Replace Pluri_cell_prolif_migr.py

Cell_behavior_initial_steps/Pluri_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
 
@@ -21,29 +21,26 @@ if os.path.isdir(path_simulation) == False :
     os.mkdir(path_simulation)
         
 #Reopening choosen surface
-with open('G_surface_empty.pkl', '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="copper_r")
-# plt.show()
 #Gs is ground seeded, a copy of the choosen surface to seed the cells,
 Gs = copy.deepcopy(Gts)
 
 #Milticelular seeding
 for i in range (4,L-6):
     for j in range (4,L-7):
-        if Gs[i,j]==0.5:
-            Gs[i,j]=1.5
+        if Gs[i,j]==1:
+            Gs[i,j]+=0.5
         else:
-            Gs[i,j]=1
+            Gs[i,j]=1.5
             
 #images of the cell in the surface
-couture= plt.imshow(Gs, cmap="copper_r")
+couture= plt.imshow(Gs, cmap="bone")
+plt.title("Gts, Inital seeding",
+             size=20)
 plt.show()
 
-            
-
 
 #Variable deffinition for PDE proliferation & migration model
 Cd =  1*10**-5 #Cell density
@@ -60,24 +57,26 @@ 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):
+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
+                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
-                        im2 = plt.imshow(Gs, cmap="copper_r", norm = None, aspect ='equal', vmin=0 ,vmax=12)
+                    if Gs[mi,mj]>0 and Gs[mi,mj]!=1:
+                        Gs[mi,mj]=1.5
+                        plt.title("Gts, Proliferation and migration",
+                                  size=20)
+                        im2 = plt.imshow(Gs, cmap="bone")
                         plt.show()
                         name = 'Single_cell_migr_prolif'+str(iter)+'.png'
-                        # plt.imsave(os.path.join(path_simulation, name), Gs, cmap="copper_r")
+                        plt.imsave(os.path.join(path_simulation, name), Gs, cmap="bone")
                         filename = name
                         ls_images.append(im2)
                         iter+=1
                         
-WD().create_gif_from_images(files_path=results_path+os.sep+"prolif_migr",results_path=path_simulation_gif,filename='Cell_behavior.gif', time_lapse= time_lapse, deleteOriginFiles=0)
\ No newline at end of file
+WD().create_gif_from_images(files_path=results_path+os.sep+"prolif_migr",results_path=path_simulation_gif,filename='Multiple_cell_behavior.gif', time_lapse= time_lapse, deleteOriginFiles=0)
\ No newline at end of file