New layout algorithms

msi.gama.core/src/msi/gaml/operators/Graphs.java

@@ -23,6 +23,13 @@
 import org.apache.commons.lang.ArrayUtils;
 import org.jgrapht.alg.clique.BronKerboschCliqueFinder;
 import org.jgrapht.alg.connectivity.ConnectivityInspector;
+import org.jgrapht.alg.drawing.FRLayoutAlgorithm2D;
+import org.jgrapht.alg.drawing.IndexedFRLayoutAlgorithm2D;
+import org.jgrapht.alg.drawing.MedianGreedyTwoLayeredBipartiteLayout2D;
+import org.jgrapht.alg.drawing.model.Box2D;
+import org.jgrapht.alg.drawing.model.LayoutModel2D;
+import org.jgrapht.alg.drawing.model.MapLayoutModel2D;
+import org.jgrapht.alg.drawing.model.Point2D;
 import org.jgrapht.alg.flow.EdmondsKarpMFImpl;
 import org.jgrapht.alg.interfaces.MaximumFlowAlgorithm.MaximumFlow;
 import org.jgrapht.generate.BarabasiAlbertGraphGenerator;
@@ -36,6 +43,7 @@
 import org.jgrapht.util.SupplierUtil;
 import org.locationtech.jts.geom.Coordinate;
 
+import msi.gama.common.geometry.Envelope3D;
 import msi.gama.common.geometry.GeometryUtils;
 import msi.gama.common.interfaces.IKeyword;
 import msi.gama.metamodel.agent.IAgent;
@@ -1859,6 +1867,74 @@ public static IGraph layoutForce(final IScope scope, final GamaGraph graph, fina
 		return graph;
 	}
 
+
+	@operator (
+			value = "layout_force_FR",
+			content_type = ITypeProvider.CONTENT_TYPE_AT_INDEX + 1,
+			index_type = ITypeProvider.KEY_TYPE_AT_INDEX + 1,
+
+			category = { IOperatorCategory.GRAPH },
+			concept = { IConcept.GRAPH })
+	@doc (
+			value = "layouts a GAMA graph using Fruchterman and Reingold Force-Directed Placement Algorithm (in a given spatial bound, normalization factor and max_iteration parameters). ",
+			masterDoc = true,
+			special_cases = "usage: layoutForce(graph, bounds, normalization_factor, max_iteration, equilibirum criterion). graph is the graph to which "
+					+ "applied the layout;  bounds is the shape (geometry) in which the graph should be located; normalization_factor is the normalization factor for the optimal distance, typical value is 1.0; "
+					+ "  max_iteration is the maximal number of iterations")
+	@no_test
+	public static IGraph layoutForceFR(final IScope scope, final GamaGraph graph, final IShape bounds,
+			final double normalization_factor,  final int maxIteration) {
+		final FRLayoutAlgorithm2D sim = new FRLayoutAlgorithm2D(maxIteration,normalization_factor,scope.getSimulation().getRandomGenerator().getGenerator());
+		LayoutModel2D model = toModel(graph,bounds);
+		sim.layout(graph, model);
+		return update_loc(graph,model);
+	}
+
+	@operator (
+			value = "layout_force_FR_indexed",
+			content_type = ITypeProvider.CONTENT_TYPE_AT_INDEX + 1,
+			index_type = ITypeProvider.KEY_TYPE_AT_INDEX + 1,
+
+			category = { IOperatorCategory.GRAPH },
+			concept = { IConcept.GRAPH })
+	@doc (
+			value = "layouts a GAMA graph using Fruchterman and Reingold Force-Directed Placement Algorithm with The Barnes-Hut indexing technique(in a given spatial bound, theta, normalization factor and max_iteration parameters). ",
+			masterDoc = true,
+			special_cases = "usage: layoutForce(graph, bounds, normalization_factor, max_iteration, equilibirum criterion). graph is the graph to which "
+					+ "applied the layout;  bounds is the shape (geometry) in which the graph should be located; theta value for approximation using the Barnes-Hut technique, typical value is 0.5; normalization_factor is the normalization factor for the optimal distance, typical value is 1.0; "
+					+ "  max_iteration is the maximal number of iterations")
+	@no_test
+	public static IGraph indexedFRLayout(final IScope scope, final GamaGraph graph, final IShape bounds,
+			final double theta, final double normalizationFactor,  final int maxIteration) {
+		final IndexedFRLayoutAlgorithm2D sim = new IndexedFRLayoutAlgorithm2D(maxIteration,theta, normalizationFactor,scope.getSimulation().getRandomGenerator().getGenerator());
+		LayoutModel2D model = toModel(graph,bounds);
+		sim.layout(graph, model);
+		return update_loc(graph,model);
+	}
+
+
+
+	static IGraph update_loc(IGraph graph, LayoutModel2D model) {
+		for (Object s : graph.vertexSet()) {
+			if (s instanceof IShape) {
+				Point2D pt = model.get(s);
+				((IShape) s).setLocation(new GamaPoint(pt.getX(), pt.getY()));
+			}
+		}
+		return graph;
+	}
+
+	static LayoutModel2D toModel(final GamaGraph graph, final IShape bounds) {
+		Envelope3D env = bounds.getEnvelope();
+		LayoutModel2D model = new MapLayoutModel2D<>(new Box2D(env.getMinY(), env.getMinY(), env.getWidth(), env.getHeight()));
+		for (Object s : graph.vertexSet()) {
+			if (s instanceof IShape) {
+				model.put(s, new Point2D(((IShape)s).getLocation().getX(), ((IShape)s).getLocation().getY()));
+			}
+		}
+		return model;
+	}
+
 	@operator (
 			value = "layout_force",
 			content_type = ITypeProvider.CONTENT_TYPE_AT_INDEX + 1,

msi.gama.ext/META-INF/MANIFEST.MF

@@ -444,6 +444,8 @@ Export-Package: com.conversantmedia.util.collection,
  org.jgrapht.alg.connectivity,
  org.jgrapht.alg.cycle,
  org.jgrapht.alg.decomposition,
+ org.jgrapht.alg.drawing,
+ org.jgrapht.alg.drawing.model,
  org.jgrapht.alg.flow,
  org.jgrapht.alg.flow.mincost,
  org.jgrapht.alg.interfaces,

msi.gama.models/models/Modeling/Spatial Topology/Graphs/models/Graph Loading Layout.gaml

@@ -1,7 +1,7 @@
 /**
 * Name: Graph from DGS File and Layout Changed
 * Author: Patrick Taillandier
-* Description: Model which shows how to load a graph from a DGS File, and change its layout. 
+* Description: Model which shows how to load a graph from a graphml File, and change its layout. 
 * Tags: graph, load_file, dgs
 */
 
@@ -12,17 +12,18 @@ global {
 	string barabasi_file <- "../includes/simple.graphml";
 	geometry shape <- rectangle(500,500);
 	string layout_type;
-	int layout_time <- 1000 min: 0 max: 10000 parameter: "Max number of iterations" category: "Force";
+	int layout_time <- 1000 min: 0 max: 10000 parameter: "Max number of iterations" ;
 	float coeff_force <- 0.8 min: 0.1 max: 1.0 parameter: "Force coefficient" category: "Force";
 	float cooling_coefficient <- 0.1 min: 0.01 max: 0.5 parameter: "Decreasing coefficient of the temperature" category: "Force"; 
 	float coeff_nb_places <- 1.2 min: 0.0 max: 2.0 parameter: "Coefficient for the number of places to locate the vertices" category: "Grid"; 
+	float normalizationFactor <- 0.5 min: 0.1 max: 2.0 parameter: "Coefficient for the number of places to locate the vertices" category: "Force_FR"; 
+	float theta <- 0.5 min: 0.1 max: 2.0 parameter: "Coefficient for the number of places to locate the vertices" category: "Force_FR_indexed"; 
 
 
 	//The operator load_graph_from_file generates the graph from the file, and chose the vertices as agents of node_agent 
 	//species, and edges as edge_agent agents
 	init {
 		the_graph <- graphml_file("../includes/simple.graphml", node_agent, edge_agent).contents;
-		write the_graph.edges;
 	}
 
 	//In case the layout type is forcedirected or random, the reflex will change at each step the layout of the graph
@@ -31,6 +32,12 @@ global {
 			match "Force" {
 				the_graph <- layout_force(the_graph, world.shape,coeff_force , cooling_coefficient, layout_time);
 			}
+			match "Force FR" {
+				the_graph <- layout_force_FR(the_graph, world.shape,normalizationFactor,layout_time);
+			}
+			match "Force FR Indexed" {
+				the_graph <- layout_force_FR_indexed(the_graph, world.shape,theta,normalizationFactor,layout_time);
+			}
 			match "Circular" {
 				the_graph <- layout_circle(the_graph, world.shape, false);
 			}
@@ -54,7 +61,7 @@ species node_agent {
 }
 
 experiment loadgraph type: gui {
-	parameter "Layout type" var: layout_type among:["Force", "Circular", "Grid"] init:"Circular";
+	parameter "Layout type" var: layout_type among:["Force FR","Force FR Indexed" , "Force", "Circular", "Grid"] init:"Force FR";
 	output {
 		display map type: opengl{
 			species edge_agent ;