changes in figure2

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)))
 
 
 
@@ -134,4 +145,4 @@ if __name__ == '__main__':
 
     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)

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]
+        value: [10,0,0]
-        #p0: [0,1333.223874]
+        p0: [0,1333.223874]
-        value: [10,1000,0.01]
+        #value: [10,1000,0.01]
-        p0: [47,1333.223874]
+        #p0: [47,1333.223874]
     - 
         id: 4
         type: 'windkessel'
-        #value: [250,0,0]
+        value: [250,0,0]
-        #p0: [0,1333.223874]
+        p0: [0,1333.223874]
-        value: [250,8000,0.0001]
+        #value: [250,8000,0.0001]
-        p0: [47,1333.223874]
+        #p0: [47,1333.223874]
         
     - 
         id: 5
         type: 'windkessel'
-        #value: [250,0,0]
+        value: [250,0,0]
-        #p0: [0,1333.223874]
+        p0: [0,1333.223874]
-        value: [250,8000,0.0001]
+        #value: [250,8000,0.0001]
-        p0: [47,1333.223874]
+        #p0: [47,1333.223874]
     - 
         id: 6
         type: 'windkessel'
-        #value: [250,0,0]
+        value: [250,0,0]
-        #p0: [0,1333.223874]
+        p0: [0,1333.223874]
-        value: [250,8000,0.0001]
+        #value: [250,8000,0.0001]
-        p0: [47,1333.223874]
+        #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
+            id: 3
-        #    type: 'windkessel'
+            type: 'windkessel'
-        #    initial_stddev: 1
+            initial_stddev: 1
-        #- 
+        - 
-        #   id: 4
+            id: 4
-        #    type: 'windkessel'
+            type: 'windkessel'
-        #   initial_stddev: 1
+            initial_stddev: 1
-        #- 
+        - 
-        #   id: 5
+            id: 5
-        #   type: 'windkessel'
+            type: 'windkessel'
-        #   initial_stddev: 1
+            initial_stddev: 1
-        #- 
+        - 
-        #    id: 6
+            id: 6
-        #    type: 'windkessel'
+            type: 'windkessel'
-        #    initial_stddev: 1
+            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'
+            xdmf_file: 'measurements/aorta_master_s100/u_all.xdmf'
-            #file_root: 'measurements/aorta_C/Perturbation/Ks12V120/u{i}.h5'
+            file_root: 'measurements/aorta_master_s100/u{i}.h5'
-            xdmf_file: 'measurements/aorta_C/u_all.xdmf'
-            file_root: 'measurements/aorta_C/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

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: [10,0.0008,2400]
-        #value: [94,1794,0.0014] #paper windk
+        #value: [10,0,2400]
-        value: [94,0,0]
+        p0: [80,1333.223874]
-        p0: [0,1333.223874]
+        #p0: [0,1333.223874]
     - 
         id: 4
         type: 'windkessel'
-        #value: [250,8000,0.0001] #paper corr
+        value: [60,0.00034,4200]
-        #value: [250,10000,0.0004] #paper windk
+        #value: [60,0,4200] #safe
-        value: [250,0,0] #paper
+        p0: [80,1333.223874]
-        p0: [0,1333.223874]
+        #p0: [0,1333.223874]
     - 
         id: 5
         type: 'windkessel'
-        #value: [250,8000,0.0001] #paper corr
+        value: [220,0.00034,11000]
-        #value: [683,12960,0.0002] #paper windk
+        #value: [220,0,11000] #safe
-        value: [683,0,0] 
+        p0: [80,1333.223874]
-        p0: [0,1333.223874]
+        #p0: [0,1333.223874]
     - 
         id: 6
         type: 'windkessel'
-        #value: [250,8000,0.0001] #paper corr
+        value: [160,0.00034,7800]
-        #value: [615,11664,0.0002] #paper windk
+        #value: [160,0,7800] #safe
-        value: [615,0,0]
+        p0: [80,1333.223874]
-        p0: [0,1333.223874]
+        #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
+    T: 0.8      # end time
-    dt: 0.001
+    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
@@ -148,8 +154,10 @@ estimation:
         -
             mesh: './meshes/coaortaH3_leo2.0.h5'
             fe_degree: 1
-            xdmf_file: 'measurements/aorta_C/u_all.xdmf'
+            #xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V50/u_all.xdmf'
-            file_root: 'measurements/aorta_C/u{i}.h5'
+            #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