Voronoi Tesselation based Discrete Space (#2084)

This feature allows the user to build a discrete space based on a random sample of points, where neighbors are defined by Delaunay Triangulation.

More specifically, Delaunay Triangulation is a dual-graph representation of the Voronoi Tesselation. Using this algorithm, we can easily find nearest neighbors without delimiting cells edges.

Author: vitorfrois

mesa/experimental/cell_space/__init__.py

@@ -9,6 +9,7 @@
     OrthogonalVonNeumannGrid,
 )
 from mesa.experimental.cell_space.network import Network
+from mesa.experimental.cell_space.voronoi import VoronoiGrid
 
 __all__ = [
     "CellCollection",
@@ -20,4 +21,5 @@
     "OrthogonalMooreGrid",
     "OrthogonalVonNeumannGrid",
     "Network",
+    "VoronoiGrid",
 ]

mesa/experimental/cell_space/voronoi.py

@@ -0,0 +1,264 @@
+from collections.abc import Sequence
+from itertools import combinations
+from random import Random
+
+import numpy as np
+
+from mesa.experimental.cell_space.cell import Cell
+from mesa.experimental.cell_space.discrete_space import DiscreteSpace
+
+
+class Delaunay:
+    """
+    Class to compute a Delaunay triangulation in 2D
+    ref: http://github.com/jmespadero/pyDelaunay2D
+    """
+
+    def __init__(self, center: tuple = (0, 0), radius: int = 9999) -> None:
+        """
+        Init and create a new frame to contain the triangulation
+        center: Optional position for the center of the frame. Default (0,0)
+        radius: Optional distance from corners to the center.
+        """
+        center = np.asarray(center)
+        # Create coordinates for the corners of the frame
+        self.coords = [
+            center + radius * np.array((-1, -1)),
+            center + radius * np.array((+1, -1)),
+            center + radius * np.array((+1, +1)),
+            center + radius * np.array((-1, +1)),
+        ]
+
+        # Create two dicts to store triangle neighbours and circumcircles.
+        self.triangles = {}
+        self.circles = {}
+
+        # Create two CCW triangles for the frame
+        triangle1 = (0, 1, 3)
+        triangle2 = (2, 3, 1)
+        self.triangles[triangle1] = [triangle2, None, None]
+        self.triangles[triangle2] = [triangle1, None, None]
+
+        # Compute circumcenters and circumradius for each triangle
+        for t in self.triangles:
+            self.circles[t] = self._circumcenter(t)
+
+    def _circumcenter(self, triangle: list) -> tuple:
+        """
+        Compute circumcenter and circumradius of a triangle in 2D.
+        """
+        points = np.asarray([self.coords[v] for v in triangle])
+        points2 = np.dot(points, points.T)
+        a = np.bmat([[2 * points2, [[1], [1], [1]]], [[[1, 1, 1, 0]]]])
+
+        b = np.hstack((np.sum(points * points, axis=1), [1]))
+        x = np.linalg.solve(a, b)
+        bary_coords = x[:-1]
+        center = np.dot(bary_coords, points)
+
+        radius = np.sum(np.square(points[0] - center))  # squared distance
+        return (center, radius)
+
+    def _in_circle(self, triangle: list, point: list) -> bool:
+        """
+        Check if point p is inside of precomputed circumcircle of triangle.
+        """
+        center, radius = self.circles[triangle]
+        return np.sum(np.square(center - point)) <= radius
+
+    def add_point(self, point: Sequence) -> None:
+        """
+        Add a point to the current DT, and refine it using Bowyer-Watson.
+        """
+        point_index = len(self.coords)
+        self.coords.append(np.asarray(point))
+
+        bad_triangles = []
+        for triangle in self.triangles:
+            if self._in_circle(triangle, point):
+                bad_triangles.append(triangle)
+
+        boundary = []
+        triangle = bad_triangles[0]
+        edge = 0
+
+        while True:
+            opposite_triangle = self.triangles[triangle][edge]
+            if opposite_triangle not in bad_triangles:
+                boundary.append(
+                    (
+                        triangle[(edge + 1) % 3],
+                        triangle[(edge - 1) % 3],
+                        opposite_triangle,
+                    )
+                )
+                edge = (edge + 1) % 3
+                if boundary[0][0] == boundary[-1][1]:
+                    break
+            else:
+                edge = (self.triangles[opposite_triangle].index(triangle) + 1) % 3
+                triangle = opposite_triangle
+
+        for triangle in bad_triangles:
+            del self.triangles[triangle]
+            del self.circles[triangle]
+
+        new_triangles = []
+        for e0, e1, opposite_triangle in boundary:
+            triangle = (point_index, e0, e1)
+            self.circles[triangle] = self._circumcenter(triangle)
+            self.triangles[triangle] = [opposite_triangle, None, None]
+            if opposite_triangle:
+                for i, neighbor in enumerate(self.triangles[opposite_triangle]):
+                    if neighbor and e1 in neighbor and e0 in neighbor:
+                        self.triangles[opposite_triangle][i] = triangle
+
+            new_triangles.append(triangle)
+
+        n = len(new_triangles)
+        for i, triangle in enumerate(new_triangles):
+            self.triangles[triangle][1] = new_triangles[(i + 1) % n]  # next
+            self.triangles[triangle][2] = new_triangles[(i - 1) % n]  # previous
+
+    def export_triangles(self) -> list:
+        """
+        Export the current list of Delaunay triangles
+        """
+        triangles_list = [
+            (a - 4, b - 4, c - 4)
+            for (a, b, c) in self.triangles
+            if a > 3 and b > 3 and c > 3
+        ]
+        return triangles_list
+
+    def export_voronoi_regions(self):
+        """
+        Export coordinates and regions of Voronoi diagram as indexed data.
+        """
+        use_vertex = {i: [] for i in range(len(self.coords))}
+        vor_coors = []
+        index = {}
+        for triangle_index, (a, b, c) in enumerate(sorted(self.triangles)):
+            vor_coors.append(self.circles[(a, b, c)][0])
+            use_vertex[a] += [(b, c, a)]
+            use_vertex[b] += [(c, a, b)]
+            use_vertex[c] += [(a, b, c)]
+
+            index[(a, b, c)] = triangle_index
+            index[(c, a, b)] = triangle_index
+            index[(b, c, a)] = triangle_index
+
+        regions = {}
+        for i in range(4, len(self.coords)):
+            vertex = use_vertex[i][0][0]
+            region = []
+            for _ in range(len(use_vertex[i])):
+                triangle = next(
+                    triangle for triangle in use_vertex[i] if triangle[0] == vertex
+                )
+                region.append(index[triangle])
+                vertex = triangle[1]
+            regions[i - 4] = region
+
+        return vor_coors, regions
+
+
+def round_float(x: float) -> int:
+    return int(x * 500)
+
+
+class VoronoiGrid(DiscreteSpace):
+    triangulation: Delaunay
+    voronoi_coordinates: list
+    regions: list
+
+    def __init__(
+        self,
+        centroids_coordinates: Sequence[Sequence[float]],
+        capacity: float | None = None,
+        random: Random | None = None,
+        cell_klass: type[Cell] = Cell,
+        capacity_function: callable = round_float,
+        cell_coloring_property: str | None = None,
+    ) -> None:
+        """
+        A Voronoi Tessellation Grid.
+
+        Given a set of points, this class creates a grid where a cell is centered in each point,
+        its neighbors are given by Voronoi Tessellation cells neighbors
+        and the capacity by the polygon area.
+
+        Args:
+            centroids_coordinates: coordinates of centroids to build the tessellation space
+            capacity (int) : capacity of the cells in the discrete space
+            random (Random): random number generator
+            CellKlass (type[Cell]): type of cell class
+            capacity_function (Callable): function to compute (int) capacity according to (float) area
+            cell_coloring_property (str): voronoi visualization polygon fill property
+        """
+        super().__init__(capacity=capacity, random=random, cell_klass=cell_klass)
+        self.centroids_coordinates = centroids_coordinates
+        self._validate_parameters()
+
+        self._cells = {
+            i: cell_klass(self.centroids_coordinates[i], capacity, random=self.random)
+            for i in range(len(self.centroids_coordinates))
+        }
+
+        self.regions = None
+        self.triangulation = None
+        self.voronoi_coordinates = None
+        self.capacity_function = capacity_function
+        self.cell_coloring_property = cell_coloring_property
+
+        self._connect_cells()
+        self._build_cell_polygons()
+
+    def _connect_cells(self) -> None:
+        """
+        Connect cells to neighbors based on given centroids and using Delaunay Triangulation
+        """
+        self.triangulation = Delaunay()
+        for centroid in self.centroids_coordinates:
+            self.triangulation.add_point(centroid)
+
+        for point in self.triangulation.export_triangles():
+            for i, j in combinations(point, 2):
+                self._cells[i].connect(self._cells[j])
+                self._cells[j].connect(self._cells[i])
+
+    def _validate_parameters(self) -> None:
+        if self.capacity is not None and not isinstance(self.capacity, float | int):
+            raise ValueError("Capacity must be a number or None.")
+        if not isinstance(self.centroids_coordinates, Sequence) or not isinstance(
+            self.centroids_coordinates[0], Sequence
+        ):
+            raise ValueError("Centroids should be a list of lists")
+        dimension_1 = len(self.centroids_coordinates[0])
+        for coordinate in self.centroids_coordinates:
+            if dimension_1 != len(coordinate):
+                raise ValueError("Centroid coordinates should be a homogeneous array")
+
+    def _get_voronoi_regions(self) -> tuple:
+        if self.voronoi_coordinates is None or self.regions is None:
+            self.voronoi_coordinates, self.regions = (
+                self.triangulation.export_voronoi_regions()
+            )
+        return self.voronoi_coordinates, self.regions
+
+    @staticmethod
+    def _compute_polygon_area(polygon: list) -> float:
+        polygon = np.array(polygon)
+        x = polygon[:, 0]
+        y = polygon[:, 1]
+        return 0.5 * np.abs(np.dot(x, np.roll(y, 1)) - np.dot(y, np.roll(x, 1)))
+
+    def _build_cell_polygons(self):
+        coordinates, regions = self._get_voronoi_regions()
+        for region in regions:
+            polygon = [coordinates[i] for i in regions[region]]
+            self._cells[region].properties["polygon"] = polygon
+            polygon_area = self._compute_polygon_area(polygon)
+            self._cells[region].properties["area"] = polygon_area
+            self._cells[region].capacity = self.capacity_function(polygon_area)
+            self._cells[region].properties[self.cell_coloring_property] = 0

mesa/visualization/components/matplotlib.py

@@ -6,6 +6,7 @@
 from matplotlib.ticker import MaxNLocator
 
 import mesa
+from mesa.experimental.cell_space import VoronoiGrid
 
 
 @solara.component
@@ -20,6 +21,8 @@ def SpaceMatplotlib(model, agent_portrayal, dependencies: list[any] | None = Non
         _draw_network_grid(space, space_ax, agent_portrayal)
     elif isinstance(space, mesa.space.ContinuousSpace):
         _draw_continuous_space(space, space_ax, agent_portrayal)
+    elif isinstance(space, VoronoiGrid):
+        _draw_voronoi(space, space_ax, agent_portrayal)
     else:
         _draw_grid(space, space_ax, agent_portrayal)
     solara.FigureMatplotlib(space_fig, format="png", dependencies=dependencies)
@@ -150,6 +153,56 @@ def portray(space):
     _split_and_scatter(portray(space), space_ax)
 
 
+def _draw_voronoi(space, space_ax, agent_portrayal):
+    def portray(g):
+        x = []
+        y = []
+        s = []  # size
+        c = []  # color
+
+        for cell in g.all_cells:
+            for agent in cell.agents:
+                data = agent_portrayal(agent)
+                x.append(cell.coordinate[0])
+                y.append(cell.coordinate[1])
+                if "size" in data:
+                    s.append(data["size"])
+                if "color" in data:
+                    c.append(data["color"])
+        out = {"x": x, "y": y}
+        # This is the default value for the marker size, which auto-scales
+        # according to the grid area.
+        out["s"] = s
+        if len(c) > 0:
+            out["c"] = c
+
+        return out
+
+    x_list = [i[0] for i in space.centroids_coordinates]
+    y_list = [i[1] for i in space.centroids_coordinates]
+    x_max = max(x_list)
+    x_min = min(x_list)
+    y_max = max(y_list)
+    y_min = min(y_list)
+
+    width = x_max - x_min
+    x_padding = width / 20
+    height = y_max - y_min
+    y_padding = height / 20
+    space_ax.set_xlim(x_min - x_padding, x_max + x_padding)
+    space_ax.set_ylim(y_min - y_padding, y_max + y_padding)
+    space_ax.scatter(**portray(space))
+
+    for cell in space.all_cells:
+        polygon = cell.properties["polygon"]
+        space_ax.fill(
+            *zip(*polygon),
+            alpha=min(1, cell.properties[space.cell_coloring_property]),
+            c="red",
+        )  # Plot filled polygon
+        space_ax.plot(*zip(*polygon), color="black")  # Plot polygon edges in red
+
+
 @solara.component
 def PlotMatplotlib(model, measure, dependencies: list[any] | None = None):
     fig = Figure()

tests/test_cell_space.py

@@ -11,6 +11,7 @@
     Network,
     OrthogonalMooreGrid,
     OrthogonalVonNeumannGrid,
+    VoronoiGrid,
 )
 
 
@@ -372,6 +373,28 @@ def test_networkgrid():
             assert connection.coordinate in G.neighbors(i)
 
 
+def test_voronoigrid():
+    points = [[0, 1], [1, 3], [1.1, 1], [1, 1]]
+
+    grid = VoronoiGrid(points)
+
+    assert len(grid._cells) == len(points)
+
+    # Check cell neighborhood
+    assert len(grid._cells[0]._connections) == 2
+    for connection in grid._cells[0]._connections:
+        assert connection.coordinate in [[1, 1], [1, 3]]
+
+    with pytest.raises(ValueError):
+        VoronoiGrid(points, capacity="str")
+
+    with pytest.raises(ValueError):
+        VoronoiGrid((1, 1))
+
+    with pytest.raises(ValueError):
+        VoronoiGrid([[0, 1], [0, 1, 1]])
+
+
 def test_empties_space():
     import networkx as nx