Replace single_cell_prolif_migr.py

Cell_behavior_initial_steps/single_cell_prolif_migr.py

@@ -8,7 +8,7 @@ import random
 from scipy import ndimage
 from bio2mslib.inout.inout import WriteData as WD
 import os
-from Gts_selection import L, Lx, Ly
+from Gts_selection import L
 from bio2mslib.analysis.models import CellModels as DM
 from matplotlib.pyplot import figure
 
@@ -21,18 +21,20 @@ if os.path.isdir(path_simulation) == False :
     os.mkdir(path_simulation)
         
 #Reopening choosen surface
-with open('Gts_Sample_100.cvs', 'rb') as csv_file:
+with open('Gts_Sample.cvs', 'rb') as csv_file:
      Gts = pickle.load(csv_file)
 
-# #Visual preentation in image of the matrix
-# im1 = plt.imshow(Gts, cmap="bone")
-# plt.show()
 #Gs is ground seeded, a copy of the choosen surface to seed the cells,
 Gs = copy.deepcopy(Gts)
 
 #uni_cell is the seeding of a single cell inside the treated surface.
-uni_cell = Gs[(86,8)]
-Gs[(86,8)] = 1
+uni_cell = Gs[(8,8)]
+Gs[(8,8)] = 1.5
+plt.title("Gts, Inital seeding",
+             size=20)
+#images of the cell in the surface
+couture= plt.imshow(Gs, cmap="bone")
+plt.show()
 
 #Variable deffinition for PDE proliferation & migration model
 Cd =  1*10**-5 #Cell density
@@ -48,20 +50,21 @@ time_lapse = 0.1
 Gscopy = copy.deepcopy(Gs)
 Laplace = ndimage.laplace(Gs)
 #Migration 
-iter = 0
-while iter<= 15:
-    for mi in range(1, len(Lx)-1):
-        for mj in range(1, len(Ly)-1):
+iter = 1
+while iter<= 5:
+    for mi in range(1, L-1):
+        for mj in range(1, L-1):
                 x = random.randint(-1,1)#horizontal value for the movement of the cell
                 y = random.randint(-1,1)#vertival value for the movement of the cell
-                if Gs[mi,mj]==1 and (x != 0 or y!= 0) and ((mi+x)<len(Lx)) and ((mj+y)< len(Ly)):
-                    Gs[mi+x,mj+y]= 1
-                    Gs[mi,mj]=0
+                if Gs[mi,mj]==1.5 and (x != 0 or y!= 0) and ((mi+x)<L) and ((mj+y)< L):
+                    Gs[mi+x,mj+y]= 1.5
+                    Gs[mi,mj]+=0
                     #Proliferation after migration
                     Gs[mi,mj] = Gscopy[mi,mj] + dt*Dm*Laplace[mi,mj]*(1-(Gscopy[mi,mj]/Cdmax))+CRgrw*1*Gscopy[mi,mj]*(1-(Gscopy[mi,mj]/Cdmax))                
-                    if Gs[mi,mj]>0 and Gs[mi,mj]!=0.7 and Gs[mi,mj]!=0.5 :
-                        Gs[mi,mj]=1
-                        zoom = True
+                    if Gs[mi,mj]>0 and Gs[mi,mj]!=1 :
+                        Gs[mi,mj]=1.5
+                        plt.title('Cell migration & proliferation '+str(iter),
+                                  size=20)
                         im2 = plt.imshow(Gs, cmap="bone", norm = None)
                         plt.show()
                         name = 'Single_cell_SMAT_sample'+str(iter)+'.png'