From 7c6740f91ae37c0e271459de36e314d11ba68a6e Mon Sep 17 00:00:00 2001
From: encinass1u <jessica-maria.encinas-silvas4@etu.univ-lorraine.fr>
Date: Wed, 18 May 2022 12:20:14 +0000
Subject: [PATCH] Replace Pluri_cell_prolif_migr.py
---
.../Pluri_cell_prolif_migr.py | 41 +++++++++----------
1 file changed, 20 insertions(+), 21 deletions(-)
diff --git a/Cell_behavior_initial_steps/Pluri_cell_prolif_migr.py b/Cell_behavior_initial_steps/Pluri_cell_prolif_migr.py
index 13de283..ce1c4b5 100644
--- a/Cell_behavior_initial_steps/Pluri_cell_prolif_migr.py
+++ b/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
--
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