Cell behavior Codes

Cell_behavior_initial_steps/Gts_selection.py

+#Gst generator,it is possible to choose a type of texture for the cell couture.
+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
+
+#Selection of desire treated surface, Gts
+First_Pickle= True
+square_grid=False
+highs_grid=False
+diagonal=True
+
+if First_Pickle== True:
+    #L is the matrix dimension
+    L =12
+    Lx =np.linspace(0, L, 12)
+    Ly =np.linspace(0, L, 12)
+    #G is the ground, an empty matrix to add the desire surface
+    G= np.zeros((L,L))
+    #Gts us the ground for treated surface
+    Gts = copy.deepcopy(G)
+    if square_grid==True:
+        # #Square grid
+        for i in range (1,len(Lx)-1):
+            for j in range(1,len(Ly)-1):
+                if ((i % 2) !=0) or ((j % 2) ==0):
+                    Gts[i,j] = 0.5
+    elif highs_grid==True:
+        for i in range (1,len(Lx)-1):
+            for j in range(1,len(Ly)-1):
+                if i==0 or j==0 or i==len(Lx)-1 or j==len(Ly)-1:
+                    Gst[i,j] = 0.5
+                elif i==1 or j==1 or i==len(Lx)-2 or j==len(Ly)-2:
+                    Gts[i,j] = 0.7
+    elif diagonal==True:
+        for i in range (1,len(Lx)-1):
+            for j in range (1,len(Ly)-1):
+                if (i == j):
+                    Gts[i,j]=0.5
+else:
+    with open('G_surface_empty.pkl', 'rb') as csv_file:
+        Gts = pickle.load(csv_file)
+
+with open('G_surface_empty.pkl', 'wb') as csv_file:
+    pickle.dump(Gts,csv_file)
+
+im = plt.imshow(Gts, cmap="copper_r")
+plt.show()
+