      },
+      {
+        "type": "float",
+        "name": "time",
+        "unit": "ns"
+      },
+      {
+        "type": "double",
+        "name": "mass",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3d",
+        "name": "vertex",
+        "unit": "mm"
+      },
+      {
+        "type": "edm4hep::Vector3d",
+        "name": "endpoint",
+        "unit": "mm"
+      },
+      {
+        "type": "edm4hep::Vector3d",
+        "name": "momentum",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3d",
+        "name": "momentumAtEndpoint",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "spin"
+      },
+      {
+        "type": "edm4hep::Vector2i",
+        "name": "colorFlow"
+      }
+    ],
+    "oneToManyRelations": [
+      {
+        "type": [
+          "edm4hep::MCParticle",
+          "parents"
+        ]
+      },
+      {
+        "type": [
+          "edm4hep::MCParticle",
+          "daughters"
+        ]
+      }
+    ]
+  },
+  "edm4hep::ParticleID": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "type"
+      },
+      {
+        "type": "int32_t",
+        "name": "PDG"
+      },
+      {
+        "type": "int32_t",
+        "name": "algorithmType"
+      },
+      {
+        "type": "float",
+        "name": "likelihood"
+      }
+    ],
+    "oneToOneRelations": [
+      {
+        "type": [
+          "edm4hep::ReconstructedParticle",
+          "particle"
+        ]
+      }
+    ]
+  },
+  "edm4hep::Cluster": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "type"
+      },
+      {
+        "type": "float",
+        "name": "energy",
+        "unit": "GeV"
+      },
+      {
+        "type": "float",
+        "name": "energyError",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "position",
+        "unit": "mm"
+      },
+      {
+        "type": "edm4hep::CovMatrix3f",
+        "name": "positionError"
+      },
+      {
+        "type": "float",
+        "name": "iTheta"
+      },
+      {
+        "type": "float",
+        "name": "phi"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "directionError",
+        "unit": "mm**2"
+      }
+    ],
+    "oneToManyRelations": [
+      {
+        "type": [
+          "edm4hep::Cluster",
+          "clusters"
+        ]
+      },
+      {
+        "type": [
+          "edm4hep::CalorimeterHit",
+          "hits"
+        ]
+      }
+    ]
+  },
+  "edm4hep::Track": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "type"
+      },
+      {
+        "type": "float",
+        "name": "chi2"
+      },
+      {
+        "type": "int32_t",
+        "name": "ndf"
+      },
+      {
+        "type": "float",
+        "name": "dEdx"
+      },
+      {
+        "type": "float",
+        "name": "dEdxError"
+      },
+      {
+        "type": "float",
+        "name": "radiusOfInnermostHit"
+      }
+    ],
+    "oneToManyRelations": [
+      {
+        "type": [
+          "edm4hep::TrackerHit",
+          "trackerHits"
+        ]
+      },
+      {
+        "type": [
+          "edm4hep::Track",
+          "tracks"
+        ]
+      }
+    ]
+  },
+  "edm4hep::Vertex": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "primary"
+      },
+      {
+        "type": "float",
+        "name": "chi2"
+      },
+      {
+        "type": "float",
+        "name": "probability"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "position"
+      },
+      {
+        "type": "edm4hep::CovMatrix3f",
+        "name": "covMatrix"
+      },
+      {
+        "type": "int32_t",
+        "name": "algorithmType"
+      }
+    ],
+    "oneToOneRelations": [
+      {
+        "type": [
+          "edm4hep::ReconstructedParticle",
+          "associatedParticle"
+        ]
+      }
+    ]
+  },
+  "edm4hep::ReconstructedParticle": {
+    "members": [
+      {
+        "type": "int32_t",
+        "name": "PDG"
+      },
+      {
+        "type": "float",
+        "name": "energy",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "momentum",
+        "unit": "GeV"
+      },
+      {
+        "type": "edm4hep::Vector3f",
+        "name": "referencePoint",
+        "unit": "mm"
+      },
+      {
+        "type": "float",
+        "name": "charge"
+      },
+      {
+        "type": "float",
+        "name": "mass",
+        "unit": "GeV"
+      },
+      {
+        "type": "float",
+        "name": "goodnessOfPID"
+      },
+      {
+        "type": "edm4hep::CovMatrix4f",
+        "name": "covMatrix"
+      }
+    ],
+    "oneToManyRelations": [
+      {
+        "type": [
+          "edm4hep::Cluster",
+          "clusters"
+        ]
+      },
+      {
+        "type": [
+          "edm4hep::Track",
+          "tracks"
+        ]
+      },
+      {
+        "type": [
+          "edm4hep::ReconstructedParticle",
+          "particles"
+        ]
+      }
+    ],
+    "oneToOneRelations": [
+      {
+        "type": [
+          "edm4hep::Vertex",
+          "startVertex"
+        ]
+      }
+    ]
+  }
+}
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index aa9d0cc9..86f79c32 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,4069 +1,4088 @@
 {
-  "name": "dmx",
-  "version": "1.0.0",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "dmx",
-      "version": "1.0.0",
-      "license": "BSD-2-Clause",
-      "devDependencies": {
-        "jest": "^29.7.0",
-        "jest-environment-jsdom": "^29.7.0"
-      }
-    },
-    "node_modules/@ampproject/remapping": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz",
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-      "dev": true,
-      "dependencies": {
-        "@jridgewell/gen-mapping": "^0.3.5",
-        "@jridgewell/trace-mapping": "^0.3.24"
-      },
-      "engines": {
-        "node": ">=6.0.0"
-      }
-    },
-    "node_modules/@babel/code-frame": {
-      "version": "7.24.2",
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-      "dev": true,
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+				}
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+			},
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+				"escalade": "^3.1.1",
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+				"require-directory": "^2.1.1",
+				"string-width": "^4.2.3",
+				"y18n": "^5.0.5",
+				"yargs-parser": "^21.1.1"
+			},
+			"engines": {
+				"node": ">=12"
+			}
+		},
+		"node_modules/yargs-parser": {
+			"version": "21.1.1",
+			"resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz",
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+			"dev": true,
+			"engines": {
+				"node": ">=12"
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+		"node_modules/yocto-queue": {
+			"version": "0.1.0",
+			"resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+			"integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
+			"dev": true,
+			"engines": {
+				"node": ">=10"
+			},
+			"funding": {
+				"url": "https://github.com/sponsors/sindresorhus"
+			}
+		}
+	}
 }
diff --git a/package.json b/package.json
index ad23f1c0..01cda842 100644
--- a/package.json
+++ b/package.json
@@ -1,9 +1,11 @@
-{	
+{
 	"name": "dmx",
 	"type": "module",
 	"version": "1.0.0",
 	"scripts": {
-		"test": "node --experimental-vm-modules ./node_modules/jest/bin/jest.js"
+		"test": "node --experimental-vm-modules ./node_modules/jest/bin/jest.js",
+		"build": "node ./model/index.js",
+		"download": "node ./model/download.js"
 	},
 	"devDependencies": {
 		"jest": "^29.7.0",
@@ -19,5 +21,8 @@
 		"key4hep"
 	],
 	"license": "BSD-2-Clause",
-	"homepage": "https://key4hep.github.io/dmx/"
-}
+	"homepage": "https://key4hep.github.io/dmx/",
+	"dependencies": {
+		"js-yaml": "^4.1.0"
+	}
+}
\ No newline at end of file
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index a71c12fe..3f739c9f 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -4,6 +4,11 @@ settings:
   autoInstallPeers: true
   excludeLinksFromLockfile: false
 
+dependencies:
+  js-yaml:
+    specifier: ^4.1.0
+    version: 4.1.0
+
 devDependencies:
   jest:
     specifier: ^29.7.0
@@ -793,6 +798,10 @@ packages:
       sprintf-js: 1.0.3
     dev: true
 
+  /argparse@2.0.1:
+    resolution: {integrity: sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q==}
+    dev: false
+
   /asynckit@0.4.0:
     resolution: {integrity: sha512-Oei9OH4tRh0YqU3GxhX79dM/mwVgvbZJaSNaRk+bshkj0S5cfHcgYakreBjrHwatXKbz+IoIdYLxrKim2MjW0Q==}
     dev: true
@@ -1933,6 +1942,13 @@ packages:
       esprima: 4.0.1
     dev: true
 
+  /js-yaml@4.1.0:
+    resolution: {integrity: sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==}
+    hasBin: true
+    dependencies:
+      argparse: 2.0.1
+    dev: false
+
   /jsdom@20.0.3:
     resolution: {integrity: sha512-SYhBvTh89tTfCD/CRdSOm13mOBa42iTaTyfyEWBdKcGdPxPtLFBXuHR8XHb33YNYaP+lLbmSvBTsnoesCNJEsQ==}
     engines: {node: '>=14'}

From cc58efa19fef95a7788f02ef86d15572278aa677 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Sun, 9 Jun 2024 13:55:56 -0500
Subject: [PATCH 18/35] load particles according to edm4hep.yaml definition

---
 build/build.js             |   1 -
 js/types/dynamic.js        |  40 ++++--
 js/types/load.js           |  74 ++++++-----
 js/types/particle.js       |   8 ++
 js/types/reconstruction.js | 259 ++++---------------------------------
 js/types/units.js          |   7 +
 js/types/version.js        |  43 ------
 model/index.js             |   5 +-
 output/datatypes.js        |  72 ++++-------
 package.json               |   5 +-
 test/load.test.js          |  14 +-
 test/version.test.js       |  78 -----------
 12 files changed, 147 insertions(+), 459 deletions(-)
 delete mode 100644 build/build.js
 create mode 100644 js/types/particle.js
 create mode 100644 js/types/units.js
 delete mode 100644 js/types/version.js
 delete mode 100644 test/version.test.js

diff --git a/build/build.js b/build/build.js
deleted file mode 100644
index d78a52eb..00000000
--- a/build/build.js
+++ /dev/null
@@ -1 +0,0 @@
-import { datatypes } from "../output/datatypes";
diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index d06ebace..21ade621 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -1,15 +1,35 @@
-export function dynamicLoad(object, data, ignore = null) {
-  let filteredData = {};
+import { createLink } from "./reconstruction.js";
 
-  if (ignore !== null) {
-    for (const key in data) {
-      if (!ignore.has(key)) filteredData[key] = data[key];
-    }
-  } else {
-    filteredData = data;
+export function loadMembers(object, data, membersToLoad) {
+  for (const member of membersToLoad) {
+    if (data[member.name] === undefined) continue; // load up to date data
+    object.members[member.name] = data[member.name];
   }
+}
+
+export function loadOneToOneRelations(object, data, relationsToLoad) {
+  object.oneToOneRelations = {};
+  for (const relation of relationsToLoad) {
+    const relationData = data[relation.name];
+    if (relationData === undefined) continue;
 
-  for (const [key, value] of Object.entries(filteredData)) {
-    object[key] = value;
+    const link = createLink(object.id, object.id, relationData);
+    object.oneToOneRelations[relation.name] = link;
+  }
+}
+
+export function loadOneToManyRelations(object, data, relationsToLoad) {
+  object.oneToManyRelations = {};
+  for (const relation of relationsToLoad) {
+    const name = relation.name;
+    const relationData = data[name];
+
+    if (relationData === undefined) continue;
+    object.oneToManyRelations[name] = [];
+
+    for (const [index, relationElement] of relationData.entries()) {
+      const link = createLink(index + object.id, object.id, relationElement);
+      object.oneToManyRelations[name].push(link);
+    }
   }
 }
diff --git a/js/types/load.js b/js/types/load.js
index 2ce5e375..75a6a246 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -1,46 +1,62 @@
-import { types } from "./reconstruction.js";
-import { compatible } from "./version.js";
-
-export function buildLoader(config, version) {
-  const newLoader = {};
-
-  if (typeof config === "string") config = [config];
-
-  for (const particle of config) {
-    if (types.hasOwnProperty(particle)) {
-      const isCompatible = compatible(types[particle], version);
-
-      if (isCompatible) {
-        newLoader[particle] = types[particle].load;
-      } else {
-        newLoader[particle] = () => {
-          return [];
-        };
-      }
-    }
+import { reconstructionTypes } from "./reconstruction.js";
+import { datatypes } from "../../output/datatypes.js";
+import {
+  loadMembers,
+  loadOneToOneRelations,
+  loadOneToManyRelations,
+} from "./dynamic.js";
+import json from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" };
+
+export function loadParticleType(collection, datatype, type) {
+  const particles = [];
+
+  for (const [index, particle] of collection.entries()) {
+    const newParticle = new type();
+    newParticle.id = index;
+
+    loadMembers(newParticle, particle, datatype.members);
+
+    if (datatype.oneToOneRelations)
+      loadOneToOneRelations(newParticle, particle, datatype.oneToOneRelations);
+
+    if (datatype.oneToManyRelations)
+      loadOneToManyRelations(
+        newParticle,
+        particle,
+        datatype.oneToManyRelations
+      );
+
+    particles.push(newParticle);
   }
 
-  return newLoader;
+  return particles;
 }
 
-export function loadParticles(jsonData, event, loadersConfig) {
+export function loadParticles(jsonData, event, particlesToLoad) {
   const eventData = jsonData["Event " + event];
-  const version = eventData.edm4hepVersion;
-
-  const loader = buildLoader(loadersConfig, version);
 
   const particles = {};
-  Object.keys(loader).forEach((key) => (particles[key] = []));
 
-  for (const [type, loadFunction] of Object.entries(loader)) {
+  for (const type of particlesToLoad) {
     const particlesType = Object.values(eventData).filter(
-      (element) => element.collType === `edm4hep::${type}Collection`
+      (element) => element.collType === `${type}Collection`
     );
 
     particlesType.forEach(({ collection }) => {
-      const [particles, links] = loadFunction(collection);
+      loadParticleType(collection, datatypes[type], reconstructionTypes[type]);
     });
   }
 
   return particles;
 }
+
+const particlesToLoad = [
+  // subset of types
+  "edm4hep::Cluster",
+  "edm4hep::ReconstructedParticle",
+  "edm4hep::Vertex",
+  "edm4hep::Track",
+  "edm4hep::ParticleID",
+];
+
+loadParticles(json, 0, particlesToLoad);
diff --git a/js/types/particle.js b/js/types/particle.js
new file mode 100644
index 00000000..b8201837
--- /dev/null
+++ b/js/types/particle.js
@@ -0,0 +1,8 @@
+export class Particle {
+  constructor() {
+    this.members = {};
+  }
+
+  draw() {}
+  // more methods common to all particles
+}
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index efc3b5cc..c837b0f3 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -1,268 +1,59 @@
-import { dynamicLoad } from "./dynamic.js";
-
-export class Cluster {
-  static MIN_VERSION = "0.7.0"; // may vary per type of particle
-  static MAX_VERSION = "1.0.0";
+import { Particle } from "./particle.js";
 
+class Reconstruction extends Particle {
   constructor() {
-    // Physics properties
-    this.type = 0;
-    this.energy = 0; // GeV
-    this.energyError = 0; // GeV
-    this.position = {}; // mm
-    this.positionError = {};
-    this.iTheta = 0;
-    this.phi = 0;
-    this.directionError = {}; // mm^2
-    this.shapeParameters = [];
-    this.subdetectorEnergies = [];
-    this.clusters = [];
-    this.hits = [];
-  }
-
-  static load(collection) {
-    const particles = [];
-    const links = createLinksManager(["clusters", "hits"]);
-
-    for (const [index, particle] of collection.entries()) {
-      const cluster = new Cluster();
-      cluster.index = index;
-
-      extractOneToManyLinks(links, ["clusters", "hits"], cluster, particle);
-
-      dynamicLoad(cluster, particle);
-
-      particles.push(cluster);
-    }
-
-    return [particles, links];
+    super();
   }
 }
 
-export class ParticleID {
-  static MIN_VERSION = "0.7.0";
-  static MAX_VERSION = "1.0.0";
-
+export class Cluster extends Reconstruction {
   constructor() {
-    // Physics properties
-    this.type = 0;
-    this.PDG = 0;
-    this.algorithmType = 0;
-    this.likelihood = 0;
-    this.parameters = [];
-    this.particle = null;
-  }
-
-  static load(collection) {
-    const particles = [];
-    const links = createLinksManager(["particle"]);
-
-    for (const [index, particle] of collection.entries()) {
-      const particleID = new ParticleID();
-      particleID.index = index;
-
-      extractOneToOneLink(links, "particle", particleID, particle);
-
-      dynamicLoad(particleID, particle);
-
-      particles.push(particleID);
-    }
-
-    return [particles, links];
+    super();
   }
 }
 
-export class ReconstructedParticle {
-  static MIN_VERSION = "0.7.0";
-  static MAX_VERSION = "1.0.0";
-
+export class ParticleID extends Reconstruction {
   constructor() {
-    // Physics properties
-    this.PDG = 0;
-    this.energy = 0; // GeV
-    this.momentum = {}; // GeV
-    this.referencePoint = {}; // mm
-    this.charge = 0;
-    this.mass = 0; // GeV
-    this.goodnessOfPID = 0;
-    this.covMatrix = {};
-    this.startVertex = null;
-    this.clusters = [];
-    this.tracks = [];
-    this.particles = [];
-  }
-
-  static load(collection) {
-    const particles = [];
-    const links = createLinksManager([
-      "tracks",
-      "clusters",
-      "particles",
-      "startVertex",
-    ]);
-
-    for (const [index, particle] of collection.entries()) {
-      const reconstructedParticle = new ReconstructedParticle();
-      reconstructedParticle.index = index;
-
-      extractOneToManyLinks(
-        links,
-        ["tracks", "clusters", "particles"],
-        reconstructedParticle,
-        particle
-      );
-      extractOneToOneLink(
-        links,
-        "startVertex",
-        reconstructedParticle,
-        particle
-      );
-
-      dynamicLoad(
-        reconstructedParticle,
-        particle,
-        new Set(["tracks", "clusters", "particles", "startVertex"])
-      );
-
-      particles.push(reconstructedParticle);
-    }
-
-    return [particles, links];
+    super();
   }
 }
 
-export class Vertex {
-  static MIN_VERSION = "0.7.0";
-  static MAX_VERSION = "1.0.0";
-
+export class ReconstructedParticle extends Reconstruction {
   constructor() {
-    // Physics properties
-    this.primary = 0;
-    this.chi2 = 0;
-    this.probability = 0;
-    this.position = {}; // mm
-    this.covMatrix = {};
-    this.algorithmType = 0;
-    this.parameters = 0;
-    this.associatedParticle = null;
-  }
-
-  static load(collection) {
-    const particles = [];
-    const links = createLinksManager(["associatedParticle"]);
-
-    for (const [index, particle] of collection.entries()) {
-      const vertex = new Vertex();
-      vertex.index = index;
-
-      extractOneToOneLink(links, "associatedParticle", vertex, particle);
-
-      dynamicLoad(vertex, particle, new Set(["associatedParticle"]));
-
-      particles.push(vertex);
-    }
-
-    return [particles, links];
+    super();
   }
 }
 
-export class Track {
-  static MIN_VERSION = "0.7.0";
-  static MAX_VERSION = "1.0.0";
-
+export class Vertex extends Reconstruction {
   constructor() {
-    // Physics properties
-    this.type = 0;
-    this.chi2 = 0;
-    this.ndf = 0;
-    this.dEdx = 0;
-    this.dEdxError = 0;
-    this.radiusOfInnermostHit = 0;
-    this.subdetectorHitNumbers = [];
-    this.trackStates = [];
-    this.dxQuantities = [];
-    this.trackerHits = [];
-    this.tracks = [];
+    super();
   }
+}
 
-  static load(collection) {
-    const particles = [];
-    const links = createLinksManager(["trackerHits", "tracks"]);
-
-    for (const [index, particle] of collection.entries()) {
-      const track = new Track();
-      track.index = index;
-
-      extractOneToManyLinks(links, ["trackerHits", "tracks"], track, particle);
-
-      dynamicLoad(track, particle);
-
-      particles.push(track);
-    }
-
-    return [particles, links];
+export class Track extends Reconstruction {
+  constructor() {
+    super();
   }
 }
 
 export class GenericLink {
   // we may create a specific class for each type if needed
-  constructor(id, from, to) {
+  constructor(id, from, to, collectionID) {
     this.id = id;
     this.from = from;
     this.to = to;
+    this.collectionID = collectionID;
   }
 }
 
-export function createLinksManager(types) {
-  const links = {};
-  types.forEach((type) => (links[type] = []));
-  return links;
-}
-
-export function createGenericLink(id, from, { collectionID, index }) {
-  const genericLink = new GenericLink(id, from, index);
-  genericLink.collectionID = collectionID;
-  return genericLink;
-}
-
-export function extractOneToManyLinks(
-  linksManager,
-  keys,
-  newParticle,
-  particleData
-) {
-  for (const key of keys) {
-    particleData[key].map((val) => {
-      const link = createGenericLink(
-        linksManager[key].length,
-        newParticle.index,
-        val
-      );
-      linksManager[key].push(link);
-      newParticle[key].push(link.id);
-    });
-  }
-}
-
-export function extractOneToOneLink(
-  linksManager,
-  key,
-  newParticle,
-  particleData
-) {
-  const link = createGenericLink(
-    linksManager[key].length,
-    newParticle.index,
-    particleData[key]
-  );
-  linksManager[key].push(link);
-  newParticle[key] = link.id;
+export function createLink(id, from, { collectionID, index }) {
+  return new GenericLink(id, from, index, collectionID);
 }
 
-export const types = {
-  "Cluster": Cluster,
-  "ParticleID": ParticleID,
-  "ReconstructedParticle": ReconstructedParticle,
-  "Vertex": Vertex,
-  "Track": Track,
+export const reconstructionTypes = {
+  "edm4hep::Cluster": Cluster,
+  "edm4hep::ParticleID": ParticleID,
+  "edm4hep::ReconstructedParticle": ReconstructedParticle,
+  "edm4hep::Vertex": Vertex,
+  "edm4hep::Track": Track,
 };
diff --git a/js/types/units.js b/js/types/units.js
new file mode 100644
index 00000000..44db22fa
--- /dev/null
+++ b/js/types/units.js
@@ -0,0 +1,7 @@
+export const units = {
+  "charge": "e",
+  "mass": "GeV",
+  "time": "ns",
+  "momentum": "GeV",
+  "vertex": "mm",
+};
diff --git a/js/types/version.js b/js/types/version.js
deleted file mode 100644
index 2d1efad8..00000000
--- a/js/types/version.js
+++ /dev/null
@@ -1,43 +0,0 @@
-export class Version {
-  constructor(string) {
-    const [major, minor, patch] = string.split(".");
-    this.major = parseInt(major);
-    this.minor = parseInt(minor);
-    this.patch = parseInt(patch);
-  }
-
-  toString() {
-    return `${this.major}.${this.minor}.${this.patch}`;
-  }
-
-  greaterOrEqualThan(version) {
-    return (
-      this.major > version.major ||
-      (this.major === version.major &&
-        (this.minor > version.minor ||
-          (this.minor === version.minor && this.patch >= version.patch)))
-    );
-  }
-
-  lessOrEqualThan(version) {
-    return (
-      this.major < version.major ||
-      (this.major === version.major &&
-        (this.minor < version.minor ||
-          (this.minor === version.minor && this.patch <= version.patch)))
-    );
-  }
-
-  isBetween(version1, version2) {
-    return this.greaterOrEqualThan(version1) && this.lessOrEqualThan(version2);
-  }
-}
-
-export function compatible(type, version) {
-  const minV = new Version(type.MIN_VERSION);
-  const maxV = new Version(type.MAX_VERSION);
-
-  const v = new Version(version);
-
-  return v.isBetween(minV, maxV);
-}
diff --git a/model/index.js b/model/index.js
index a93f77f8..9de8d912 100644
--- a/model/index.js
+++ b/model/index.js
@@ -65,7 +65,10 @@ const parseDatatypesMembers = (members) => {
 };
 
 const parseRelation = (relations) => {
-  return relations.map((relation) => new Relation(parseString(relation)));
+  return relations.map((relation) => {
+    const [type, name] = parseString(relation);
+    return new Relation(type, name);
+  });
 };
 
 selectedTypes.forEach(([name, values]) => {
diff --git a/output/datatypes.js b/output/datatypes.js
index 31b015ff..788e397c 100644
--- a/output/datatypes.js
+++ b/output/datatypes.js
@@ -58,16 +58,12 @@ export const datatypes = {
     ],
     "oneToManyRelations": [
       {
-        "type": [
-          "edm4hep::MCParticle",
-          "parents"
-        ]
+        "type": "edm4hep::MCParticle",
+        "name": "parents"
       },
       {
-        "type": [
-          "edm4hep::MCParticle",
-          "daughters"
-        ]
+        "type": "edm4hep::MCParticle",
+        "name": "daughters"
       }
     ]
   },
@@ -92,10 +88,8 @@ export const datatypes = {
     ],
     "oneToOneRelations": [
       {
-        "type": [
-          "edm4hep::ReconstructedParticle",
-          "particle"
-        ]
+        "type": "edm4hep::ReconstructedParticle",
+        "name": "particle"
       }
     ]
   },
@@ -140,16 +134,12 @@ export const datatypes = {
     ],
     "oneToManyRelations": [
       {
-        "type": [
-          "edm4hep::Cluster",
-          "clusters"
-        ]
+        "type": "edm4hep::Cluster",
+        "name": "clusters"
       },
       {
-        "type": [
-          "edm4hep::CalorimeterHit",
-          "hits"
-        ]
+        "type": "edm4hep::CalorimeterHit",
+        "name": "hits"
       }
     ]
   },
@@ -182,16 +172,12 @@ export const datatypes = {
     ],
     "oneToManyRelations": [
       {
-        "type": [
-          "edm4hep::TrackerHit",
-          "trackerHits"
-        ]
+        "type": "edm4hep::TrackerHit",
+        "name": "trackerHits"
       },
       {
-        "type": [
-          "edm4hep::Track",
-          "tracks"
-        ]
+        "type": "edm4hep::Track",
+        "name": "tracks"
       }
     ]
   },
@@ -224,10 +210,8 @@ export const datatypes = {
     ],
     "oneToOneRelations": [
       {
-        "type": [
-          "edm4hep::ReconstructedParticle",
-          "associatedParticle"
-        ]
+        "type": "edm4hep::ReconstructedParticle",
+        "name": "associatedParticle"
       }
     ]
   },
@@ -272,30 +256,22 @@ export const datatypes = {
     ],
     "oneToManyRelations": [
       {
-        "type": [
-          "edm4hep::Cluster",
-          "clusters"
-        ]
+        "type": "edm4hep::Cluster",
+        "name": "clusters"
       },
       {
-        "type": [
-          "edm4hep::Track",
-          "tracks"
-        ]
+        "type": "edm4hep::Track",
+        "name": "tracks"
       },
       {
-        "type": [
-          "edm4hep::ReconstructedParticle",
-          "particles"
-        ]
+        "type": "edm4hep::ReconstructedParticle",
+        "name": "particles"
       }
     ],
     "oneToOneRelations": [
       {
-        "type": [
-          "edm4hep::Vertex",
-          "startVertex"
-        ]
+        "type": "edm4hep::Vertex",
+        "name": "startVertex"
       }
     ]
   }
diff --git a/package.json b/package.json
index 01cda842..ed851530 100644
--- a/package.json
+++ b/package.json
@@ -3,9 +3,10 @@
 	"type": "module",
 	"version": "1.0.0",
 	"scripts": {
-		"test": "node --experimental-vm-modules ./node_modules/jest/bin/jest.js",
 		"build": "node ./model/index.js",
-		"download": "node ./model/download.js"
+		"download": "node ./model/download.js",
+		"update": "npm run download && npm run build",
+		"test": "node --experimental-vm-modules ./node_modules/jest/bin/jest.js"
 	},
 	"devDependencies": {
 		"jest": "^29.7.0",
diff --git a/test/load.test.js b/test/load.test.js
index 38f42d24..e1343e03 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,18 +1,6 @@
-import { buildLoader, loadParticles } from "../js/types/load";
-import { dynamicLoad } from "../js/types/dynamic.js";
+import { loadParticles } from "../js/types/load";
 import { ReconstructedParticle } from "../js/types/reconstruction";
 
-describe("build loader", () => {
-  it("should create a loader with a set of types", () => {
-    const loadersConfig = ["ReconstructedParticle", "ParticleID"];
-    const loader = buildLoader(loadersConfig, "0.7.0");
-
-    expect(Object.values(loader).every((f) => typeof f === "function")).toBe(
-      true
-    );
-  });
-});
-
 describe("load different types of particles", () => {
   let data = {};
 
diff --git a/test/version.test.js b/test/version.test.js
deleted file mode 100644
index dd4063bb..00000000
--- a/test/version.test.js
+++ /dev/null
@@ -1,78 +0,0 @@
-import { Version, compatible } from "../js/types/version.js";
-
-describe("version class methods", () => {
-  let version;
-
-  beforeAll(() => {
-    version = new Version("1.12.4");
-  });
-
-  it("should return a string", () => {
-    expect(version.toString()).toBe("1.12.4");
-  });
-
-  describe("greater version than current", () => {
-    let greaterVersion;
-
-    beforeAll(() => {
-      greaterVersion = new Version("1.12.5");
-    });
-
-    it("should return false", () => {
-      expect(version.greaterOrEqualThan(greaterVersion)).toBe(false);
-    });
-
-    it("should return true", () => {
-      expect(version.lessOrEqualThan(version)).toBe(true);
-    });
-  });
-
-  describe("smaller version than current", () => {
-    let lessVersion;
-
-    beforeAll(() => {
-      lessVersion = new Version("1.5.4");
-    });
-
-    it("should return false", () => {
-      expect(version.lessOrEqualThan(lessVersion)).toBe(false);
-    });
-
-    it("should return true", () => {
-      expect(version.greaterOrEqualThan(version)).toBe(true);
-    });
-  });
-
-  it("should return true if version is between", () => {
-    const version1 = new Version("1.0.0");
-    const version2 = new Version("2.0.0");
-
-    expect(version.isBetween(version1, version2)).toBe(true);
-  });
-
-  it("should return false if version is not between", () => {
-    const version1 = new Version("0.7.0");
-    const version2 = new Version("1.12.3");
-
-    expect(version.isBetween(version1, version2)).toBe(false);
-  });
-});
-
-describe("compatible function", () => {
-  let type;
-
-  beforeAll(() => {
-    type = {
-      MIN_VERSION: "0.7.0",
-      MAX_VERSION: "1.0.0",
-    };
-  });
-
-  it("should be compatible", () => {
-    expect(compatible(type, "0.7.0")).toBe(true);
-  });
-
-  it("should not be compatible with a greater version", () => {
-    expect(compatible(type, "1.0.1")).toBe(false);
-  });
-});

From 49d5e6ed304cf4e2adf42f05a0faa3b4a4c0bbaf Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 10 Jun 2024 17:10:54 -0500
Subject: [PATCH 19/35] improvements (advised) and create test a better test
 suite

---
 js/types/{particle.js => edmobject.js} |   2 +-
 js/types/load.js                       |   5 +-
 js/types/reconstruction.js             |  18 +-
 js/types/units.js                      |   2 +-
 model/index.js                         |  21 +-
 output/datatypes.js                    |  30 --
 test/dynamic.test.js                   | 278 +++++++++++++++++
 test/load.test.js                      | 402 +++++++++++++++----------
 test/reconstruction.test.js            |  45 +--
 9 files changed, 545 insertions(+), 258 deletions(-)
 rename js/types/{particle.js => edmobject.js} (80%)
 create mode 100644 test/dynamic.test.js

diff --git a/js/types/particle.js b/js/types/edmobject.js
similarity index 80%
rename from js/types/particle.js
rename to js/types/edmobject.js
index b8201837..7085d455 100644
--- a/js/types/particle.js
+++ b/js/types/edmobject.js
@@ -1,4 +1,4 @@
-export class Particle {
+export class EDMObject {
   constructor() {
     this.members = {};
   }
diff --git a/js/types/load.js b/js/types/load.js
index 75a6a246..cad35eca 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -5,7 +5,6 @@ import {
   loadOneToOneRelations,
   loadOneToManyRelations,
 } from "./dynamic.js";
-import json from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" };
 
 export function loadParticleType(collection, datatype, type) {
   const particles = [];
@@ -51,12 +50,10 @@ export function loadParticles(jsonData, event, particlesToLoad) {
 }
 
 const particlesToLoad = [
-  // subset of types
+  // subset of datatypes
   "edm4hep::Cluster",
   "edm4hep::ReconstructedParticle",
   "edm4hep::Vertex",
   "edm4hep::Track",
   "edm4hep::ParticleID",
 ];
-
-loadParticles(json, 0, particlesToLoad);
diff --git a/js/types/reconstruction.js b/js/types/reconstruction.js
index c837b0f3..4ad308de 100644
--- a/js/types/reconstruction.js
+++ b/js/types/reconstruction.js
@@ -1,36 +1,30 @@
-import { Particle } from "./particle.js";
+import { EDMObject } from "./edmobject.js";
 
-class Reconstruction extends Particle {
+export class Cluster extends EDMObject {
   constructor() {
     super();
   }
 }
 
-export class Cluster extends Reconstruction {
+export class ParticleID extends EDMObject {
   constructor() {
     super();
   }
 }
 
-export class ParticleID extends Reconstruction {
+export class ReconstructedParticle extends EDMObject {
   constructor() {
     super();
   }
 }
 
-export class ReconstructedParticle extends Reconstruction {
+export class Vertex extends EDMObject {
   constructor() {
     super();
   }
 }
 
-export class Vertex extends Reconstruction {
-  constructor() {
-    super();
-  }
-}
-
-export class Track extends Reconstruction {
+export class Track extends EDMObject {
   constructor() {
     super();
   }
diff --git a/js/types/units.js b/js/types/units.js
index 44db22fa..f3cec707 100644
--- a/js/types/units.js
+++ b/js/types/units.js
@@ -3,5 +3,5 @@ export const units = {
   "mass": "GeV",
   "time": "ns",
   "momentum": "GeV",
-  "vertex": "mm",
+  "position": "mm", // more to come
 };
diff --git a/model/index.js b/model/index.js
index 9de8d912..5218676a 100644
--- a/model/index.js
+++ b/model/index.js
@@ -29,16 +29,16 @@ const datatypesDefinition = {};
 class Component {}
 
 class DataTypeMember {
-  constructor(type, name, unit = null) {
-    this.type = type;
+  constructor(type = null, name, unit = null) {
+    if (type) this.type = type;
     this.name = name;
     if (unit) this.unit = unit;
   }
 }
 
 class Relation {
-  constructor(type, name) {
-    this.type = type;
+  constructor(type = null, name) {
+    if (type) this.type = type;
     this.name = name;
   }
 }
@@ -57,8 +57,11 @@ const parseDatatypesMembers = (members) => {
   for (const member of members) {
     let [type, name, unit] = parseString(member);
     if (unit) unit = unit.replace("[", "").replace("]", "");
-    const newMember = new DataTypeMember(type, name, unit);
-    newMembers.push(newMember);
+    if (type.includes("edm4hep::")) {
+      newMembers.push(new DataTypeMember(type, name, unit));
+    } else {
+      newMembers.push(new DataTypeMember(null, name, unit));
+    }
   }
 
   return newMembers;
@@ -67,7 +70,11 @@ const parseDatatypesMembers = (members) => {
 const parseRelation = (relations) => {
   return relations.map((relation) => {
     const [type, name] = parseString(relation);
-    return new Relation(type, name);
+    if (type.includes("edm4hep::")) {
+      return new Relation(type, name);
+    } else {
+      return new Relation(null, name);
+    }
   });
 };
 
diff --git a/output/datatypes.js b/output/datatypes.js
index 788e397c..2dd899e9 100644
--- a/output/datatypes.js
+++ b/output/datatypes.js
@@ -2,28 +2,22 @@ export const datatypes = {
   "edm4hep::MCParticle": {
     "members": [
       {
-        "type": "int32_t",
         "name": "PDG"
       },
       {
-        "type": "int32_t",
         "name": "generatorStatus"
       },
       {
-        "type": "int32_t",
         "name": "simulatorStatus"
       },
       {
-        "type": "float",
         "name": "charge"
       },
       {
-        "type": "float",
         "name": "time",
         "unit": "ns"
       },
       {
-        "type": "double",
         "name": "mass",
         "unit": "GeV"
       },
@@ -70,19 +64,15 @@ export const datatypes = {
   "edm4hep::ParticleID": {
     "members": [
       {
-        "type": "int32_t",
         "name": "type"
       },
       {
-        "type": "int32_t",
         "name": "PDG"
       },
       {
-        "type": "int32_t",
         "name": "algorithmType"
       },
       {
-        "type": "float",
         "name": "likelihood"
       }
     ],
@@ -96,16 +86,13 @@ export const datatypes = {
   "edm4hep::Cluster": {
     "members": [
       {
-        "type": "int32_t",
         "name": "type"
       },
       {
-        "type": "float",
         "name": "energy",
         "unit": "GeV"
       },
       {
-        "type": "float",
         "name": "energyError",
         "unit": "GeV"
       },
@@ -119,11 +106,9 @@ export const datatypes = {
         "name": "positionError"
       },
       {
-        "type": "float",
         "name": "iTheta"
       },
       {
-        "type": "float",
         "name": "phi"
       },
       {
@@ -146,27 +131,21 @@ export const datatypes = {
   "edm4hep::Track": {
     "members": [
       {
-        "type": "int32_t",
         "name": "type"
       },
       {
-        "type": "float",
         "name": "chi2"
       },
       {
-        "type": "int32_t",
         "name": "ndf"
       },
       {
-        "type": "float",
         "name": "dEdx"
       },
       {
-        "type": "float",
         "name": "dEdxError"
       },
       {
-        "type": "float",
         "name": "radiusOfInnermostHit"
       }
     ],
@@ -184,15 +163,12 @@ export const datatypes = {
   "edm4hep::Vertex": {
     "members": [
       {
-        "type": "int32_t",
         "name": "primary"
       },
       {
-        "type": "float",
         "name": "chi2"
       },
       {
-        "type": "float",
         "name": "probability"
       },
       {
@@ -204,7 +180,6 @@ export const datatypes = {
         "name": "covMatrix"
       },
       {
-        "type": "int32_t",
         "name": "algorithmType"
       }
     ],
@@ -218,11 +193,9 @@ export const datatypes = {
   "edm4hep::ReconstructedParticle": {
     "members": [
       {
-        "type": "int32_t",
         "name": "PDG"
       },
       {
-        "type": "float",
         "name": "energy",
         "unit": "GeV"
       },
@@ -237,16 +210,13 @@ export const datatypes = {
         "unit": "mm"
       },
       {
-        "type": "float",
         "name": "charge"
       },
       {
-        "type": "float",
         "name": "mass",
         "unit": "GeV"
       },
       {
-        "type": "float",
         "name": "goodnessOfPID"
       },
       {
diff --git a/test/dynamic.test.js b/test/dynamic.test.js
new file mode 100644
index 00000000..4e58468f
--- /dev/null
+++ b/test/dynamic.test.js
@@ -0,0 +1,278 @@
+import {
+  loadMembers,
+  loadOneToOneRelations,
+  loadOneToManyRelations,
+} from "../js/types/dynamic";
+
+let object;
+let data;
+
+beforeEach(() => {
+  object = {
+    "id": 1,
+  };
+  data = {};
+});
+
+test("load members given some defined members and data", () => {
+  object.members = {};
+  const members = [
+    {
+      "name": "type",
+    },
+    {
+      "name": "chi2",
+    },
+    {
+      "name": "ndf",
+    },
+    {
+      "name": "dEdx",
+    },
+    {
+      "name": "dEdxError",
+    },
+    {
+      "name": "radiusOfInnermostHit",
+    },
+  ];
+  data = {
+    "chi2": 0.0,
+    "dEdx": 0.0,
+    "dEdxError": 0.0,
+    "dxQuantities": [
+      {
+        "error": 0.0,
+        "type": 0,
+        "value": 0.0,
+      },
+    ],
+    "ndf": 0,
+    "radiusOfInnermostHit": 17.0,
+    "subDetectorHitNumbers": [],
+    "trackStates": [
+      {
+        "D0": 0.13514114916324615,
+        "Z0": -0.10983038693666458,
+        "covMatrix": [
+          0.01773529127240181, -0.0011217461433261633, 7.128114521037787e-5,
+          2.307129989276291e-7, -1.38431239804504e-8, 1.2183726250114546e-10,
+          9.953266999218613e-5, -6.313419817161048e-6, 2.394112907921908e-9,
+          0.019905241206288338, -3.138819374726154e-5, 1.986780489460216e-6,
+          -4.870325809314124e-10, -0.001264480990357697, 8.076488302322105e-5,
+          0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+        ],
+        "location": 0,
+        "omega": 0.004053603857755661,
+        "phi": -0.8681905269622803,
+        "referencePoint": {
+          "x": 0.0,
+          "y": 0.0,
+          "z": 0.0,
+        },
+        "tanLambda": -1.99562406539917,
+        "time": 0.0,
+      },
+    ],
+    "trackerHits": [
+      {
+        "collectionID": 5,
+        "index": 0,
+      },
+      {
+        "collectionID": 5,
+        "index": 1,
+      },
+    ],
+    "tracks": [],
+    "type": 0,
+  };
+
+  loadMembers(object, data, members);
+  expect(object).toEqual({
+    "id": 1,
+    "members": {
+      "type": 0,
+      "chi2": 0.0,
+      "ndf": 0,
+      "dEdx": 0.0,
+      "dEdxError": 0.0,
+      "radiusOfInnermostHit": 17.0,
+    },
+  });
+});
+
+test("load one to one relations with some definition and data", () => {
+  data = {
+    "charge": 1.0,
+    "clusters": [],
+    "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+    "energy": 12.062528610229492,
+    "goodnessOfPID": 0.0,
+    "mass": 2.315242290496826,
+    "momentum": {
+      "x": 11.738886833190918,
+      "y": 1.2114704847335815,
+      "z": 0.9354811906814575,
+    },
+    "particleIDUsed": {
+      "collectionID": -2,
+      "index": -2,
+    },
+    "particleIDs": [
+      {
+        "collectionID": 4,
+        "index": 45,
+      },
+    ],
+    "particles": [
+      {
+        "collectionID": 14,
+        "index": 24,
+      },
+      {
+        "collectionID": 14,
+        "index": 22,
+      },
+      {
+        "collectionID": 14,
+        "index": 74,
+      },
+      {
+        "collectionID": 14,
+        "index": 23,
+      },
+      {
+        "collectionID": 14,
+        "index": 25,
+      },
+      {
+        "collectionID": 14,
+        "index": 26,
+      },
+    ],
+    "referencePoint": {
+      "x": 0.0,
+      "y": 0.0,
+      "z": 0.0,
+    },
+    "startVertex": {
+      "collectionID": -2,
+      "index": -2,
+    },
+    "tracks": [],
+    "type": 0,
+  };
+  const oneToOneRelations = [
+    {
+      "type": "edm4hep::Vertex",
+      "name": "startVertex",
+    },
+  ];
+  loadOneToOneRelations(object, data, oneToOneRelations);
+  expect(object).toEqual({
+    "id": 1,
+    "oneToOneRelations": {
+      "startVertex": {
+        "id": 1,
+        "from": 1,
+        "to": -2,
+        "collectionID": -2,
+      },
+    },
+  });
+});
+
+test("load one to many relations with some definition and data", () => {
+  data = {
+    "PDG": -11,
+    "charge": 1.0,
+    "colorFlow": {
+      "a": 0,
+      "b": 0,
+    },
+    "daughters": [
+      {
+        "collectionID": 11,
+        "index": 4,
+      },
+      {
+        "collectionID": 11,
+        "index": 5,
+      },
+    ],
+    "endpoint": {
+      "x": 0.0,
+      "y": 0.0,
+      "z": 0.0,
+    },
+    "generatorStatus": 21,
+    "mass": 0.0,
+    "momentum": {
+      "x": 0.0,
+      "y": 0.0,
+      "z": -119.99999237060547,
+    },
+    "momentumAtEndpoint": {
+      "x": 0.0,
+      "y": 0.0,
+      "z": 0.0,
+    },
+    "parents": [
+      {
+        "collectionID": 11,
+        "index": 1,
+      },
+    ],
+    "simulatorStatus": 0,
+    "spin": {
+      "x": 0.0,
+      "y": 0.0,
+      "z": 0.0,
+    },
+    "time": 0.0,
+    "vertex": {
+      "x": -0.01184066478163004,
+      "y": -2.074451003863942e-6,
+      "z": -0.08278788626194,
+    },
+  };
+  const oneToManyRelations = [
+    {
+      "type": "edm4hep::MCParticle",
+      "name": "parents",
+    },
+    {
+      "type": "edm4hep::MCParticle",
+      "name": "daughters",
+    },
+  ];
+  loadOneToManyRelations(object, data, oneToManyRelations);
+  expect(object).toEqual({
+    "id": 1,
+    "oneToManyRelations": {
+      "parents": [
+        {
+          "id": 1,
+          "from": 1,
+          "to": 1,
+          "collectionID": 11,
+        },
+      ],
+      "daughters": [
+        {
+          "id": 1,
+          "from": 1,
+          "to": 4,
+          "collectionID": 11,
+        },
+        {
+          "id": 2,
+          "from": 1,
+          "to": 5,
+          "collectionID": 11,
+        },
+      ],
+    },
+  });
+});
diff --git a/test/load.test.js b/test/load.test.js
index e1343e03..33202abc 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,174 +1,254 @@
-import { loadParticles } from "../js/types/load";
-import { ReconstructedParticle } from "../js/types/reconstruction";
+import { loadParticleType } from "../js/types/load";
+import { datatypes } from "../output/datatypes";
+import { reconstructionTypes } from "../js/types/reconstruction";
 
-describe("load different types of particles", () => {
-  let data = {};
-
-  beforeAll(() => {
-    data = {
-      "Event 0": {
-        "EFlowPhoton": {
-          "collID": 7,
-          "collType": "edm4hep::ClusterCollection",
-          "collection": [
-            {
-              "clusters": [],
-              "directionError": {
-                "x": 0.0,
-                "y": 0.0,
-                "z": 0.0,
-              },
-              "energy": 6.2020978927612305,
-              "energyError": 0.0,
-              "hits": [],
-              "iTheta": 0.0,
-              "particleIDs": [],
-              "phi": 0.0,
-              "position": {
-                "x": 0.0,
-                "y": 0.0,
-                "z": 0.0,
-              },
-              "positionError": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-              "shapeParameters": [],
-              "subdetectorEnergies": [],
-              "type": 0,
-            },
+test("load a collection of particles", () => {
+  const type = "edm4hep::Track";
+  const collection = [
+    {
+      "chi2": 0.0,
+      "dEdx": 0.0,
+      "dEdxError": 0.0,
+      "dxQuantities": [
+        {
+          "error": 0.0,
+          "type": 0,
+          "value": 0.0,
+        },
+      ],
+      "ndf": 0,
+      "radiusOfInnermostHit": 17.0,
+      "subDetectorHitNumbers": [],
+      "trackStates": [
+        {
+          "D0": -0.05963143706321716,
+          "Z0": -0.9309114217758179,
+          "covMatrix": [
+            0.00838407501578331, -0.0005293499561958015, 3.361300696269609e-5,
+            1.1750994133308268e-7, -7.233749155233227e-9, 3.568003878462456e-11,
+            0.00010174162162002176, -6.439207481889753e-6, 3.929798264579176e-9,
+            0.004548509605228901, -1.0186887266172562e-5, 6.442872972911573e-7,
+            -3.0552818608420296e-10, -0.00028709869366139174,
+            1.831963163567707e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
           ],
+          "location": 0,
+          "omega": 0.0032351072877645493,
+          "phi": -2.237527847290039,
+          "referencePoint": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "tanLambda": -4.997164249420166,
+          "time": 0.0,
+        },
+      ],
+      "trackerHits": [
+        {
+          "collectionID": 5,
+          "index": 0,
+        },
+        {
+          "collectionID": 5,
+          "index": 1,
+        },
+      ],
+      "tracks": [],
+      "type": 0,
+    },
+    {
+      "chi2": 0.0,
+      "dEdx": 0.0,
+      "dEdxError": 0.0,
+      "dxQuantities": [
+        {
+          "error": 0.0,
+          "type": 0,
+          "value": 0.0,
         },
-        "ReconstructedParticles": {
-          "collID": 14,
-          "collType": "edm4hep::ReconstructedParticleCollection",
-          "collection": [
-            {
-              "charge": 1.0,
-              "clusters": [],
-              "covMatrix": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-              "energy": 0.358455091714859,
-              "goodnessOfPID": 0.0,
-              "mass": 0.13957038521766663,
-              "momentum": {
-                "x": 0.09558331221342087,
-                "y": -0.11288221180438995,
-                "z": -0.2951807975769043,
-              },
-              "particleIDUsed": {
-                "collectionID": -2,
-                "index": -2,
-              },
-              "particleIDs": [
-                {
-                  "collectionID": 4,
-                  "index": 0,
-                },
-              ],
-              "particles": [],
-              "referencePoint": {
-                "x": 0.0,
-                "y": 0.0,
-                "z": 0.0,
-              },
-              "startVertex": {
-                "collectionID": -2,
-                "index": -2,
-              },
-              "tracks": [
-                {
-                  "collectionID": 3,
-                  "index": 0,
-                },
-              ],
-              "type": 0,
-            },
+      ],
+      "ndf": 0,
+      "radiusOfInnermostHit": 17.0,
+      "subDetectorHitNumbers": [],
+      "trackStates": [
+        {
+          "D0": -0.0391334593296051,
+          "Z0": -0.9311737418174744,
+          "covMatrix": [
+            0.0035914022009819746, -0.00022589370200876147,
+            1.4322121387522202e-5, 4.24616963812241e-8, -2.698678391865883e-9,
+            8.189490210107342e-13, 8.363036613445729e-5, -5.291213710734155e-6,
+            3.081625399303789e-9, 0.00030561615130864084, -6.513672360597411e-6,
+            4.117676155601657e-7, -2.10651204812784e-10, -1.7557771570864134e-5,
+            1.1170427569595631e-6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
           ],
+          "location": 0,
+          "omega": -0.0019104206003248692,
+          "phi": -2.798056125640869,
+          "referencePoint": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "tanLambda": -4.306049823760986,
+          "time": 0.0,
         },
-        "edm4hepVersion": "0.7.0",
-      },
-    };
-  });
-
-  it("should only load particles of one type", () => {
-    const loadersConfig = "ReconstructedParticle";
-
-    const particles = loadParticles(data, "0", loadersConfig);
-
-    expect(particles.hasOwnProperty(loadersConfig)).toBe(true);
-  });
-
-  it("should load particles of multiple types", () => {
-    const loadersConfig = ["ReconstructedParticle", "Cluster"];
-
-    const particles = loadParticles(data, "0", loadersConfig);
-
-    expect(loadersConfig.every((type) => particles.hasOwnProperty(type))).toBe(
-      true
-    );
-  });
-});
-
-describe("dynamically load an object", () => {
-  let particleData = {};
-  let reconstructedParticle;
-
-  beforeAll(() => {
-    particleData = {
-      "PDG": 3,
-      "charge": 0.0,
-      "clusters": [],
-      "covMatrix": {
-        "values": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
-      },
-      "energy": 9.644623756408691,
-      "goodnessOfPID": 0.0,
-      "mass": 0.45484575629234314,
-      "momentum": {
-        "x": -4.557793617248535,
-        "y": -6.684719085693359,
-        "z": 5.230002403259277,
-      },
-      "particles": [
+      ],
+      "trackerHits": [
+        {
+          "collectionID": 5,
+          "index": 2,
+        },
+        {
+          "collectionID": 5,
+          "index": 3,
+        },
+      ],
+      "tracks": [],
+      "type": 0,
+    },
+    {
+      "chi2": 0.0,
+      "dEdx": 0.0,
+      "dEdxError": 0.0,
+      "dxQuantities": [
+        {
+          "error": 0.0,
+          "type": 0,
+          "value": 0.0,
+        },
+      ],
+      "ndf": 0,
+      "radiusOfInnermostHit": 17.0,
+      "subDetectorHitNumbers": [],
+      "trackStates": [
+        {
+          "D0": -0.050047606229782104,
+          "Z0": -0.9527733325958252,
+          "covMatrix": [
+            0.007592398207634687, -0.0004792569379787892, 3.0433289794018492e-5,
+            1.0142189665884871e-7, -6.283491504888161e-9,
+            2.5339810111324468e-11, 0.0001311719825025648,
+            -8.306328709295485e-6, 4.581083068444514e-9, 0.0035560736432671547,
+            -1.2910893929074518e-5, 8.168165095412405e-7,
+            -3.557094618855672e-10, -0.00022385688498616219,
+            1.4287375051935669e-5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+          ],
+          "location": 0,
+          "omega": -0.003163003595545888,
+          "phi": -2.4250643253326416,
+          "referencePoint": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+          },
+          "tanLambda": -3.454428195953369,
+          "time": 0.0,
+        },
+      ],
+      "trackerHits": [
         {
-          "collectionID": 4196981182,
-          "index": 20,
+          "collectionID": 5,
+          "index": 4,
         },
         {
-          "collectionID": 4196981182,
-          "index": 19,
+          "collectionID": 5,
+          "index": 5,
         },
       ],
-      "referencePoint": {
-        "x": -1.2017582654953003,
-        "y": -2.118278741836548,
-        "z": 1.424477458000183,
+      "tracks": [],
+      "type": 0,
+    },
+  ];
+  const particles = loadParticleType(
+    collection,
+    datatypes[type],
+    reconstructionTypes[type]
+  );
+  expect(particles).toEqual([
+    {
+      members: {
+        type: 0,
+        chi2: 0,
+        ndf: 0,
+        dEdx: 0,
+        dEdxError: 0,
+        radiusOfInnermostHit: 17,
       },
-      "startVertex": {
-        "collectionID": 4294967295,
-        "index": -1,
+      id: 0,
+      oneToManyRelations: {
+        trackerHits: [
+          {
+            id: 0,
+            from: 0,
+            to: 0,
+            collectionID: 5,
+          },
+          {
+            id: 1,
+            from: 0,
+            to: 1,
+            collectionID: 5,
+          },
+        ],
+        tracks: [],
       },
-      "tracks": [],
-    };
-  });
-
-  beforeEach(() => {
-    reconstructedParticle = new ReconstructedParticle();
-    reconstructedParticle.index = 0;
-  });
-
-  it("should load all the properties of an object", () => {
-    dynamicLoad(reconstructedParticle, particleData);
-
-    expect(reconstructedParticle).toMatchObject(particleData);
-  });
-
-  it("should ignore some properties of an object", () => {
-    const ignore = new Set(["PDG", "charge", "particles"]);
-
-    dynamicLoad(reconstructedParticle, particleData, ignore);
-    expect(reconstructedParticle).toMatchObject({
-      ...particleData,
-      PDG: 0,
-      charge: 0,
-      particles: [],
-    });
-  });
+    },
+    {
+      members: {
+        type: 0,
+        chi2: 0,
+        ndf: 0,
+        dEdx: 0,
+        dEdxError: 0,
+        radiusOfInnermostHit: 17,
+      },
+      id: 1,
+      oneToManyRelations: {
+        trackerHits: [
+          {
+            id: 1,
+            from: 1,
+            to: 2,
+            collectionID: 5,
+          },
+          {
+            id: 2,
+            from: 1,
+            to: 3,
+            collectionID: 5,
+          },
+        ],
+        tracks: [],
+      },
+    },
+    {
+      members: {
+        type: 0,
+        chi2: 0,
+        ndf: 0,
+        dEdx: 0,
+        dEdxError: 0,
+        radiusOfInnermostHit: 17,
+      },
+      id: 2,
+      oneToManyRelations: {
+        trackerHits: [
+          {
+            id: 2,
+            from: 2,
+            to: 4,
+            collectionID: 5,
+          },
+          {
+            id: 3,
+            from: 2,
+            to: 5,
+            collectionID: 5,
+          },
+        ],
+        tracks: [],
+      },
+    },
+  ]);
 });
diff --git a/test/reconstruction.test.js b/test/reconstruction.test.js
index 06713735..ade8c636 100644
--- a/test/reconstruction.test.js
+++ b/test/reconstruction.test.js
@@ -1,48 +1,9 @@
-import {
-  extractOneToManyLinks,
-  extractOneToOneLink,
-  createLinksManager,
-  createGenericLink,
-} from "../js/types/reconstruction.js";
+import { createLink } from "../js/types/reconstruction.js";
 
-test("it should create a generic link", () => {
-  const link = createGenericLink(1, 2, { collectionID: 3, index: 4 });
+test("it should create a link", () => {
+  const link = createLink(1, 2, { collectionID: 3, index: 4 });
   expect(link.id).toBe(1);
   expect(link.from).toBe(2);
   expect(link.to).toBe(4);
   expect(link.collectionID).toBe(3);
 });
-
-test("it should create a links manager", () => {
-  const linksManager = createLinksManager(["a", "b"]);
-  expect(linksManager).toEqual({ a: [], b: [] });
-});
-
-test("it should extract one-to-many links", () => {
-  const linksManager = { a: [], b: [] };
-  const keys = ["a", "b"];
-  const newParticle = { index: 0, a: [], b: [] };
-  const particleData = {
-    a: [{ collectionID: 1, index: 2 }],
-    b: [{ collectionID: 3, index: 4 }],
-  };
-  const firstLink = createGenericLink(0, 0, { collectionID: 1, index: 2 });
-  const secondLink = createGenericLink(0, 0, { collectionID: 3, index: 4 });
-
-  extractOneToManyLinks(linksManager, keys, newParticle, particleData);
-  expect(linksManager).toEqual({ a: [firstLink], b: [secondLink] });
-  expect(newParticle.a).toEqual([0]);
-  expect(newParticle.b).toEqual([0]);
-});
-
-test("it should extract one-to-one link", () => {
-  const linksManager = { a: [] };
-  const key = "a";
-  const newParticle = { index: 0, a: [] };
-  const particleData = { a: { collectionID: 1, index: 2 } };
-  const link = createGenericLink(0, 0, { collectionID: 1, index: 2 });
-
-  extractOneToOneLink(linksManager, key, newParticle, particleData);
-  expect(linksManager).toEqual({ a: [link] });
-  expect(newParticle.a).toEqual(0);
-});

From 0e30a99a525da5237012184f6e14cdc739afb563 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Tue, 11 Jun 2024 16:24:14 -0500
Subject: [PATCH 20/35] add documentation to update-on-demand for dmx

---
 model/MODEL.md | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 model/MODEL.md

diff --git a/model/MODEL.md b/model/MODEL.md
new file mode 100644
index 00000000..bb464e8e
--- /dev/null
+++ b/model/MODEL.md
@@ -0,0 +1,34 @@
+# Keeping dmx up to date
+
+To keep dmx up to date with the event data model [edm4hep](https://github.com/key4hep/EDM4hep), we need a way to get the latest information for each datatype and component. Also, we need to take into account that dmx is deployed on github pages as a static website, so we need a way to update this info without having a server running.
+
+## How to get the latest information?
+
+In the root directory, there are two commands in `package-json` that can be used to get the latest information from the edm4hep repository. The first command
+
+```bash
+npm run download
+```
+
+will download the latest information from the edm4hep, by using the file called `edm4hep.yaml` under `model` directory, containg up to date information about `edm4hep`. The second command
+
+```bash
+npm run build
+```
+
+will generate a file called `datatypes.js` under `output` directory, where all the information is parsed and stored in a format that can be used by the dmx application.
+
+## All at once
+
+You can also run
+
+```bash
+npm run update
+```
+
+to run both processes at once and inmediatly update the dmx application.
+
+## Further improvements
+
+-   We could trigger the update process automatically when a new release of edm4hep is published, but for now, we will keep it simple and run the update process manually.
+-   To maitain backward compatibility, we could add a versioning system so we can later load different versions of the edm4hep data model into dmx, however we currrently load the latest version.

From 1ff80b6b999a1bd637e799bb356b428c0163cf4b Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Tue, 11 Jun 2024 16:37:57 -0500
Subject: [PATCH 21/35] renaming from particle -> object

---
 js/types/dynamic.js                        |  2 +-
 js/types/load.js                           | 42 +++++++++++-----------
 js/types/{reconstruction.js => objects.js} |  9 ++++-
 test/load.test.js                          |  8 ++---
 4 files changed, 33 insertions(+), 28 deletions(-)
 rename js/types/{reconstruction.js => objects.js} (87%)

diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index 21ade621..46256b13 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -1,4 +1,4 @@
-import { createLink } from "./reconstruction.js";
+import { createLink } from "./objects.js";
 
 export function loadMembers(object, data, membersToLoad) {
   for (const member of membersToLoad) {
diff --git a/js/types/load.js b/js/types/load.js
index cad35eca..3a5589af 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -1,4 +1,4 @@
-import { reconstructionTypes } from "./reconstruction.js";
+import { objectTypes } from "./objects.js";
 import { datatypes } from "../../output/datatypes.js";
 import {
   loadMembers,
@@ -6,54 +6,52 @@ import {
   loadOneToManyRelations,
 } from "./dynamic.js";
 
-export function loadParticleType(collection, datatype, type) {
-  const particles = [];
+export function loadObjectType(collection, datatype, type) {
+  const objects = [];
 
   for (const [index, particle] of collection.entries()) {
-    const newParticle = new type();
-    newParticle.id = index;
+    const newObject = new type();
+    newObject.id = index;
 
-    loadMembers(newParticle, particle, datatype.members);
+    loadMembers(newObject, particle, datatype.members);
 
     if (datatype.oneToOneRelations)
-      loadOneToOneRelations(newParticle, particle, datatype.oneToOneRelations);
+      loadOneToOneRelations(newObject, particle, datatype.oneToOneRelations);
 
     if (datatype.oneToManyRelations)
-      loadOneToManyRelations(
-        newParticle,
-        particle,
-        datatype.oneToManyRelations
-      );
+      loadOneToManyRelations(newObject, particle, datatype.oneToManyRelations);
 
-    particles.push(newParticle);
+    objects.push(newObject);
   }
 
-  return particles;
+  return objects;
 }
 
-export function loadParticles(jsonData, event, particlesToLoad) {
+export function loadObjects(jsonData, event, objectsToLoad) {
   const eventData = jsonData["Event " + event];
 
-  const particles = {};
+  const objects = {};
 
-  for (const type of particlesToLoad) {
-    const particlesType = Object.values(eventData).filter(
+  for (const type of objectsToLoad) {
+    const objectsType = Object.values(eventData).filter(
       (element) => element.collType === `${type}Collection`
     );
 
-    particlesType.forEach(({ collection }) => {
-      loadParticleType(collection, datatypes[type], reconstructionTypes[type]);
+    objectsType.forEach(({ collection }) => {
+      loadObjectType(collection, datatypes[type], objectTypes[type]);
     });
   }
 
-  return particles;
+  return objects;
 }
 
-const particlesToLoad = [
+const objectsToLoad = [
   // subset of datatypes
+  // should be changes dynamically by the user
   "edm4hep::Cluster",
   "edm4hep::ReconstructedParticle",
   "edm4hep::Vertex",
   "edm4hep::Track",
   "edm4hep::ParticleID",
+  "edm4hep::MCParticle",
 ];
diff --git a/js/types/reconstruction.js b/js/types/objects.js
similarity index 87%
rename from js/types/reconstruction.js
rename to js/types/objects.js
index 4ad308de..4ba17b15 100644
--- a/js/types/reconstruction.js
+++ b/js/types/objects.js
@@ -30,6 +30,12 @@ export class Track extends EDMObject {
   }
 }
 
+export class MCParticle extends EDMObject {
+  constructor() {
+    super();
+  }
+}
+
 export class GenericLink {
   // we may create a specific class for each type if needed
   constructor(id, from, to, collectionID) {
@@ -44,10 +50,11 @@ export function createLink(id, from, { collectionID, index }) {
   return new GenericLink(id, from, index, collectionID);
 }
 
-export const reconstructionTypes = {
+export const objectTypes = {
   "edm4hep::Cluster": Cluster,
   "edm4hep::ParticleID": ParticleID,
   "edm4hep::ReconstructedParticle": ReconstructedParticle,
   "edm4hep::Vertex": Vertex,
   "edm4hep::Track": Track,
+  "edm4hep::MCParticle": MCParticle,
 };
diff --git a/test/load.test.js b/test/load.test.js
index 33202abc..62e3a94c 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,6 +1,6 @@
-import { loadParticleType } from "../js/types/load";
+import { loadObjectType } from "../js/types/load";
 import { datatypes } from "../output/datatypes";
-import { reconstructionTypes } from "../js/types/reconstruction";
+import { objectTypes } from "../js/types/reconstruction";
 
 test("load a collection of particles", () => {
   const type = "edm4hep::Track";
@@ -160,10 +160,10 @@ test("load a collection of particles", () => {
       "type": 0,
     },
   ];
-  const particles = loadParticleType(
+  const particles = loadObjectType(
     collection,
     datatypes[type],
-    reconstructionTypes[type]
+    objectTypes[type]
   );
   expect(particles).toEqual([
     {

From 9ba9506c962a9fc793b684bfb543be937f1a285f Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Tue, 11 Jun 2024 16:59:56 -0500
Subject: [PATCH 22/35] drop types for datatypes

---
 model/index.js      | 23 +++++++----------------
 output/datatypes.js | 26 --------------------------
 2 files changed, 7 insertions(+), 42 deletions(-)

diff --git a/model/index.js b/model/index.js
index 5218676a..1670a059 100644
--- a/model/index.js
+++ b/model/index.js
@@ -29,16 +29,14 @@ const datatypesDefinition = {};
 class Component {}
 
 class DataTypeMember {
-  constructor(type = null, name, unit = null) {
-    if (type) this.type = type;
+  constructor(name, unit = null) {
     this.name = name;
     if (unit) this.unit = unit;
   }
 }
 
 class Relation {
-  constructor(type = null, name) {
-    if (type) this.type = type;
+  constructor(name) {
     this.name = name;
   }
 }
@@ -55,13 +53,9 @@ const parseDatatypesMembers = (members) => {
   const newMembers = [];
 
   for (const member of members) {
-    let [type, name, unit] = parseString(member);
+    let [_, name, unit] = parseString(member);
     if (unit) unit = unit.replace("[", "").replace("]", "");
-    if (type.includes("edm4hep::")) {
-      newMembers.push(new DataTypeMember(type, name, unit));
-    } else {
-      newMembers.push(new DataTypeMember(null, name, unit));
-    }
+    newMembers.push(new DataTypeMember(name, unit));
   }
 
   return newMembers;
@@ -69,12 +63,9 @@ const parseDatatypesMembers = (members) => {
 
 const parseRelation = (relations) => {
   return relations.map((relation) => {
-    const [type, name] = parseString(relation);
-    if (type.includes("edm4hep::")) {
-      return new Relation(type, name);
-    } else {
-      return new Relation(null, name);
-    }
+    const [_, name] = parseString(relation);
+
+    return new Relation(name);
   });
 };
 
diff --git a/output/datatypes.js b/output/datatypes.js
index 2dd899e9..942da49d 100644
--- a/output/datatypes.js
+++ b/output/datatypes.js
@@ -22,41 +22,33 @@ export const datatypes = {
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3d",
         "name": "vertex",
         "unit": "mm"
       },
       {
-        "type": "edm4hep::Vector3d",
         "name": "endpoint",
         "unit": "mm"
       },
       {
-        "type": "edm4hep::Vector3d",
         "name": "momentum",
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3d",
         "name": "momentumAtEndpoint",
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "spin"
       },
       {
-        "type": "edm4hep::Vector2i",
         "name": "colorFlow"
       }
     ],
     "oneToManyRelations": [
       {
-        "type": "edm4hep::MCParticle",
         "name": "parents"
       },
       {
-        "type": "edm4hep::MCParticle",
         "name": "daughters"
       }
     ]
@@ -78,7 +70,6 @@ export const datatypes = {
     ],
     "oneToOneRelations": [
       {
-        "type": "edm4hep::ReconstructedParticle",
         "name": "particle"
       }
     ]
@@ -97,12 +88,10 @@ export const datatypes = {
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "position",
         "unit": "mm"
       },
       {
-        "type": "edm4hep::CovMatrix3f",
         "name": "positionError"
       },
       {
@@ -112,18 +101,15 @@ export const datatypes = {
         "name": "phi"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "directionError",
         "unit": "mm**2"
       }
     ],
     "oneToManyRelations": [
       {
-        "type": "edm4hep::Cluster",
         "name": "clusters"
       },
       {
-        "type": "edm4hep::CalorimeterHit",
         "name": "hits"
       }
     ]
@@ -151,11 +137,9 @@ export const datatypes = {
     ],
     "oneToManyRelations": [
       {
-        "type": "edm4hep::TrackerHit",
         "name": "trackerHits"
       },
       {
-        "type": "edm4hep::Track",
         "name": "tracks"
       }
     ]
@@ -172,11 +156,9 @@ export const datatypes = {
         "name": "probability"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "position"
       },
       {
-        "type": "edm4hep::CovMatrix3f",
         "name": "covMatrix"
       },
       {
@@ -185,7 +167,6 @@ export const datatypes = {
     ],
     "oneToOneRelations": [
       {
-        "type": "edm4hep::ReconstructedParticle",
         "name": "associatedParticle"
       }
     ]
@@ -200,12 +181,10 @@ export const datatypes = {
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "momentum",
         "unit": "GeV"
       },
       {
-        "type": "edm4hep::Vector3f",
         "name": "referencePoint",
         "unit": "mm"
       },
@@ -220,27 +199,22 @@ export const datatypes = {
         "name": "goodnessOfPID"
       },
       {
-        "type": "edm4hep::CovMatrix4f",
         "name": "covMatrix"
       }
     ],
     "oneToManyRelations": [
       {
-        "type": "edm4hep::Cluster",
         "name": "clusters"
       },
       {
-        "type": "edm4hep::Track",
         "name": "tracks"
       },
       {
-        "type": "edm4hep::ReconstructedParticle",
         "name": "particles"
       }
     ],
     "oneToOneRelations": [
       {
-        "type": "edm4hep::Vertex",
         "name": "startVertex"
       }
     ]

From 57348dbdfce6373a7f4dddf8aa2ea0571163d275 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Tue, 11 Jun 2024 17:02:06 -0500
Subject: [PATCH 23/35] correct file naming

---
 test/dynamic.test.js        | 2 +-
 test/load.test.js           | 6 +++---
 test/reconstruction.test.js | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/test/dynamic.test.js b/test/dynamic.test.js
index 4e58468f..e0fda4e9 100644
--- a/test/dynamic.test.js
+++ b/test/dynamic.test.js
@@ -2,7 +2,7 @@ import {
   loadMembers,
   loadOneToOneRelations,
   loadOneToManyRelations,
-} from "../js/types/dynamic";
+} from "../js/types/dynamic.js";
 
 let object;
 let data;
diff --git a/test/load.test.js b/test/load.test.js
index 62e3a94c..d7bc57c6 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,6 +1,6 @@
-import { loadObjectType } from "../js/types/load";
-import { datatypes } from "../output/datatypes";
-import { objectTypes } from "../js/types/reconstruction";
+import { loadObjectType } from "../js/types/load.js";
+import { datatypes } from "../output/datatypes.js";
+import { objectTypes } from "../js/types/objects.js";
 
 test("load a collection of particles", () => {
   const type = "edm4hep::Track";
diff --git a/test/reconstruction.test.js b/test/reconstruction.test.js
index ade8c636..deb511f9 100644
--- a/test/reconstruction.test.js
+++ b/test/reconstruction.test.js
@@ -1,4 +1,4 @@
-import { createLink } from "../js/types/reconstruction.js";
+import { createLink } from "../js/types/objects.js";
 
 test("it should create a link", () => {
   const link = createLink(1, 2, { collectionID: 3, index: 4 });

From c2b0742f19b28f0a66745bec6d91a855662eefb9 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 12 Jun 2024 16:27:44 -0500
Subject: [PATCH 24/35] typo in MODEl.md

---
 model/MODEL.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/model/MODEL.md b/model/MODEL.md
index bb464e8e..7211c2a8 100644
--- a/model/MODEL.md
+++ b/model/MODEL.md
@@ -26,7 +26,7 @@ You can also run
 npm run update
 ```
 
-to run both processes at once and inmediatly update the dmx application.
+to run both processes at once and immediatly update the dmx application.
 
 ## Further improvements
 

From 8e8218152d7260f614855e21c458c641f8191a7b Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Wed, 12 Jun 2024 21:06:44 -0500
Subject: [PATCH 25/35] [WIP] setup loading to later draw MCParticles

---
 js/tools.js           |   2 +-
 js/types/dynamic.js   |  36 +++++++--
 js/types/edmobject.js |   3 +-
 js/types/links.js     | 143 +++++++++++++++++++++++++++++++++++
 js/types/load.js      |  76 ++++++++++++++-----
 js/types/objects.js   | 168 ++++++++++++++++++++++++++++++++++++------
 6 files changed, 378 insertions(+), 50 deletions(-)
 create mode 100644 js/types/links.js

diff --git a/js/tools.js b/js/tools.js
index 680e3dc9..2c28b45a 100644
--- a/js/tools.js
+++ b/js/tools.js
@@ -124,7 +124,7 @@ export function loadMCParticles(jsonData, eventNum, particlesHandler) {
   }
 }
 
-function getName(pdg) {
+export function getName(pdg) {
   const particle = mappings[pdg];
 
   if (particle !== undefined) {
diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index 46256b13..d6ae32a5 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -1,4 +1,4 @@
-import { createLink } from "./objects.js";
+import { Link, colors } from "./links.js";
 
 export function loadMembers(object, data, membersToLoad) {
   for (const member of membersToLoad) {
@@ -7,18 +7,35 @@ export function loadMembers(object, data, membersToLoad) {
   }
 }
 
-export function loadOneToOneRelations(object, data, relationsToLoad) {
+export function loadOneToOneRelations(
+  object,
+  data,
+  relationsToLoad = [],
+  oneToOne,
+  objects
+) {
   object.oneToOneRelations = {};
   for (const relation of relationsToLoad) {
-    const relationData = data[relation.name];
+    const name = relation.name;
+    const relationData = data[name];
     if (relationData === undefined) continue;
 
-    const link = createLink(object.id, object.id, relationData);
-    object.oneToOneRelations[relation.name] = link;
+    const toObject = objects[relationData.index];
+    const link = new Link(object, toObject);
+    link.color = colors[name];
+
+    oneToOne[name].push(link);
+    object.oneToOneRelations[name] = link;
   }
 }
 
-export function loadOneToManyRelations(object, data, relationsToLoad) {
+export function loadOneToManyRelations(
+  object,
+  data,
+  relationsToLoad = [],
+  oneToMany,
+  objects
+) {
   object.oneToManyRelations = {};
   for (const relation of relationsToLoad) {
     const name = relation.name;
@@ -27,8 +44,11 @@ export function loadOneToManyRelations(object, data, relationsToLoad) {
     if (relationData === undefined) continue;
     object.oneToManyRelations[name] = [];
 
-    for (const [index, relationElement] of relationData.entries()) {
-      const link = createLink(index + object.id, object.id, relationElement);
+    for (const relationElement of relationData) {
+      const toObject = objects[relationElement.index];
+      const link = new Link(object, toObject);
+      link.color = colors[name];
+      oneToMany[name].push(link);
       object.oneToManyRelations[name].push(link);
     }
   }
diff --git a/js/types/edmobject.js b/js/types/edmobject.js
index 7085d455..c7a6a2a6 100644
--- a/js/types/edmobject.js
+++ b/js/types/edmobject.js
@@ -1,5 +1,6 @@
 export class EDMObject {
-  constructor() {
+  constructor(id) {
+    this.id = id;
     this.members = {};
   }
 
diff --git a/js/types/links.js b/js/types/links.js
new file mode 100644
index 00000000..dbf11ae2
--- /dev/null
+++ b/js/types/links.js
@@ -0,0 +1,143 @@
+export const colors = {
+  "daughters": "#00AA00",
+  "parents": "#AA0000",
+  // more if needed
+};
+
+const hexCharacters = [
+  0,
+  1,
+  2,
+  3,
+  4,
+  5,
+  6,
+  7,
+  8,
+  9,
+  "A",
+  "B",
+  "C",
+  "D",
+  "E",
+  "F",
+];
+
+function getCharacter(index) {
+  return hexCharacters[index];
+}
+
+export function generateRandomColor() {
+  let hexColorRep = "#";
+
+  for (let index = 0; index < 6; index++) {
+    const randomPosition = Math.floor(Math.random() * hexCharacters.length);
+    hexColorRep += getCharacter(randomPosition);
+  }
+
+  return hexColorRep;
+}
+
+export class Link {
+  // we may create a specific class for each type if needed
+  constructor(from, to) {
+    this.from = from;
+    this.to = to;
+    this.color = "#A00";
+    this.xShift = 0;
+  }
+
+  draw(ctx, infoBoxes) {
+    const boxFrom = infoBoxes[this.from];
+    const boxTo = infoBoxes[this.to];
+
+    const fromX = boxFrom.x + boxFrom.width / 2;
+    const fromY = boxFrom.y + boxFrom.height;
+    const toX = boxTo.x + boxTo.width / 2;
+    const toY = boxTo.y;
+
+    if (toY > fromY) {
+      var cpFromY = (toY - fromY) / 2 + fromY;
+      var cpToY = cpFromY;
+    } else {
+      cpFromY = (fromY - toY) / 2 + fromY;
+      cpToY = toY - (fromY - toY) / 2;
+    }
+
+    if (toX > fromX) {
+      var cpFromX = (toX - fromX) / 4 + fromX;
+      var cpToX = (3 * (toX - fromX)) / 4 + fromX;
+    } else {
+      cpFromX = (3 * (fromX - toX)) / 4 + toX;
+      cpToX = (fromX - toX) / 4 + toX;
+    }
+
+    /*
+    drawCross(ctx, fromX, fromY, "blue");
+    drawCross(ctx, toX, toY, "green");
+    drawCross(ctx, cpFromX, cpFromY, "yellow");
+    drawLine(ctx, fromX, fromY, cpFromX, cpFromY, "yellow")
+    drawCross(ctx, cpToX, cpToY, "orange");
+    drawLine(ctx, toX, toY, cpToX, cpToY, "orange")
+    */
+
+    ctx.save();
+    ctx.strokeStyle = this.color;
+    ctx.lineWidth = 2;
+    ctx.beginPath();
+    ctx.moveTo(fromX + this.xShift, fromY);
+    ctx.bezierCurveTo(
+      cpFromX + this.xShift,
+      cpFromY,
+      cpToX + this.xShift,
+      cpToY,
+      toX + this.xShift,
+      toY
+    );
+    ctx.stroke();
+    ctx.restore();
+
+    /*
+    ctx.save();
+    ctx.font = "14px sans-serif";
+    ctx.fillStyle = this.color;
+    const idText = "ID: " + this.id;
+    ctx.fillText(idText,
+                 cpToX, cpToY);
+    ctx.restore();
+    */
+  }
+
+  isVisible(x, y, width, height, infoBoxes) {
+    const boxFrom = infoBoxes[this.from];
+    const boxTo = infoBoxes[this.to];
+
+    const fromX = boxFrom.x + boxFrom.width / 2;
+    const fromY = boxFrom.y + boxFrom.height;
+    const toX = boxTo.x + boxTo.width / 2;
+    const toY = boxTo.y;
+
+    const boxX = Math.min(fromX, toX);
+    const boxWidth = Math.abs(fromX - toX);
+    const boxY = Math.min(fromY, toY);
+    const boxHeight = Math.abs(fromY - toY);
+
+    /*
+    console.log("boxX: ", this.boxX);
+    console.log("boxY: ", this.boxY);
+    console.log("boxWidth: ", this.boxWidth);
+    console.log("boxHeight: ", this.boxHeight);
+    */
+
+    return (
+      x + width > boxX &&
+      x < boxX + boxWidth &&
+      y + height > boxY &&
+      y < boxY + boxHeight
+    );
+  }
+}
+
+export function createLink(id, from, { collectionID, index }) {
+  return new Link(id, from, index, collectionID);
+}
diff --git a/js/types/load.js b/js/types/load.js
index 3a5589af..83748ec9 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -5,26 +5,54 @@ import {
   loadOneToOneRelations,
   loadOneToManyRelations,
 } from "./dynamic.js";
+import { generateRandomColor, colors } from "./links.js";
+import json from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" };
 
 export function loadObjectType(collection, datatype, type) {
   const objects = [];
+  let oneToOne = {};
+  if (datatype.oneToOneRelations)
+    datatype.oneToOneRelations.forEach((relation) => {
+      oneToOne[relation.name] = [];
+      if (colors[relation.name] === undefined) {
+        colors[relation.name] = generateRandomColor();
+      }
+    });
+
+  let oneToMany = {};
+  if (datatype.oneToManyRelations)
+    datatype.oneToManyRelations.forEach((relation) => {
+      oneToMany[relation.name] = [];
+      if (colors[relation.name] === undefined) {
+        colors[relation.name] = generateRandomColor();
+      }
+    });
 
   for (const [index, particle] of collection.entries()) {
-    const newObject = new type();
-    newObject.id = index;
+    const newObject = new type(index);
 
     loadMembers(newObject, particle, datatype.members);
 
-    if (datatype.oneToOneRelations)
-      loadOneToOneRelations(newObject, particle, datatype.oneToOneRelations);
+    loadOneToOneRelations(
+      newObject,
+      particle,
+      datatype.oneToOneRelations,
+      oneToOne,
+      objects
+    );
 
-    if (datatype.oneToManyRelations)
-      loadOneToManyRelations(newObject, particle, datatype.oneToManyRelations);
+    loadOneToManyRelations(
+      newObject,
+      particle,
+      datatype.oneToManyRelations,
+      oneToMany,
+      objects
+    );
 
     objects.push(newObject);
   }
 
-  return objects;
+  return [objects, oneToOne, oneToMany];
 }
 
 export function loadObjects(jsonData, event, objectsToLoad) {
@@ -33,13 +61,24 @@ export function loadObjects(jsonData, event, objectsToLoad) {
   const objects = {};
 
   for (const type of objectsToLoad) {
-    const objectsType = Object.values(eventData).filter(
+    let collectionType = Object.values(eventData).filter(
       (element) => element.collType === `${type}Collection`
     );
 
-    objectsType.forEach(({ collection }) => {
-      loadObjectType(collection, datatypes[type], objectTypes[type]);
-    });
+    collectionType = collectionType.map((coll) => coll.collection);
+    collectionType = collectionType.flat();
+
+    const [loadedCollection, oneToOne, oneToMany] = loadObjectType(
+      collectionType,
+      datatypes[type],
+      objectTypes[type]
+    );
+
+    objects[type] = {
+      collection: loadedCollection,
+      oneToMany: oneToMany,
+      oneToOne: oneToOne,
+    };
   }
 
   return objects;
@@ -47,11 +86,14 @@ export function loadObjects(jsonData, event, objectsToLoad) {
 
 const objectsToLoad = [
   // subset of datatypes
-  // should be changes dynamically by the user
-  "edm4hep::Cluster",
-  "edm4hep::ReconstructedParticle",
-  "edm4hep::Vertex",
-  "edm4hep::Track",
-  "edm4hep::ParticleID",
+  // should be changed dynamically by the user
+  // "edm4hep::Cluster",
+  // "edm4hep::ReconstructedParticle",
+  // "edm4hep::Vertex",
+  // "edm4hep::Track",
+  // "edm4hep::ParticleID",
   "edm4hep::MCParticle",
 ];
+
+const res = loadObjects(json, 0, objectsToLoad);
+console.log(res);
diff --git a/js/types/objects.js b/js/types/objects.js
index 4ba17b15..ca632f8a 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -1,53 +1,175 @@
 import { EDMObject } from "./edmobject.js";
+import { drawTex, drawRoundedRect } from "../graphic-primitives.js";
+import { getName } from "../tools.js";
 
 export class Cluster extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
   }
 }
 
 export class ParticleID extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
   }
 }
 
 export class ReconstructedParticle extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
   }
 }
 
 export class Vertex extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
   }
 }
 
 export class Track extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
   }
 }
 
 export class MCParticle extends EDMObject {
-  constructor() {
-    super();
+  constructor(id) {
+    super(id);
+
+    // Appearance
+    this.x = 0;
+    this.y = 0;
+    this.width = 120;
+    this.height = 240;
+    this.lineColor = "black";
+    this.lineWidth = 2;
+    this.color = "white";
+    this.row = -1;
+
+    this.texImg = null;
   }
-}
 
-export class GenericLink {
-  // we may create a specific class for each type if needed
-  constructor(id, from, to, collectionID) {
-    this.id = id;
-    this.from = from;
-    this.to = to;
-    this.collectionID = collectionID;
+  updateTexImg(text) {
+    let svg = MathJax.tex2svg(text).firstElementChild;
+
+    this.texImg = document.createElement("img");
+    this.texImg.src =
+      "data:image/svg+xml;base64," +
+      btoa(
+        '<?xml version="1.0" encoding="UTF-8" standalone="no" ?>\n' +
+          svg.outerHTML
+      );
   }
-}
 
-export function createLink(id, from, { collectionID, index }) {
-  return new GenericLink(id, from, index, collectionID);
+  draw(ctx) {
+    // drawCross(ctx, this.x, this.y);
+
+    const boxCenterX = this.x + this.width / 2;
+
+    drawRoundedRect(ctx, this.x, this.y, this.width, this.height, "#f5f5f5");
+
+    if (this.texImg.complete) {
+      drawTex(
+        ctx,
+        boxCenterX,
+        this.y + this.height * 0.4,
+        this.texImg,
+        this.width
+      );
+    } else {
+      this.texImg.onload = () => {
+        drawTex(
+          ctx,
+          boxCenterX,
+          this.y + this.height * 0.4,
+          this.texImg,
+          this.width
+        );
+      };
+    }
+
+    const {
+      generatorStatus,
+      simulatorStatus,
+      momentum,
+      vertex,
+      time,
+      mass,
+      charge,
+    } = this.members;
+
+    const topY = this.y + 20;
+    const topLines = [];
+    topLines.push("ID: " + this.id);
+    topLines.push("Gen. stat.: " + generatorStatus);
+    topLines.push("Sim. stat.: " + simulatorStatus);
+
+    const bottomY = this.y + this.height * 0.6;
+    const bottomLines = [];
+    let moment = Math.sqrt(momentum.x ** 2 + momentum.y ** 2 + momentum.z ** 2);
+    moment = Math.round(moment * 100) / 100;
+    bottomLines.push("p = " + moment + " GeV");
+    let v = Math.sqrt(vertex.x ** 2 + vertex.y ** 2 + vertex.z ** 2);
+    v = Math.round(v * 100) / 100;
+    bottomLines.push("d = " + v + " mm");
+    const t = Math.round(time * 100) / 100;
+    bottomLines.push("t = " + t + " ns");
+    let m = Math.round(mass * 100) / 100;
+    bottomLines.push("m = " + m + " GeV");
+    if (Math.abs(charge) < 1.0 && charge != 0) {
+      if (Math.round(charge * 1000) === 667) {
+        bottomLines.push("q = 2/3 e");
+      }
+      if (Math.round(charge * 1000) === -667) {
+        bottomLines.push("q = -2/3 e");
+      }
+      if (Math.round(charge * 1000) === 333) {
+        bottomLines.push("q = 1/3 e");
+      }
+      if (Math.round(charge * 1000) === -333) {
+        bottomLines.push("q = -1/3 e");
+      }
+    } else {
+      bottomLines.push("q = " + charge + " e");
+    }
+
+    ctx.save();
+    ctx.font = "16px sans-serif";
+    for (const [i, lineText] of topLines.entries()) {
+      ctx.fillText(
+        lineText,
+        boxCenterX - ctx.measureText(lineText).width / 2,
+        topY + i * 23
+      );
+    }
+
+    for (const [i, lineText] of bottomLines.entries()) {
+      ctx.fillText(
+        lineText,
+        boxCenterX - ctx.measureText(lineText).width / 2,
+        bottomY + i * 22
+      );
+    }
+    ctx.restore();
+  }
+
+  isHere(mouseX, mouseY) {
+    return (
+      mouseX > this.x &&
+      mouseX < this.x + this.width &&
+      mouseY > this.y &&
+      mouseY < this.y + this.height
+    );
+  }
+
+  isVisible(x, y, width, height) {
+    return (
+      x + width > this.x &&
+      x < this.x + this.width &&
+      y + height > this.y &&
+      y < this.y + this.height
+    );
+  }
 }
 
 export const objectTypes = {

From 27ba065cd17711e7d975b5843529d61a9b7675f3 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 08:43:38 -0500
Subject: [PATCH 26/35] fix typos in MODEL.md

---
 model/MODEL.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/model/MODEL.md b/model/MODEL.md
index 7211c2a8..3f4bf259 100644
--- a/model/MODEL.md
+++ b/model/MODEL.md
@@ -10,7 +10,7 @@ In the root directory, there are two commands in `package-json` that can be used
 npm run download
 ```
 
-will download the latest information from the edm4hep, by using the file called `edm4hep.yaml` under `model` directory, containg up to date information about `edm4hep`. The second command
+will download the latest information from the edm4hep, by using the file called `edm4hep.yaml` under `model` directory, containing up to date information about `edm4hep`. The second command
 
 ```bash
 npm run build
@@ -26,9 +26,9 @@ You can also run
 npm run update
 ```
 
-to run both processes at once and immediatly update the dmx application.
+to run both processes at once and immediately update the dmx application.
 
 ## Further improvements
 
 -   We could trigger the update process automatically when a new release of edm4hep is published, but for now, we will keep it simple and run the update process manually.
--   To maitain backward compatibility, we could add a versioning system so we can later load different versions of the edm4hep data model into dmx, however we currrently load the latest version.
+-   To maintain backward compatibility, we could add a versioning system so we can later load different versions of the edm4hep data model into dmx, however we currently load the latest version.

From e82ba4c81c4e98f4e4eebc3f82dee4bda74518db Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 08:46:42 -0500
Subject: [PATCH 27/35] implement @tmadlener random color generator

---
 js/types/links.js | 32 +-------------------------------
 1 file changed, 1 insertion(+), 31 deletions(-)

diff --git a/js/types/links.js b/js/types/links.js
index dbf11ae2..36e6f34b 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -4,38 +4,8 @@ export const colors = {
   // more if needed
 };
 
-const hexCharacters = [
-  0,
-  1,
-  2,
-  3,
-  4,
-  5,
-  6,
-  7,
-  8,
-  9,
-  "A",
-  "B",
-  "C",
-  "D",
-  "E",
-  "F",
-];
-
-function getCharacter(index) {
-  return hexCharacters[index];
-}
-
 export function generateRandomColor() {
-  let hexColorRep = "#";
-
-  for (let index = 0; index < 6; index++) {
-    const randomPosition = Math.floor(Math.random() * hexCharacters.length);
-    hexColorRep += getCharacter(randomPosition);
-  }
-
-  return hexColorRep;
+  return "#" + ((0xffffff * Math.random()) << 0).toString(16).padStart(6, "0");
 }
 
 export class Link {

From 9c0ee0a75132a63b50f2254145702751bf605322 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 16:45:20 -0500
Subject: [PATCH 28/35] minimal drawing for MCParticle

---
 js/draw.js               |  22 ++--
 js/main.js               | 250 +++++++++++++++++++--------------------
 js/menu/filter/filter.js |   6 +-
 js/types/links.js        |  12 +-
 js/types/load.js         |   3 -
 js/types/objects.js      | 110 +++++++++++++++++
 6 files changed, 254 insertions(+), 149 deletions(-)

diff --git a/js/draw.js b/js/draw.js
index 6bfdd8ae..b88dc088 100644
--- a/js/draw.js
+++ b/js/draw.js
@@ -1,23 +1,23 @@
 import { canvas, ctx } from "./main.js";
 
-export function drawAll(ctx, currentParticles) {
-  const { parentLinks, childrenLinks, infoBoxes } = currentParticles;
-
+export function drawAll(ctx, loadedObjects) {
   ctx.clearRect(0, 0, canvas.width, canvas.height);
   // console.time("drawParentLinks");
-  for (const link of parentLinks) {
-    link.draw(ctx, infoBoxes);
+
+  for (const elements of Object.values(loadedObjects)) {
+    const { collection, oneToMany, oneToOne } = elements;
+
+    for (const object of collection) object.draw(ctx);
+    for (const links of Object.values(oneToMany)) {
+      for (const link of links) link.draw(ctx);
+    }
+    for (const link of Object.values(oneToOne)) link.draw(ctx);
   }
+
   // console.timeEnd("drawParentLinks");
   // console.time("drawChildrenLinks");
-  for (const link of childrenLinks) {
-    link.draw(ctx, infoBoxes);
-  }
   // console.timeEnd("drawChildrenLinks");
   // console.time("drawBoxes");
-  for (const infoBox of infoBoxes) {
-    if (infoBox !== null) infoBox.draw(ctx);
-  }
   // console.timeEnd("drawBoxes");
 }
 
diff --git a/js/main.js b/js/main.js
index 3187794d..af7eeced 100644
--- a/js/main.js
+++ b/js/main.js
@@ -17,6 +17,8 @@ import {
   getVisible,
   onScroll,
 } from "./events.js";
+import { loadObjects } from "./types/load.js";
+import { objectTypes } from "./types/objects.js";
 
 const canvas = document.getElementById("canvas");
 const ctx = canvas.getContext("2d");
@@ -31,117 +33,107 @@ canvas.height = window.innerHeight;
 let jsonData = {};
 
 const dragTools = {
-  draggedInfoBox: -1,
+  draggedInfoBox: null,
   isDragging: false,
   prevMouseX: 0,
   prevMouseY: 0,
 };
 
-const particlesHandler = {
-  infoBoxes: [],
-  parentLinks: [],
-  childrenLinks: [],
-};
-
-const currentParticles = {
-  infoBoxes: [],
-  parentLinks: [],
-  childrenLinks: [],
-};
+let loadedObjects = {};
 
-const visibleParticles = {
-  infoBoxes: [],
-  parentLinks: [],
-  childrenLinks: [],
-};
+let currentObjects = {};
 
-function start(particlesHandler, visibleParticles) {
-  const { infoBoxes } = particlesHandler;
+let visibleObjects = {};
 
-  if (!infoBoxes) {
-    return;
+function start(loadedObjects, visibleObjects) {
+  for (const [key, value] of Object.entries(loadedObjects)) {
+    const classType = objectTypes[key];
+    const collection = value.collection;
+    classType.setup(collection);
   }
 
-  // Get How many rows
-  const rows = infoBoxes.map((obj) => {
-    return obj.row;
-  });
-  const maxRow = Math.max(...rows);
-
-  // Order infoBoxes into rows
-  const boxRows = [];
-  for (let i = 0; i <= maxRow; i++) {
-    boxRows.push([]);
-  }
-  for (const box of infoBoxes) {
-    boxRows[box.row].push(box.id);
-  }
-  const rowWidths = boxRows.map((obj) => {
-    return obj.length;
-  });
-  const maxRowWidth = Math.max(...rowWidths);
-
-  const boxWidth = infoBoxes[0].width;
-  const boxHeight = infoBoxes[0].height;
-  const horizontalGap = boxWidth * 0.4;
-  const verticalGap = boxHeight * 0.3;
-
-  canvas.width =
-    boxWidth * (maxRowWidth + 1) + horizontalGap * (maxRowWidth + 1);
-  canvas.height = boxHeight * (maxRow + 1) + verticalGap * (maxRow + 2);
-
-  for (const [i, row] of boxRows.entries()) {
-    for (const [j, boxId] of row.entries()) {
-      const box = infoBoxes[boxId];
-
-      if (row.length % 2 === 0) {
-        const distanceFromCenter = j - row.length / 2;
-        if (distanceFromCenter < 0) {
-          box.x =
-            canvas.width / 2 -
-            boxWidth -
-            horizontalGap / 2 +
-            (distanceFromCenter + 1) * boxWidth +
-            (distanceFromCenter + 1) * horizontalGap;
-        } else {
-          box.x =
-            canvas.width / 2 +
-            horizontalGap / 2 +
-            distanceFromCenter * boxWidth +
-            distanceFromCenter * horizontalGap;
-        }
-      } else {
-        const distanceFromCenter = j - row.length / 2;
-        box.x =
-          canvas.width / 2 -
-          boxWidth / 2 +
-          distanceFromCenter * boxWidth +
-          distanceFromCenter * horizontalGap;
-      }
-      box.y = i * verticalGap + verticalGap + i * boxHeight;
-    }
-  }
-
-  drawAll(ctx, particlesHandler);
-
-  getVisible(particlesHandler, visibleParticles);
+  // const { infoBoxes } = particlesHandler;
+
+  // // Get How many rows
+  // const rows = infoBoxes.map((obj) => {
+  //   return obj.row;
+  // });
+  // const maxRow = Math.max(...rows);
+
+  // // Order infoBoxes into rows
+  // const boxRows = [];
+  // for (let i = 0; i <= maxRow; i++) {
+  //   boxRows.push([]);
+  // }
+  // for (const box of infoBoxes) {
+  //   boxRows[box.row].push(box.id);
+  // }
+  // const rowWidths = boxRows.map((obj) => {
+  //   return obj.length;
+  // });
+  // const maxRowWidth = Math.max(...rowWidths);
+
+  // const boxWidth = infoBoxes[0].width;
+  // const boxHeight = infoBoxes[0].height;
+  // const horizontalGap = boxWidth * 0.4;
+  // const verticalGap = boxHeight * 0.3;
+
+  // canvas.width =
+  //   boxWidth * (maxRowWidth + 1) + horizontalGap * (maxRowWidth + 1);
+  // canvas.height = boxHeight * (maxRow + 1) + verticalGap * (maxRow + 2);
+
+  // for (const [i, row] of boxRows.entries()) {
+  //   for (const [j, boxId] of row.entries()) {
+  //     const box = infoBoxes[boxId];
+
+  //     if (row.length % 2 === 0) {
+  //       const distanceFromCenter = j - row.length / 2;
+  //       if (distanceFromCenter < 0) {
+  //         box.x =
+  //           canvas.width / 2 -
+  //           boxWidth -
+  //           horizontalGap / 2 +
+  //           (distanceFromCenter + 1) * boxWidth +
+  //           (distanceFromCenter + 1) * horizontalGap;
+  //       } else {
+  //         box.x =
+  //           canvas.width / 2 +
+  //           horizontalGap / 2 +
+  //           distanceFromCenter * boxWidth +
+  //           distanceFromCenter * horizontalGap;
+  //       }
+  //     } else {
+  //       const distanceFromCenter = j - row.length / 2;
+  //       box.x =
+  //         canvas.width / 2 -
+  //         boxWidth / 2 +
+  //         distanceFromCenter * boxWidth +
+  //         distanceFromCenter * horizontalGap;
+  //     }
+  //     box.y = i * verticalGap + verticalGap + i * boxHeight;
+  //   }
+  // }
+
+  drawAll(ctx, loadedObjects);
+
+  // getVisible(loadedObjects, visibleObjects);
 }
 
-canvas.onmousedown = (event) => {
-  mouseDown(event, currentParticles, visibleParticles, dragTools);
-};
-canvas.onmouseup = (event) => {
-  mouseUp(event, currentParticles, dragTools);
-};
-canvas.onmouseout = (event) => {
-  mouseOut(event, dragTools);
-};
-canvas.onmousemove = (event) => {
-  mouseMove(event, currentParticles, visibleParticles, dragTools);
-};
-window.onscroll = () => {
-  onScroll(currentParticles, visibleParticles);
-};
+// canvas.onmousedown = (event) => {
+//   mouseDown(event, currentParticles, visibleParticles, dragTools);
+// };
+// canvas.onmouseup = (event) => {
+//   mouseUp(event, currentParticles, dragTools);
+// };
+// canvas.onmouseout = (event) => {
+//   mouseOut(event, dragTools);
+// };
+// canvas.onmousemove = (event) => {
+//   mouseMove(event, currentParticles, visibleParticles, dragTools);
+// };
+// window.onscroll = () => {
+//   onScroll(currentParticles, visibleParticles);
+// };
 
 /*
 function showInputModal() {
@@ -187,45 +179,51 @@ document
     event.preventDefault();
     const eventNum = document.getElementById("event-number").value;
 
-    loadMCParticles(jsonData, eventNum, particlesHandler);
+    const objects = loadObjects(jsonData, eventNum, ["edm4hep::MCParticle"]);
+
+    for (const [key, value] of Object.entries(objects))
+      loadedObjects[key] = value;
 
-    currentParticles.infoBoxes = particlesHandler.infoBoxes;
-    currentParticles.parentLinks = particlesHandler.parentLinks;
-    currentParticles.childrenLinks = particlesHandler.childrenLinks;
+    for (const [key, value] of Object.entries(loadedObjects))
+      currentObjects[key] = value;
 
-    if (particlesHandler.infoBoxes.length === 0) {
+    const length = Object.values(loadedObjects)
+      .map((obj) => obj.collection.length)
+      .reduce((a, b) => a + b, 0);
+
+    if (length === 0) {
       errorMsg("Provided file does not contain any MC particle tree!");
       return;
     }
     for (const eventNum in jsonData) {
       delete jsonData[eventNum];
     }
-    start(currentParticles, visibleParticles);
+    start(currentObjects, visibleObjects);
     hideInputModal();
     window.scroll((canvas.width - window.innerWidth) / 2, 0);
 
-    for (const tool of manipulationTools) {
-      tool.style.display = "flex";
-    }
+    // for (const tool of manipulationTools) {
+    //   tool.style.display = "flex";
+    // }
 
-    const { infoBoxes } = currentParticles;
+    // const { infoBoxes } = currentParticles;
 
-    infoBoxes.forEach((infoBox) => {
-      genStatus.add(infoBox.genStatus);
-    });
-    genStatus.setCheckBoxes();
-    renderRangeParameters(filters, parametersRange);
-    const width = getWidthFilterContent();
-    filter.style.width = width;
-
-    renderGenSim(bits, genStatus, filters);
-
-    const pdgToggle = new PdgToggle("show-pdg");
-    pdgToggle.init(() => {
-      pdgToggle.toggle(infoBoxes, () => {
-        drawAll(ctx, currentParticles);
-      });
-    });
+    // infoBoxes.forEach((infoBox) => {
+    //   genStatus.add(infoBox.genStatus);
+    // });
+    // genStatus.setCheckBoxes();
+    // renderRangeParameters(filters, parametersRange);
+    // const width = getWidthFilterContent();
+    // filter.style.width = width;
+
+    // renderGenSim(bits, genStatus, filters);
+
+    // const pdgToggle = new PdgToggle("show-pdg");
+    // pdgToggle.init(() => {
+    //   pdgToggle.toggle(infoBoxes, () => {
+    //     drawAll(ctx, currentParticles);
+    //   });
+    // });
   });
 
-export { canvas, ctx, visibleParticles, particlesHandler, currentParticles };
+export { canvas, ctx, loadedObjects, currentObjects, visibleObjects };
diff --git a/js/menu/filter/filter.js b/js/menu/filter/filter.js
index 8399e8fb..aa6c2d16 100644
--- a/js/menu/filter/filter.js
+++ b/js/menu/filter/filter.js
@@ -1,9 +1,9 @@
 import { drawAll } from "../../draw.js";
 import {
   ctx,
-  particlesHandler,
-  currentParticles,
-  visibleParticles,
+  loadedObjects,
+  currentObjects,
+  visibleObjects,
 } from "../../main.js";
 import { CheckboxBuilder, BitFieldBuilder } from "./builders.js";
 import { Range, Checkbox, buildCriteriaFunction } from "./parameters.js";
diff --git a/js/types/links.js b/js/types/links.js
index 36e6f34b..30addf05 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -17,9 +17,9 @@ export class Link {
     this.xShift = 0;
   }
 
-  draw(ctx, infoBoxes) {
-    const boxFrom = infoBoxes[this.from];
-    const boxTo = infoBoxes[this.to];
+  draw(ctx) {
+    const boxFrom = this.from;
+    const boxTo = this.to;
 
     const fromX = boxFrom.x + boxFrom.width / 2;
     const fromY = boxFrom.y + boxFrom.height;
@@ -78,9 +78,9 @@ export class Link {
     */
   }
 
-  isVisible(x, y, width, height, infoBoxes) {
-    const boxFrom = infoBoxes[this.from];
-    const boxTo = infoBoxes[this.to];
+  isVisible(x, y, width, height) {
+    const boxFrom = this.from;
+    const boxTo = this.to;
 
     const fromX = boxFrom.x + boxFrom.width / 2;
     const fromY = boxFrom.y + boxFrom.height;
diff --git a/js/types/load.js b/js/types/load.js
index 83748ec9..dcf8f914 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -94,6 +94,3 @@ const objectsToLoad = [
   // "edm4hep::ParticleID",
   "edm4hep::MCParticle",
 ];
-
-const res = loadObjects(json, 0, objectsToLoad);
-console.log(res);
diff --git a/js/types/objects.js b/js/types/objects.js
index ca632f8a..d0930c0c 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -1,6 +1,7 @@
 import { EDMObject } from "./edmobject.js";
 import { drawTex, drawRoundedRect } from "../graphic-primitives.js";
 import { getName } from "../tools.js";
+import { canvas } from "../main.js";
 
 export class Cluster extends EDMObject {
   constructor(id) {
@@ -170,6 +171,115 @@ export class MCParticle extends EDMObject {
       y < this.y + this.height
     );
   }
+
+  static setup(mcCollection) {
+    for (const mcParticle of mcCollection) {
+      const parentLength = mcParticle.oneToManyRelations["parents"].length;
+      const daughterLength = mcParticle.oneToManyRelations["daughters"].length;
+
+      if (parentLength === 0 && daughterLength === 0) {
+        mcParticle.row = -1;
+        console.log("WARNING: Standalone particle!");
+      }
+
+      if (parentLength === 0) {
+        mcParticle.row = 0;
+      }
+
+      const name = getName(mcParticle.members.PDG);
+      mcParticle.name = name;
+      mcParticle.updateTexImg(name);
+    }
+
+    const getMaxRow = (parentLinks) => {
+      let maxRow = -1;
+      for (const parentLink of parentLinks) {
+        const parent = parentLink.to;
+        if (parent.row === -1) {
+          return -1;
+        }
+
+        if (parent.row > maxRow) {
+          maxRow = parent.row;
+        }
+      }
+
+      return maxRow;
+    };
+
+    let repeat = true;
+    while (repeat) {
+      repeat = false;
+      for (const mcParticle of mcCollection) {
+        if (mcParticle.row >= 0) {
+          continue;
+        }
+        const parentRow = getMaxRow(mcParticle.oneToManyRelations["parents"]);
+        if (parentRow >= 0) {
+          mcParticle.row = parentRow + 1;
+        } else {
+          repeat = true;
+        }
+      }
+    }
+
+    const rows = mcCollection.map((obj) => {
+      return obj.row;
+    });
+    const maxRow = Math.max(...rows);
+
+    // Order infoBoxes into rows
+    const mcRows = [];
+    for (let i = 0; i <= maxRow; i++) {
+      mcRows.push([]);
+    }
+    for (const box of mcCollection) {
+      mcRows[box.row].push(box);
+    }
+    const rowWidths = mcRows.map((obj) => {
+      return obj.length;
+    });
+    const maxRowWidth = Math.max(...rowWidths);
+
+    const boxWidth = mcCollection[0].width;
+    const boxHeight = mcCollection[0].height;
+    const horizontalGap = boxWidth * 0.4;
+    const verticalGap = boxHeight * 0.3;
+
+    canvas.width =
+      boxWidth * (maxRowWidth + 1) + horizontalGap * (maxRowWidth + 1);
+    canvas.height = boxHeight * (maxRow + 1) + verticalGap * (maxRow + 2);
+
+    for (const [i, row] of mcRows.entries()) {
+      for (const [j, box] of row.entries()) {
+        if (row.length % 2 === 0) {
+          const distanceFromCenter = j - row.length / 2;
+          if (distanceFromCenter < 0) {
+            box.x =
+              canvas.width / 2 -
+              boxWidth -
+              horizontalGap / 2 +
+              (distanceFromCenter + 1) * boxWidth +
+              (distanceFromCenter + 1) * horizontalGap;
+          } else {
+            box.x =
+              canvas.width / 2 +
+              horizontalGap / 2 +
+              distanceFromCenter * boxWidth +
+              distanceFromCenter * horizontalGap;
+          }
+        } else {
+          const distanceFromCenter = j - row.length / 2;
+          box.x =
+            canvas.width / 2 -
+            boxWidth / 2 +
+            distanceFromCenter * boxWidth +
+            distanceFromCenter * horizontalGap;
+        }
+        box.y = i * verticalGap + verticalGap + i * boxHeight;
+      }
+    }
+  }
 }
 
 export const objectTypes = {

From cd53b06f1db457850afc789912b57f80bdc3ccc6 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 17:40:14 -0500
Subject: [PATCH 29/35] good working drawing

---
 js/draw.js          | 11 +++-----
 js/main.js          | 62 ---------------------------------------------
 js/types/dynamic.js | 12 ++++-----
 js/types/links.js   | 27 +++++++++++++++++---
 js/types/load.js    | 22 +++++-----------
 js/types/objects.js |  2 +-
 6 files changed, 41 insertions(+), 95 deletions(-)

diff --git a/js/draw.js b/js/draw.js
index b88dc088..0976c057 100644
--- a/js/draw.js
+++ b/js/draw.js
@@ -2,23 +2,18 @@ import { canvas, ctx } from "./main.js";
 
 export function drawAll(ctx, loadedObjects) {
   ctx.clearRect(0, 0, canvas.width, canvas.height);
-  // console.time("drawParentLinks");
 
   for (const elements of Object.values(loadedObjects)) {
     const { collection, oneToMany, oneToOne } = elements;
 
-    for (const object of collection) object.draw(ctx);
     for (const links of Object.values(oneToMany)) {
       for (const link of links) link.draw(ctx);
     }
+
     for (const link of Object.values(oneToOne)) link.draw(ctx);
-  }
 
-  // console.timeEnd("drawParentLinks");
-  // console.time("drawChildrenLinks");
-  // console.timeEnd("drawChildrenLinks");
-  // console.time("drawBoxes");
-  // console.timeEnd("drawBoxes");
+    for (const object of collection) object.draw(ctx);
+  }
 }
 
 export function drawVisible(currentParticles, visibleParticles) {
diff --git a/js/main.js b/js/main.js
index af7eeced..3f082902 100644
--- a/js/main.js
+++ b/js/main.js
@@ -52,68 +52,6 @@ function start(loadedObjects, visibleObjects) {
     classType.setup(collection);
   }
 
-  // const { infoBoxes } = particlesHandler;
-
-  // // Get How many rows
-  // const rows = infoBoxes.map((obj) => {
-  //   return obj.row;
-  // });
-  // const maxRow = Math.max(...rows);
-
-  // // Order infoBoxes into rows
-  // const boxRows = [];
-  // for (let i = 0; i <= maxRow; i++) {
-  //   boxRows.push([]);
-  // }
-  // for (const box of infoBoxes) {
-  //   boxRows[box.row].push(box.id);
-  // }
-  // const rowWidths = boxRows.map((obj) => {
-  //   return obj.length;
-  // });
-  // const maxRowWidth = Math.max(...rowWidths);
-
-  // const boxWidth = infoBoxes[0].width;
-  // const boxHeight = infoBoxes[0].height;
-  // const horizontalGap = boxWidth * 0.4;
-  // const verticalGap = boxHeight * 0.3;
-
-  // canvas.width =
-  //   boxWidth * (maxRowWidth + 1) + horizontalGap * (maxRowWidth + 1);
-  // canvas.height = boxHeight * (maxRow + 1) + verticalGap * (maxRow + 2);
-
-  // for (const [i, row] of boxRows.entries()) {
-  //   for (const [j, boxId] of row.entries()) {
-  //     const box = infoBoxes[boxId];
-
-  //     if (row.length % 2 === 0) {
-  //       const distanceFromCenter = j - row.length / 2;
-  //       if (distanceFromCenter < 0) {
-  //         box.x =
-  //           canvas.width / 2 -
-  //           boxWidth -
-  //           horizontalGap / 2 +
-  //           (distanceFromCenter + 1) * boxWidth +
-  //           (distanceFromCenter + 1) * horizontalGap;
-  //       } else {
-  //         box.x =
-  //           canvas.width / 2 +
-  //           horizontalGap / 2 +
-  //           distanceFromCenter * boxWidth +
-  //           distanceFromCenter * horizontalGap;
-  //       }
-  //     } else {
-  //       const distanceFromCenter = j - row.length / 2;
-  //       box.x =
-  //         canvas.width / 2 -
-  //         boxWidth / 2 +
-  //         distanceFromCenter * boxWidth +
-  //         distanceFromCenter * horizontalGap;
-  //     }
-  //     box.y = i * verticalGap + verticalGap + i * boxHeight;
-  //   }
-  // }
-
   drawAll(ctx, loadedObjects);
 
   // getVisible(loadedObjects, visibleObjects);
diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index d6ae32a5..14dfd886 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -1,4 +1,4 @@
-import { Link, colors } from "./links.js";
+import { linkTypes } from "./links.js";
 
 export function loadMembers(object, data, membersToLoad) {
   for (const member of membersToLoad) {
@@ -21,10 +21,10 @@ export function loadOneToOneRelations(
     if (relationData === undefined) continue;
 
     const toObject = objects[relationData.index];
-    const link = new Link(object, toObject);
-    link.color = colors[name];
+    const linkType = linkTypes[name];
+    const link = new linkType(object, toObject);
 
-    oneToOne[name].push(link);
+    oneToOne[name] = link;
     object.oneToOneRelations[name] = link;
   }
 }
@@ -46,8 +46,8 @@ export function loadOneToManyRelations(
 
     for (const relationElement of relationData) {
       const toObject = objects[relationElement.index];
-      const link = new Link(object, toObject);
-      link.color = colors[name];
+      const linkType = linkTypes[name];
+      const link = new linkType(object, toObject);
       oneToMany[name].push(link);
       object.oneToManyRelations[name].push(link);
     }
diff --git a/js/types/links.js b/js/types/links.js
index 30addf05..45e52326 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -8,7 +8,7 @@ export function generateRandomColor() {
   return "#" + ((0xffffff * Math.random()) << 0).toString(16).padStart(6, "0");
 }
 
-export class Link {
+class Link {
   // we may create a specific class for each type if needed
   constructor(from, to) {
     this.from = from;
@@ -108,6 +108,27 @@ export class Link {
   }
 }
 
-export function createLink(id, from, { collectionID, index }) {
-  return new Link(id, from, index, collectionID);
+class ParentLink extends Link {
+  constructor(from, to) {
+    super(to, from);
+    this.color = colors["parents"];
+    this.xShift = 3;
+    // parent is this.from
+    // current object is this.to
+  }
+}
+
+class DaughterLink extends Link {
+  constructor(from, to) {
+    super(from, to);
+    this.color = colors["daughters"];
+    this.xShift = -3;
+    // current object is this.from
+    // daughter is this.to
+  }
 }
+
+export const linkTypes = {
+  "parents": ParentLink,
+  "daughters": DaughterLink,
+};
diff --git a/js/types/load.js b/js/types/load.js
index dcf8f914..ea7340b9 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -6,14 +6,13 @@ import {
   loadOneToManyRelations,
 } from "./dynamic.js";
 import { generateRandomColor, colors } from "./links.js";
-import json from "../../input/p8_ee_ZH_ecm240_edm4hep.edm4hep.json" assert { type: "json" };
 
 export function loadObjectType(collection, datatype, type) {
   const objects = [];
   let oneToOne = {};
   if (datatype.oneToOneRelations)
     datatype.oneToOneRelations.forEach((relation) => {
-      oneToOne[relation.name] = [];
+      oneToOne[relation.name] = null;
       if (colors[relation.name] === undefined) {
         colors[relation.name] = generateRandomColor();
       }
@@ -33,6 +32,12 @@ export function loadObjectType(collection, datatype, type) {
 
     loadMembers(newObject, particle, datatype.members);
 
+    objects.push(newObject);
+  }
+
+  for (const [index, particle] of collection.entries()) {
+    const newObject = objects[index];
+
     loadOneToOneRelations(
       newObject,
       particle,
@@ -48,8 +53,6 @@ export function loadObjectType(collection, datatype, type) {
       oneToMany,
       objects
     );
-
-    objects.push(newObject);
   }
 
   return [objects, oneToOne, oneToMany];
@@ -83,14 +86,3 @@ export function loadObjects(jsonData, event, objectsToLoad) {
 
   return objects;
 }
-
-const objectsToLoad = [
-  // subset of datatypes
-  // should be changed dynamically by the user
-  // "edm4hep::Cluster",
-  // "edm4hep::ReconstructedParticle",
-  // "edm4hep::Vertex",
-  // "edm4hep::Track",
-  // "edm4hep::ParticleID",
-  "edm4hep::MCParticle",
-];
diff --git a/js/types/objects.js b/js/types/objects.js
index d0930c0c..d44c7204 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -194,7 +194,7 @@ export class MCParticle extends EDMObject {
     const getMaxRow = (parentLinks) => {
       let maxRow = -1;
       for (const parentLink of parentLinks) {
-        const parent = parentLink.to;
+        const parent = parentLink.from;
         if (parent.row === -1) {
           return -1;
         }

From aeb04e23004a572d2e306d8b88fb096c0d4116f5 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 18:13:05 -0500
Subject: [PATCH 30/35] dmx works with new loading functionality

---
 js/draw.js            |  31 ++++-----
 js/events.js          | 147 +++++++++++++++++++-----------------------
 js/main.js            |  46 ++++++-------
 js/types/dynamic.js   |   5 +-
 js/types/edmobject.js |   1 -
 js/types/objects.js   |  40 +++++-------
 6 files changed, 123 insertions(+), 147 deletions(-)

diff --git a/js/draw.js b/js/draw.js
index 0976c057..65159e75 100644
--- a/js/draw.js
+++ b/js/draw.js
@@ -16,15 +16,7 @@ export function drawAll(ctx, loadedObjects) {
   }
 }
 
-export function drawVisible(currentParticles, visibleParticles) {
-  const {
-    infoBoxes: visibleBoxes,
-    parentLinks: visibleParentLinks,
-    childrenLinks: visibleChildrenLinks,
-  } = visibleParticles;
-
-  const { parentLinks, childrenLinks, infoBoxes } = currentParticles;
-
+export function drawVisible(visibleObjects) {
   const boundigClientRect = canvas.getBoundingClientRect();
   ctx.clearRect(
     0 - boundigClientRect.x,
@@ -32,15 +24,16 @@ export function drawVisible(currentParticles, visibleParticles) {
     window.innerWidth,
     window.innerHeight
   );
-  for (const linkId of visibleParentLinks) {
-    if (parentLinks[linkId] !== undefined)
-      parentLinks[linkId].draw(ctx, infoBoxes);
-  }
-  for (const linkId of visibleChildrenLinks) {
-    if (childrenLinks[linkId] !== undefined)
-      childrenLinks[linkId].draw(ctx, infoBoxes);
-  }
-  for (const boxId of visibleBoxes) {
-    infoBoxes[boxId].draw(ctx);
+
+  for (const elements of Object.values(visibleObjects)) {
+    const { collection, oneToMany, oneToOne } = elements;
+
+    for (const links of Object.values(oneToMany)) {
+      for (const link of links) link.draw(ctx);
+    }
+
+    for (const link of Object.values(oneToOne)) link.draw(ctx);
+
+    for (const object of collection) object.draw(ctx);
   }
 }
diff --git a/js/events.js b/js/events.js
index 193d71e9..660ec57b 100644
--- a/js/events.js
+++ b/js/events.js
@@ -1,12 +1,7 @@
 import { canvas, ctx } from "./main.js";
 import { drawAll, drawVisible } from "./draw.js";
 
-const mouseDown = function (
-  event,
-  currentParticles,
-  visibleParticles,
-  dragTools
-) {
+const mouseDown = function (event, visibleObjects, dragTools) {
   event.preventDefault();
   const boundigClientRect = canvas.getBoundingClientRect();
   const mouseX = parseInt(event.clientX - boundigClientRect.x);
@@ -15,18 +10,18 @@ const mouseDown = function (
   dragTools.prevMouseX = mouseX;
   dragTools.prevMouseY = mouseY;
 
-  const infoBoxes = currentParticles.infoBoxes;
-  const visibleBoxes = visibleParticles.infoBoxes;
-  for (let i = visibleBoxes.length - 1; i >= 0; i--) {
-    if (infoBoxes[visibleBoxes[i]].isHere(mouseX, mouseY)) {
-      dragTools.draggedInfoBox = visibleBoxes[i];
-      dragTools.isDragging = true;
-      return;
+  for (const { collection } of Object.values(visibleObjects)) {
+    for (const object of collection) {
+      if (object.isHere(mouseX, mouseY)) {
+        dragTools.draggedObject = object;
+        dragTools.isDragging = true;
+        return;
+      }
     }
   }
 };
 
-const mouseUp = function (event, particlesHandler, dragTools) {
+const mouseUp = function (event, currentObjects, dragTools) {
   if (!dragTools.isDragging) {
     return;
   }
@@ -35,7 +30,7 @@ const mouseUp = function (event, particlesHandler, dragTools) {
   dragTools.isDragging = false;
 
   // console.time("drawAll");
-  drawAll(ctx, particlesHandler);
+  drawAll(ctx, currentObjects);
   // console.timeEnd("drawAll");
 };
 
@@ -48,12 +43,7 @@ const mouseOut = function (event, dragTools) {
   dragTools.isDragging = false;
 };
 
-const mouseMove = function (
-  event,
-  currentParticles,
-  visibleParticles,
-  dragTools
-) {
+const mouseMove = function (event, visibleObjects, dragTools) {
   if (!dragTools.isDragging) {
     return;
   }
@@ -66,82 +56,81 @@ const mouseMove = function (
   const dx = mouseX - dragTools.prevMouseX;
   const dy = mouseY - dragTools.prevMouseY;
 
-  const infoBox = currentParticles.infoBoxes[dragTools.draggedInfoBox];
-  infoBox.x += dx;
-  infoBox.y += dy;
+  const draggedObject = dragTools.draggedObject;
+  draggedObject.x += dx;
+  draggedObject.y += dy;
 
   // console.time("drawVisible");
-  drawVisible(currentParticles, visibleParticles);
+  drawVisible(visibleObjects);
   // console.timeEnd("drawVisible");
 
   dragTools.prevMouseX = mouseX;
   dragTools.prevMouseY = mouseY;
 };
 
-const getVisible = function (currentParticles, visibleParticles) {
+const getVisible = function (loadedObjects, visibleObjects) {
   const boundigClientRect = canvas.getBoundingClientRect();
 
-  const { infoBoxes, parentLinks, childrenLinks } = currentParticles;
-
-  const visibleBoxes = [];
-  const visibleParentLinks = [];
-  const visibleChildrenLinks = [];
-
-  for (const box of infoBoxes) {
-    if (box === null) continue;
-    if (
-      box.isVisible(
-        0 - boundigClientRect.x,
-        0 - boundigClientRect.y,
-        window.innerWidth,
-        window.innerHeight
-      )
-    ) {
-      visibleBoxes.push(box.id);
+  for (const [objectType, elements] of Object.entries(loadedObjects)) {
+    const { collection, oneToMany, oneToOne } = elements;
+
+    visibleObjects[objectType] = {
+      collection: [],
+      oneToMany: {},
+      oneToOne: {},
+    };
+
+    for (const object of collection) {
+      if (
+        object.isVisible(
+          0 - boundigClientRect.x,
+          0 - boundigClientRect.y,
+          window.innerWidth,
+          window.innerHeight
+        )
+      ) {
+        visibleObjects[objectType].collection.push(object);
+      }
     }
-  }
 
-  for (const link of parentLinks) {
-    if (
-      link.isVisible(
-        0 - boundigClientRect.x,
-        0 - boundigClientRect.y,
-        window.innerWidth,
-        window.innerHeight,
-        infoBoxes
-      )
-    ) {
-      visibleParentLinks.push(link.id);
+    for (const [name, links] of Object.entries(oneToMany)) {
+      visibleObjects[objectType].oneToMany[name] = [];
+
+      for (const link of links) {
+        if (
+          link.isVisible(
+            0 - boundigClientRect.x,
+            0 - boundigClientRect.y,
+            window.innerWidth,
+            window.innerHeight
+          )
+        ) {
+          visibleObjects[objectType].oneToMany[name].push(link);
+        }
+      }
     }
-  }
 
-  for (const link of childrenLinks) {
-    if (
-      link.isVisible(
-        0 - boundigClientRect.x,
-        0 - boundigClientRect.y,
-        window.innerWidth,
-        window.innerHeight,
-        infoBoxes
-      )
-    ) {
-      visibleChildrenLinks.push(link.id);
+    for (const [name, links] of Object.entries(oneToOne)) {
+      visibleObjects[objectType].oneToOne[name] = null;
+
+      for (const link of links) {
+        if (
+          link.isVisible(
+            0 - boundigClientRect.x,
+            0 - boundigClientRect.y,
+            window.innerWidth,
+            window.innerHeight
+          )
+        ) {
+          visibleObjects[objectType].oneToOne[name] = link;
+        }
+      }
     }
   }
-
-  /*
-  console.log("Visible boxes: ", visibleBoxes);
-  console.log("Visible parentLinks: ", visibleParentLinks);
-  console.log("Visible childrenLinks: ", visibleChildrenLinks);
-  */
-
-  visibleParticles.infoBoxes = visibleBoxes;
-  visibleParticles.parentLinks = visibleParentLinks;
-  visibleParticles.childrenLinks = visibleChildrenLinks;
 };
 
-const onScroll = function (currentParticles, visibleParticles) {
-  getVisible(currentParticles, visibleParticles);
+const onScroll = function (currentObjects, visibleObjects) {
+  getVisible(currentObjects, visibleObjects);
 };
 
 export { mouseDown, mouseUp, mouseOut, mouseMove, getVisible, onScroll };
diff --git a/js/main.js b/js/main.js
index 3f082902..01059d00 100644
--- a/js/main.js
+++ b/js/main.js
@@ -33,45 +33,45 @@ canvas.height = window.innerHeight;
 let jsonData = {};
 
 const dragTools = {
-  draggedInfoBox: null,
+  draggedObject: null,
   isDragging: false,
   prevMouseX: 0,
   prevMouseY: 0,
 };
 
-let loadedObjects = {};
+const loadedObjects = {};
 
-let currentObjects = {};
+const currentObjects = {};
 
-let visibleObjects = {};
+const visibleObjects = {};
 
-function start(loadedObjects, visibleObjects) {
-  for (const [key, value] of Object.entries(loadedObjects)) {
+function start(currentObjects, visibleObjects) {
+  for (const [key, value] of Object.entries(currentObjects)) {
     const classType = objectTypes[key];
     const collection = value.collection;
     classType.setup(collection);
   }
 
-  drawAll(ctx, loadedObjects);
+  drawAll(ctx, currentObjects);
 
-  // getVisible(loadedObjects, visibleObjects);
+  getVisible(currentObjects, visibleObjects);
 }
 
-// canvas.onmousedown = (event) => {
-//   mouseDown(event, currentParticles, visibleParticles, dragTools);
-// };
-// canvas.onmouseup = (event) => {
-//   mouseUp(event, currentParticles, dragTools);
-// };
-// canvas.onmouseout = (event) => {
-//   mouseOut(event, dragTools);
-// };
-// canvas.onmousemove = (event) => {
-//   mouseMove(event, currentParticles, visibleParticles, dragTools);
-// };
-// window.onscroll = () => {
-//   onScroll(currentParticles, visibleParticles);
-// };
+canvas.onmousedown = (event) => {
+  mouseDown(event, visibleObjects, dragTools);
+};
+canvas.onmouseup = (event) => {
+  mouseUp(event, currentObjects, dragTools);
+};
+canvas.onmouseout = (event) => {
+  mouseOut(event, dragTools);
+};
+canvas.onmousemove = (event) => {
+  mouseMove(event, visibleObjects, dragTools);
+};
+window.onscroll = () => {
+  onScroll(currentObjects, visibleObjects);
+};
 
 /*
 function showInputModal() {
diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index 14dfd886..eb722a61 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -2,8 +2,9 @@ import { linkTypes } from "./links.js";
 
 export function loadMembers(object, data, membersToLoad) {
   for (const member of membersToLoad) {
-    if (data[member.name] === undefined) continue; // load up to date data
-    object.members[member.name] = data[member.name];
+    const name = member.name;
+    if (data[name] === undefined) continue; // load up to date data
+    object[name] = data[name];
   }
 }
 
diff --git a/js/types/edmobject.js b/js/types/edmobject.js
index c7a6a2a6..52332c34 100644
--- a/js/types/edmobject.js
+++ b/js/types/edmobject.js
@@ -1,7 +1,6 @@
 export class EDMObject {
   constructor(id) {
     this.id = id;
-    this.members = {};
   }
 
   draw() {}
diff --git a/js/types/objects.js b/js/types/objects.js
index d44c7204..dcbca391 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -89,49 +89,43 @@ export class MCParticle extends EDMObject {
       };
     }
 
-    const {
-      generatorStatus,
-      simulatorStatus,
-      momentum,
-      vertex,
-      time,
-      mass,
-      charge,
-    } = this.members;
-
     const topY = this.y + 20;
     const topLines = [];
     topLines.push("ID: " + this.id);
-    topLines.push("Gen. stat.: " + generatorStatus);
-    topLines.push("Sim. stat.: " + simulatorStatus);
+    topLines.push("Gen. stat.: " + this.generatorStatus);
+    topLines.push("Sim. stat.: " + this.simulatorStatus);
 
     const bottomY = this.y + this.height * 0.6;
     const bottomLines = [];
-    let moment = Math.sqrt(momentum.x ** 2 + momentum.y ** 2 + momentum.z ** 2);
+    let moment = Math.sqrt(
+      this.momentum.x ** 2 + this.momentum.y ** 2 + this.momentum.z ** 2
+    );
     moment = Math.round(moment * 100) / 100;
     bottomLines.push("p = " + moment + " GeV");
-    let v = Math.sqrt(vertex.x ** 2 + vertex.y ** 2 + vertex.z ** 2);
+    let v = Math.sqrt(
+      this.vertex.x ** 2 + this.vertex.y ** 2 + this.vertex.z ** 2
+    );
     v = Math.round(v * 100) / 100;
     bottomLines.push("d = " + v + " mm");
-    const t = Math.round(time * 100) / 100;
+    const t = Math.round(this.time * 100) / 100;
     bottomLines.push("t = " + t + " ns");
-    let m = Math.round(mass * 100) / 100;
+    let m = Math.round(this.mass * 100) / 100;
     bottomLines.push("m = " + m + " GeV");
-    if (Math.abs(charge) < 1.0 && charge != 0) {
-      if (Math.round(charge * 1000) === 667) {
+    if (Math.abs(this.charge) < 1.0 && this.charge != 0) {
+      if (Math.round(this.charge * 1000) === 667) {
         bottomLines.push("q = 2/3 e");
       }
-      if (Math.round(charge * 1000) === -667) {
+      if (Math.round(this.charge * 1000) === -667) {
         bottomLines.push("q = -2/3 e");
       }
-      if (Math.round(charge * 1000) === 333) {
+      if (Math.round(this.charge * 1000) === 333) {
         bottomLines.push("q = 1/3 e");
       }
-      if (Math.round(charge * 1000) === -333) {
+      if (Math.round(this.charge * 1000) === -333) {
         bottomLines.push("q = -1/3 e");
       }
     } else {
-      bottomLines.push("q = " + charge + " e");
+      bottomLines.push("q = " + this.charge + " e");
     }
 
     ctx.save();
@@ -186,7 +180,7 @@ export class MCParticle extends EDMObject {
         mcParticle.row = 0;
       }
 
-      const name = getName(mcParticle.members.PDG);
+      const name = getName(mcParticle.PDG);
       mcParticle.name = name;
       mcParticle.updateTexImg(name);
     }

From fc4540941584956dff6fe49145b961dc4572aba1 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 20:31:06 -0500
Subject: [PATCH 31/35] dmx completely using new loading function

---
 js/lib/copy.js              | 25 ++++++++++++
 js/main.js                  | 54 ++++++++++++-------------
 js/menu/filter/filter.js    | 63 ++++++++---------------------
 js/menu/filter/reconnect.js | 78 +++++-------------------------------
 js/menu/show-pdg.js         | 19 ++++++---
 js/types/objects.js         | 80 ++++++++++++++++++++++++++++++-------
 js/types/units.js           | 34 ++++++++++++----
 7 files changed, 183 insertions(+), 170 deletions(-)
 create mode 100644 js/lib/copy.js

diff --git a/js/lib/copy.js b/js/lib/copy.js
new file mode 100644
index 00000000..f87cbc03
--- /dev/null
+++ b/js/lib/copy.js
@@ -0,0 +1,25 @@
+export function copyObject(objToCopy, updatedObject) {
+  for (const [key, value] of Object.entries(objToCopy)) {
+    updatedObject[key] = value;
+  }
+}
+
+export function emptyCopyObject(objToCopy, updatedObject) {
+  for (const [objectType, elements] of Object.entries(objToCopy)) {
+    const { _, oneToMany, oneToOne } = elements;
+
+    updatedObject[objectType] = {
+      collection: [],
+      oneToMany: {},
+      oneToOne: {},
+    };
+
+    for (const name in oneToMany) {
+      updatedObject[objectType].oneToMany[name] = [];
+    }
+
+    for (const name in oneToOne) {
+      updatedObject[objectType].oneToOne[name] = null;
+    }
+  }
+}
diff --git a/js/main.js b/js/main.js
index 01059d00..a0d261e7 100644
--- a/js/main.js
+++ b/js/main.js
@@ -1,4 +1,4 @@
-import { errorMsg, loadMCParticles } from "./tools.js";
+import { errorMsg } from "./tools.js";
 import { PdgToggle } from "./menu/show-pdg.js";
 import { drawAll } from "./draw.js";
 import {
@@ -19,6 +19,7 @@ import {
 } from "./events.js";
 import { loadObjects } from "./types/load.js";
 import { objectTypes } from "./types/objects.js";
+import { copyObject } from "./lib/copy.js";
 
 const canvas = document.getElementById("canvas");
 const ctx = canvas.getContext("2d");
@@ -117,13 +118,11 @@ document
     event.preventDefault();
     const eventNum = document.getElementById("event-number").value;
 
-    const objects = loadObjects(jsonData, eventNum, ["edm4hep::MCParticle"]);
+    const selectedObjectTypes = ["edm4hep::MCParticle"];
+    const objects = loadObjects(jsonData, eventNum, selectedObjectTypes);
 
-    for (const [key, value] of Object.entries(objects))
-      loadedObjects[key] = value;
-
-    for (const [key, value] of Object.entries(loadedObjects))
-      currentObjects[key] = value;
+    copyObject(objects, loadedObjects);
+    copyObject(objects, currentObjects);
 
     const length = Object.values(loadedObjects)
       .map((obj) => obj.collection.length)
@@ -140,28 +139,27 @@ document
     hideInputModal();
     window.scroll((canvas.width - window.innerWidth) / 2, 0);
 
-    // for (const tool of manipulationTools) {
-    //   tool.style.display = "flex";
-    // }
-
-    // const { infoBoxes } = currentParticles;
-
-    // infoBoxes.forEach((infoBox) => {
-    //   genStatus.add(infoBox.genStatus);
-    // });
-    // genStatus.setCheckBoxes();
-    // renderRangeParameters(filters, parametersRange);
-    // const width = getWidthFilterContent();
-    // filter.style.width = width;
-
-    // renderGenSim(bits, genStatus, filters);
+    for (const tool of manipulationTools) {
+      tool.style.display = "flex";
+    }
 
-    // const pdgToggle = new PdgToggle("show-pdg");
-    // pdgToggle.init(() => {
-    //   pdgToggle.toggle(infoBoxes, () => {
-    //     drawAll(ctx, currentParticles);
-    //   });
-    // });
+    const mcObjects = loadedObjects["edm4hep::MCParticle"].collection;
+    mcObjects.forEach((mcObject) => {
+      genStatus.add(mcObject.generatorStatus);
+    });
+    genStatus.setCheckBoxes();
+    renderRangeParameters(filters, parametersRange);
+    const width = getWidthFilterContent();
+    filter.style.width = width;
+
+    renderGenSim(bits, genStatus, filters);
+
+    const pdgToggle = new PdgToggle("show-pdg");
+    pdgToggle.init(() => {
+      pdgToggle.toggle(currentObjects, () => {
+        drawAll(ctx, currentObjects);
+      });
+    });
   });
 
 export { canvas, ctx, loadedObjects, currentObjects, visibleObjects };
diff --git a/js/menu/filter/filter.js b/js/menu/filter/filter.js
index aa6c2d16..febe3cd1 100644
--- a/js/menu/filter/filter.js
+++ b/js/menu/filter/filter.js
@@ -9,6 +9,8 @@ import { CheckboxBuilder, BitFieldBuilder } from "./builders.js";
 import { Range, Checkbox, buildCriteriaFunction } from "./parameters.js";
 import { reconnect } from "./reconnect.js";
 import { getVisible } from "../../events.js";
+import { units } from "../../types/units.js";
+import { copyObject } from "../../lib/copy.js";
 
 const filterButton = document.getElementById("filter-button");
 const openFilter = document.getElementById("open-filter");
@@ -72,31 +74,7 @@ export function renderGenSim(sim, gen, container) {
   container.appendChild(div);
 }
 
-// TODO: Check in the future for other types of particles
-let parametersRange = [
-  {
-    property: "momentum",
-    unit: "GeV",
-  },
-  {
-    property: "mass",
-    unit: "GeV",
-  },
-  {
-    property: "charge",
-    unit: "e",
-  },
-  {
-    property: "vertex",
-    unit: "mm",
-  },
-  {
-    property: "time",
-    unit: "ns",
-  },
-];
-
-parametersRange = parametersRange.sort((a, b) =>
+let parametersRange = units.sort((a, b) =>
   a.property.localeCompare(b.property)
 );
 
@@ -114,15 +92,15 @@ const SimStatusBitFieldDisplayValues = {
 };
 
 const bits = new BitFieldBuilder(
-  "simStatus",
+  "simulatorStatus",
   "Simulation status",
   SimStatusBitFieldDisplayValues
 );
 bits.setCheckBoxes();
 
-const genStatus = new CheckboxBuilder("genStatus", "Generator status");
+const genStatus = new CheckboxBuilder("generatorStatus", "Generator status");
 
-function applyFilter(particlesHandler, currentParticles, visibleParticles) {
+function applyFilter(loadedObjects, currentObjects, visibleObjects) {
   const rangeFunctions = Range.buildFilter(parametersRange);
   const checkboxFunctions = Checkbox.buildFilter(bits.checkBoxes);
   const genStatusFunctions = Checkbox.buildFilter(genStatus.checkBoxes);
@@ -133,28 +111,21 @@ function applyFilter(particlesHandler, currentParticles, visibleParticles) {
     genStatusFunctions
   );
 
-  const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-    criteriaFunction,
-    particlesHandler
-  );
+  const filteredObjects = reconnect(criteriaFunction, loadedObjects);
 
-  currentParticles.parentLinks = newParentLinks;
-  currentParticles.childrenLinks = newChildrenLinks;
-  currentParticles.infoBoxes = filteredParticles;
+  copyObject(filteredObjects, currentObjects);
 
-  drawAll(ctx, currentParticles);
+  drawAll(ctx, currentObjects);
 
-  getVisible(currentParticles, visibleParticles);
+  getVisible(currentObjects, visibleObjects);
 }
 
-function removeFilter(particlesHandler, currentParticles, visibleParticles) {
-  currentParticles.parentLinks = particlesHandler.parentLinks;
-  currentParticles.childrenLinks = particlesHandler.childrenLinks;
-  currentParticles.infoBoxes = particlesHandler.infoBoxes;
+function removeFilter(loadedObjects, currentObjects, visibleObjects) {
+  copyObject(loadedObjects, currentObjects);
 
-  drawAll(ctx, currentParticles);
+  drawAll(ctx, currentObjects);
 
-  getVisible(currentParticles, visibleParticles);
+  getVisible(currentObjects, visibleObjects);
 
   filters.innerHTML = "";
 
@@ -163,17 +134,17 @@ function removeFilter(particlesHandler, currentParticles, visibleParticles) {
 }
 
 apply.addEventListener("click", () =>
-  applyFilter(particlesHandler, currentParticles, visibleParticles)
+  applyFilter(loadedObjects, currentObjects, visibleObjects)
 );
 
 document.addEventListener("keydown", (event) => {
   if (event.key === "Enter" && active) {
-    applyFilter(particlesHandler, currentParticles, visibleParticles);
+    applyFilter(loadedObjects, currentObjects, visibleObjects);
   }
 });
 
 reset.addEventListener("click", () =>
-  removeFilter(particlesHandler, currentParticles, visibleParticles)
+  removeFilter(loadedObjects, currentObjects, visibleObjects)
 );
 
 export { bits, genStatus, parametersRange };
diff --git a/js/menu/filter/reconnect.js b/js/menu/filter/reconnect.js
index c60b2f1f..e33e4eee 100644
--- a/js/menu/filter/reconnect.js
+++ b/js/menu/filter/reconnect.js
@@ -1,76 +1,16 @@
-import { Link } from "../../objects.js";
+import { emptyCopyObject } from "../../lib/copy.js";
+import { objectTypes } from "../../types/objects.js";
 
-export function reconnect(criteriaFunction, particlesHandler) {
-  const { parentLinks, childrenLinks, infoBoxes } = particlesHandler;
+export function reconnect(criteriaFunction, loadedObjects) {
+  const filteredObjects = {};
 
-  const newParentLinks = [];
-  const newChildrenLinks = [];
-  const filteredParticles = [];
+  emptyCopyObject(loadedObjects, filteredObjects);
 
-  for (const particle of infoBoxes) {
-    if (!criteriaFunction(particle)) {
-      filteredParticles.push(null);
+  for (const [key, value] of Object.entries(loadedObjects)) {
+    const filterFunction = objectTypes[key].filter;
 
-      const parentParticles = [];
-      const childrenParticles = [];
-
-      for (const parent of particle.parents) {
-        if (criteriaFunction(infoBoxes[parent])) {
-          parentParticles.push(parent);
-        }
-      }
-
-      for (const child of particle.children) {
-        if (criteriaFunction(infoBoxes[child])) {
-          childrenParticles.push(child);
-        }
-      }
-
-      for (const parent of parentParticles) {
-        for (const child of childrenParticles) {
-          const linkToParent = new Link(newParentLinks.length, parent, child);
-          linkToParent.xShift = 3;
-          const linkToChild = new Link(newChildrenLinks.length, parent, child);
-          linkToChild.color = "#0A0";
-          linkToChild.xShift = -3;
-
-          newParentLinks.push(linkToParent);
-          newChildrenLinks.push(linkToChild);
-        }
-      }
-    } else {
-      filteredParticles.push(particle);
-
-      for (const parentLinkId of particle.parentLinks) {
-        const parentLink = parentLinks[parentLinkId];
-        const parent = infoBoxes[parentLink.from];
-        if (criteriaFunction(parent)) {
-          const parentLinkCopy = new Link(
-            newParentLinks.length,
-            parentLink.from,
-            parentLink.to
-          );
-          parentLinkCopy.xShift = 3;
-          newParentLinks.push(parentLinkCopy);
-        }
-      }
-
-      for (const childrenLinkId of particle.childrenLinks) {
-        const childrenLink = childrenLinks[childrenLinkId];
-        const child = infoBoxes[childrenLink.to];
-        if (criteriaFunction(child)) {
-          const childrenLinkCopy = new Link(
-            newChildrenLinks.length,
-            childrenLink.from,
-            childrenLink.to
-          );
-          childrenLinkCopy.color = "#0A0";
-          childrenLinkCopy.xShift = -3;
-          newChildrenLinks.push(childrenLinkCopy);
-        }
-      }
-    }
+    filterFunction(value, filteredObjects, criteriaFunction);
   }
 
-  return [newParentLinks, newChildrenLinks, filteredParticles];
+  return filteredObjects;
 }
diff --git a/js/menu/show-pdg.js b/js/menu/show-pdg.js
index e78627a7..eb577d5a 100644
--- a/js/menu/show-pdg.js
+++ b/js/menu/show-pdg.js
@@ -1,4 +1,3 @@
-// const slider = document.getElementById("show-pdg");
 import { Toggle } from "./toggle.js";
 
 export class PdgToggle extends Toggle {
@@ -6,14 +5,22 @@ export class PdgToggle extends Toggle {
     super(id);
   }
 
-  toggle(infoBoxes, redraw) {
+  toggle(currentObjects, redraw) {
+    const validParticles = ["edm4hep::MCParticle"];
+
     if (this.isSliderActive) {
-      for (const infoBox of infoBoxes) {
-        infoBox.updateTexImg(`${infoBox.pdg}`);
+      for (const objectType of validParticles) {
+        const collection = currentObjects[objectType].collection;
+        for (const object of collection) {
+          object.updateTexImg(`${object.PDG}`);
+        }
       }
     } else {
-      for (const infoBox of infoBoxes) {
-        infoBox.updateTexImg(infoBox.name);
+      for (const objectType of validParticles) {
+        const collection = currentObjects[objectType].collection;
+        for (const object of collection) {
+          object.updateTexImg(`${object.name}`);
+        }
       }
     }
 
diff --git a/js/types/objects.js b/js/types/objects.js
index dcbca391..647ee6f2 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -2,6 +2,7 @@ import { EDMObject } from "./edmobject.js";
 import { drawTex, drawRoundedRect } from "../graphic-primitives.js";
 import { getName } from "../tools.js";
 import { canvas } from "../main.js";
+import { linkTypes } from "./links.js";
 
 export class Cluster extends EDMObject {
   constructor(id) {
@@ -97,20 +98,10 @@ export class MCParticle extends EDMObject {
 
     const bottomY = this.y + this.height * 0.6;
     const bottomLines = [];
-    let moment = Math.sqrt(
-      this.momentum.x ** 2 + this.momentum.y ** 2 + this.momentum.z ** 2
-    );
-    moment = Math.round(moment * 100) / 100;
-    bottomLines.push("p = " + moment + " GeV");
-    let v = Math.sqrt(
-      this.vertex.x ** 2 + this.vertex.y ** 2 + this.vertex.z ** 2
-    );
-    v = Math.round(v * 100) / 100;
-    bottomLines.push("d = " + v + " mm");
-    const t = Math.round(this.time * 100) / 100;
-    bottomLines.push("t = " + t + " ns");
-    let m = Math.round(this.mass * 100) / 100;
-    bottomLines.push("m = " + m + " GeV");
+    bottomLines.push("p = " + this.momentum + " GeV");
+    bottomLines.push("d = " + this.vertex + " mm");
+    bottomLines.push("t = " + this.time + " ns");
+    bottomLines.push("m = " + this.mass + " GeV");
     if (Math.abs(this.charge) < 1.0 && this.charge != 0) {
       if (Math.round(this.charge * 1000) === 667) {
         bottomLines.push("q = 2/3 e");
@@ -183,6 +174,21 @@ export class MCParticle extends EDMObject {
       const name = getName(mcParticle.PDG);
       mcParticle.name = name;
       mcParticle.updateTexImg(name);
+      mcParticle.momentum = Math.sqrt(
+        Math.pow(mcParticle.momentum.x, 2) +
+          Math.pow(mcParticle.momentum.y, 2) +
+          Math.pow(mcParticle.momentum.z, 2)
+      );
+      mcParticle.momentum = Math.round(mcParticle.momentum * 100) / 100;
+      mcParticle.vertex = Math.sqrt(
+        Math.pow(mcParticle.vertex.x, 2) +
+          Math.pow(mcParticle.vertex.y, 2) +
+          Math.pow(mcParticle.vertex.z, 2)
+      );
+      mcParticle.vertex = Math.round(mcParticle.vertex * 100) / 100;
+
+      mcParticle.time = Math.round(mcParticle.time * 100) / 100;
+      mcParticle.mass = Math.round(mcParticle.mass * 100) / 100;
     }
 
     const getMaxRow = (parentLinks) => {
@@ -274,6 +280,52 @@ export class MCParticle extends EDMObject {
       }
     }
   }
+
+  static filter({ collection }, filteredObjects, criteriaFunction) {
+    for (const mcParticle of collection) {
+      if (!criteriaFunction(mcParticle)) {
+        const parentParticles = mcParticle.oneToManyRelations["parents"]
+          .map((link) => link.from)
+          .filter((parent) => criteriaFunction(parent));
+        const childrenParticles = mcParticle.oneToManyRelations["daughters"]
+          .map((link) => link.to)
+          .filter((child) => criteriaFunction(child));
+
+        for (const parent of parentParticles) {
+          for (const child of childrenParticles) {
+            const linkToParent = new linkTypes["parents"](parent, mcParticle);
+
+            const linkToChild = new linkTypes["daughters"](mcParticle, child);
+
+            filteredObjects["edm4hep::MCParticle"].oneToMany["parents"].push(
+              linkToParent
+            );
+            filteredObjects["edm4hep::MCParticle"].oneToMany["daughters"].push(
+              linkToChild
+            );
+          }
+        }
+      } else {
+        filteredObjects["edm4hep::MCParticle"].collection.push(mcParticle);
+
+        for (const link of mcParticle.oneToManyRelations["parents"]) {
+          if (criteriaFunction(link.from)) {
+            filteredObjects["edm4hep::MCParticle"].oneToMany["parents"].push(
+              link
+            );
+          }
+        }
+
+        for (const link of mcParticle.oneToManyRelations["daughters"]) {
+          if (criteriaFunction(link.to)) {
+            filteredObjects["edm4hep::MCParticle"].oneToMany["daughters"].push(
+              link
+            );
+          }
+        }
+      }
+    }
+  }
 }
 
 export const objectTypes = {
diff --git a/js/types/units.js b/js/types/units.js
index f3cec707..164fc1c3 100644
--- a/js/types/units.js
+++ b/js/types/units.js
@@ -1,7 +1,27 @@
-export const units = {
-  "charge": "e",
-  "mass": "GeV",
-  "time": "ns",
-  "momentum": "GeV",
-  "position": "mm", // more to come
-};
+// TODO: Check in the future for other types of particles
+export const units = [
+  {
+    property: "momentum",
+    unit: "GeV",
+  },
+  {
+    property: "mass",
+    unit: "GeV",
+  },
+  {
+    property: "charge",
+    unit: "e",
+  },
+  {
+    property: "vertex",
+    unit: "mm",
+  },
+  {
+    property: "time",
+    unit: "ns",
+  },
+  {
+    property: "position",
+    unit: "mm",
+  },
+];

From bb0bc73c1e18e25ea949e051a1b02f987688b1a4 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 20:42:47 -0500
Subject: [PATCH 32/35] remove old files + fix filter function + fix lib

---
 js/lib/getName.js   |  13 +++
 js/objects.js       | 247 --------------------------------------------
 js/tools.js         | 124 ----------------------
 js/types/objects.js |   6 +-
 4 files changed, 16 insertions(+), 374 deletions(-)
 create mode 100644 js/lib/getName.js
 delete mode 100644 js/objects.js

diff --git a/js/lib/getName.js b/js/lib/getName.js
new file mode 100644
index 00000000..edfbc1f5
--- /dev/null
+++ b/js/lib/getName.js
@@ -0,0 +1,13 @@
+import { mappings } from "../../data/particles.js";
+
+export function getName(pdg) {
+  const particle = mappings[pdg];
+
+  if (particle !== undefined) {
+    console.log("Name: " + particle);
+    return particle;
+  }
+
+  console.log("PDG: " + pdg.toString());
+  return "PDG: " + pdg.toString();
+}
diff --git a/js/objects.js b/js/objects.js
deleted file mode 100644
index 7249e2b9..00000000
--- a/js/objects.js
+++ /dev/null
@@ -1,247 +0,0 @@
-import { drawTex, drawRoundedRect } from "./graphic-primitives.js";
-
-export class InfoBox {
-  constructor(id) {
-    this.id = parseInt(id);
-
-    // Appearance
-    this.x = 0;
-    this.y = 0;
-    this.width = 120;
-    this.height = 240;
-    this.lineColor = "black";
-    this.lineWidth = 2;
-    this.color = "white";
-    this.row = -1;
-
-    this.texImg = null;
-
-    // Physics data
-    this.name = "";
-    this.momentum = 0; // GeV
-    this.px = 0; // GeV
-    this.py = 0; // GeV
-    this.pz = 0; // GeV
-    this.vertex = 0; // mm, distance from 0, 0, 0
-    this.vx = 0; // mm
-    this.vy = 0; // mm
-    this.vz = 0; // mm
-    this.time = 0; // ns
-    this.mass = 0; // GeV
-    this.charge = 0; // e
-    this.pdg = 0;
-    this.genStatus = 0;
-    this.simStatus = 0;
-    this.parents = [];
-    this.children = [];
-
-    this.parentLinks = [];
-    this.childrenLinks = [];
-  }
-
-  updateTexImg(text) {
-    let svg = MathJax.tex2svg(text).firstElementChild;
-
-    this.texImg = document.createElement("img");
-    this.texImg.src =
-      "data:image/svg+xml;base64," +
-      btoa(
-        '<?xml version="1.0" encoding="UTF-8" standalone="no" ?>\n' +
-          svg.outerHTML
-      );
-  }
-
-  draw(ctx) {
-    // drawCross(ctx, this.x, this.y);
-
-    const boxCenterX = this.x + this.width / 2;
-
-    drawRoundedRect(ctx, this.x, this.y, this.width, this.height, "#f5f5f5");
-
-    if (this.texImg.complete) {
-      drawTex(
-        ctx,
-        boxCenterX,
-        this.y + this.height * 0.4,
-        this.texImg,
-        this.width
-      );
-    } else {
-      this.texImg.onload = () => {
-        drawTex(
-          ctx,
-          boxCenterX,
-          this.y + this.height * 0.4,
-          this.texImg,
-          this.width
-        );
-      };
-    }
-
-    const topY = this.y + 20;
-    const topLines = [];
-    topLines.push("ID: " + this.id);
-    topLines.push("Gen. stat.: " + this.genStatus);
-    topLines.push("Sim. stat.: " + this.simStatus);
-
-    const bottomY = this.y + this.height * 0.6;
-    const bottomLines = [];
-    bottomLines.push("p = " + this.momentum + " GeV");
-    bottomLines.push("d = " + this.vertex + " mm");
-    bottomLines.push("t = " + this.time + " ns");
-    bottomLines.push("m = " + this.mass + " GeV");
-    if (Math.abs(this.charge) < 1.0 && this.charge != 0) {
-      if (Math.round(this.charge * 1000) === 667) {
-        bottomLines.push("q = 2/3 e");
-      }
-      if (Math.round(this.charge * 1000) === -667) {
-        bottomLines.push("q = -2/3 e");
-      }
-      if (Math.round(this.charge * 1000) === 333) {
-        bottomLines.push("q = 1/3 e");
-      }
-      if (Math.round(this.charge * 1000) === -333) {
-        bottomLines.push("q = -1/3 e");
-      }
-    } else {
-      bottomLines.push("q = " + this.charge + " e");
-    }
-
-    ctx.save();
-    ctx.font = "16px sans-serif";
-    for (const [i, lineText] of topLines.entries()) {
-      ctx.fillText(
-        lineText,
-        boxCenterX - ctx.measureText(lineText).width / 2,
-        topY + i * 23
-      );
-    }
-
-    for (const [i, lineText] of bottomLines.entries()) {
-      ctx.fillText(
-        lineText,
-        boxCenterX - ctx.measureText(lineText).width / 2,
-        bottomY + i * 22
-      );
-    }
-    ctx.restore();
-  }
-
-  isHere(mouseX, mouseY) {
-    return (
-      mouseX > this.x &&
-      mouseX < this.x + this.width &&
-      mouseY > this.y &&
-      mouseY < this.y + this.height
-    );
-  }
-
-  isVisible(x, y, width, height) {
-    return (
-      x + width > this.x &&
-      x < this.x + this.width &&
-      y + height > this.y &&
-      y < this.y + this.height
-    );
-  }
-}
-
-export class Link {
-  constructor(id, boxFrom, boxTo) {
-    this.id = parseInt(id);
-    this.from = boxFrom;
-    this.to = boxTo;
-    this.color = "#A00";
-    this.xShift = 0;
-  }
-
-  draw(ctx, infoBoxes) {
-    const boxFrom = infoBoxes[this.from];
-    const boxTo = infoBoxes[this.to];
-
-    const fromX = boxFrom.x + boxFrom.width / 2;
-    const fromY = boxFrom.y + boxFrom.height;
-    const toX = boxTo.x + boxTo.width / 2;
-    const toY = boxTo.y;
-
-    if (toY > fromY) {
-      var cpFromY = (toY - fromY) / 2 + fromY;
-      var cpToY = cpFromY;
-    } else {
-      cpFromY = (fromY - toY) / 2 + fromY;
-      cpToY = toY - (fromY - toY) / 2;
-    }
-
-    if (toX > fromX) {
-      var cpFromX = (toX - fromX) / 4 + fromX;
-      var cpToX = (3 * (toX - fromX)) / 4 + fromX;
-    } else {
-      cpFromX = (3 * (fromX - toX)) / 4 + toX;
-      cpToX = (fromX - toX) / 4 + toX;
-    }
-
-    /*
-    drawCross(ctx, fromX, fromY, "blue");
-    drawCross(ctx, toX, toY, "green");
-    drawCross(ctx, cpFromX, cpFromY, "yellow");
-    drawLine(ctx, fromX, fromY, cpFromX, cpFromY, "yellow")
-    drawCross(ctx, cpToX, cpToY, "orange");
-    drawLine(ctx, toX, toY, cpToX, cpToY, "orange")
-    */
-
-    ctx.save();
-    ctx.strokeStyle = this.color;
-    ctx.lineWidth = 2;
-    ctx.beginPath();
-    ctx.moveTo(fromX + this.xShift, fromY);
-    ctx.bezierCurveTo(
-      cpFromX + this.xShift,
-      cpFromY,
-      cpToX + this.xShift,
-      cpToY,
-      toX + this.xShift,
-      toY
-    );
-    ctx.stroke();
-    ctx.restore();
-
-    /*
-    ctx.save();
-    ctx.font = "14px sans-serif";
-    ctx.fillStyle = this.color;
-    const idText = "ID: " + this.id;
-    ctx.fillText(idText,
-                 cpToX, cpToY);
-    ctx.restore();
-    */
-  }
-
-  isVisible(x, y, width, height, infoBoxes) {
-    const boxFrom = infoBoxes[this.from];
-    const boxTo = infoBoxes[this.to];
-
-    const fromX = boxFrom.x + boxFrom.width / 2;
-    const fromY = boxFrom.y + boxFrom.height;
-    const toX = boxTo.x + boxTo.width / 2;
-    const toY = boxTo.y;
-
-    const boxX = Math.min(fromX, toX);
-    const boxWidth = Math.abs(fromX - toX);
-    const boxY = Math.min(fromY, toY);
-    const boxHeight = Math.abs(fromY - toY);
-
-    /*
-    console.log("boxX: ", this.boxX);
-    console.log("boxY: ", this.boxY);
-    console.log("boxWidth: ", this.boxWidth);
-    console.log("boxHeight: ", this.boxHeight);
-    */
-
-    return (
-      x + width > boxX &&
-      x < boxX + boxWidth &&
-      y + height > boxY &&
-      y < boxY + boxHeight
-    );
-  }
-}
diff --git a/js/tools.js b/js/tools.js
index 2c28b45a..4b24f73e 100644
--- a/js/tools.js
+++ b/js/tools.js
@@ -1,6 +1,3 @@
-import { InfoBox, Link } from "./objects.js";
-import { mappings } from "../data/particles.js";
-
 export function infoMsg(msg) {
   const msgDiv = document.getElementById("input-message");
   msgDiv.classList.add("mb-20");
@@ -14,124 +11,3 @@ export function errorMsg(msg) {
   msgDiv.style.color = "red";
   msgDiv.innerHTML = "<p>ERROR: " + msg + "</p>";
 }
-
-export function loadMCParticles(jsonData, eventNum, particlesHandler) {
-  const { infoBoxes, parentLinks, childrenLinks } = particlesHandler;
-
-  const eventData = jsonData["Event " + eventNum];
-  try {
-    const mcParticles = Object.values(eventData).find(
-      (element) => element.collType == "edm4hep::MCParticleCollection"
-    );
-    for (const [i, particle] of mcParticles.collection.entries()) {
-      const box = new InfoBox(i);
-      box.pdg = particle.PDG;
-      box.genStatus = particle.generatorStatus;
-      box.simStatus = particle.simulatorStatus;
-      box.momentum = Math.sqrt(
-        Math.pow(particle.momentum.x, 2) +
-          Math.pow(particle.momentum.y, 2) +
-          Math.pow(particle.momentum.z, 2)
-      );
-      box.momentum = Math.round(box.momentum * 100) / 100;
-      box.vertex = Math.sqrt(
-        Math.pow(particle.vertex.x, 2) +
-          Math.pow(particle.vertex.y, 2) +
-          Math.pow(particle.vertex.z, 2)
-      );
-      box.vertex = Math.round(box.vertex * 100) / 100;
-      box.px = Math.round(particle.momentum.x * 100) / 100;
-      box.py = Math.round(particle.momentum.y * 100) / 100;
-      box.pz = Math.round(particle.momentum.z * 100) / 100;
-
-      box.vx = particle.vertex.x;
-      box.vy = particle.vertex.y;
-      box.vz = particle.vertex.z;
-
-      box.charge = particle.charge;
-      box.time = Math.round(particle.time * 100) / 100;
-      box.mass = Math.round(particle.mass * 100) / 100;
-
-      box.name = getName(particle.PDG);
-      box.updateTexImg(box.name);
-
-      if (particle.parents.length === 0 && particle.daughters.length === 0) {
-        box.row = -1;
-        console.log("WARNING: Standalone particle!");
-      }
-
-      if (particle.parents.length === 0) {
-        box.row = 0;
-      }
-
-      for (const j in particle.parents) {
-        const parentId = particle.parents[j].index;
-        box.parents.push(parentId);
-        const link = new Link(parseInt(parentLinks.length), parentId, i);
-        link.color = "#A00"; // Darkish red
-        link.xShift = 3;
-        parentLinks.push(link);
-        box.parentLinks.push(link.id);
-      }
-
-      for (const j in particle.daughters) {
-        const childrenId = particle.daughters[j].index;
-        box.children.push(childrenId);
-        const link = new Link(parseInt(childrenLinks.length), i, childrenId);
-        link.color = "#0A0"; // Darkish green
-        link.xShift = -3;
-        childrenLinks.push(link);
-        box.childrenLinks.push(link.id);
-      }
-
-      infoBoxes.push(box);
-    }
-  } catch (err) {
-    if (err instanceof TypeError) {
-      return;
-    }
-  }
-
-  const getMaxRow = function (parentIds) {
-    let maxRow = -1;
-    for (const parentId of parentIds) {
-      if (infoBoxes[parentId].row === -1) {
-        return -1;
-      }
-
-      if (infoBoxes[parentId].row > maxRow) {
-        maxRow = infoBoxes[parentId].row;
-      }
-    }
-
-    return maxRow;
-  };
-
-  let repeat = true;
-  while (repeat) {
-    repeat = false;
-    for (const infoBox of infoBoxes) {
-      if (infoBox.row >= 0) {
-        continue;
-      }
-      const parentRow = getMaxRow(infoBox.parents);
-      if (parentRow >= 0) {
-        infoBox.row = parentRow + 1;
-      } else {
-        repeat = true;
-      }
-    }
-  }
-}
-
-export function getName(pdg) {
-  const particle = mappings[pdg];
-
-  if (particle !== undefined) {
-    console.log("Name: " + particle);
-    return particle;
-  }
-
-  console.log("PDG: " + pdg.toString());
-  return "PDG: " + pdg.toString();
-}
diff --git a/js/types/objects.js b/js/types/objects.js
index 647ee6f2..18756893 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -1,6 +1,6 @@
 import { EDMObject } from "./edmobject.js";
 import { drawTex, drawRoundedRect } from "../graphic-primitives.js";
-import { getName } from "../tools.js";
+import { getName } from "../lib/getName.js";
 import { canvas } from "../main.js";
 import { linkTypes } from "./links.js";
 
@@ -293,9 +293,9 @@ export class MCParticle extends EDMObject {
 
         for (const parent of parentParticles) {
           for (const child of childrenParticles) {
-            const linkToParent = new linkTypes["parents"](parent, mcParticle);
+            const linkToParent = new linkTypes["parents"](child, parent);
 
-            const linkToChild = new linkTypes["daughters"](mcParticle, child);
+            const linkToChild = new linkTypes["daughters"](parent, child);
 
             filteredObjects["edm4hep::MCParticle"].oneToMany["parents"].push(
               linkToParent

From 26597eed4ca3b2506ac0d02143bcbd7e3922f89c Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Thu, 13 Jun 2024 21:22:07 -0500
Subject: [PATCH 33/35] new loading is done. [WIP] new test suite

---
 js/main.js                  |  2 +-
 js/types/links.js           |  6 +--
 js/types/objects.js         |  3 +-
 test/dynamic.test.js        | 18 +++----
 test/objects.test.js        | 99 +++++++++++--------------------------
 test/reconstruction.test.js |  9 ----
 6 files changed, 41 insertions(+), 96 deletions(-)
 delete mode 100644 test/reconstruction.test.js

diff --git a/js/main.js b/js/main.js
index a0d261e7..4f43c2cb 100644
--- a/js/main.js
+++ b/js/main.js
@@ -50,7 +50,7 @@ function start(currentObjects, visibleObjects) {
   for (const [key, value] of Object.entries(currentObjects)) {
     const classType = objectTypes[key];
     const collection = value.collection;
-    classType.setup(collection);
+    classType.setup(collection, canvas);
   }
 
   drawAll(ctx, currentObjects);
diff --git a/js/types/links.js b/js/types/links.js
index 45e52326..c5145754 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -8,7 +8,7 @@ export function generateRandomColor() {
   return "#" + ((0xffffff * Math.random()) << 0).toString(16).padStart(6, "0");
 }
 
-class Link {
+export class Link {
   // we may create a specific class for each type if needed
   constructor(from, to) {
     this.from = from;
@@ -108,7 +108,7 @@ class Link {
   }
 }
 
-class ParentLink extends Link {
+export class ParentLink extends Link {
   constructor(from, to) {
     super(to, from);
     this.color = colors["parents"];
@@ -118,7 +118,7 @@ class ParentLink extends Link {
   }
 }
 
-class DaughterLink extends Link {
+export class DaughterLink extends Link {
   constructor(from, to) {
     super(from, to);
     this.color = colors["daughters"];
diff --git a/js/types/objects.js b/js/types/objects.js
index 18756893..d0fe160f 100644
--- a/js/types/objects.js
+++ b/js/types/objects.js
@@ -1,7 +1,6 @@
 import { EDMObject } from "./edmobject.js";
 import { drawTex, drawRoundedRect } from "../graphic-primitives.js";
 import { getName } from "../lib/getName.js";
-import { canvas } from "../main.js";
 import { linkTypes } from "./links.js";
 
 export class Cluster extends EDMObject {
@@ -157,7 +156,7 @@ export class MCParticle extends EDMObject {
     );
   }
 
-  static setup(mcCollection) {
+  static setup(mcCollection, canvas) {
     for (const mcParticle of mcCollection) {
       const parentLength = mcParticle.oneToManyRelations["parents"].length;
       const daughterLength = mcParticle.oneToManyRelations["daughters"].length;
diff --git a/test/dynamic.test.js b/test/dynamic.test.js
index e0fda4e9..dfec0eb6 100644
--- a/test/dynamic.test.js
+++ b/test/dynamic.test.js
@@ -15,7 +15,6 @@ beforeEach(() => {
 });
 
 test("load members given some defined members and data", () => {
-  object.members = {};
   const members = [
     {
       "name": "type",
@@ -91,14 +90,12 @@ test("load members given some defined members and data", () => {
   loadMembers(object, data, members);
   expect(object).toEqual({
     "id": 1,
-    "members": {
-      "type": 0,
-      "chi2": 0.0,
-      "ndf": 0,
-      "dEdx": 0.0,
-      "dEdxError": 0.0,
-      "radiusOfInnermostHit": 17.0,
-    },
+    "type": 0,
+    "chi2": 0.0,
+    "ndf": 0,
+    "dEdx": 0.0,
+    "dEdxError": 0.0,
+    "radiusOfInnermostHit": 17.0,
   });
 });
 
@@ -169,7 +166,8 @@ test("load one to one relations with some definition and data", () => {
       "name": "startVertex",
     },
   ];
-  loadOneToOneRelations(object, data, oneToOneRelations);
+  const oneToOne = {};
+  loadOneToOneRelations(object, data, oneToOneRelations, oneToOne, []);
   expect(object).toEqual({
     "id": 1,
     "oneToOneRelations": {
diff --git a/test/objects.test.js b/test/objects.test.js
index 52860261..b52328dd 100644
--- a/test/objects.test.js
+++ b/test/objects.test.js
@@ -1,67 +1,36 @@
-import { InfoBox, Link } from "../js/objects";
+import { MCParticle } from "../js/types/objects";
+import { Link } from "../js/types/links";
 
-describe("InfoBox", () => {
-  let infoBox;
+describe("MCParticle", () => {
+  let mcParticle;
 
   beforeEach(() => {
-    infoBox = new InfoBox(1);
+    mcParticle = new MCParticle(1);
   });
 
   afterEach(() => {
-    infoBox = null;
-  });
-
-  it("should initialize with correct values", () => {
-    expect(infoBox.id).toBe(1);
-    expect(infoBox.x).toBe(0);
-    expect(infoBox.y).toBe(0);
-    expect(infoBox.width).toBe(120);
-    expect(infoBox.height).toBe(240);
-    expect(infoBox.lineColor).toBe("black");
-    expect(infoBox.lineWidth).toBe(2);
-    expect(infoBox.color).toBe("white");
-    expect(infoBox.row).toBe(-1);
-    expect(infoBox.texImg).toBe(null);
-    expect(infoBox.name).toBe("");
-    expect(infoBox.momentum).toBe(0);
-    expect(infoBox.px).toBe(0);
-    expect(infoBox.py).toBe(0);
-    expect(infoBox.pz).toBe(0);
-    expect(infoBox.vertex).toBe(0);
-    expect(infoBox.vx).toBe(0);
-    expect(infoBox.vy).toBe(0);
-    expect(infoBox.vz).toBe(0);
-    expect(infoBox.time).toBe(0);
-    expect(infoBox.mass).toBe(0);
-    expect(infoBox.charge).toBe(0);
-    expect(infoBox.pdg).toBe(0);
-    expect(infoBox.genStatus).toBe(0);
-    expect(infoBox.simStatus).toBe(0);
-    expect(infoBox.parents).toEqual([]);
-    expect(infoBox.children).toEqual([]);
-    expect(infoBox.parentLinks).toEqual([]);
-    expect(infoBox.childrenLinks).toEqual([]);
+    mcParticle = null;
   });
 
   it("should return true if (x, y) coordinates are within the box", () => {
     const x = 60;
     const y = 120;
 
-    expect(infoBox.isHere(x, y)).toBe(true);
+    expect(mcParticle.isHere(x, y)).toBe(true);
   });
 
   it("should return false if x coordinate is outside the box", () => {
     const x = 200;
     const y = 120;
 
-    expect(infoBox.isHere(x, y)).toBe(false);
+    expect(mcParticle.isHere(x, y)).toBe(false);
   });
 
   it("should return false if y coordinate is outside the box", () => {
     const x = 50;
     const y = -1;
 
-    expect(infoBox.isHere(x, y)).toBe(false);
+    expect(mcParticle.isHere(x, y)).toBe(false);
   });
 
   it("should return true if box is visible within the given area", () => {
@@ -70,85 +39,73 @@ describe("InfoBox", () => {
     const width = 200;
     const height = 200;
 
-    expect(infoBox.isVisible(x, y, width, height)).toBe(true);
+    expect(mcParticle.isVisible(x, y, width, height)).toBe(true);
   });
 
   it("should return false if the box is to the right of the area", () => {
-    infoBox.x = 300;
+    mcParticle.x = 300;
     const x = 0;
     const y = 0;
     const width = 200;
     const height = 200;
 
-    expect(infoBox.isVisible(x, y, width, height)).toBe(false);
+    expect(mcParticle.isVisible(x, y, width, height)).toBe(false);
   });
 
   it("should return false if the box is to the left of the area", () => {
-    infoBox.x = -300;
+    mcParticle.x = -300;
     const x = 0;
     const y = 0;
     const width = 200;
     const height = 200;
 
-    expect(infoBox.isVisible(x, y, width, height)).toBe(false);
+    expect(mcParticle.isVisible(x, y, width, height)).toBe(false);
   });
 
   it("should return false if the box is below the area", () => {
-    infoBox.y = 300;
+    mcParticle.y = 300;
     const x = 0;
     const y = 0;
     const width = 200;
     const height = 200;
 
-    expect(infoBox.isVisible(x, y, width, height)).toBe(false);
+    expect(mcParticle.isVisible(x, y, width, height)).toBe(false);
   });
 
   it("should return false if the box is above the area", () => {
-    infoBox.y = -300;
+    mcParticle.y = -300;
     const x = 0;
     const y = 0;
     const width = 200;
     const height = 200;
 
-    expect(infoBox.isVisible(x, y, width, height)).toBe(false);
+    expect(mcParticle.isVisible(x, y, width, height)).toBe(false);
   });
 });
 
 describe("Link", () => {
   let link;
+  let firstObject, secondObject;
 
   beforeEach(() => {
-    link = new Link(1, 0, 1);
-  });
-
-  afterEach(() => {
-    link = null;
+    firstObject = new MCParticle(0);
+    secondObject = new MCParticle(1);
+    link = new Link(firstObject, secondObject);
   });
 
   it("should construct correctly", () => {
-    expect(link.id).toBe(1);
-    expect(link.from).toBe(0);
-    expect(link.to).toBe(1);
-    expect(link.color).toBe("#A00");
-    expect(link.xShift).toBe(0);
-  });
-
-  let firstInfoBox, secondInfoBox, infoBoxes;
-
-  beforeEach(() => {
-    firstInfoBox = new InfoBox(0);
-    secondInfoBox = new InfoBox(1);
-    infoBoxes = [firstInfoBox, secondInfoBox];
+    expect(link.from).toBe(firstObject);
+    expect(link.to).toBe(secondObject);
   });
 
   it("should return true if the link is visible", () => {
-    secondInfoBox.x = 140;
-    secondInfoBox.y = 250;
+    secondObject.x = 140;
+    secondObject.y = 250;
 
-    expect(link.isVisible(0, 0, 250, 250, infoBoxes)).toBe(true);
+    expect(link.isVisible(0, 0, 250, 250)).toBe(true);
   });
 
   it("should return false if the link is not visible", () => {
-    expect(link.isVisible(10, 10, 50, 50, infoBoxes)).toBe(false);
+    expect(link.isVisible(10, 10, 50, 50)).toBe(false);
   });
 });
diff --git a/test/reconstruction.test.js b/test/reconstruction.test.js
deleted file mode 100644
index deb511f9..00000000
--- a/test/reconstruction.test.js
+++ /dev/null
@@ -1,9 +0,0 @@
-import { createLink } from "../js/types/objects.js";
-
-test("it should create a link", () => {
-  const link = createLink(1, 2, { collectionID: 3, index: 4 });
-  expect(link.id).toBe(1);
-  expect(link.from).toBe(2);
-  expect(link.to).toBe(4);
-  expect(link.collectionID).toBe(3);
-});

From 0c1538b7747184c8115722f02c6c597c5caa8a6b Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Fri, 14 Jun 2024 23:11:54 -0500
Subject: [PATCH 34/35] add very basic tests for new loading logic

---
 js/types/links.js             |   2 +
 test/dynamic.test.js          |  55 ++------
 test/filter.test.js           | 216 ------------------------------
 test/filterMCParticle.test.js | 241 ++++++++++++++++++++++++++++++++++
 test/load.test.js             |  93 +------------
 5 files changed, 262 insertions(+), 345 deletions(-)
 delete mode 100644 test/filter.test.js
 create mode 100644 test/filterMCParticle.test.js

diff --git a/js/types/links.js b/js/types/links.js
index c5145754..c95fc73c 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -131,4 +131,6 @@ export class DaughterLink extends Link {
 export const linkTypes = {
   "parents": ParentLink,
   "daughters": DaughterLink,
+  "trackerHits": Link,
+  "startVertex": Link,
 };
diff --git a/test/dynamic.test.js b/test/dynamic.test.js
index dfec0eb6..0fed4546 100644
--- a/test/dynamic.test.js
+++ b/test/dynamic.test.js
@@ -154,8 +154,8 @@ test("load one to one relations with some definition and data", () => {
       "z": 0.0,
     },
     "startVertex": {
-      "collectionID": -2,
-      "index": -2,
+      "collectionID": 2,
+      "index": 2,
     },
     "tracks": [],
     "type": 0,
@@ -166,19 +166,11 @@ test("load one to one relations with some definition and data", () => {
       "name": "startVertex",
     },
   ];
-  const oneToOne = {};
+  const oneToOne = {
+    "startVertex": null,
+  };
   loadOneToOneRelations(object, data, oneToOneRelations, oneToOne, []);
-  expect(object).toEqual({
-    "id": 1,
-    "oneToOneRelations": {
-      "startVertex": {
-        "id": 1,
-        "from": 1,
-        "to": -2,
-        "collectionID": -2,
-      },
-    },
-  });
+  expect(object.oneToOneRelations).not.toBeNull();
 });
 
 test("load one to many relations with some definition and data", () => {
@@ -245,32 +237,11 @@ test("load one to many relations with some definition and data", () => {
       "name": "daughters",
     },
   ];
-  loadOneToManyRelations(object, data, oneToManyRelations);
-  expect(object).toEqual({
-    "id": 1,
-    "oneToManyRelations": {
-      "parents": [
-        {
-          "id": 1,
-          "from": 1,
-          "to": 1,
-          "collectionID": 11,
-        },
-      ],
-      "daughters": [
-        {
-          "id": 1,
-          "from": 1,
-          "to": 4,
-          "collectionID": 11,
-        },
-        {
-          "id": 2,
-          "from": 1,
-          "to": 5,
-          "collectionID": 11,
-        },
-      ],
-    },
-  });
+  const oneToMany = {
+    "parents": [],
+    "daughters": [],
+  };
+  loadOneToManyRelations(object, data, oneToManyRelations, oneToMany, []);
+  expect(object.oneToManyRelations.daughters.length).toEqual(2);
+  expect(object.oneToManyRelations.parents.length).toEqual(1);
 });
diff --git a/test/filter.test.js b/test/filter.test.js
deleted file mode 100644
index a4046fc3..00000000
--- a/test/filter.test.js
+++ /dev/null
@@ -1,216 +0,0 @@
-import { reconnect } from "../js/menu/filter/reconnect.js";
-import { InfoBox, Link } from "../js/objects.js";
-import {
-  Range,
-  Checkbox,
-  buildCriteriaFunction,
-} from "../js/menu/filter/parameters.js";
-
-const parentLinks = [];
-const childrenLinks = [];
-const infoBoxes = [];
-
-beforeAll(() => {
-  for (let i = 0; i < 5; i++) {
-    const particle = new InfoBox(i);
-    particle.momentum = i * 100;
-    particle.charge = i;
-    particle.mass = i * 10;
-    particle.simStatus = i + 23;
-    infoBoxes.push(particle);
-  }
-
-  parentLinks.push(new Link(0, 0, 1));
-  parentLinks.push(new Link(1, 0, 2));
-  parentLinks.push(new Link(2, 2, 4));
-  parentLinks.push(new Link(3, 1, 3));
-  parentLinks.push(new Link(4, 3, 4));
-
-  childrenLinks.push(new Link(0, 0, 1));
-  childrenLinks.push(new Link(1, 0, 2));
-  childrenLinks.push(new Link(2, 1, 3));
-  childrenLinks.push(new Link(3, 2, 4));
-  childrenLinks.push(new Link(4, 3, 4));
-
-  infoBoxes[0].children = [1, 2];
-  infoBoxes[0].childrenLinks = [0, 1];
-
-  infoBoxes[1].parents = [0];
-  infoBoxes[1].children = [3];
-  infoBoxes[1].parentLinks = [0];
-  infoBoxes[1].childrenLinks = [2];
-
-  infoBoxes[2].parents = [0];
-  infoBoxes[2].children = [4];
-  infoBoxes[2].parentLinks = [1];
-  infoBoxes[2].childrenLinks = [3];
-
-  infoBoxes[3].parents = [1];
-  infoBoxes[3].children = [4];
-  infoBoxes[3].parentLinks = [3];
-  infoBoxes[3].childrenLinks = [4];
-
-  infoBoxes[4].parents = [2, 3];
-  infoBoxes[4].parentLinks = [2, 4];
-});
-
-const particlesHandler = {
-  parentLinks,
-  childrenLinks,
-  infoBoxes,
-};
-
-describe("filter by ranges", () => {
-  it("filter by a single range parameter", () => {
-    const momentum = new Range({
-      property: "momentum",
-      unit: "GeV",
-    });
-    momentum.min = 300;
-    momentum.max = 1000;
-    const rangeFilters = Range.buildFilter([momentum]);
-    const criteriaFunction = buildCriteriaFunction(rangeFilters);
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newChildrenLinks.map((link) => link.id)).toEqual([0]);
-    expect(newParentLinks.map((link) => link.id)).toEqual([0]);
-    expect(
-      filteredParticles.filter((p) => p).map((particle) => particle.id)
-    ).toEqual([3, 4]);
-  });
-
-  it("filter by a combination of ranges", () => {
-    const charge = new Range({
-      property: "charge",
-      unit: "e",
-    });
-    charge.min = 3;
-    const mass = new Range({
-      property: "mass",
-      unit: "GeV",
-    });
-    mass.min = 20;
-    mass.max = 40;
-    const rangeFilters = Range.buildFilter([mass, charge]);
-    const criteriaFunction = buildCriteriaFunction(rangeFilters);
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newChildrenLinks.map((link) => link.id)).toEqual([0]);
-    expect(newParentLinks.map((link) => link.id)).toEqual([0]);
-    expect(
-      filteredParticles.filter((p) => p).map((particle) => particle.id)
-    ).toEqual([3, 4]);
-  });
-});
-
-describe("filter by checkboxes", () => {
-  it("filter by a single checkbox", () => {
-    const simulatorStatus = new Checkbox("simStatus", 23);
-    simulatorStatus.checked = true;
-    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
-    const criteriaFunction = buildCriteriaFunction(checkboxFilters);
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newChildrenLinks.map((link) => link.id)).toEqual([]);
-    expect(newParentLinks.map((link) => link.id)).toEqual([]);
-    expect(
-      filteredParticles.filter((p) => p).map((particle) => particle.id)
-    ).toEqual([0]);
-  });
-
-  it("filter by a combination of checkboxes", () => {
-    const simulatorStatus1 = new Checkbox("simStatus", 23);
-    simulatorStatus1.checked = true;
-    const simulatorStatus2 = new Checkbox("simStatus", 26);
-    simulatorStatus2.checked = true;
-    const simulatorStatus3 = new Checkbox("simStatus", 27);
-    simulatorStatus3.checked = true;
-    const checkboxFilters = Checkbox.buildFilter([
-      simulatorStatus1,
-      simulatorStatus2,
-      simulatorStatus3,
-    ]);
-    const criteriaFunction = buildCriteriaFunction(checkboxFilters);
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newChildrenLinks.map((link) => link.id)).toEqual([0, 1, 2]);
-    expect(newParentLinks.map((link) => link.id)).toEqual([0, 1, 2]);
-    expect(
-      filteredParticles.filter((p) => p).map((particle) => particle.id)
-    ).toEqual([0, 3, 4]);
-  });
-});
-
-describe("filter by ranges and checkboxes", () => {
-  it("show all particles when no kind of filter is applied", () => {
-    const charge = new Range({
-      property: "charge",
-      unit: "e",
-    });
-    const simulatorStatus = new Checkbox("simStatus", 26);
-    const rangeFilters = Range.buildFilter([charge]);
-    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
-    const criteriaFunction = buildCriteriaFunction(
-      rangeFilters,
-      checkboxFilters
-    );
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newParentLinks.map((link) => link.id).sort()).toEqual([
-      0, 1, 2, 3, 4,
-    ]);
-    expect(newChildrenLinks.map((link) => link.id).sort()).toEqual([
-      0, 1, 2, 3, 4,
-    ]);
-    expect(filteredParticles.map((particle) => particle.id)).toEqual([
-      0, 1, 2, 3, 4,
-    ]);
-  });
-
-  it("filter by a combination of ranges and checkboxes", () => {
-    const charge = new Range({
-      property: "charge",
-      unit: "e",
-    });
-    charge.max = 3;
-    const simulatorStatus = new Checkbox("simStatus", 23);
-    simulatorStatus.checked = true;
-    const rangeFilters = Range.buildFilter([charge]);
-    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
-    const criteriaFunction = buildCriteriaFunction(
-      rangeFilters,
-      checkboxFilters
-    );
-
-    const [newParentLinks, newChildrenLinks, filteredParticles] = reconnect(
-      criteriaFunction,
-      particlesHandler
-    );
-
-    expect(newChildrenLinks.map((link) => link.id)).toEqual([]);
-    expect(newParentLinks.map((link) => link.id)).toEqual([]);
-    expect(
-      filteredParticles.filter((p) => p).map((particle) => particle.id)
-    ).toEqual([0]);
-  });
-});
diff --git a/test/filterMCParticle.test.js b/test/filterMCParticle.test.js
new file mode 100644
index 00000000..c3c54ca3
--- /dev/null
+++ b/test/filterMCParticle.test.js
@@ -0,0 +1,241 @@
+import { reconnect } from "../js/menu/filter/reconnect.js";
+import { loadObjects } from "../js/types/load.js";
+import {
+  Range,
+  Checkbox,
+  buildCriteriaFunction,
+} from "../js/menu/filter/parameters.js";
+import { CheckboxBuilder } from "../js/menu/filter/builders.js";
+
+let objects = {};
+
+const data = {
+  "Event 0": {
+    "Collection": {
+      "collType": "edm4hep::MCParticleCollection",
+      "collection": [
+        {
+          "momentum": 0,
+          "charge": 0,
+          "mass": 0,
+          "simStatus": 70,
+          "parents": [],
+          "daughters": [
+            {
+              "collectionID": 0,
+              "index": 1,
+            },
+          ],
+        },
+        {
+          "momentum": 100,
+          "charge": 1,
+          "mass": 10,
+          "simStatus": 24,
+          "daughters": [
+            {
+              "collectionID": 0,
+              "index": 3,
+            },
+          ],
+          "parents": [
+            {
+              "collectionID": 0,
+              "index": 0,
+            },
+          ],
+        },
+        {
+          "momentum": 200,
+          "charge": 2,
+          "mass": 20,
+          "simStatus": 25,
+          "daughters": [
+            {
+              "collectionID": 0,
+              "index": 4,
+            },
+          ],
+          "parents": [
+            {
+              "collectionID": 0,
+              "index": 0,
+            },
+          ],
+        },
+        {
+          "momentum": 300,
+          "charge": 3,
+          "mass": 30,
+          "simStatus": 26,
+          "daughters": [
+            {
+              "collectionID": 0,
+              "index": 4,
+            },
+          ],
+          "parents": [
+            {
+              "collectionID": 0,
+              "index": 1,
+            },
+          ],
+        },
+        {
+          "momentum": 400,
+          "charge": 4,
+          "mass": 40,
+          "simStatus": 27,
+          "parents": [
+            {
+              "collectionID": 0,
+              "index": 2,
+            },
+            {
+              "collectionID": 0,
+              "index": 3,
+            },
+          ],
+          "daughters": [],
+        },
+      ],
+    },
+  },
+};
+
+beforeAll(() => {
+  objects = loadObjects(data, 0, ["edm4hep::MCParticle"]);
+});
+
+describe("filter by ranges", () => {
+  it("filter by a single range parameter", () => {
+    const momentum = new Range({
+      property: "momentum",
+      unit: "GeV",
+    });
+    momentum.min = 300;
+    momentum.max = 1000;
+    const rangeFilters = Range.buildFilter([momentum]);
+    const criteriaFunction = buildCriteriaFunction(rangeFilters);
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([3, 4]);
+  });
+
+  it("filter by a combination of ranges", () => {
+    const charge = new Range({
+      property: "charge",
+      unit: "e",
+    });
+    charge.min = 3;
+    const mass = new Range({
+      property: "mass",
+      unit: "GeV",
+    });
+    mass.min = 20;
+    mass.max = 40;
+    const rangeFilters = Range.buildFilter([mass, charge]);
+    const criteriaFunction = buildCriteriaFunction(rangeFilters);
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([3, 4]);
+  });
+});
+
+describe("filter by checkboxes", () => {
+  it("filter by a single checkbox", () => {
+    const simulatorStatus = new Checkbox("simStatus", 23);
+    simulatorStatus.checked = true;
+    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
+    const criteriaFunction = buildCriteriaFunction(checkboxFilters);
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([]);
+  });
+
+  it("filter by a combination of checkboxes", () => {
+    const simulatorStatus1 = new Checkbox("simStatus", 23);
+    simulatorStatus1.checked = true;
+    const simulatorStatus2 = new Checkbox("simStatus", 26);
+    simulatorStatus2.checked = true;
+    const simulatorStatus3 = new Checkbox("simStatus", 27);
+    simulatorStatus3.checked = true;
+    const checkboxFilters = Checkbox.buildFilter([
+      simulatorStatus1,
+      simulatorStatus2,
+      simulatorStatus3,
+    ]);
+    const criteriaFunction = buildCriteriaFunction(checkboxFilters);
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([]);
+  });
+});
+
+describe("filter by ranges and checkboxes", () => {
+  it("show all particles when no kind of filter is applied", () => {
+    const charge = new Range({
+      property: "charge",
+      unit: "e",
+    });
+    const simulatorStatus = new Checkbox("simStatus", 26);
+    const rangeFilters = Range.buildFilter([charge]);
+    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
+    const criteriaFunction = buildCriteriaFunction(
+      rangeFilters,
+      checkboxFilters
+    );
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([0, 1, 2, 3, 4]);
+  });
+
+  it("filter by a combination of ranges and checkboxes", () => {
+    const charge = new Range({
+      property: "charge",
+      unit: "e",
+    });
+    charge.max = 3;
+    const simulatorStatus = new Checkbox("simStatus", 23);
+    simulatorStatus.checked = true;
+    const rangeFilters = Range.buildFilter([charge]);
+    const checkboxFilters = Checkbox.buildFilter([simulatorStatus]);
+    const criteriaFunction = buildCriteriaFunction(
+      rangeFilters,
+      checkboxFilters
+    );
+
+    const filteredObjects = reconnect(criteriaFunction, objects);
+
+    expect(
+      filteredObjects["edm4hep::MCParticle"].collection.map(
+        (mcParticle) => mcParticle.id
+      )
+    ).toEqual([]);
+  });
+});
diff --git a/test/load.test.js b/test/load.test.js
index d7bc57c6..a795c391 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -160,95 +160,14 @@ test("load a collection of particles", () => {
       "type": 0,
     },
   ];
-  const particles = loadObjectType(
+  const [objects, oneToOne, { trackerHits, tracks }] = loadObjectType(
     collection,
     datatypes[type],
     objectTypes[type]
   );
-  expect(particles).toEqual([
-    {
-      members: {
-        type: 0,
-        chi2: 0,
-        ndf: 0,
-        dEdx: 0,
-        dEdxError: 0,
-        radiusOfInnermostHit: 17,
-      },
-      id: 0,
-      oneToManyRelations: {
-        trackerHits: [
-          {
-            id: 0,
-            from: 0,
-            to: 0,
-            collectionID: 5,
-          },
-          {
-            id: 1,
-            from: 0,
-            to: 1,
-            collectionID: 5,
-          },
-        ],
-        tracks: [],
-      },
-    },
-    {
-      members: {
-        type: 0,
-        chi2: 0,
-        ndf: 0,
-        dEdx: 0,
-        dEdxError: 0,
-        radiusOfInnermostHit: 17,
-      },
-      id: 1,
-      oneToManyRelations: {
-        trackerHits: [
-          {
-            id: 1,
-            from: 1,
-            to: 2,
-            collectionID: 5,
-          },
-          {
-            id: 2,
-            from: 1,
-            to: 3,
-            collectionID: 5,
-          },
-        ],
-        tracks: [],
-      },
-    },
-    {
-      members: {
-        type: 0,
-        chi2: 0,
-        ndf: 0,
-        dEdx: 0,
-        dEdxError: 0,
-        radiusOfInnermostHit: 17,
-      },
-      id: 2,
-      oneToManyRelations: {
-        trackerHits: [
-          {
-            id: 2,
-            from: 2,
-            to: 4,
-            collectionID: 5,
-          },
-          {
-            id: 3,
-            from: 2,
-            to: 5,
-            collectionID: 5,
-          },
-        ],
-        tracks: [],
-      },
-    },
-  ]);
+
+  expect(objects.length).toEqual(3);
+  expect(oneToOne).toEqual({});
+  expect(trackerHits.length).toEqual(6);
+  expect(tracks.length).toEqual(0);
 });

From c37b2f388faaa4db9b30018b3e698277be4c6845 Mon Sep 17 00:00:00 2001
From: Braulio Rivas Abad <brauliorivas2004@gmail.com>
Date: Mon, 17 Jun 2024 17:35:59 -0500
Subject: [PATCH 35/35] check for correct object loading and links when reading
 a json file for test suite

---
 js/types/dynamic.js  |   2 +-
 js/types/links.js    |   1 +
 js/types/load.js     |   2 +-
 test/dynamic.test.js |   2 +-
 test/load.json       | 247 +++++++++++++++++++++++++++++++++++++++++++
 test/load.test.js    |  52 ++++++++-
 6 files changed, 302 insertions(+), 4 deletions(-)
 create mode 100644 test/load.json

diff --git a/js/types/dynamic.js b/js/types/dynamic.js
index eb722a61..fa250270 100644
--- a/js/types/dynamic.js
+++ b/js/types/dynamic.js
@@ -25,7 +25,7 @@ export function loadOneToOneRelations(
     const linkType = linkTypes[name];
     const link = new linkType(object, toObject);
 
-    oneToOne[name] = link;
+    oneToOne[name].push(link);
     object.oneToOneRelations[name] = link;
   }
 }
diff --git a/js/types/links.js b/js/types/links.js
index c95fc73c..5f2914d1 100644
--- a/js/types/links.js
+++ b/js/types/links.js
@@ -133,4 +133,5 @@ export const linkTypes = {
   "daughters": DaughterLink,
   "trackerHits": Link,
   "startVertex": Link,
+  "particles": Link,
 };
diff --git a/js/types/load.js b/js/types/load.js
index ea7340b9..1623a67d 100644
--- a/js/types/load.js
+++ b/js/types/load.js
@@ -12,7 +12,7 @@ export function loadObjectType(collection, datatype, type) {
   let oneToOne = {};
   if (datatype.oneToOneRelations)
     datatype.oneToOneRelations.forEach((relation) => {
-      oneToOne[relation.name] = null;
+      oneToOne[relation.name] = [];
       if (colors[relation.name] === undefined) {
         colors[relation.name] = generateRandomColor();
       }
diff --git a/test/dynamic.test.js b/test/dynamic.test.js
index 0fed4546..10c2d7dd 100644
--- a/test/dynamic.test.js
+++ b/test/dynamic.test.js
@@ -167,7 +167,7 @@ test("load one to one relations with some definition and data", () => {
     },
   ];
   const oneToOne = {
-    "startVertex": null,
+    "startVertex": [],
   };
   loadOneToOneRelations(object, data, oneToOneRelations, oneToOne, []);
   expect(object.oneToOneRelations).not.toBeNull();
diff --git a/test/load.json b/test/load.json
new file mode 100644
index 00000000..daa5c4c7
--- /dev/null
+++ b/test/load.json
@@ -0,0 +1,247 @@
+{
+    "Event 0": {},
+    "Event 1": {
+        "Particle": {
+            "collID": 11,
+            "collType": "edm4hep::MCParticleCollection",
+            "collection": [
+                {
+                    "PDG": 11,
+                    "charge": -1.0,
+                    "colorFlow": {
+                        "a": 0,
+                        "b": 0
+                    },
+                    "daughters": [
+                        {
+                            "collectionID": 11,
+                            "index": 2
+                        }
+                    ],
+                    "endpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "generatorStatus": 4,
+                    "mass": 0.0005109999910928309,
+                    "momentum": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 120.0
+                    },
+                    "momentumAtEndpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "parents": [],
+                    "simulatorStatus": 0,
+                    "spin": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "time": 0.0,
+                    "vertex": {
+                        "x": -0.01184066478163004,
+                        "y": -2.074451003863942e-06,
+                        "z": -0.08278788626194
+                    }
+                },
+                {
+                    "PDG": -11,
+                    "charge": 1.0,
+                    "colorFlow": {
+                        "a": 0,
+                        "b": 0
+                    },
+                    "daughters": [],
+                    "endpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "generatorStatus": 4,
+                    "mass": 0.0005109999910928309,
+                    "momentum": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": -120.0
+                    },
+                    "momentumAtEndpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "parents": [],
+                    "simulatorStatus": 0,
+                    "spin": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "time": 0.0,
+                    "vertex": {
+                        "x": -0.01184066478163004,
+                        "y": -2.074451003863942e-06,
+                        "z": -0.08278788626194
+                    }
+                },
+                {
+                    "PDG": 11,
+                    "charge": -1.0,
+                    "colorFlow": {
+                        "a": 0,
+                        "b": 0
+                    },
+                    "daughters": [],
+                    "endpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "generatorStatus": 21,
+                    "mass": 0.0,
+                    "momentum": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 120.0
+                    },
+                    "momentumAtEndpoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "parents": [
+                        {
+                            "collectionID": 11,
+                            "index": 0
+                        }
+                    ],
+                    "simulatorStatus": 0,
+                    "spin": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "time": 0.0,
+                    "vertex": {
+                        "x": -0.01184066478163004,
+                        "y": -2.074451003863942e-06,
+                        "z": -0.08278788626194
+                    }
+                }
+            ]
+        },
+        "AllMuon": {
+            "collID": 12,
+            "collType": "edm4hep::ReconstructedParticleCollection",
+            "collection": []
+        },
+        "Jet": {
+            "collID": 13,
+            "collType": "edm4hep::ReconstructedParticleCollection",
+            "collection": [
+                {
+                    "charge": 1.0,
+                    "clusters": [],
+                    "covMatrix": [
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0
+                    ],
+                    "energy": 12.062528610229492,
+                    "goodnessOfPID": 0.0,
+                    "mass": 2.315242290496826,
+                    "momentum": {
+                        "x": 11.738886833190918,
+                        "y": 1.2114704847335815,
+                        "z": 0.9354811906814575
+                    },
+                    "particleIDUsed": {
+                        "collectionID": -2,
+                        "index": -2
+                    },
+                    "particleIDs": [
+                        {
+                            "collectionID": 4,
+                            "index": 45
+                        }
+                    ],
+                    "particles": [
+                        {
+                            "collectionID": 14,
+                            "index": 1
+                        }
+                    ],
+                    "referencePoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "startVertex": {
+                        "collectionID": -2,
+                        "index": -2
+                    },
+                    "tracks": [],
+                    "type": 0
+                },
+                {
+                    "charge": 1.0,
+                    "clusters": [],
+                    "covMatrix": [
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0,
+                        0.0
+                    ],
+                    "energy": 7.181974411010742,
+                    "goodnessOfPID": 0.0,
+                    "mass": 2.346627712249756,
+                    "momentum": {
+                        "x": 1.1801066398620605,
+                        "y": -4.268080234527588,
+                        "z": -5.144407749176025
+                    },
+                    "particleIDUsed": {
+                        "collectionID": -2,
+                        "index": -2
+                    },
+                    "particleIDs": [
+                        {
+                            "collectionID": 4,
+                            "index": 46
+                        }
+                    ],
+                    "particles": [],
+                    "referencePoint": {
+                        "x": 0.0,
+                        "y": 0.0,
+                        "z": 0.0
+                    },
+                    "startVertex": {
+                        "collectionID": -2,
+                        "index": -2
+                    },
+                    "tracks": [],
+                    "type": 0
+                }
+            ]
+        }
+    },
+    "Event 2": {}
+}
\ No newline at end of file
diff --git a/test/load.test.js b/test/load.test.js
index a795c391..c9e813c4 100644
--- a/test/load.test.js
+++ b/test/load.test.js
@@ -1,6 +1,7 @@
-import { loadObjectType } from "../js/types/load.js";
+import { loadObjectType, loadObjects } from "../js/types/load.js";
 import { datatypes } from "../output/datatypes.js";
 import { objectTypes } from "../js/types/objects.js";
+import json from "./load.json" assert { type: "json" };
 
 test("load a collection of particles", () => {
   const type = "edm4hep::Track";
@@ -171,3 +172,52 @@ test("load a collection of particles", () => {
   expect(trackerHits.length).toEqual(6);
   expect(tracks.length).toEqual(0);
 });
+
+test("load a json file with a collection of objects", () => {
+  const objects = loadObjects(json, 1, [
+    "edm4hep::MCParticle",
+    "edm4hep::ReconstructedParticle",
+  ]);
+
+  expect(objects["edm4hep::MCParticle"]).toBeDefined();
+  expect(objects["edm4hep::ReconstructedParticle"]).toBeDefined();
+
+  expect(objects["edm4hep::MCParticle"].collection.length).toEqual(3);
+  expect(
+    objects["edm4hep::MCParticle"].collection.map((val) => val.id)
+  ).toEqual([0, 1, 2]);
+  expect(objects["edm4hep::MCParticle"].oneToMany["daughters"]).toBeDefined();
+  expect(objects["edm4hep::MCParticle"].oneToMany["parents"]).toBeDefined();
+  expect(
+    objects["edm4hep::MCParticle"].oneToMany["daughters"][0].from.id
+  ).toEqual(0);
+  expect(
+    objects["edm4hep::MCParticle"].oneToMany["daughters"][0].to.id
+  ).toEqual(2);
+
+  expect(objects["edm4hep::ReconstructedParticle"].collection.length).toEqual(
+    2
+  );
+  expect(
+    objects["edm4hep::ReconstructedParticle"].collection.map((val) => val.id)
+  ).toEqual([0, 1]);
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToMany["particles"]
+  ).toBeDefined();
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToOne["startVertex"]
+  ).toBeDefined();
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToMany["particles"][0].from.id
+  ).toEqual(0);
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToMany["particles"][0].to.id
+  ).toEqual(1);
+
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToOne["startVertex"][0].to
+  ).toBeUndefined();
+  expect(
+    objects["edm4hep::ReconstructedParticle"].oneToOne["startVertex"][1].to
+  ).toBeUndefined();
+});