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encinass1u
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885a50ec
Cell behavior Codes
· 885a50ec
encinass1u
authored
3 years ago
Cell_behavior_initial_steps/Pluri_cell_prolif_migr.py
0 → 100644
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0
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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
from
Gts_selection
import
L
,
Lx
,
Ly
from
bio2mslib.analysis.models
import
CellModels
as
DM
from
matplotlib.pyplot
import
figure
#Declaring saving paths for results
ls_images
=
[]
results_path
=
os
.
getcwd
()
+
os
.
sep
+
"
Pluri_cell
"
path_simulation_gif
=
os
.
getcwd
()
+
os
.
sep
+
"
Pluri_cell
"
path_simulation
=
results_path
+
os
.
sep
+
"
prolif_migr
"
if
os
.
path
.
isdir
(
path_simulation
)
==
False
:
os
.
mkdir
(
path_simulation
)
#Reopening choosen surface
with
open
(
'
G_surface_empty.pkl
'
,
'
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
else
:
Gs
[
i
,
j
]
=
1
#images of the cell in the surface
couture
=
plt
.
imshow
(
Gs
,
cmap
=
"
copper_r
"
)
plt
.
show
()
#Variable deffinition for PDE proliferation & migration model
Cd
=
1
*
10
**-
5
#Cell density
NO2
=
10
**
2
#nutrient concentration
Cdmax
=
10
**
7
#maximum cell density
Dm
=
0.001
#Cell motility coefficient
CRgrw
=
1
#rate of cell growth
CRNO2
=
10
**-
8
#Consumption rate of nutrients
DNO2
=
2
*
10
**-
5
dt
=
1
#time step
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
):
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
#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
)
plt
.
show
()
name
=
'
Single_cell_migr_prolif
'
+
str
(
iter
)
+
'
.png
'
# plt.imsave(os.path.join(path_simulation, name), Gs, cmap="copper_r")
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
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