Insert Neuropercolation(+Coupled) class

examples/just a test.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Aug 16 22:17:28 2023
+
+@author: astral
+"""
+import pygame
+pygame.init()
+win = pygame.display.set_mode((500, 500))
+pygame.display.set_caption("Test")
+black = (0, 0, 0)
+sysfont = pygame.font.SysFont(None, 50)
+win.fill((255, 255, 255))
+
+running = True
+while running:
+    win.fill((255, 255, 255))
+    digit = sysfont.render("Test", 1, black)
+    win.blit(digit, (50, 50))
+    pygame.display.update()
+    for event in pygame.event.get():
+        if event.type == pygame.QUIT:
+            running = False
+            
+pygame.quit()

neuropercolation/__init__.py

@@ -17,5 +17,5 @@ limitations under the License.
 
 from .neighborhood import Neighborhood, MooreNeighborhood, RadialNeighborhood, VonNeumannNeighborhood, \
                           HexagonalNeighborhood, EdgeRule
-from .automaton import CellularAutomaton
+from .automaton import Neuropercolation, NeuropercolationCoupled
 from .display import CAWindow

neuropercolation/automaton.py

@@ -19,9 +19,12 @@ from typing import Sequence
 import abc
 import itertools
 import recordclass
+import random
 
-from cellular_automaton import Neighborhood
+from cellular_automaton import Neighborhood, VonNeumannNeighborhood, EdgeRule
 
+ALIVE = [1]
+DEAD = [0]
 
 CELL = recordclass.make_dataclass("Cell",
                                   ("state", "is_active", "is_dirty", "neighbors"),
@@ -42,6 +45,7 @@ class CellularAutomatonCreator(abc.ABC):
         self._current_state = {}
         self._next_state = {}
         self.__make_cellular_automaton_state()
+        self.dumped = False
 
     def get_dimension(self):
         return self._dimension
@@ -53,7 +57,7 @@ class CellularAutomatonCreator(abc.ABC):
         self.__add_neighbors()
 
     def __make_cells(self):
-        for coord in itertools.product(*[range(d) for d in self._dimension]):
+        for coord in itertools.product(*[range(d) for d in [*self._dimension]]): # doubled the layers in thrid dimension
             cell_state = self.init_cell_state(coord)
             self._current_state[coord] = CELL(cell_state)
             self._next_state[coord] = CELL(cell_state)
@@ -62,9 +66,10 @@ class CellularAutomatonCreator(abc.ABC):
         calculate_neighbor_coordinates = self._neighborhood.calculate_cell_neighbor_coordinates
         coordinates = self._current_state.keys()
         for coordinate, cell_c, cell_n in zip(coordinates, self._current_state.values(), self._next_state.values()):
-            n_coord = calculate_neighbor_coordinates(coordinate, self._dimension)
+            pre_coord = calculate_neighbor_coordinates(coordinate, [*self._dimension[:2]])
-            cell_c.neighbors = list([self._current_state[nc] for nc in n_coord])
+            n_coord = tuple([(*coord,*coordinate[2:]) for coord in pre_coord])
-            cell_n.neighbors = list([self._next_state[nc] for nc in n_coord])
+            cell_c.neighbors = list([self._current_state[nc] for nc in n_coord if nc!=coordinate])
+            cell_n.neighbors = list([self._next_state[nc] for nc in n_coord if nc!=coordinate])
 
     def init_cell_state(self, cell_coordinate: Sequence) -> Sequence:  # pragma: no cover
         """ Will be called to initialize a cells state.
@@ -74,35 +79,17 @@ class CellularAutomatonCreator(abc.ABC):
         raise NotImplementedError
 
 
-class CellularAutomaton(CellularAutomatonCreator, abc.ABC):
+class Neuropercolation(CellularAutomatonCreator, abc.ABC):
-    """ This class represents a cellular automaton.
+    """ Cellular automaton with the evolution rules of conways game of life """
-    It can be created with n dimensions and can handle different neighborhood definitions.
     
-    It is intended to be uses as base class.
+    def __init__(self, dim, eps, *args, **kwargs):
-    Override `init_cell_state()` to define the state the cell(s) are initiated with.
+        super().__init__(dimension=[dim, dim, 2],
-    Override `evolve()` to define the rule that is aplied on every evolution step of this automaton.
+                         neighborhood=VonNeumannNeighborhood(EdgeRule.FIRST_AND_LAST_CELL_OF_DIMENSION_ARE_NEIGHBORS))
-    """
-    def __init__(self, neighborhood: Neighborhood, *args, **kwargs):
-        """ Initiates a cellular automaton by the use of the `init_cell_state` method.
-        :param neighborhood: Defines which cells are considered neighbors.
-        :param dimension: Iterable of len = dimensions
-                          (e.g. [4, 3, 3, 3] = 4 x 3 x 3 x 3 cells in a four dimensional cube).
-        """
-        super().__init__(neighborhood=neighborhood, *args, **kwargs)
         self._evolution_step = 0
-        self._active = True
+        self.epsilon = eps
         
-    def is_active(self):
+    def init_cell_state(self, coord):  # pylint: disable=no-self-use
-        return self._active
+        return DEAD
-
-    def reactivate(self):
-        """ Sets all cells active again """
-        for cell in self._current_state.values():
-            cell.is_active = True
-            cell.is_dirty = True
-        self._active = True
-
-    active = property(is_active)
 
     def get_cells(self):
         return self._current_state
@@ -126,7 +113,6 @@ class CellularAutomaton(CellularAutomatonCreator, abc.ABC):
         :param times: The number of evolution steps processed with one call of this method.
         """
         for _ in itertools.repeat(None, times):
-            self._active = False
             self.__evolve_cells(self._current_state, self._next_state)
             self._current_state, self._next_state = self._next_state, self._current_state
             self._evolution_step += 1
@@ -134,28 +120,122 @@ class CellularAutomaton(CellularAutomatonCreator, abc.ABC):
     def __evolve_cells(self, this_state, next_state):
         evolve_cell = self.__evolve_cell
         evolution_rule = self.evolve_rule
-        for old, new in zip(this_state.values(), next_state.values()):
+        for coord, old, new in zip(this_state.keys(), this_state.values(), next_state.values()):
-            if old.is_active:
+            coord_c = tuple([*coord[:2],int(1-coord[2])])
-                new_state = evolution_rule(old.state.copy(), [n.state for n in old.neighbors])
+            old_c = this_state[coord_c]
-                old.is_active = False
+            new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state for n in old.neighbors], coord[2], coord_c[2]) #inverse the inhibitory layer's action
-                evolve_cell(old, new, new_state)
+            
+            evolve_cell(old, new, new_state)
 
     def __evolve_cell(self, old, cell, new_state):
         changed = new_state != old.state
         cell.state = new_state
         cell.is_dirty |= changed
         old.is_dirty |= changed
-        self._active |= changed
-        if changed:
-            cell.is_active = True
-            for n in cell.neighbors:
-                n.is_active = True
         
-    def evolve_rule(self, last_cell_state: Sequence, neighbors_last_states: Sequence) -> Sequence:  # pragma: no cover
+    def evolve_rule(self, last_cell_state, link_last_state, neighbors_last_states, cell_lay, link_cell_lay):
-        """ Calculates and sets new state of 'cell'.
+        new_cell_state = last_cell_state
-        A cells evolution will only be called if it or at least one of its neighbors has changed last evolution_step.
+        if link_cell_lay==0:
-        :param last_cell_state:         The cells state previous to the evolution step.
+            alive_neighbours = self.__count_alive_neighbours(neighbors_last_states)+link_last_state[0] # adjust for excitatory link cells
-        :param neighbors_last_states:   The cells neighbors current states.
+        else:
-        :return: New state.             The state after this evolution step
+            alive_neighbours = self.__count_alive_neighbours(neighbors_last_states)+(1-link_last_state[0]) # adjust for inhibitory link cells
+        
+        CASE = (random.random()>=self.epsilon)
+        if alive_neighbours > 2:
+            if CASE:
+                new_cell_state = ALIVE
+            else:
+                new_cell_state = DEAD
+        else:
+            if CASE:
+                new_cell_state = DEAD
+            else:
+                new_cell_state = ALIVE
+        return new_cell_state
+    
+    @staticmethod
+    def __count_alive_neighbours(neighbours):
+        alive_neighbors = []
+        for n in neighbours:
+            if n == ALIVE:
+                alive_neighbors.append(1)
+        return len(alive_neighbors)
+    
+class NeuropercolationCoupled(CellularAutomatonCreator, abc.ABC):
+    
+    def __init__(self, dim, eps, coupling=[], *args, **kwargs):
+        super().__init__(dimension=[dim, dim, 2, 2],
+                         neighborhood=VonNeumannNeighborhood(EdgeRule.FIRST_AND_LAST_CELL_OF_DIMENSION_ARE_NEIGHBORS))
+        self._evolution_step = 0
+        self.epsilon = eps
+        self.coupling = coupling
+        
+    def init_cell_state(self, coord):  # pylint: disable=no-self-use
+        return DEAD
+    
+    def get_cells(self):
+        return self._current_state
+
+    def set_cells(self, cells):
+        """ Sets the cell states both as current and next states """
+        for (coordinate, c_cell), n_cell in zip(self._current_state.items(), self._next_state.values()):
+            new_cell_state = cells[coordinate].state
+            c_cell.state = new_cell_state
+            n_cell.state = new_cell_state
+
+    cells = property(get_cells, set_cells)
+
+    def get_evolution_step(self):
+        return self._evolution_step
+
+    evolution_step = property(get_evolution_step)
+
+    def evolve(self, times=1):
+        """ Evolve all cells x times.
+        :param times: The number of evolution steps processed with one call of this method.
         """
-        raise NotImplementedError
+        for _ in itertools.repeat(None, times):
+            self.__evolve_cells(self._current_state, self._next_state)
+            self._current_state, self._next_state = self._next_state, self._current_state
+            self._evolution_step += 1
+
+    def __evolve_cells(self, this_state, next_state): #this will be overwritten by heir
+        evolve_cell = self.__evolve_cell
+        evolution_rule = self.evolve_rule
+        for coord, old, new in zip(this_state.keys(), this_state.values(), next_state.values()):
+            if coord[:2] in self.coupling:
+                coord_c = tuple([*coord[:2],coord[2],int(1-coord[3])])
+                old_c = this_state[coord_c]
+                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state for n in old.neighbors], 0)
+            else:
+                coord_c = tuple([*coord[:2],int(1-coord[2]),coord[3]])
+                old_c = this_state[coord_c]
+                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state for n in old.neighbors], coord_c[2]) #inverse the inhibitory layer's action
+                
+            evolve_cell(old, new, new_state)
+
+    def __evolve_cell(self, old, cell, new_state):
+        changed = new_state != old.state
+        cell.state = new_state
+        cell.is_dirty |= changed
+        old.is_dirty |= changed
+        
+    def evolve_rule(self, last_cell_state, link_last_state, neighbors_last_states, other_layer):
+        new_cell_state = last_cell_state
+        if other_layer==0:
+            alive_neighbours = self.__count_alive_neighbours(neighbors_last_states)+link_last_state[0] # adjust for excitatory link cells
+        else:
+            alive_neighbours = self.__count_alive_neighbours(neighbors_last_states)+(1-link_last_state[0]) # adjust for inhibitory link cells
+        
+        CASE = (random.random()>=self.epsilon)
+        if alive_neighbours > 2:
+            if CASE:
+                new_cell_state = ALIVE
+            else:
+                new_cell_state = DEAD
+        else:
+            if CASE:
+                new_cell_state = DEAD
+            else:
+                new_cell_state = ALIVE
+        return new_cell_state

neuropercolation/display.py

@@ -22,7 +22,7 @@ import collections
 import contextlib
 from typing import Sequence
 
-from . import CellularAutomaton
+from . import Neuropercolation, NeuropercolationCoupled
 
 _Rect = collections.namedtuple(typename="Rect",
                                field_names=["left", "top", "width", "height"])
@@ -65,7 +65,7 @@ class PygameEngine:
 
 class CAWindow:
     def __init__(self,
-                 cellular_automaton: CellularAutomaton,
+                 cellular_automaton: Neuropercolation,
                  window_size=(1000, 800),
                  stretch_cells=False,
                  draw_engine=None,
@@ -117,8 +117,7 @@ class CAWindow:
                 time.sleep(rest_time)
 
     def _not_at_the_end(self, last_evolution_step):
-        return (self._cellular_automaton.evolution_step < last_evolution_step or last_evolution_step <= 0) \
+        return (self._cellular_automaton.evolution_step < last_evolution_step or last_evolution_step <= 0)
-               and self._cellular_automaton.active
 
     def __calculate_cell_display_size(self, stretch_cells):  # pragma: no cover
         grid_dimension = self._cellular_automaton.dimension