Merge pull request #123 from MaxRobinsonTheGreat/develop

Develop

Changelog.md

@@ -1,18 +1,20 @@
 # Changelog
 
-## 1.0.3 (current dev)
+## 1.0.3 (4/15/2022)
 
 ### UI Enhancements:
-- Improved input box styling
+- Improved styling
 
 ### Simulation Enhancements:
-- 
+- Added ability to save/load organisms
+- Added ability to save/load worlds
 
 ### Bug Fixes:
 - charste changed to charset
+- Fixed species tracking
 
 
-Thanks to contributors: 
+Thanks to contributors: @TerraMaster85
 
 ## 1.0.2 (12/21/2021)
 

dist/index.html

@@ -6,7 +6,6 @@
 		<link rel="icon" href="./img/icon.png">
 		<link rel="stylesheet" href="./css/style.css">
 		<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
-		<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
 		<script type="text/javascript" src="https://canvasjs.com/assets/script/canvasjs.min.js"></script>
 
 	</head>
@@ -21,7 +20,7 @@
 				<div class='vertical-buttons'>
 					<button class="reset-view" title="Reset View. Hotkey: A"><i class="fa fa-video-camera"></i></button>
 					<button class="edit-mode-btn drag-view" id="drag-view" title="Drag View. Hotkey: S"><i class="fa fa-arrows"></i></button>
-					<button class="edit-mode-btn wall-drop" id="wall-drop" title="Drop/Remove Wall. Hotkey: D"><i class="fa fa-square"></i></button>
+					<button class="edit-mode-btn wall-drop" id="wall-drop" title="Drop/Remove Wall. Hotkey: D"><i class="fa fa-th"></i></button>
 					<button class="edit-mode-btn food-drop selected" id="food-drop" title="Drop/Remove Food. Hotkey: F"><i class="fa fa-cutlery"></i></button>
 					<button class="edit-mode-btn click-kill" id="click-kill" title="Click to kill. Hotkey: G"><i class="fa fa-bolt"></i></button>
 				</div>
@@ -78,6 +77,9 @@
 							<button class="edit-mode-btn select" id="select" title="Select organism from world. Hotkey: Z"><i class="fa fa-hand-pointer-o"></i></button>
 							<button class="edit-mode-btn edit" id="edit" title="Edit organism. Hotkey: X"><i class="fa fa-pencil"></i></button>
 							<button class="edit-mode-btn drop-org" id="drop-org" title="Drop organism in world. Hotkey: C"><i class="fa fa-plus"></i></button>
+							<button id="save-org" title="Save Organism"><i class="fa fa-save"></i></button>
+							<button id="load-org" title="Load Organism"><i class="fa fa-upload"></i></button>
+							<input id="upload-org" style="display: none;" type="file">
 						</div>
 						<div id='editor-env'>
 							<canvas id='editor-canvas'></canvas>
@@ -187,6 +189,15 @@
 						<br>
 						<label for="clear-walls-reset" title='When on, walls will be cleared when the environment resets'>Clear walls on reset</label>
 						<input type="checkbox" id="clear-walls-reset">
+						<br>
+						<button id='save-env' title="Download save file for entire world">Save World</button>
+						<label for="save-env-name" title='Save World as:'>Save As:</label>
+						<input type="text" id="save-env-name" value="world" style="text-align: center;">.json
+						<br>
+						<button id='load-env' title="Load world save file">Load World</button>
+						<label for="override-controls" title='Override the current evolution controls with those from the loaded world'>Override Evolution Controls</label>
+						<input type="checkbox" id="override-controls" checked>
+						<input id="upload-env" style="display: none;" type="file">
 					</div>
 				</div>
 				<div id='hyperparameters' class='tab'>
@@ -238,7 +249,7 @@
 						<button id='save-controls' title="Save all Evolution Controls in a .json file">Save & Download</button>
 						<button id='load-controls' title="Load saved Evolution Controls with a .json file">Load</button>
 						<a id="download-el" style="display: none;"></a>
-						<input id="upload-el" style="display: none;" type="file">
+						<input id="upload-hyperparams" style="display: none;" type="file">
 					</div>
 				</div>
 				<div id='stats' class='tab'>
@@ -268,7 +279,7 @@
 		<div class='hot-controls'>
 			<button class="reset-view" title="Reset View. Hotkey: A"><i class="fa fa-video-camera"></i></button>
 			<button class="edit-mode-btn drag-view" id="drag-view" title="Drag View. Hotkey: S"><i class="fa fa-arrows"></i></button>
-			<button class="edit-mode-btn wall-drop" id="wall-drop" title="Drop/Remove Wall. Hotkey: D"><i class="fa fa-square"></i></button>
+			<button class="edit-mode-btn wall-drop" id="wall-drop" title="Drop/Remove Wall. Hotkey: D"><i class="fa fa-th"></i></button>
 			<button class="edit-mode-btn food-drop selected" id="food-drop" title="Drop/Remove Food. Hotkey: F"><i class="fa fa-cutlery"></i></button>
 			<button class="edit-mode-btn click-kill" id="click-kill" title="Click to kill. Hotkey: G"><i class="fa fa-bolt"></i></button>
 			<button class="headless" title="Toggle rendering. Hotkey: H"><i class="fa fa-eye-slash"></i></button>

package-lock.json

@@ -198,9 +198,9 @@
       "dev": true
     },
     "ajv": {
-      "version": "6.12.2",
+      "version": "6.12.6",
-      "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.2.tgz",
+      "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz",
-      "integrity": "sha512-k+V+hzjm5q/Mr8ef/1Y9goCmlsK4I6Sm74teeyGvFk1XrOsbsKLjEdrvny42CZ+a8sXbk8KWpY/bDwS+FLL2UQ==",
+      "integrity": "sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==",
       "dev": true,
       "requires": {
         "fast-deep-equal": "^3.1.1",
@@ -2048,9 +2048,9 @@
       }
     },
     "minimist": {
-      "version": "1.2.5",
+      "version": "1.2.6",
-      "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.5.tgz",
+      "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.6.tgz",
-      "integrity": "sha512-FM9nNUYrRBAELZQT3xeZQ7fmMOBg6nWNmJKTcgsJeaLstP/UODVpGsr5OhXhhXg6f+qtJ8uiZ+PUxkDWcgIXLw==",
+      "integrity": "sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q==",
       "dev": true
     },
     "mississippi": {

src/Controllers/ControlPanel.js

@@ -1,7 +1,6 @@
 const Hyperparams = require("../Hyperparameters");
 const Modes = require("./ControlModes");
 const StatsPanel = require("../Stats/StatsPanel");
-const RandomOrganismGenerator = require("../Organism/RandomOrganismGenerator")
 const WorldConfig = require("../WorldConfig");
 
 class ControlPanel {
@@ -48,6 +47,8 @@ class ControlPanel {
 
     defineHotkeys() {
         $('body').keydown( (e) => {
+            let focused = document.activeElement;
+            if (focused.tagName === "INPUT" && focused.type === "text") return;
             switch (e.key.toLowerCase()) {
                 // hot bar controls
                 case 'a':
@@ -206,6 +207,43 @@ class ControlPanel {
             this.env_controller.add_new_species = true;
             this.env_controller.dropOrganism(org, center[0], center[1])
         });
+        $('#save-env').click( () => {
+            let was_running = this.engine.running;
+            this.setPaused(true);
+            let env = this.engine.env.serialize();
+            let data = "data:text/json;charset=utf-8," + encodeURIComponent(JSON.stringify(env));
+            let downloadEl = document.getElementById('download-el');
+            downloadEl.setAttribute("href", data);
+            downloadEl.setAttribute("download", $('#save-env-name').val()+".json");
+            downloadEl.click();
+            if (was_running)
+                this.setPaused(false);
+        });
+        $('#load-env').click(() => {
+            $('#upload-env').click();
+        });
+        $('#upload-env').change((e)=>{
+            let files = e.target.files;
+            if (!files.length) {return;};
+            let reader = new FileReader();
+            reader.onload = (e) => {
+                try {
+                    let was_running = this.engine.running;
+                    this.setPaused(true);
+                    let env = JSON.parse(e.target.result);
+                    this.engine.env.loadRaw(env);
+                    if (was_running)
+                        this.setPaused(false);
+                    this.updateHyperparamUIValues();
+                    this.env_controller.resetView();
+                } catch(except) {
+                    console.error(except)
+                    alert('Failed to load world');
+                }
+                $('#upload-env')[0].value = '';
+            };
+            reader.readAsText(files[0]);
+        });
     }
 
     defineHyperparameterControls() {
@@ -279,9 +317,9 @@ class ControlPanel {
             downloadEl.click();
         });
         $('#load-controls').click(() => {
-            $('#upload-el').click();
+            $('#upload-hyperparams').click();
         });
-        $('#upload-el').change((e)=>{
+        $('#upload-hyperparams').change((e)=>{
             let files = e.target.files;
             if (!files.length) {return;};
             let reader = new FileReader();
@@ -290,7 +328,7 @@ class ControlPanel {
                 Hyperparams.loadJsonObj(result);
                 this.updateHyperparamUIValues();
                 // have to clear the value so change() will be triggered if the same file is uploaded again
-                $('#upload-el')[0].value = '';
+                $('#upload-hyperparams')[0].value = '';
             };
             reader.readAsText(files[0]);
         });
@@ -428,7 +466,6 @@ class ControlPanel {
             this.env_controller.org_to_clone = this.engine.organism_editor.getCopyOfOrg();
             this.env_controller.add_new_species = this.editor_controller.new_species;
             this.editor_controller.new_species = false;
-            // console.log(this.env_controller.add_new_species)
         }
     }
 

src/Controllers/EditorController.js

@@ -13,6 +13,7 @@ class EditorController extends CanvasController{
         this.new_species = false;
         this.defineCellTypeSelection();
         this.defineEditorDetails();
+        this.defineSaveLoad();
     }
 
     mouseMove() {
@@ -109,6 +110,43 @@ class EditorController extends CanvasController{
         }.bind(this));
     }
 
+    defineSaveLoad() {
+        $('#save-org').click(()=>{
+            let org = this.env.organism.serialize();
+            let data = "data:text/json;charset=utf-8," + encodeURIComponent(JSON.stringify(org));
+            let downloadEl = document.getElementById('download-el');
+            downloadEl.setAttribute("href", data);
+            downloadEl.setAttribute("download", "organism.json");
+            downloadEl.click();
+        });
+        $('#load-org').click(() => {
+            $('#upload-org').click();
+        });
+        $('#upload-org').change((e)=>{
+            let files = e.target.files;
+            if (!files.length) {return;};
+            let reader = new FileReader();
+            reader.onload = (e) => {
+                try {
+                    let org=JSON.parse(e.target.result);
+                    this.env.clear();
+                    this.env.organism.loadRaw(org);
+                    this.refreshDetailsPanel();
+                    this.env.organism.updateGrid();
+                    this.env.renderFull();
+                    if (this.mode === Modes.Clone)
+                        $('#drop-org').click();
+                    // have to clear the value so change() will be triggered if the same file is uploaded again
+                    $('#upload-org')[0].value = '';
+                } catch(except) {
+                    console.error(except)
+                    alert('Failed to load organism');
+                }
+            };
+            reader.readAsText(files[0]);
+        });
+    }
+
     clearDetailsPanel() {
         $('#organism-details').css('display', 'none');
         $('#edit-organism-details').css('display', 'none');

src/Environments/WorldEnvironment.js

@@ -7,6 +7,8 @@ const EnvironmentController = require('../Controllers/EnvironmentController');
 const Hyperparams = require('../Hyperparameters.js');
 const FossilRecord = require('../Stats/FossilRecord');
 const WorldConfig = require('../WorldConfig');
+const SerializeHelper = require('../Utils/SerializeHelper');
+const Species = require('../Stats/Species');
 
 class WorldEnvironment extends Environment{
     constructor(cell_size) {
@@ -164,6 +166,57 @@ class WorldEnvironment extends Environment{
         this.num_rows = Math.ceil(this.renderer.height / cell_size);
         this.grid_map.resize(this.num_cols, this.num_rows, cell_size);
     }
+
+    serialize() {
+        let env = SerializeHelper.copyNonObjects(this);
+        env.grid = this.grid_map.serialize();
+        env.organisms = [];
+        for (let org of this.organisms){
+            env.organisms.push(org.serialize());
+        }
+        env.fossil_record = FossilRecord.serialize();
+        env.controls = Hyperparams;
+        return env;
+    }
+
+    loadRaw(env) { // species name->stats map, evolution controls, 
+        this.organisms = [];
+        FossilRecord.clear_record();
+        this.resizeGridColRow(this.grid_map.cell_size, env.grid.cols, env.grid.rows)
+        this.grid_map.loadRaw(env.grid);
+
+        // create species map
+        let species = {};
+        for (let name in env.fossil_record.species) {
+            let s = new Species(null, null, 0);
+            SerializeHelper.overwriteNonObjects(env.fossil_record.species[name], s)
+            species[name] = s; // the species needs an anatomy obj still
+        }
+
+        for (let orgRaw of env.organisms) {
+            let org = new Organism(orgRaw.col, orgRaw.row, this);
+            org.loadRaw(orgRaw);
+            this.addOrganism(org);
+            let s = species[orgRaw.species_name];
+            if (!s){ // ideally, every organisms species should exists, but there is a bug somewhere
+                s = new Species(org.anatomy, null, env.total_ticks);
+                species[orgRaw.species_name] = s;
+            }
+            if (!s.anatomy) {
+                //if the species doesn't have anatomy we need to initialize it
+                s.anatomy = org.anatomy;
+                s.calcAnatomyDetails();
+            }
+            org.species = s;
+        }
+        for (let name in species)
+            FossilRecord.addSpeciesObj(species[name]);
+        FossilRecord.loadRaw(env.fossil_record);
+        SerializeHelper.overwriteNonObjects(env, this);
+        if ($('#override-controls').is(':checked'))
+            Hyperparams.loadJsonObj(env.controls)
+        this.renderer.renderFullGrid(this.grid_map.grid);
+    }
 }
 
 module.exports = WorldEnvironment;

src/Grid/GridMap.js

@@ -78,6 +78,34 @@ class GridMap {
             r = 0;
         return [c, r];
     }
+
+    serialize() {
+        // Rather than store every single cell, we will store non organism cells (food+walls)
+        // and assume everything else is empty. Organism cells will be set when the organism
+        // list is loaded. This reduces filesize and complexity.
+        let grid = {cols:this.cols, rows:this.rows};
+        grid.food = [];
+        grid.walls = [];
+        for (let col of this.grid) {
+            for (let cell of col) {
+                if (cell.state===CellStates.wall || cell.state===CellStates.food){
+                    let c = {c: cell.col, r: cell.row}; // no need to store state
+                    if (cell.state===CellStates.food)
+                        grid.food.push(c)
+                    else
+                        grid.walls.push(c)
+                }
+            }
+        }
+        return grid;
+    }
+
+    loadRaw(grid) {
+        for (let f of grid.food)
+            this.setCellType(f.c, f.r, CellStates.food);
+        for (let w of grid.walls)
+            this.setCellType(w.c, w.r, CellStates.wall);
+    }
 }
 
 module.exports = GridMap;

src/Organism/Anatomy.js

@@ -1,14 +1,19 @@
 const CellStates = require("./Cell/CellStates");
 const BodyCellFactory = require("./Cell/BodyCells/BodyCellFactory");
+const SerializeHelper = require("../Utils/SerializeHelper");
 
 class Anatomy {
     constructor(owner) {
         this.owner = owner;
+        this.birth_distance = 4;
+        this.clear();
+    }
+
+    clear() {
         this.cells = [];
         this.is_producer = false;
         this.is_mover = false;
         this.has_eyes = false;
-        this.birth_distance = 4;
     }
 
     canAddCellAt(c, r) {
@@ -61,7 +66,7 @@ class Anatomy {
                 break;
             }
         }
-        this.checkTypeChange(cell.state);
+        this.checkTypeChange();
         return true;
     }
 
@@ -93,9 +98,7 @@ class Anatomy {
     }
 
     getNeighborsOfCell(col, row) {
-
         var neighbors = [];
-
         for (var x = -1; x <= 1; x++) {
             for (var y = -1; y <= 1; y++) {
 
@@ -107,6 +110,37 @@ class Anatomy {
 
         return neighbors;
     }
+
+    isEqual(anatomy) { // currently unused helper func. inefficient, avoid usage in prod.
+        if (this.cells.length !== anatomy.cells.length) return false;
+        for (let i in this.cells) {
+            let my_cell = this.cells[i];
+            let their_cell = anatomy.cells[i];
+            if (my_cell.loc_col !== their_cell.loc_col ||
+                my_cell.loc_row !== their_cell.loc_row ||
+                my_cell.state !== their_cell.state)
+                return false;
+        }
+        return true;
+    }
+
+    serialize() {
+        let anatomy = SerializeHelper.copyNonObjects(this);
+        anatomy.cells = [];
+        for (let cell of this.cells) {
+            let newcell = SerializeHelper.copyNonObjects(cell);
+            newcell.state = {name: cell.state.name};
+            anatomy.cells.push(newcell)
+        }
+        return anatomy;
+    }
+
+    loadRaw(anatomy) {
+        this.clear();
+        for (let cell of anatomy.cells){
+            this.addInheritCell(cell);
+        }
+    }
 }
 
 module.exports = Anatomy;

src/Organism/Cell/BodyCells/KillerCell.js

@@ -18,7 +18,6 @@ class KillerCell extends BodyCell{
     }
 
     killNeighbor(n_cell) {
-        // console.log(n_cell)
         if(n_cell == null || n_cell.owner == null || n_cell.owner == this.org || !n_cell.owner.living || n_cell.state == CellStates.armor) 
             return;
         var is_hit = n_cell.state == CellStates.killer; // has to be calculated before death

src/Organism/Organism.js

@@ -5,6 +5,7 @@ const Directions = require("./Directions");
 const Anatomy = require("./Anatomy");
 const Brain = require("./Perception/Brain");
 const FossilRecord = require("../Stats/FossilRecord");
+const SerializeHelper = require("../Utils/SerializeHelper");
 
 class Organism {
     constructor(col, row, env, parent=null) {
@@ -33,15 +34,12 @@ class Organism {
         this.move_range = parent.move_range;
         this.mutability = parent.mutability;
         this.species = parent.species;
-        // this.birth_distance = parent.birth_distance;
         for (var c of parent.anatomy.cells){
             //deep copy parent cells
             this.anatomy.addInheritCell(c);
         }
-        if(parent.anatomy.is_mover) {
+        if(parent.anatomy.is_mover && parent.anatomy.has_eyes) {
-            for (var i in parent.brain.decisions) {
+            this.brain.copy(parent.brain);
-                this.brain.decisions[i] = parent.brain.decisions[i];
-            }
         }
     }
 
@@ -104,7 +102,6 @@ class Organism {
         var new_c = this.c + (direction_c*basemovement) + (direction_c*offset);
         var new_r = this.r + (direction_r*basemovement) + (direction_r*offset);
 
-        // console.log(org.isClear(new_c, new_r, org.rotation, true))
         if (org.isClear(new_c, new_r, org.rotation, true) && org.isStraightPath(new_c, new_r, this.c, this.r, this)){
             org.c = new_c;
             org.r = new_r;
@@ -118,11 +115,12 @@ class Organism {
             }
         }
         Math.max(this.food_collected -= this.foodNeeded(), 0);
-
     }
 
     mutate() {
-        let mutated = false;
+        let added = false;
+        let changed = false;
+        let removed = false;
         if (this.calcRandomChance(Hyperparams.addProb)) {
             let branch = this.anatomy.getRandomCell();
             let state = CellStates.getRandomLivingType();//branch.state;
@@ -130,7 +128,7 @@ class Organism {
             let c = branch.loc_col+growth_direction[0];
             let r = branch.loc_row+growth_direction[1];
             if (this.anatomy.canAddCellAt(c, r)){
-                mutated = true;
+                added = true;
                 this.anatomy.addRandomizedCell(state, c, r);
             }
         }
@@ -138,15 +136,15 @@ class Organism {
             let cell = this.anatomy.getRandomCell();
             let state = CellStates.getRandomLivingType();
             this.anatomy.replaceCell(state, cell.loc_col, cell.loc_row);
-            mutated = true;
+            changed = true;
         }
         if (this.calcRandomChance(Hyperparams.removeProb)){
             if(this.anatomy.cells.length > 1) {
                 let cell = this.anatomy.getRandomCell();
-                mutated = this.anatomy.removeCell(cell.loc_col, cell.loc_row);
+                removed = this.anatomy.removeCell(cell.loc_col, cell.loc_row);
             }
         }
-        return mutated;
+        return added || changed || removed;
     }
 
     calcRandomChance(prob) {
@@ -319,6 +317,22 @@ class Organism {
         return this.env.grid_map.cellAt(real_c, real_r);
     }
 
+    serialize() {
+        let org = SerializeHelper.copyNonObjects(this);
+        org.anatomy = this.anatomy.serialize();
+        if (this.anatomy.is_mover && this.anatomy.has_eyes)
+            org.brain = this.brain.serialize();
+        org.species_name = this.species.name;
+        return org;
+    }
+
+    loadRaw(org) {
+        SerializeHelper.overwriteNonObjects(org, this);
+        this.anatomy.loadRaw(org.anatomy)
+        if (org.brain)
+            this.brain.copy(org.brain)
+    }
+
 }
 
 module.exports = Organism;

src/Organism/Perception/Brain.js

@@ -20,16 +20,18 @@ class Brain {
         this.observations = [];
 
         // corresponds to CellTypes
-        this.decisions = [];
+        this.decisions = {};
-        this.decisions[CellStates.empty.name] = Decision.neutral;
+        for (let cell of CellStates.all) {
+            this.decisions[cell.name] = Decision.neutral;
+        }
         this.decisions[CellStates.food.name] = Decision.chase;
-        this.decisions[CellStates.wall.name] = Decision.neutral;
-        this.decisions[CellStates.mouth.name] = Decision.neutral;
-        this.decisions[CellStates.producer.name] = Decision.neutral;
-        this.decisions[CellStates.mover.name] = Decision.neutral;
         this.decisions[CellStates.killer.name] = Decision.retreat;
-        this.decisions[CellStates.armor.name] = Decision.neutral;
+    }
-        this.decisions[CellStates.eye.name] = Decision.neutral;
+
+    copy(brain) {
+        for (let dec in brain.decisions) {
+            this.decisions[dec] = brain.decisions[dec];
+        }
     }
 
     randomizeDecisions(randomize_all=false) {
@@ -58,9 +60,7 @@ class Brain {
                 continue;
             }
             if (obs.distance < closest) {
-                // console.log(obs.cell.state)
                 decision = this.decisions[obs.cell.state.name];
-                // console.log(decision)
                 move_direction = obs.direction;
                 closest = obs.distance;
             }
@@ -81,6 +81,10 @@ class Brain {
         this.decisions[CellStates.getRandomName()] = Decision.getRandom();
         this.decisions[CellStates.empty.name] = Decision.neutral; // if the empty cell has a decision it gets weird
     }
+    
+    serialize() {
+        return {decisions: this.decisions};
+    }
 }
 
 Brain.Decision = Decision;

src/Stats/FossilRecord.js

@@ -1,4 +1,5 @@
 const CellStates = require("../Organism/Cell/CellStates");
+const SerializeHelper = require("../Utils/SerializeHelper");
 const Species = require("./Species");
 
 const FossilRecord = {
@@ -18,7 +19,6 @@ const FossilRecord = {
     },
 
     addSpecies: function(org, ancestor) {
-        // console.log("Adding Species")
         var new_species = new Species(org.anatomy, ancestor, this.env.total_ticks);
         this.extant_species.push(new_species);
         org.species = new_species;
@@ -26,33 +26,30 @@ const FossilRecord = {
     },
 
     addSpeciesObj: function(species) {
-        // console.log("Adding Species")
         this.extant_species.push(species);
         return species;
     },
 
     fossilize: function(species) {
-        // console.log("Extinction")
         species.end_tick = this.env.total_ticks;
         for (i in this.extant_species) {
             var s = this.extant_species[i];
             if (s == species) {
                 this.extant_species.splice(i, 1);
+                species.ancestor = undefined; // garbage collect dead species
+                // if (species.ancestor)
+                //     species.ancestor.ancestor = undefined;
                 if (species.cumulative_pop < this.min_pop) {
                     return false;
                 }
                 // disabled for now, causes memory problems on long runs
                 // this.extinct_species.push(s);
-                
-                // console.log("Extant species:", this.extant_species.length)
-                // console.log("Extinct species:", this.extinct_species.length)
                 return true;
             }
         }
     },
 
     resurrect: function(species) {
-        // console.log("Resurrecting species")
         if (species.extinct) {
             for (i in this.extinct_species) {
                 var s = this.extinct_species[i];
@@ -67,12 +64,13 @@ const FossilRecord = {
 
     setData() {
         // all parallel arrays
-        this.tick_record = [0];
+        this.tick_record = [];
-        this.pop_counts = [0];
+        this.pop_counts = [];
-        this.species_counts = [0];
+        this.species_counts = [];
-        this.av_mut_rates = [0];
+        this.av_mut_rates = [];
-        this.av_cells = [0];
+        this.av_cells = [];
-        this.av_cell_counts = [this.calcCellCountAverages()];
+        this.av_cell_counts = [];
+        this.updateData();
     },
 
     updateData() {
@@ -121,12 +119,39 @@ const FossilRecord = {
         this.av_cell_counts.push(cell_counts);
     },
 
-    clear_record: function() {
+    clear_record() {
         this.extant_species = [];
         this.extinct_species = [];
         this.setData();
     },
 
+    serialize() {
+        this.updateData();
+        let record = SerializeHelper.copyNonObjects(this);
+        record.records = {
+            tick_record:this.tick_record,
+            pop_counts:this.pop_counts,
+            species_counts:this.species_counts,
+            av_mut_rates:this.av_mut_rates,
+            av_cells:this.av_cells,
+            av_cell_counts:this.av_cell_counts,
+        };
+        let species = {};
+        for (let s of this.extant_species) {
+            species[s.name] = SerializeHelper.copyNonObjects(s);
+            delete species[s.name].name; // the name will be used as the key, so remove it from the value
+        }
+        record.species = species;
+        return record;
+    },
+
+    loadRaw(record) {
+        SerializeHelper.overwriteNonObjects(record, this);
+        for (let key in record.records) {
+            this[key] = record.records[key];
+        }
+    }
+
 }
 
 FossilRecord.init();

src/Stats/Species.js

@@ -1,19 +1,26 @@
 const CellStates = require("../Organism/Cell/CellStates");
+let FossilRecord = undefined; // workaround to a circular dependency problem
+const getFossilRecord = () => {
+    if (!FossilRecord)
+        FossilRecord = require("./FossilRecord");
+    return FossilRecord;
+}
 
 class Species {
     constructor(anatomy, ancestor, start_tick) {
         this.anatomy = anatomy;
-        // this.ancestor = ancestor; // garbage collect ancestors to avoid memory problems
+        this.ancestor = ancestor; // eventually need to garbage collect ancestors to avoid memory problems
         this.population = 1;
         this.cumulative_pop = 1;
         this.start_tick = start_tick;
         this.end_tick = -1;
-        this.name = '_' + Math.random().toString(36).substr(2, 9);
+        this.name = Math.random().toString(36).substr(2, 10);
         this.extinct = false;
         this.calcAnatomyDetails();
     }
 
     calcAnatomyDetails() {
+        if (!this.anatomy) return;
         var cell_counts = {};
         for (let c of CellStates.living) {
             cell_counts[c.name] = 0;
@@ -33,8 +40,7 @@ class Species {
         this.population--;
         if (this.population <= 0) {
             this.extinct = true;
-            const FossilRecord = require("./FossilRecord");
+            getFossilRecord().fossilize(this);
-            FossilRecord.fossilize(this);
         }
     }
 

src/Utils/SerializeHelper.js

@@ -0,0 +1,20 @@
+const SerializeHelper = {
+    copyNonObjects(obj) {
+        let newobj = {};
+        for (let key in obj) {
+            if (typeof obj[key] !== 'object')
+                newobj[key] = obj[key];
+        }
+        return newobj;
+    },
+    overwriteNonObjects(copyFrom, copyTo) {
+        for (let key in copyFrom) {
+            if (typeof copyFrom[key] !== 'object' && typeof copyTo[key] !== 'object') {
+                // only overwrite if neither are objects
+                copyTo[key] = copyFrom[key];
+            }
+        }
+    }
+}
+
+module.exports = SerializeHelper;

webpack.config.js

@@ -1,4 +1,5 @@
 const path = require('path');
+const webpack = require("webpack");
 
 module.exports = {
     entry: './src/index.js',
@@ -6,7 +7,9 @@ module.exports = {
         filename: 'bundle.js',
         path: path.resolve(__dirname, 'dist/js/'),
     },
-    externals: {
+    plugins: [
-        jquery: 'jQuery'
+        new webpack.ProvidePlugin({
-    }
+            $: "jquery",
+        })
+    ]
 };