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update

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jeremias 1 year ago
parent
commit
d7f4709593
  1. 101
      kalman/graphics/figure2.py
  2. 244
      kalman/graphics/figure3.py
  3. 90
      kalman/input_files/aorta.yaml
  4. 0
      presentations/press_course1/images/4dflow.png
  5. 0
      presentations/press_course1/images/MRI.jpg
  6. BIN
      presentations/press_course1/images/aorta_healthy.JPG
  7. BIN
      presentations/press_course1/images/aortic_stenosis_1.png
  8. BIN
      presentations/press_course1/images/aortic_stenosis_2.png
  9. BIN
      presentations/press_course1/images/aortic_stenosis_3.png
  10. 0
      presentations/press_course1/images/aortic_stenosis_4.png
  11. 0
      presentations/press_course1/images/catheter.png
  12. 0
      presentations/press_course1/images/p.png
  13. BIN
      presentations/press_course1/images/p2.png

101
kalman/graphics/figure2.py

@ -52,42 +52,31 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -52,42 +52,31 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
inputfile = yaml.full_load(file)
#true_values = {
# 3: 3400,
# 4: 4200,
# 5: 11000,
# 6: 7800,
# 2: 100
# }
true_values = {
3: 4800,
4: 7020,
4: 7200,
5: 11520,
6: 11520,
2: 75
}
true_values_C = {
3: 0.0004,
4: 0.0004,
5: 0.0003,
6: 0.0003,
}
true_values_c = {
3: 0.0008,
4: 0.00034,
5: 0.00034,
6: 0.00034,
2: 100
}
true_values_rp = {
3: 10,
4: 60,
5: 220,
6: 160,
2: 100
}
meas_flag = False
RC_mod = True
line_split = 1.5
current_val = []
current_val_C = []
ids_type = []
labels = []
ids = []
@ -97,14 +86,23 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -97,14 +86,23 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
for bnd_set in inputfile['boundary_conditions']:
if bnd_c['id'] == bnd_set['id']:
ids.append(bnd_c['id'])
ids_type.append('windkessel')
current_val.append(bnd_set['parameters']['R_d'])
labels.append('$R_' + str(bnd_c['id']))
if RC_mod:
current_val_C.append(bnd_set['parameters']['C'])
labels.append('$C_' + str(bnd_c['id']))
elif 'dirichlet' in bnd_c['type']:
current_val.append(inputfile['boundary_conditions'][0]['parameters']['U'])
ids.append(bnd_c['id'])
ids_type.append('dirichlet')
labels.append('$U')
dim = dat['theta'].shape[-1]
fig1, axes = plt.subplots(1,1,figsize=(8,6))
@ -116,9 +114,12 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -116,9 +114,12 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
col = cycle(['C0', 'C1', 'C2', 'C3','C4'])
ls = cycle(['-', '-', '--', '--', ':', ':', '-.', '-.'])
#legends = cycle(['$R_3$','$R_4$','$R_5$','$R_6$','$U$'])
legends = cycle(labels)
if meas_flag:
t_und = t[0::30]
t_und = np.append( t_und , [t[-1]])
meas_mark = t_und*0
col_ = next(col)
ls_ = next(ls)
@ -127,23 +128,51 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -127,23 +128,51 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
if dim == 1:
theta = theta.reshape((-1, 1))
P = P.reshape((-1, 1, 1))
for i in range(dim):
true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
rec_value = np.round(2**theta[-1, i]*current_val[i],2)
idx = 0
idc = 0
for i in range(len(ids)):
cur_key = ids[i]
axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
axes.fill_between(t, theta[:, i] + 1.5*i - np.sqrt(P[:, i, i]),
theta[:, i] + 1.5*i + np.sqrt(P[:, i, i]), alpha=0.3,
color=col_)
true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
rec_value = np.round(2**theta[-1, idx]*current_val[i],2)
#curve = theta[:,i] + line_split*i
#dash_curve = line_split*i + t*0 + true_level
curve = theta[:,idx] + line_split*idx - true_level
dash_curve = line_split*idx + t*0
axes.plot(t, curve , '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
axes.fill_between(t, curve - np.sqrt(P[:, idx, idx]), curve + np.sqrt(P[:, idx, idx]), alpha=0.3, color=col_)
legends_=next(legends)
axes.plot(t, dash_curve , color=col_,ls='--')
if RC_mod:
if i<len(current_val_C):
true_level_C = np.log(true_values_C[ids[i]]/current_val_C[i])/np.log(2)
rec_value_C = np.round(2**theta[-1, idc]*current_val_C[idc],6)
curve_C = theta[:,idx+1] + line_split*(idx+1) - true_level_C
dash_curve_C = line_split*(idx+1) + t*0
#print(true_values_C[cur_key_C])
axes.plot(t, curve_C , '-', color=col_,label= legends_ + '= ' + str(rec_value_C) + '/' + str(true_values_C[cur_key]) + '$')
axes.fill_between(t, curve_C - np.sqrt(P[:, idx+1, idx+1]), curve_C + np.sqrt(P[:, idx+1, idx+1]), alpha=0.3, color=col_)
axes.plot(t, dash_curve_C , color=col_,ls='--')
legends_=next(legends)
idx +=1
idc +=1
if meas_flag:
axes.plot(t_und, meas_mark + line_split*idx, marker = 'x', color='red')
axes.plot(t,1.5*i + t*0 + true_level , color=col_,ls='--')
col_ = next(col)
legends_=next(legends)
idx +=1
axes.legend(fontsize=14,loc='lower right')
axes.set_xlim([-0.01,0.81])
@ -152,7 +181,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -152,7 +181,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
print('Final value theta: \t {}'.format(theta[-1, :]))
print('Deparameterized: 2^theta_end: \t {}'.format(2**theta[-1, :]))
print('Real values: \t {}'.format(true_values))
print('Recon values: \t {a}:{b} '.format(a=ids[:],b=np.round(2**theta[-1, :]*current_val,2)))
#print('Recon values: \t {a}:{b} '.format(a=ids[:],b=np.round(2**theta[-1, :]*current_val,2)))

244
kalman/graphics/figure3.py

@ -0,0 +1,244 @@ @@ -0,0 +1,244 @@
import matplotlib.pyplot as plt
import numpy as np
from itertools import cycle
import argparse
import pickle
import yaml
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
rc('text', usetex=True)
import matplotlib.font_manager
def is_ipython():
''' Check if script is run in IPython.
Returns:
bool: True if IPython, else False '''
try:
get_ipython()
ipy = True
except NameError:
ipy = False
return ipy
def load_data(file):
''' Load numpy data from file.
Returns
dict: data dictionary
'''
dat = np.load(file)
return dat
def plot_parameters(dat, input_file, deparameterize=False, ref=None):
''' Plot the parameters in separate subplots with uncertainties.
Args:
dat (dict): data dictionary
deparameterize (bool): flag indicating if parameters should be
deparameterized via 2**theta
ref: reference value to be plotted with parameters
'''
if is_ipython():
plt.ion()
idx_a = input_file.find('/')
idx_b = input_file[idx_a+1::].find('/')
name_file = input_file[idx_a+1:idx_b+idx_a+1]
inputfile_path = 'results/' + name_file + '/input.yaml'
with open(inputfile_path) as file:
inputfile = yaml.full_load(file)
true_values = {
3: 4800,
4: 7200,
5: 11520,
6: 11520,
2: 75
}
true_values_C = {
3: 0.0004,
4: 0.0004,
5: 0.0003,
6: 0.0003,
}
meas_flag = False
RC_flag = False
line_split = 1.5
current_val = []
current_val_C = []
ids_type = []
labels = []
ids = []
for bnd_c in inputfile['estimation']['boundary_conditions']:
if 'windkessel' in bnd_c['type']:
for bnd_set in inputfile['boundary_conditions']:
if bnd_c['id'] == bnd_set['id']:
ids.append(bnd_c['id'])
ids_type.append('windkessel')
current_val.append(bnd_set['parameters']['R_d'])
labels.append('$R_' + str(bnd_c['id']))
if RC_flag:
current_val_C.append(bnd_set['parameters']['C'])
labels.append('$C_' + str(bnd_c['id']))
elif 'dirichlet' in bnd_c['type']:
current_val.append(inputfile['boundary_conditions'][0]['parameters']['U'])
ids.append(bnd_c['id'])
ids_type.append('dirichlet')
labels.append('$U')
dim = dat['theta'].shape[-1]
fig1, axes1 = plt.subplots(1,1,figsize=(12,6))
if RC_flag:
fig2, axes2 = plt.subplots(1,1,figsize=(12,6))
t = dat['times']
theta = dat['theta']
P = dat['P_theta']
col = cycle(['C0', 'C1', 'C2', 'C3','C4'])
ls = cycle(['-', '-', '--', '--', ':', ':', '-.', '-.'])
legends = cycle(labels)
if meas_flag:
t_und = t[0::30]
t_und = np.append( t_und , [t[-1]])
meas_mark = t_und*0
col_ = next(col)
ls_ = next(ls)
legends_=next(legends)
if dim == 1:
theta = theta.reshape((-1, 1))
P = P.reshape((-1, 1, 1))
idx = 0
idc = 0
for i in range(len(ids)):
cur_key = ids[i]
true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
rec_value = np.round(2**theta[-1, idx]*current_val[i],2)
#curve = theta[:,idx] + line_split*idx - true_level
#dash_curve = line_split*idx + t*0
curve = 2**theta[:, idx]*current_val[i]
std_down = 2**(-np.sqrt(P[:, idx, idx]))*curve
std_up = 2**np.sqrt(P[:, idx, idx])*curve
dash_curve = true_values[ids[i]] + t*0
if ids_type[i] == 'dirichlet':
pass
#axes3.plot(t, curve , '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
#axes3.fill_between(t, curve - np.sqrt(P[:, idx, idx]), curve + np.sqrt(P[:, idx, idx]), alpha=0.3, color=col_)
#legends_=next(legends)
#axes3.plot(t, dash_curve , color=col_,ls='--')
else:
axes1.plot(t, curve , '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$', linewidth = 2)
axes1.fill_between(t, std_down, std_up, alpha=0.3, color=col_)
axes1.plot(t, dash_curve , color=col_,ls='--')
legends_=next(legends)
if RC_flag:
if i<len(current_val_C):
true_level_C = np.log(true_values_C[ids[i]]/current_val_C[i])/np.log(2)
rec_value_C = np.round(2**theta[-1, idc]*current_val_C[idc],6)
curve_C = 2**theta[:, idx+1]*current_val_C[idc]
dash_curve_C = true_values_C[ids[i]] + t*0
std_C_down = 2**(-np.sqrt(P[:, idx+1, idx+1]))*curve_C
std_C_up = 2**np.sqrt(P[:, idx+1, idx+1])*curve_C
axes2.plot(t, curve_C , '-', color=col_,label= legends_ + '= ' + str(rec_value_C) + '/' + str(true_values_C[cur_key]) + '$', linewidth = 2)
axes2.fill_between(t, std_C_down, std_C_up, alpha=0.3, color=col_)
axes2.plot(t, dash_curve_C , color=col_,ls='--')
legends_=next(legends)
idx +=1
idc +=1
if meas_flag:
axes1.plot(t_und, meas_mark + line_split*idx, marker = 'x', color='red')
col_ = next(col)
idx +=1
axes1.set_ylabel(r'$R_d$',fontsize=22)
axes1.legend(fontsize=18,loc='upper right')
axes1.set_xlim([-0.01,0.81])
axes1.set_xlabel(r'$t (s)$',fontsize=22)
plt.savefig('C.png')
if RC_flag:
axes2.set_ylabel(r'$C$',fontsize=22)
axes2.legend(fontsize=18,loc='upper right')
axes2.set_xlim([-0.01,0.81])
axes2.set_xlabel(r'$t (s)$',fontsize=22)
fig2.savefig('C.png')
fig1.savefig('Rd.png')
if not is_ipython():
plt.show()
def get_parser():
parser = argparse.ArgumentParser(
description='''
Plot the time evolution of the ROUKF estimated parameters.
To execute in IPython::
%run plot_roukf_parameters.py [-d] [-r N [N \
...]] file
''',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('file', type=str, help='path to ROUKF stats file')
parser.add_argument('-d', '--deparameterize', action='store_true',
help='deparameterize the parameters by 2**theta')
parser.add_argument('-r', '--ref', metavar='N', nargs='+', default=None,
type=float, help='Reference values for parameters')
return parser
if __name__ == '__main__':
args = get_parser().parse_args()
dat = load_data(args.file)
plot_parameters(dat, args.file,deparameterize=args.deparameterize, ref=args.ref)

90
kalman/input_files/aorta.yaml

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid
# Physical parameters of the fluid
fluid:
density: 1.2
dynamic_viscosity: 0.035
@ -8,7 +8,7 @@ fluid: @@ -8,7 +8,7 @@ fluid:
implicit_windkessel: True
io:
write_path: 'results/aorta25_zPb_3R'
write_path: 'results/Rz_Pa_vnoise'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -26,9 +26,10 @@ boundary_conditions: @@ -26,9 +26,10 @@ boundary_conditions:
# -U*sin(DOLFIN_PI*(t-1.6)/Th)*(t<= 1.6+Th )*(t>1.6) + (t<2.4)*(1.6+Th<t)*(U*DOLFIN_PI/Th*(t-1.6-Th)*exp(-(t-1.6-Th)*beta))' ]
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
parameters:
#U: 75
#U: 150 #Pa
U: 40 #Pb
#U: 75 #P0
U: 150 #Pa
#U: 100 #Pg
#U: 40 #Pc
Th: 0.36
beta: 70
t: 0
@ -41,10 +42,8 @@ boundary_conditions: @@ -41,10 +42,8 @@ boundary_conditions:
type: 'windkessel'
parameters:
R_p: 200
C: 0.0005
#R_d: 4800
#R_d: 9000 #Pa
R_d: 2000 #Pb
C: 0.0004
R_d: 4800
p0: 85
conv: 1333.223874
-
@ -52,10 +51,16 @@ boundary_conditions: @@ -52,10 +51,16 @@ boundary_conditions:
type: 'windkessel'
parameters:
R_p: 480
C: 0.00045
#R_d: 7200
#R_d: 12000 #Pa
R_d: 4000 #Pb
#C: 0.0004 # P0
C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 7200 #P0
R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 10000 #Pg
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
@ -63,10 +68,17 @@ boundary_conditions: @@ -63,10 +68,17 @@ boundary_conditions:
type: 'windkessel'
parameters:
R_p: 520
C: 0.00045
#R_d: 11520
#R_d: 23000 #Pa
R_d: 6000 #Pb
#C: 0.0003 # REFERENCE
C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 11520 # REFERENCE
R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 26280 #Pc x3
#R_d: 10000 #Pg
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
@ -74,10 +86,17 @@ boundary_conditions: @@ -74,10 +86,17 @@ boundary_conditions:
type: 'windkessel'
parameters:
R_p: 520
C: 0.00045
R_d: 11520
#R_d: 23000 #Pa
#R_d: 6000 #Pb
#C: 0.0003 # REFERENCE
C: 0.0005 #Pa
#C: 0.0010 #Pb
#C: 0.0001 #Pc
#C: 0.0008 #Pg
#R_d: 11520 # REFERENCE
R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 26280 #Pc x3
#R_d: 10000 #Pg
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
@ -143,22 +162,25 @@ linear_solver: @@ -143,22 +162,25 @@ linear_solver:
estimation:
boundary_conditions:
#-
# id: 3
# type: 'windkessel'
# initial_stddev: 1
-
id: 3
id: 4
type: 'windkessel'
mode: 'Rd'
initial_stddev: 1
-
id: 4
id: 5
type: 'windkessel'
mode: 'Rd'
initial_stddev: 1
-
id: 5
id: 6
type: 'windkessel'
mode: 'Rd'
initial_stddev: 1
#-
# id: 6
# type: 'windkessel'
# initial_stddev: 1
-
id: 2
type: 'dirichlet'
@ -171,13 +193,13 @@ estimation: @@ -171,13 +193,13 @@ estimation:
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
#mesh: './meshes/coaortaH1.h5'
fe_degree: 1
xdmf_file: 'measurements/aorta25_z/Perturbation/Mg15V120/u_all.xdmf'
file_root: 'measurements/aorta25_z/Perturbation/Mg15V120/u{i}.h5'
#xdmf_file: 'measurements/aorta25_z/u_all.xdmf'
#file_root: 'measurements/aorta25_z/u{i}.h5'
#xdmf_file: 'measurements/aorta_zdir/Perturbation/Mg15V120/u_all.xdmf'
#file_root: 'measurements/aorta_zdir/Perturbation/Mg15V120/u{i}.h5'
xdmf_file: 'measurements/aorta_zdir_vnoise/u_all.xdmf'
file_root: 'measurements/aorta_zdir_vnoise/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: [0,0,1]
noise_stddev: 55 # standard deviation of Gaussian noise
noise_stddev: 45 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
@ -185,4 +207,4 @@ estimation: @@ -185,4 +207,4 @@ estimation:
reparameterize: True
ODV_functional:
enable: False
VENC: 102 # 102,120% 59,70% 42 50%, 21,25%
VENC: 244

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