Dev

.gitignore

@@ -1,4 +1,3 @@
-docs/
 .vscode/
 environment/
 tests/

README.md

@@ -85,7 +85,7 @@ The template system was created in an effort to decrease the risk of entering in
 * timesteps: integer > 0.
 * sim_type: str takes value of 'visual' or 'full'.
 * tempurature: int between 1 and 5
-* struct_mode: str takes values of 'static', 'blinker', 'toad', 'glider', 'pulsar', 'beacon', 'gun', 'pentadecon', 'heavyglider' and 'none' (no structure added).
+* struct_mode: str takes values of 'static', 'blinker', 'toad', 'glider' and 'none' (no structure added).
 * dyn_mode: str takes values of 'cyclic', 'absorbing', 'half', 'dynamic', 'cut' and 'none' (default start state)
 * prob: list (array object in json terms) of length 3.
 * *cahn simulation*: all values other than the default first three are floating point numbers.

main.py

@@ -8,7 +8,7 @@ def main():
     general_utils.check_directories()
 
     # gets name of module python files tools/utils
-    modules = general_utils.get_py_files(general_utils.MODULEPATH)
+    modules = general_utils.get_py_files(general_utils.MODULE_PATH)
 
     # resolves module class names into a list (references to classes)
     module_class = [general_utils.str_to_class("tools", module) for module in modules]

packages/__init__.py

@@ -1,4 +1,4 @@
 from tools.utils import general_utils
 
-__all__ = general_utils.get_py_files(general_utils.SIMPATH)
+__all__ = general_utils.get_py_files(general_utils.SIM_PATH)
 

packages/controller/simulationPlane.py

@@ -22,7 +22,6 @@ def __init__(self, dimensions, timesteps):
 
     def create_figure(self):
         """ Creates the figure elements for the simulations """
-        plt.rcParams.update(general_utils.returnGraphConfigs("anim"))
         self.fig = plt.figure()
         self.axes = plt.axes()
         self.axes.set_xlabel("Cells In X (Columns)")
@@ -74,11 +73,11 @@ def check_all_nieghbours(self, coordinate):
 
     def d_index(self, coord):
         """Decrease index number in array in up or right directions"""
-        return coord - 1 if coord - 1 < 0 else self.dimensions - 1
+        return coord - 1 if coord - 1 >= 0 else self.dimensions - 1
 
     def i_index(self, coord):
         """Increase index number in array in down or left directions"""
-        return coord + 1 if coord + 1 > self.dimensions - 1 else 0
+        return coord + 1 if coord + 1 <= self.dimensions - 1 else 0
 
     def end_simulation(self):
         time.sleep(1)

packages/reaction.py

@@ -0,0 +1,60 @@
+import numpy as np
+from packages.controller import SimulationPlane
+from tools.utils import sim_utils
+
+class Reaction(SimulationPlane):
+    def __init__(self, dimensions, timesteps, k, sigma, dt):
+        super().__init__(dimensions, timesteps)
+        self.k = k
+        self.sigma = sigma
+        self.dt = dt
+
+    #override
+    def start_sim(self):
+        self.create_cells()
+        self.create_figure()
+        super().start_sim()
+
+    #override
+    def create_figure(self):
+        super().create_figure()
+        self.axes.set_title("Reaction-Diffusion Simulation For {} Cells".format(self.dimensions ** 2))
+        self.im = self.axes.imshow(self.cells, interpolation = "nearest", animated = True)
+        self.fig.colorbar(self.im)
+    #override
+    def create_cells(self):
+        self.cells = np.random.uniform(low=-0.1, high=0.1, size=(self.dimensions, self.dimensions))
+        for i in range(self.dimensions):
+            for j in range(self.dimensions):
+                self.cells[i, j] += 0.5
+
+    #override
+    def anim_func(self, i):
+        self.new_cells = np.copy(self.cells)
+        for i in range(self.dimensions):
+            for j in range(self.dimensions):
+                self.new_cells[i, j] = self.reaction_procedure(i, j)
+        self.cells = np.copy(self.new_cells)
+        self.im.set_array(self.cells)
+        self.check_sim()
+        yield self.im
+
+    def reaction_procedure(self, i , j):
+        laplacian = self.dt * (
+            self.cells[self.i_index(i), j] + \
+                self.cells[self.d_index(i), j] + \
+                    self.cells[i, self.i_index(j)] + \
+                        self.cells[i, self.d_index(j)] - \
+                            4 * self.cells[i, j]
+        )
+        constants = self.dt * self.calc_row(i, j) - self.k * self.cells[i, j]
+        new_value = laplacian + constants
+        return new_value
+
+    def calc_row(self, i , j):
+        i_component = i - (self.dimensions / 2)
+        j_component = j - (self.dimensions / 2)
+        mag_r  = np.sqrt(i_component ** 2 + j_component ** 2)
+        row = np.exp(-(mag_r ** 2) / (self.sigma ** 2))
+        return row
+

params/gol - 2019,04,05 12,20,40.124700.json

@@ -4,5 +4,5 @@
     "default_values": [50, 100, null, "glider"],
     "timesteps": null,
     "percentage": null,
-    "struct_mode": "fafaf"
+    "struct_mode": "glider"
 }

params/reaction - 2019,04,24 11,42,32.211440.json

@@ -0,0 +1,9 @@
+{
+	"mode": "reaction",
+	"dimensions": 50,
+	"timesteps": 1000,
+    "default_values":[50, 10000, 0, 0, 0],
+    "k": 1,
+    "sigma": 0.1,
+    "dt": 0.1
+}

templates/files/commands.txt

@@ -0,0 +1,6 @@
+--new-template <arguement>: creates new template file
+--new-simulation <arguement>: creates new simulation and corresponding template file
+--new-module <arguement>: creates new module
+--shortcut <arguement>: jumps to module
+--readme: opens the programme readme
+--help-commands: displays command line call syntax (You Just Called It)

templates/files/module.py

@@ -0,0 +1,6 @@
+import numpy as np
+from tools.utils import UtilityBase, general_utils
+
+class {}(UtilityBase):
+    def __init__(self):
+        super().__init__()

templates/files/params.json

@@ -0,0 +1,6 @@
+{
+    "mode": null,
+    "dimensions": null,
+    "timesteps": null,
+    "default_values": []
+}

templates/files/sim.py

@@ -0,0 +1,35 @@
+import numpy as np
+from tools.utils import sim_utils
+from packages.controller import SimulationPlane
+
+class {}(SimulationPlane):
+    def __init__(self, dimensions, timesteps):
+        super().__init__(dimensions, timesteps)
+
+    #override
+    def start_sim(self):
+        # override to add different simulation types visual or full
+        super().start_sim()
+
+    #override
+    def create_figure(self):
+        super().create_figure()
+        self.im = self.axes.imshow(self.cells, interpolation = "nearest", animated = True)
+        self.fig.colorbar(self.im)
+
+    #override
+    def create_cells(self):
+        """
+        self.cells = np.random.normal(
+            size=(self.dimensions, self.dimensions)) # loc and scale for noise
+        self.cells = np.random.uniform(
+            size=self.dimensions, self.dimensions) # high or low
+        """
+        pass
+
+    #override
+    def anim_func(self, i):
+        yield self.im
+
+
+

templates/sims/reaction.json

@@ -0,0 +1,9 @@
+{
+	"mode": "reaction",
+	"dimensions": null,
+	"timesteps": null,
+    "default_values":[50, 10000, 0, 0, 0],
+    "k": null,
+    "sigma": null,
+    "dt": null
+}

tools/__init__.py

@@ -1,3 +1,3 @@
 from tools.utils import general_utils
 
-__all__ = general_utils.get_py_files(general_utils.MODULEPATH)
+__all__ = general_utils.get_py_files(general_utils.MODULE_PATH)

tools/grapher.py

@@ -23,7 +23,6 @@ def setup(self):
     def create_figure(self):
         """Creates figure for plotting and subplotting"""
         self.figure = plt.figure()
-        plt.rcParams.update(general_utils.returnGraphConfigs("subplots"))
 
     def plot_data(self, file_name):
         """Plots the data based on simulations chosen"""