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changes in figure2

master
jeremias 10 months ago
parent
commit
b8c951afcc
  1. 33
      kalman/graphics/figure2.py
  2. 76
      kalman/input_files/aorta.yaml
  3. 62
      kalman/input_files/aorta_C.yaml

33
kalman/graphics/figure2.py

@ -30,7 +30,7 @@ def load_data(file):
return dat
def plot_parameters(dat, deparameterize=False, ref=None):
def plot_parameters(dat, input_file, deparameterize=False, ref=None):
''' Plot the parameters in separate subplots with uncertainties.
Args:
@ -42,21 +42,29 @@ def plot_parameters(dat, deparameterize=False, ref=None):
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'
inputfile_path = 'results/aorta_C/input.yaml'
with open(inputfile_path) as file:
inputfile = yaml.full_load(file)
#true_val = [10,250,250,250,30]
true_val = [94,250,683,615,30]
true_val = [10,60,220,160,100]
current_val = []
current_val.append(inputfile['boundary_conditions'][2]['value'][0])
current_val.append(inputfile['boundary_conditions'][3]['value'][0])
current_val.append(inputfile['boundary_conditions'][4]['value'][0])
current_val.append(inputfile['boundary_conditions'][5]['value'][0])
current_val.append(inputfile['boundary_conditions'][1]['parameters']['U'])
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']:
current_val.append(bnd_set['value'][0])
current_val.append(inputfile['boundary_conditions'][1]['parameters']['U'])
dim = dat['theta'].shape[-1]
fig1, axes = plt.subplots(1,1,figsize=(8,6))
@ -72,6 +80,8 @@ def plot_parameters(dat, 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(['$R_3$','$U$'])
col_ = next(col)
ls_ = next(ls)
@ -100,7 +110,8 @@ def plot_parameters(dat, deparameterize=False, ref=None):
# print('theta_peak: \t {}'.format(theta[round(len(theta)/2), :]))
print('Final value theta: \t {}'.format(theta[-1, :]))
print('Deparameterized: 2^theta_end: \t {}'.format(2**theta[-1, :]))
print('Real values: \t {}'.format(np.round(2**theta[-1, :]*current_val,2)))
print('Real values: \t {}'.format(true_val))
print('Recon values: \t {}'.format(np.round(2**theta[-1, :]*current_val,2)))
@ -133,5 +144,5 @@ if __name__ == '__main__':
args = get_parser().parse_args()
dat = load_data(args.file)
plot_parameters(dat, deparameterize=args.deparameterize, ref=args.ref)
plot_parameters(dat, args.file,deparameterize=args.deparameterize, ref=args.ref)

76
kalman/input_files/aorta.yaml

@ -6,7 +6,7 @@ fluid:
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta_C'
write_path: 'results/aorta_master'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -31,32 +31,32 @@ boundary_conditions:
-
id: 3
type: 'windkessel'
#value: [10,0,0]
#p0: [0,1333.223874]
value: [10,1000,0.01]
p0: [47,1333.223874]
value: [10,0,0]
p0: [0,1333.223874]
#value: [10,1000,0.01]
#p0: [47,1333.223874]
-
id: 4
type: 'windkessel'
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,8000,0.0001]
#p0: [47,1333.223874]
-
id: 5
type: 'windkessel'
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,8000,0.0001]
#p0: [47,1333.223874]
-
id: 6
type: 'windkessel'
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,8000,0.0001]
#p0: [47,1333.223874]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -82,7 +82,7 @@ timemarching:
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.01
dt: 0.001
write_dt: 0.04
checkpoint_dt: 0.04 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
@ -120,22 +120,22 @@ linear_solver:
estimation:
boundary_conditions:
#-
# id: 3
# type: 'windkessel'
# initial_stddev: 1
#-
# id: 4
# type: 'windkessel'
# initial_stddev: 1
#-
# id: 5
# type: 'windkessel'
# initial_stddev: 1
#-
# id: 6
# type: 'windkessel'
# initial_stddev: 1
-
id: 3
type: 'windkessel'
initial_stddev: 1
-
id: 4
type: 'windkessel'
initial_stddev: 1
-
id: 5
type: 'windkessel'
initial_stddev: 1
-
id: 6
type: 'windkessel'
initial_stddev: 1
-
id: 2
type: 'dirichlet'
@ -147,13 +147,11 @@ estimation:
-
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
fe_degree: 1
#xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V120/u.xdmf'
#file_root: 'measurements/aorta_C/Perturbation/Ks12V120/u{i}.h5'
xdmf_file: 'measurements/aorta_C/u_all.xdmf'
file_root: 'measurements/aorta_C/u{i}.h5'
xdmf_file: 'measurements/aorta_master_s100/u_all.xdmf'
file_root: 'measurements/aorta_master_s100/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 15 # standard deviation of Gaussian noise
noise_stddev: 5 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex

62
kalman/input_files/aorta_C.yaml

@ -6,14 +6,14 @@ fluid:
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta_C0_ten'
write_path: 'results/aorta_C'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_xdmf: True
write_checkpoints: True
write_hdf5_timeseries: False
write_velocity: 'tentative' # tentative or update
write_velocity: 'update' # tentative or update
boundary_conditions:
-
@ -24,41 +24,47 @@ boundary_conditions:
id: 2
type: 'dirichlet'
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (t<=Tc)*(t>Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))
- U*sin(DOLFIN_PI*(t-Tc)/Th)*(t>Tc)*(t<= Tc + Th) + (t>Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-Tc)/Th)*exp(-(t-Tc)*10))']
- U*sin(DOLFIN_PI*(t-Tc)/Th)*(t>Tc)*(t<= Tc + Th)
+ (t<=2*Tc)*(t>Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-Tc)/Th)*exp(-(t-Tc)*10))
- U*sin(DOLFIN_PI*(t-2*Tc)/Th)*(t>2*Tc)*(t<= 2*Tc + Th)
+ (t<=3*Tc)*(t>2*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-2*Tc)/Th)*exp(-(t-2*Tc)*10))
- U*sin(DOLFIN_PI*(t-3*Tc)/Th)*(t>3*Tc)*(t<= 3*Tc + Th)
+ (t<=4*Tc)*(t>3*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-3*Tc)/Th)*exp(-(t-3*Tc)*10))
- U*sin(DOLFIN_PI*(t-4*Tc)/Th)*(t>4*Tc)*(t<= 4*Tc + Th)
+ (t<=5*Tc)*(t>4*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-4*Tc)/Th)*exp(-(t-4*Tc)*10)) ']
parameters:
U: 30
U: 100 #100 safe
Th: 0.35
Tc: 0.8
t: 0
-
id: 3
type: 'windkessel'
#value: [10,1000,0.01] #paper corr
#value: [94,1794,0.0014] #paper windk
value: [94,0,0]
p0: [0,1333.223874]
value: [10,0.0008,2400]
#value: [10,0,2400]
p0: [80,1333.223874]
#p0: [0,1333.223874]
-
id: 4
type: 'windkessel'
#value: [250,8000,0.0001] #paper corr
#value: [250,10000,0.0004] #paper windk
value: [250,0,0] #paper
p0: [0,1333.223874]
value: [60,0.00034,4200]
#value: [60,0,4200] #safe
p0: [80,1333.223874]
#p0: [0,1333.223874]
-
id: 5
type: 'windkessel'
#value: [250,8000,0.0001] #paper corr
#value: [683,12960,0.0002] #paper windk
value: [683,0,0]
p0: [0,1333.223874]
value: [220,0.00034,11000]
#value: [220,0,11000] #safe
p0: [80,1333.223874]
#p0: [0,1333.223874]
-
id: 6
type: 'windkessel'
#value: [250,8000,0.0001] #paper corr
#value: [615,11664,0.0002] #paper windk
value: [615,0,0]
p0: [0,1333.223874]
value: [160,0.00034,7800]
#value: [160,0,7800] #safe
p0: [80,1333.223874]
#p0: [0,1333.223874]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -83,8 +89,8 @@ timemarching:
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 1.6 # end time
dt: 0.001
T: 0.8 # end time
dt: 0.002
write_dt: 0.04
checkpoint_dt: 0.04 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
@ -129,7 +135,7 @@ estimation:
#-
# id: 4
# type: 'windkessel'
# initial_stddev: 1
# initial_stddev: 1
#-
# id: 5
# type: 'windkessel'
@ -148,8 +154,10 @@ estimation:
-
mesh: './meshes/coaortaH3_leo2.0.h5'
fe_degree: 1
xdmf_file: 'measurements/aorta_C/u_all.xdmf'
file_root: 'measurements/aorta_C/u{i}.h5'
#xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V50/u_all.xdmf'
#file_root: 'measurements/aorta_C/Perturbation/Ks12V50/u{i}.h5'
xdmf_file: 'measurements/aorta_C_s100/u_all.xdmf'
file_root: 'measurements/aorta_C_s100/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 15 # standard deviation of Gaussian noise
@ -160,4 +168,4 @@ estimation:
reparameterize: True
ODV_functional:
enable: False
VENC: 102 # 102,120% 59,70% 42 50%, 21,25%
VENC: 172 # 241,172
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