fixed docs problem

ingewortel · May 1, 2020 · a675115 · a675115
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diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,5 @@
 examples-dev
 examples-old
-docs
 *.swp
 build.make
 node_modules

diff --git a/docs/.esdoc.json b/docs/.esdoc.json
@@ -0,0 +1,28 @@
+{
+  "source": "./src",
+  "destination": "./docs",
+  "plugins": [
+    {
+      "name": "esdoc-standard-plugin",
+      "option": {
+        "test" : {
+          "source" : "./spec/",
+          "interfaces": ["describe", "it", "context", "suite", "test"],
+          "includes": ["(spec|Spec|test|Test)\\.js$"],
+          "excludes": ["\\.config\\.js$"]
+        },
+        "manual": {
+          "index": "./manual/index.md",
+          "asset": "./manual/asset",
+          "files": [
+            "./manual/installation.md",
+            "./manual/quickstart.md",
+	    "./manual/htmlTemplate.md"
+          ]
+        },
+        "brand": {
+          "repository": "https://github.com/ingewortel/cpmjs"
+        }
+      }
+    }]
+}
diff --git a/docs/.eslintrc.js b/docs/.eslintrc.js
@@ -0,0 +1,31 @@
+module.exports = {
+    "env": {
+        "browser": true,
+        "es6": true,
+        "node": true,
+        "jasmine" : true
+    },
+    "extends": "eslint:recommended",
+    "parserOptions": {
+        "ecmaVersion": 2015,
+        "sourceType": "module"
+    },
+    "rules": {
+        "indent": [
+            "error",
+            "tab"
+        ],
+        "linebreak-style": [
+            "error",
+            "unix"
+        ],
+        "quotes": [
+            "error",
+            "double"
+        ],
+        "semi": [
+            "error",
+            "never"
+        ]
+    }
+};
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1,4 @@
+log.txt
+*.swp
+build.make
+node_modules
diff --git a/docs/examples/NoTorusDemo.html b/docs/examples/NoTorusDemo.html
@@ -0,0 +1,191 @@
+<!DOCTYPE html>
+<html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>NoTorusDemo</title>
+<style type="text/css">
+body{
+		font-family: "HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue",
+		 Helvetica, Arial, "Lucida Grande", sans-serif;
+	 padding : 15px;
+}
+td {
+	 padding: 10px;
+	 vertical-align: top;
+}
+</style>
+
+
+<script src="./artistoo.js"></script>
+<script src="./fpsmeter.min.js"></script>
+<script>
+"use strict"
+
+
+/*	----------------------------------
+	CONFIGURATION SETTINGS
+	----------------------------------
+*/
+let config = {
+
+	// Grid settings
+	ndim : 2,
+	field_size : [500, 13],
+
+	// CPM parameters and configuration
+	conf : {
+		// Basic CPM parameters
+		torus : [false,false],				// Should the grid have linked borders?
+		seed : 1,							// Seed for random number generation.
+		T : 20,								// CPM temperature
+
+		// Constraint parameters. 
+		// Mostly these have the format of an array in which each element specifies the
+		// parameter value for one of the cellkinds on the grid.
+		// First value is always cellkind 0 (the background) and is often not used.
+
+
+		// Adhesion parameters:
+		J : [ [NaN,20,0], [20,100,200], [0,200,0] ],
+
+		// VolumeConstraint parameters
+		LAMBDA_V : [0,5,NaN],				// VolumeConstraint importance per cellkind
+		V : [0,500,NaN],					// Target volume of each cellkind
+
+		// PerimeterConstraint parameters
+		LAMBDA_P : [0,2,NaN],				// PerimeterConstraint importance per cellkind
+		P : [0,360,NaN],					// Target perimeter of each cellkind
+
+		// BarrierConstraint parameters
+		IS_BARRIER : [false, false, true ],
+
+		// ActivityConstraint parameters
+		LAMBDA_ACT : [0,700,NaN],			// ActivityConstraint importance per cellkind
+		MAX_ACT : [0,50,NaN],				// Activity memory duration per cellkind
+		ACT_MEAN : "geometric"				// Is neighborhood activity computed as a
+											// "geometric" or "arithmetic" mean?
+
+	},
+
+	// Simulation setup and configuration: this controls stuff like grid initialization,
+	// runtime, and what the output should look like.
+	simsettings : {
+
+		// Cells on the grid
+		NRCELLS : [3,0],					// Number of cells to seed for all
+											// non-background cellkinds.
+		// Runtime etc
+		BURNIN : 500,
+		RUNTIME : 1000,
+		RUNTIME_BROWSER : "Inf",
+
+		// Visualization
+		CANVASCOLOR : "eaecef",
+		CELLCOLOR : ["000000","AAAAAA"],
+		ACTCOLOR : [true,false],			// Should pixel activity values be displayed?
+		SHOWBORDERS : [false,false],				// Should cellborders be displayed?
+		zoom : 2,							// zoom in on canvas with this factor.
+
+		// Output images
+		SAVEIMG : true,						// Should a png image of the grid be saved
+											// during the simulation?
+		IMGFRAMERATE : 1,					// If so, do this every <IMGFRAMERATE> MCS.
+		SAVEPATH : "output/img/NoTorusDemo",	// ... And save the image in this folder.
+		EXPNAME : "NoTorusDemo",					// Used for the filename of output images.
+
+		// Output stats etc
+		STATSOUT : { browser: false, node: true }, // Should stats be computed?
+		LOGRATE : 10							// Output stats every <LOGRATE> MCS.
+
+	}
+}
+/*	---------------------------------- */
+let sim, meter
+
+
+function initialize(){
+	 /* 	The following functions are defined below and will be added to
+	 	the simulation object. If Custom-methods above is set to false,
+	 	this object is ignored and not used in the html/node files. */
+	 let custommethods = {
+	 	initializeGrid : initializeGrid,
+	 	buildBorder : buildBorder
+	 }
+	sim = new CPM.Simulation( config, custommethods )
+
+
+
+	meter = new FPSMeter({left:"auto", right:"5px"})
+	step()
+}
+
+
+function step(){
+	sim.step()
+	meter.tick()
+	if( sim.conf["RUNTIME_BROWSER"] == "Inf" | sim.time+1 < sim.conf["RUNTIME_BROWSER"] ){
+		requestAnimationFrame( step )
+	}
+}
+
+
+
+/* The following custom methods will be added to the simulation object*/
+function initializeGrid(){
+
+		// add the initializer if not already there
+		if( !this.helpClasses["gm"] ){ this.addGridManipulator() }
+
+		let nrcells = this.conf["NRCELLS"], cellkind, i
+		this.buildBorder()
+
+		// Seed the right number of cells for each cellkind
+		for( cellkind = 0; cellkind < nrcells.length; cellkind ++ ){
+
+			for( i = 0; i < nrcells[cellkind]; i++ ){
+				// first cell always at the midpoint. Any other cells
+				// randomly.				
+				if( i == 0 ){
+					this.gm.seedCellAt( cellkind+1, this.C.midpoint )
+				} else {
+					this.gm.seedCell( cellkind+1 )
+				}
+			}
+		}
+}
+
+function buildBorder(){
+
+		let bordervoxels
+
+		bordervoxels = this.gm.makePlane( [], 0, 0 )
+		bordervoxels = this.gm.makePlane( bordervoxels, 0, this.C.extents[0]-1)
+		bordervoxels = this.gm.makePlane( bordervoxels, 1, 0 )
+		bordervoxels = this.gm.makePlane( bordervoxels, 1, this.C.extents[1]-1)
+
+		this.gm.changeKind( bordervoxels, 2)
+
+}
+
+</script>
+</head>
+<body onload="initialize()">
+<h1>NoTorusDemo</h1>
+<p>
+The torus property of the Grid class allows you to choose if the grid boundaries are
+linked, but setting them to false may give artifacts if not done properly. Cells will
+stick to the border because at the border, they have fewer neighbors to get adhesion and/or
+perimeter constraint penalties from. To avoid this, it is best to add a border of 
+barrier pixels to the edges of the grid. This forbids cells from copying in to the
+outermost pixels, and allows you to specify the adhesion with the border specifically.
+In this example, the border is made repellant by setting its adhesive penalty
+with the cell much higher than that of the background.
+
+<br>
+Note that this would also work when you do not set the torus property to false, since the
+barrier layer prevents the cells from crossing the grid borders. However, changing the 
+torus setting is important for some internal computations (such as computing centroids).
+Especially if the grid is small (as it is here in the y dimension), these computations
+can go wrong if torus is not properly specified. It is therefore best practice to always
+set torus to false if cells cannot cross the grid border.
+</p>
+</body>
+</html>