Cell behavior Codes

Cell_behavior_initial_steps/Uni_cell_add.py

+# -*- coding: utf-8 -*-
+"""
+Created on Thu Apr 21 13:34:54 2022
+
+@author: encinass1u
+"""
+
+import numpy as np
+import pickle 
+import random 
+import matplotlib.pyplot as ptl
+import copy
+from matplotlib import pyplot as plt
+import random
+from scipy import ndimage
+from bio2mslib.inout.inout import WriteData as WD
+import os
+
+#Empty matrix size declaration
+lengthx = 12
+lengthy = 12
+G= np.zeros((lengthx,lengthy))
+ST = copy.deepcopy(G)
+
+
+#Loop to add the \ surface 
+for i in range (0,12):
+    for j in range (0,12):
+        if (i == j):
+            ST[i,j]=0.5
+
+#Pickle of the obtained matrix
+with open('Cell_grid.pkl', 'wb') as csv_file:
+    pickle.dump(ST,csv_file)
+
+with open('Cell_grid.pkl', 'rb') as csv_file:
+    data_saved = pickle.load(csv_file)
+
+    #print(data_saved)
+
+# print(type(ST))
+# #Visual preentation in image of the matrix
+#im = plt.imshow(data_saved, cmap="copper_r")
+#plt.colorbar(data_saved) #Error hereeeee
+#plt.show()
+#Create a copy of the initial surface to seed the cells
+Z = copy.deepcopy(ST)
+
+im2 = plt.imshow(Z, cmap="copper_r")
+plt.show()
+
+#incertion of a single cell to track its movement based on the simpspn model
+uni_cell = Z[(5,4)]
+Z[(5,4)] = 1
+iter = 1
+itermax = 5
+im2 = plt.imshow(Z, cmap="copper_r")
+plt.show()
+while iter<= itermax:
+    for i in range(0,12):
+        for j in range(0,12):
+    #         if Zcopy[im,jm]>= 1:
+    #             Zcopyinitial = copy.deepcopy(Zcopy[im,jm])
+
+            h = random.randint(-1,1) #horizontal value for the movement of the cell
+            v = random.randint(-1,1) #vertival value for the movement of the cell
+            if Z[i,j]>=uni_cell and (h != 0 or v!= 0):
+                    Z[h + i, v + j]+=1
+                    Z[i,j]+= uni_cell
+                    im2 = plt.imshow(Z, cmap="hot") 
+                    plt.show()
+                    with open('Cell_migration_'+str(iter)+'.pkl', 'wb') as csv_file:
+                        pickle.dump(Z,csv_file)
+                        iter +=1
+            # elif Z[i,j]>0.71 and (h != 0 or v!= 0):
+            #     Z[h + i, v + j]= Z[i,j]+1
+            #     Z[i,j]+=1
+            #         #Print the image to locate the cell each iteration.
+            #         #Saving the file of pickle
+            #     im2 = plt.imshow(Z, cmap="copper_r") 
+            #     plt.show()
+            #     with open('Cell_migration_'+str(iter)+'.pkl', 'wb') as csv_file:
+            #         pickle.dump(Z,csv_file)
+            #         iter +=1
+                    # Z[h + i, v + j]= 1
+                    # Z[i,j]= 0
+
+
+
+
+
+