def compute(N, filename, method, Ncell, diabete='N'):
# cell = [[]]
# for i in range(Ncell):
# for j in range(N):
# cell[i,j].append(membrane())
cell = [[membrane() for i in range(N)] for j in range(Ncell)]
if diabete == 'N':
for i in range(Ncell):
for j in range(N):
cell[i][j].diabete = 'No'
elif diabete == 'Y':
for i in range(Ncell):
for j in range(N):
cell[i][j].diabete = 'Yes'
else:
print('What is diabete status?')
water_trans = 0
na_trans = 0
water_para = 0
na_para = 0
#filename=input('Choose a data file: ')
#method = input('Choose a method: Newton or Broyden: ')
for i in range(Ncell):
for j in range(N):
set_params.read_params(cell[i][j], filename, 0)
#cell[i].area_init[4][5] = 0.02
#cell[i].area[4][5] = cell[i].area_init[4][5]*max(cell[i].vol[4]/cell[i].volref[4],1.0)
#cell[i].area[5][4] = cell[i].area[4][5]
boundaryBath.boundaryBath(cell[i][j], i)
for i in range(Ncell - 1):
celln = copy.deepcopy(cell[i + 1][0])
dx = 1.0e-3
if cell[0][0].segment == 'PT':
x = np.zeros(3 * NS + 7)
x[0:NS] = cell[i][0].conc[:, 0]
x[NS:2 * NS] = cell[i][0].conc[:, 1]
x[2 * NS:3 * NS] = cell[i][0].conc[:, 4]
x[3 * NS] = cell[i][0].vol[0]
x[3 * NS + 1] = cell[i][0].vol[1]
x[3 * NS + 2] = cell[i][0].vol[4]
x[3 * NS + 3] = cell[i][0].ep[0]
x[3 * NS + 4] = cell[i][0].ep[1]
x[3 * NS + 5] = cell[i][0].ep[4]
x[3 * NS + 6] = cell[i][0].pres[0]
# x[3 * NS + 6] = cell[i][0].pres[1]
steadyequations.steadyconservation_init(cell[i][0], cell[i + 1][0],
celln, dx)
fvec = steadyequations.steadyconservation_eqs(x, i)
# print(fvec)
if method == 'Newton':
sol = Newton.newton(steadyequations.steadyconservation_eqs, x,
i, cell[i][0].segment)
if method == 'Broyden':
sol = Newton.broyden(steadyequations.steadyconservation_eqs, x,
i, cell[i][0].segment)
if cell[0][0].segment == 'PT':
cell[i + 1][0].conc[:, 0] = sol[0:NS]
cell[i + 1][0].conc[:, 1] = sol[NS:NS * 2]
cell[i + 1][0].conc[:, 4] = sol[NS * 2:NS * 3]
cell[i + 1][0].vol[0] = sol[3 * NS]
cell[i + 1][0].vol[1] = sol[3 * NS + 1]
cell[i + 1][0].vol[4] = sol[3 * NS + 2]
cell[i + 1][0].ep[0] = sol[3 * NS + 3]
cell[i + 1][0].ep[1] = sol[3 * NS + 4]
cell[i + 1][0].ep[4] = sol[3 * NS + 5]
cell[i + 1][0].pres[0] = sol[3 * NS + 6]
# cell[i + 1][0].pres[1] = sol[3 * NS + 6]
# to make mdel works we should do something different
# to simulate sudden change, we need to change first cell's condition
# do change as below (change cell[0]'s lumen condition means change boundary condition)
for j in range(N):
# cell[0][j].vol[0] = cell[0][j].vol[0] * (1 + 0.1 * math.sin(2 * math.pi * j / 30))
cell[0][j].conc[14, 0] = cell[0][j].conc[14, 0] * 1.1
# update in time
for j in range(1, N):
print('This is time ' + str(0.1 * j) + 's')
for i in range(1, Ncell):
print(" ")
print('Calculating ' + str(i) + 'th Cell')
celln = copy.deepcopy(cell[i - 1][j])
dx = 1.0e-3
if cell[0][0].segment == 'PT':
x = np.zeros(3 * NS + 7)
x[0:NS] = cell[i][j - 1].conc[:, 0]
x[NS:2 * NS] = cell[i][j - 1].conc[:, 1]
x[2 * NS:3 * NS] = cell[i][j - 1].conc[:, 4]
x[3 * NS] = cell[i][j - 1].vol[0]
x[3 * NS + 1] = cell[i][j - 1].vol[1]
x[3 * NS + 2] = cell[i][j - 1].vol[4]
x[3 * NS + 3] = cell[i][j - 1].ep[0]
x[3 * NS + 4] = cell[i][j - 1].ep[1]
x[3 * NS + 5] = cell[i][j - 1].ep[4]
x[3 * NS + 6] = cell[i][j - 1].pres[0]
# x[3*NS+6]=cell[i-1][j+1].pres[1]
equations.conservation_init(cell[i][j - 1], cell[i][j], celln,
dx)
fvec = equations.conservation_eqs(x, j)
#print(fvec)
if method == 'Newton':
sol = Newton.newton(equations.conservation_eqs, x, i,
cell[i][j].segment)
if method == 'Broyden':
sol = Newton.broyden(equations.conservation_eqs, x, i,
cell[i][j].segment)
if cell[0][0].segment == 'PT':
cell[i][j].conc[:, 0] = sol[0:NS]
cell[i][j].conc[:, 1] = sol[NS:NS * 2]
cell[i][j].conc[:, 4] = sol[NS * 2:NS * 3]
cell[i][j].vol[0] = sol[3 * NS]
cell[i][j].vol[1] = sol[3 * NS + 1]
cell[i][j].vol[4] = sol[3 * NS + 2]
cell[i][j].ep[0] = sol[3 * NS + 3]
cell[i][j].ep[1] = sol[3 * NS + 4]
cell[i][j].ep[4] = sol[3 * NS + 5]
cell[i][j].pres[0] = sol[3 * NS + 6]
# cell[i][j+1].pres[1] = sol[3*NS+6]
#
# print("KKKKKKK")
# print(sol[3*NS+5])
# print(sol[3 * NS + 6])
# print(sol[0:NS])
# print( sol[3*NS+2])
# print(sol[3*NS+5])
# print("cell concentration")
# print(sol[3*NS+4])
# print(sol[3*NS+1])
# check1=0
# check2=0
# stepdiff=np.zeros(3*NS+7)
# stepdiff[0:NS]=cell[i+1].conc[:,0]-cell[i].conc[:,0]
# stepdiff[NS:2*NS] = cell[i + 1].conc[:, 1] - cell[i ].conc[:, 1]
# stepdiff[2*NS:NS*3] = cell[i + 1].conc[:, 4] - cell[i ].conc[:, 4]
# stepdiff[3*NS]=cell[i+1].vol[0]-cell[i].vol[0]
# stepdiff[3 * NS+1]=cell[i+1].vol[4]-cell[i].vol[4]
# stepdiff[3 * NS+2]=cell[i+1].ep[0]-cell[i].ep[0]
# stepdiff[3 * NS+3]=cell[i+1].ep[1]-cell[i].ep[1]
# stepdiff[3 * NS+4]=cell[i+1].ep[4]-cell[i].ep[4]
# stepdiff[3 * NS+5]=cell[i+1].pres[0]-cell[i].pres[0]
# stepdiff[3 * NS+6]=cell[i+1].pres[1]-cell[i].pres[1]
#
# diffrelative=np.zeros(3*NS+7)
# diffrelative[0:NS] = (cell[i + 1].conc[:, 0] - cell[i ].conc[:, 0])/ cell[i ].conc[:, 0]
# diffrelative[NS:2 * NS] =( cell[i + 1].conc[:, 1] - cell[i ].conc[:,1])/cell[i].conc[:, 1]
# diffrelative[2 * NS:NS * 3] =( cell[i + 1].conc[:, 4] - cell[i ].conc[:, 4])/ cell[i ].conc[:, 4]
# diffrelative[3 * NS] = (cell[i + 1].vol[0] - cell[i].vol[0])/cell[i].vol[0]
# diffrelative[3 * NS + 1] =( cell[i + 1].vol[4] - cell[i].vol[4])/cell[i].vol[4]
# diffrelative[3 * NS + 2] = (cell[i + 1].ep[0] - cell[i].ep[0])/cell[i].ep[0]
# diffrelative[3 * NS + 3] = (cell[i + 1].ep[1] - cell[i].ep[1])/cell[i].ep[1]
# diffrelative[3 * NS + 4] = (cell[i + 1].ep[4] - cell[i].ep[4])/cell[i].ep[4]
# diffrelative[3 * NS + 5] = (cell[i + 1].pres[0] - cell[i].pres[0])/cell[i].pres[0]
# diffrelative[3 * NS + 6] = (cell[i + 1].pres[1] - cell[i].pres[1])/cell[i].pres[1]
# check1=0
# # check difference on x should be small enough
# check1=max(abs(stepdiff))
# check2=max(abs(diffrelative))
# if check1<0.001 and check2<0.001:
# N=i+1
# break
# else:
# print("check1 and check2")
# print(check1)
# print(check2)
print('\n')
#================================OUTPUT IN TO FILE================================
# if cell[0].segment == 'PT':
# file=open('PToutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4],cell[N-1].conc[j,5]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
#
# elif cell[0].segment == 'S3':
# file=open('S3outlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'SDL':
# file=open('SDLoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'mTAL':
# file=open('mTALoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'cTAL':
# file=open('cTALoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4],cell[N-1].conc[j,5]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'MD':
# file=open('MDoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'DCT':
# file=open('DCToutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'CNT':
# file=open('CNToutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,2],cell[N-1].conc[j,3],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[2],cell[N-1].vol[3],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[2],cell[N-1].ep[3],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'CCD':
# file=open('CCDoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,2],cell[N-1].conc[j,3],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[2],cell[N-1].vol[3],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[2],cell[N-1].ep[3],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'OMCD':
# file=open('OMCDoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,2],cell[N-1].conc[j,3],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[2],cell[N-1].vol[3],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[2],cell[N-1].ep[3],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
# elif cell[0].segment == 'IMCD':
# file=open('IMCDoutlet'+cell[0].sex+'.txt','w')
# for j in range(NS):
# file.write('{} {} {} \n'.format(cell[N-1].conc[j,0],cell[N-1].conc[j,1],cell[N-1].conc[j,4]))
# file.write('{} {} {} \n'.format(cell[N-1].vol[0],cell[N-1].vol[1],cell[N-1].vol[4]))
# file.write('{} {} {} \n'.format(cell[N-1].ep[0],cell[N-1].ep[1],cell[N-1].ep[4]))
# file.write(str(cell[N-1].pres[0]))
# file.close()
number_of_cell = [i for i in range(1, 200)]
solute = [
'Na', 'K', 'Cl', 'HCO3', 'H2CO3', 'CO2', 'HPO4', 'H2PO4', 'urea',
'NH3', 'NH4', 'H', 'HCO2', 'H2CO2', 'glu'
]
compart = ['Lumen', 'Cell', 'ICA', 'ICB', 'LIS', 'Bath']
return cell
w_init=w_init,
iteration=iteration,
lr=lr)
gd.run()
y_predict = gd.predict(x_test)
print('SGD accuracy is: {:.2f}%'.format(gd.accuracy(y_test, y_predict)))
"""
### Part4: Newton -----------------------------------------
"""
alpha = 0.2
beta = 0.9
iteration = 5
newton = Newton.newton(x_train,
y_train,
w_init=w_init,
iteration=iteration,
alpha=alpha,
beta=beta)
newton.run()
y_predict = newton.predict(x_test)
print('Newton accuracy is: {:.2f}%'.format(
newton.accuracy(y_test, y_predict)))
"""
### Part6: Natural Gradient -------------------------------
"""
lr = 0.2
iteration = 5
ng = Natural_Gradient.ng(x_train,
y_train,
w_init=w_init,