class mean_std_plot(object):
def __init__(self,device,scale_size,exp,noise):
self.device= device
self.scale = scale_size
self.prediction = Prediction(self.scale,self.device)
self.exp = exp
self.noise = noise
def compute_mean_std(self,pos,truth,save_dir):
model = self.prediction.model(self.exp)
num = pos.shape[1]
pos_samples = np.full([num,self.scale*self.scale],0.0)
permeability_samples = np.full([num,self.scale,self.scale],0.0)
if self.exp =='inversion_16' or self.exp =='inversion_32' or self.exp =='inversion_64':
zc = pos
for i in range(num):
pos_samples[i,:] = self.prediction.permeability(self.exp,model,zc[:,i],zf=None).cpu().numpy().reshape(self.scale*self.scale,)
permeability_samples[i,:,:]=pos_samples[i,:].reshape(self.scale,self.scale)
if self.exp =='inversion_16_64':
zc = pos[:16,:]
zf = pos[16:,:]
for i in range(num):
pos_samples[i,:] = self.prediction.permeability(self.exp,model,zc[:,i],zf=zf[:,i]).cpu().numpy().reshape(self.scale*self.scale,)
permeability_samples[i,:,:]=pos_samples[i,:].reshape(self.scale,self.scale)
mean = np.mean(permeability_samples,axis = 0)
std = np.std(permeability_samples,axis = 0)
sample1 = permeability_samples[0,:,:].reshape(self.scale,self.scale)
sample2 = permeability_samples[1000,:,:].reshape(self.scale,self.scale)
sample3 = permeability_samples[1999,:,:].reshape(self.scale,self.scale)
#np.savetxt(save_dir+f'/pos_samples.dat',pos_samples)
np.savetxt(save_dir+f'/mean.dat',mean)
np.savetxt(save_dir+f'/std.dat',std)
self.plot(truth,mean,std,sample1,sample2,sample3,save_dir)
return pos_samples
def plot(self,truth,mean,std,sample1,sample2,sample3,save_dir):
samples = [np.log(truth),mean,std,sample1,sample2,sample3]
fig, _ = plt.subplots(2,3, figsize=(9, 6))
vmin1 = [np.amin(samples[0]), np.amin(samples[0]),np.amin(samples[2]),np.amin(samples[0]),np.amin(samples[0]),np.amin(samples[0])]
vmax1 = [np.amax(samples[0]), np.amax(samples[0]),np.amax(samples[2]),np.amax(samples[0]),np.amax(samples[0]),np.amax(samples[0])]
for j, ax in enumerate(fig.axes):
ax.set_aspect('equal')
ax.set_axis_off()
cax = ax.imshow(samples[j], cmap='jet', origin='upper',vmin=vmin1[j],vmax=vmax1[j])
cbar = plt.colorbar(cax, ax=ax, fraction=0.046, pad=0.04,
format=ticker.ScalarFormatter(useMathText=True))
if j == 0:
ax.set_title('Reference',fontsize=12)
if j == 1:
ax.set_title('Mean',fontsize=12)
if j == 2:
ax.set_title('Standard deviation',fontsize=12)
if j == 3:
ax.set_title('Posterior sample 1',fontsize=12)
if j == 4:
ax.set_title('Posterior sample 2',fontsize=12)
if j == 5:
ax.set_title('Posterior sample 3',fontsize=12)
plt.savefig(save_dir+f'/gaussian_statistics_{self.exp}.pdf',bbox_inches = 'tight', dpi=1000,pad_inches=0.0)
plt.close()
plt.savefig(output_dir + filename,
bbox_inches='tight',
dpi=1000,
pad_inches=0.0)
plt.close()
if __name__ == "__main__":
torch.random.manual_seed(10)
device = torch.device("cuda:3" if torch.cuda.is_available() else "cpu")
latent_c = latent_c(device)
prediction = Prediction('scale_64', device)
nz_x, nz_y = 4, 4
z = torch.randn(4, 1, nz_x, nz_y)
model = prediction.model('inversion_16')
gen_imgs = prediction.permeability('inversion_16', model, z)
samples = np.squeeze(gen_imgs.data.cpu().numpy())
condition = np.loadtxt(os.getcwd() +
f'/Gaussian/MDGM_plot/gaussian_16.dat')
zc = latent_c.coarse_latent('inversion_16_64', condition).reshape(16, )
zc = (np.ones([3, 1, 4, 4])) * zc.reshape(4, 4)
z64 = torch.randn(3, 1, 16, 16)
model = prediction.model('inversion_16_64')
gen_imgs1 = prediction.permeability('inversion_16_64', model, zc, zf=z64)
samples1 = np.squeeze(gen_imgs1.data.cpu().numpy())
samples2 = [
samples[0], samples[1], samples[2], samples[3], condition, samples1[0],
samples1[1], samples1[2]
]
filename = '/gaussian_MDGM_16_64.pdf'
prediction.plot_ite(samples2, filename)
class Plot_convergence(object):
def __init__(self):
device = torch.device("cuda:2" if torch.cuda.is_available() else "cpu") # training on GPU or CPU
self.prediction = Prediction('scale_64',device)
self.simulation = simulation()
self.true_permeability = np.loadtxt(os.getcwd()+f'/Gaussian/test_data/true_permeability_0.05.dat').reshape(64,64)
self.obs = np.loadtxt(os.getcwd()+f'/Gaussian/test_data/obs_0.05.dat')
self.sigma = np.loadtxt(os.getcwd()+f'/Gaussian/test_data/sigma_0.05.dat')
self.ref_fx,_,_,_,_,_ = self.simulation.demo64(self.true_permeability)
self.ref_sswr = np.sum(np.power((self.obs-self.ref_fx)/self.sigma,2.0) )
self.ref_rss = np.sum(np.power((self.obs-self.ref_fx),2.0) )
def compute_para_rss(self,z, exp):
num = z.shape[1]
permeability_samples = np.full((num,4096),0.0)
para_rss = np.full((num,),0.0)
if exp=='inversion_64':
model = self.prediction.model(exp)
for i in range(num):
permeability_samples[i,:] = self.prediction.permeability(exp,model,z[:,i]).cpu().numpy().reshape(4096,)
para_rss[i,] = np.sum(np.power((permeability_samples[i,:]-np.log(self.true_permeability.reshape(4096,))),2))
if exp=='inversion_16_64':
model = self.prediction.model(exp)
for i in range(num):
zc = z[:16,i]
zf = z[16:,i]
permeability_samples[i,:] = self.prediction.permeability(exp,model,zc,zf =zf).cpu().numpy().reshape(4096,)
para_rss[i,] = np.sum(np.power((permeability_samples[i,:]-np.log(self.true_permeability.reshape(4096,))),2))
return para_rss
def plot_para_rss(self,para_rss_64,para_rss_16_64):
fig,ax =plt.subplots()
# ax.set_yscale('log')
x_axix=np.linspace(0,10000,10000)
x_axix1=np.linspace(0,5000,5000)
plt.ylabel('RSS of parameter field')
plt.xlabel('Iterations')
plt.plot(x_axix, para_rss_64[0:], color='green', label='reference')
plt.plot(x_axix1, para_rss_16_64[0:], color='blue', label='16-64')
plt.legend()
plt.savefig(os.getcwd()+ f'/Gaussian/convergence/images/gaussian_para_rss_convergence.pdf',bbox_inches = 'tight', dpi=1000,pad_inches=0.0)
plt.close()
def para_rss_convergence(self):
z_64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_64/pCN_step0.08_0.05_10000_8000_all_samples.dat')
z_16_64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_16_64/pCN_step0.08_0.05_5000_3000_all_samples.dat')
para_rss_64 = self.compute_para_rss(z_64 , 'inversion_64')
para_rss_16_64 = self.compute_para_rss(z_16_64, 'inversion_16_64')
self.plot_para_rss(para_rss_64,para_rss_16_64)
def Comp_log_likelihood(self,fx):
e=self.obs-fx
rss = np.sum(np.power(e,2.0) )
sswr = np.sum(np.power(e/self.sigma,2.0) )
nsswr = sswr/self.ref_sswr
nrss = rss/self.ref_rss
return rss,nrss, sswr,nsswr
def plot_nsswr(self,nsswr64,nsswr16_64):
fig,ax =plt.subplots()
ax.set_yscale('log')
x_axix=np.linspace(0,10000,10000)
x_axix1=np.linspace(0,5000,5000)
plt.ylabel('NSSWR')
plt.xlabel('Iterations')
plt.plot(x_axix, nsswr64[0:], color='green', label='reference')
plt.plot(x_axix1, nsswr16_64[0:], color='blue', label='16-64')
plt.legend()
plt.savefig(os.getcwd()+ f'/Gaussian/convergence/images/gaussian_nsswr_convergence.pdf',bbox_inches = 'tight', dpi=1000,pad_inches=0.0)
plt.close()
def plot_obs_rss(self,rss64,rss16_64):
fig,ax =plt.subplots()
ax.set_yscale('log')
x_axix=np.linspace(0,10000,10000)
x_axix1=np.linspace(0,5000,5000)
plt.ylabel('RSS of observable pressure values')
plt.xlabel('Iterations')
plt.plot(x_axix, rss64[0:], color='green', label='reference')
plt.plot(x_axix1, rss16_64[0:], color='blue', label='16-64')
plt.legend()
plt.savefig(os.getcwd()+ f'/Gaussian/convergence/images/gaussian_obsrss_convergence.pdf',bbox_inches = 'tight', dpi=1000,pad_inches=0.0)
plt.close()
def nsswr_convergence(self):
fx64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_64/pCN_step0.08_0.05_10000_8000_fx_obs.dat')
fx16_64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_16_64/pCN_step0.08_0.05_5000_3000_fx_obs.dat')
rss64 = np.full((fx64.shape[1],1),0.0)
nrss64 = np.full((fx64.shape[1],1),0.0)
sswr64 = np.full((fx64.shape[1],1),0.0)
nsswr64 = np.full((fx64.shape[1],1),0.0)
nrss16_64 = np.full((fx16_64.shape[1],1),0.0)
rss16_64 = np.full((fx16_64.shape[1],1),0.0)
sswr16_64 = np.full((fx16_64.shape[1],1),0.0)
nsswr16_64 = np.full((fx16_64.shape[1],1),0.0)
for i in range(fx64.shape[1]):
rss64[i,:],nrss64[i,:], sswr64[i,:],nsswr64[i,:]= self.Comp_log_likelihood(fx64[:,i])
for i in range(fx16_64.shape[1]):
rss16_64[i,:],nrss16_64, sswr16_64[i,:],nsswr16_64[i,:]= self.Comp_log_likelihood(fx16_64[:,i])
self.plot_nsswr(nsswr64,nsswr16_64)
self.plot_obs_rss(rss64,rss16_64)
def plot_para_state(self):
all_samples64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_64/pCN_step0.08_0.05_10000_8000_all_samples.dat')
all_samples16_64 = np.loadtxt(os.getcwd()+f'/Gaussian/prediction/inversion_16_64/pCN_step0.08_0.05_5000_3000_all_samples.dat')
truth = np.log(np.loadtxt(os.getcwd()+f'/Gaussian/test_data/true_permeability_0.05.dat'))
samples = np.full((10,64,64),0.0)
latent_sample64 = all_samples64[:,[0,999,2999,4999,9999]]
latent_sample16_64 = all_samples16_64[:,[0,499,999,2999,4999]]
for i in range(15):
if i<5:
exp = 'inversion_64'
model = self.prediction.model(exp)
samples[i,:,:] = self.prediction.permeability(exp,model,latent_sample64[:,i]).cpu().numpy().reshape(64,64)
elif 4<i<10:
exp = 'inversion_16_64'
model = self.prediction.model(exp)
zc = latent_sample16_64[:16,i-5]
zf = latent_sample16_64[16:,i-5]
samples[i,:,:] = self.prediction.permeability(exp,model,zc,zf=zf).cpu().numpy().reshape(64,64)
fig, _ = plt.subplots(2,5, figsize=(15, 6))
vmin1 = np.amin(truth)
vmax1 = np.amax(truth)
for j, ax in enumerate(fig.axes):
ax.set_aspect('equal')
ax.set_axis_off()
cax = ax.imshow(samples[j], cmap='jet', origin='upper',vmin=vmin1,vmax=vmax1)
cbar = plt.colorbar(cax, ax=ax, fraction=0.046, pad=0.04,
format=ticker.ScalarFormatter(useMathText=True))
if j == 0:
ax.set_title('initial state',fontsize=12)
if j == 1:
ax.set_title('1000-th state',fontsize=12)
if j == 2:
ax.set_title('3000-th state',fontsize=12)
if j == 3:
ax.set_title('5000-th state',fontsize=12)
if j == 4:
ax.set_title('10000-th state',fontsize=12)
if j == 5:
ax.set_title('initial state',fontsize=12)
if j == 6:
ax.set_title('499-th state',fontsize=12)
if j == 7:
ax.set_title('1000-th state',fontsize=12)
if j == 8:
ax.set_title('3000-th state',fontsize=12)
if j == 9:
ax.set_title('5000-th state',fontsize=12)
plt.savefig(os.getcwd()+f'/Gaussian/convergence/images/gaussian_para_state.pdf',bbox_inches = 'tight', dpi=1000,pad_inches=0.0)
plt.close()
class inference(object):
def __init__(self,step,burn_in,dim,obs,sigma,true_permeability,true_pressure,obs_position,scale,device):
self.dim = dim
self.burn_in = burn_in
self.step = step
self.obs = obs
self.sigma = sigma
self.true_permeability = true_permeability
self.true_pressure = true_pressure
self.pos = obs_position
self.plot_interval = 1000
self.num_obs = 64
self.prediction = Prediction(scale,device)
def pCN(self,old_params,beta,dim):
'''
Here the prior distribution is standart Normal
'''
new_params = np.sqrt(1-beta*beta)*old_params+beta*np.random.randn(dim,)
return new_params
def fx(self,model,exp,zc,zf):
'''
compute the permeability field X using MDGM, and compute f(X) using forward model
'''
input = self.prediction.permeability(exp,model,zc,zf=zf)
like , pre = self.prediction.forward(input)
f_x = np.reshape(like,(1,-1))
return f_x,input,pre
def Comp_log_likelihood(self,obs,sigma,exp,model,zc,zf=None):
'''
compute likelihood function for inference
'''
f_x,input,pre = self.fx(model,exp,zc,zf)
e=obs-f_x
log_likelihood = -0.5 * np.sum( np.power(e/sigma,2.0))
print('log_like:',log_likelihood)
return f_x,input,pre, log_likelihood
def pCN_MH(self,init_c,init_state_f,beta,exp,noise,output_dir):
'''
MH algorithm with MDGM, two proposal distributions for latent zc and zf respectively,
where zc can capture global feature, zf is latent variable for parameter local adaption.
proposal for zc with small step size(0.01)
proposal for zf with big step size(first 50% state using 0.08, rest with 0.04)
'''
coarse_beta = 0.01
model = self.prediction.model(exp)
old_params_c = init_c
dim_c=old_params_c.shape[0]
accept_num = 0
dim = dim_c+self.dim
samples = np.zeros([dim,self.step])
fx_obs = np.zeros([self.num_obs,self.step])
log_likelihood = np.zeros([1,self.step])
old_params_f = init_state_f
old_fx,old_input,old_pre,old_log_l= self.Comp_log_likelihood(self.obs,self.sigma,exp,model,old_params_c,zf = old_params_f)
old_params = np.concatenate((old_params_c,old_params_f),axis=0)
samples[:,0] = old_params.reshape([dim,])
fx_obs[:,0] = old_fx
log_likelihood[:,0] = old_log_l
self.plot_para_field(0,old_input,old_pre,self.true_permeability, self.true_pressure,beta,'pCN',exp,noise,output_dir)
for i in tqdm(range(1,self.step)):
if i > 0.5*self.step:
beta = 0.04
new_params_c = self.pCN(old_params_c,coarse_beta,dim_c)
new_params_f = self.pCN(old_params_f,beta,self.dim)
new_fx,new_input,new_pre,new_log_l= self.Comp_log_likelihood(self.obs,self.sigma,exp,model,new_params_c,zf = new_params_f)
new_params = np.concatenate((new_params_c,new_params_f),axis=0)
ratio = np.exp(new_log_l - old_log_l)
alpha = min(1,ratio)
np.random.seed(i)
z = np.random.rand()
if z<= alpha:
print('-----------------------------------------------------------------')
log_likelihood[:,i] = new_log_l
fx_obs[:,i] = new_fx
old_fx= new_fx
samples[:,i] = new_params
old_input = new_input
old_pre = new_pre
old_params = new_params
old_params_c = new_params_c
old_params_f = new_params_f
old_log_l = new_log_l
accept_num = accept_num +1
elif z>alpha:
samples[:,i] = old_params
fx_obs[:,i] = old_fx
log_likelihood[:,i] = old_log_l
if (i+1)%self.plot_interval == 0:
self.plot_para_field(i,old_input,old_pre,self.true_permeability, self.true_pressure,beta,'pCN',exp,noise,output_dir)
post_samples = samples[:,self.burn_in:]
accept_ratio = (accept_num/self.step)
print('accept_ratio:',accept_ratio)
accept = [accept_ratio,accept_num]
return samples, post_samples,fx_obs,accept,log_likelihood
def plot_para_field(self,i,input,pre_pressure, true_permeability, true_pressure,beta,type,exp,noise,output_dir):
'''
Plot Markov chain state(log permeability)
'''
samples = [np.log(true_permeability),input.data.cpu().numpy(), true_pressure.reshape(64,64),pre_pressure]
fig, _ = plt.subplots(2,2, figsize=(6,6))
vmin1 = [np.amin(samples[0]), np.amin(samples[0]),np.amin(samples[2]), np.amin(samples[2])]
vmax1 = [np.amax(samples[0]), np.amax(samples[0]),np.amax(samples[2]), np.amax(samples[2])]
for j, ax in enumerate(fig.axes):
ax.set_aspect('equal')
ax.set_axis_off()
cax = ax.imshow(samples[j], cmap='jet',vmin=vmin1[j],vmax=vmax1[j])
cbar = plt.colorbar(cax, ax=ax, fraction=0.046, pad=0.04,
format=ticker.ScalarFormatter(useMathText=True))
plt.savefig(output_dir+f'/{type}_step_size{beta}_state_{i+1}.pdf')
plt.close()
class inference(object):
def __init__(self,step,burn_in,dim,obs,sigma,true_permeability,true_pressure,obs_position,scale,device):
self.dim = dim
self.burn_in = burn_in
self.step = step
self.obs = obs
self.sigma = sigma
self.true_permeability = true_permeability
self.true_pressure = true_pressure
self.pos = obs_position
self.Prior_type = 'Standard Normal'
self.plot_interval = 1000
self.num_obs = 64
self.prediction = Prediction(scale,device)
def pCN(self,old_params,beta):
'''
Here the prior distribution is standart Normal
'''
new_params = np.sqrt(1-beta*beta)*old_params+beta*np.random.randn(self.dim,)
return new_params
def fx(self,model,exp,z):
'''
compute the permeability field X using MDGM, and compute f(X) using forward model
'''
input = self.prediction.permeability(exp,model,z)
like , pre = self.prediction.forward(input)
fx = np.reshape(like,(1,-1))
return fx
def Comp_log_likelihood(self,z,obs,sigma,exp,model):
'''
compute likelihood function for inference
'''
fx = self.fx(model,exp,z)
e=obs-fx
log_likelihood = -0.5 * np.sum( np.power(e/sigma,2.0))
print('log_like:',log_likelihood)
return fx, log_likelihood
def pCN_MH(self,init_state,beta,exp,noise,output_dir):
'''
MH algorithm with DGM on the first scale(the coarsest scale)
proposal for latent variable z1 with big step size to explore the whole space
(first 50% state using 0.08, rest with 0.04)
'''
model = self.prediction.model(exp)
accept_num = 0
old_params = init_state
samples = np.zeros([self.dim,self.step])
log_likelihood = np.zeros([1,self.step])
fx_obs = np.zeros([self.num_obs,self.step])
old_fx ,old_log_l= self.Comp_log_likelihood(old_params,self.obs,self.sigma,exp,model)
fx_obs[:,0] = old_fx
log_likelihood[:,0] = old_log_l
samples [:,0] = old_params.reshape([self.dim,])
self.plot_para_field(0,old_params,self.true_permeability, self.true_pressure,beta,'pCN',exp,model,noise,output_dir)
for i in tqdm(range(1,self.step)):
if i > 0.5*self.step:
beta = 0.04
new_params = self.pCN(old_params,beta)
new_fx ,new_log_l = self.Comp_log_likelihood(new_params,self.obs,self.sigma,exp,model)
ratio = np.exp(new_log_l - old_log_l)
alpha = min(1,ratio)
np.random.seed(i)
z = np.random.rand()
if z<= alpha:
print('-----------------------------------------------------------------')
old_params = new_params.reshape([self.dim,])
fx_obs[:,i] = new_fx
log_likelihood[:,i] = new_log_l
samples[:,i] = new_params.reshape([self.dim,])
old_log_l = new_log_l
old_fx = new_fx
accept_num = accept_num +1
elif z>alpha:
old_params = old_params
samples[:,i] = old_params.reshape([self.dim,])
fx_obs[:,i] = old_fx
log_likelihood[:,i] = old_log_l
if (i+1)%self.plot_interval == 0:
self.plot_para_field(i,old_params,self.true_permeability, self.true_pressure,beta,'pCN',exp,model,noise,output_dir)
post_samples = samples[:,self.burn_in:]
accept_ratio = accept_num/self.step
print('accept_ratio:',accept_ratio)
accept = [accept_ratio,accept_num]
return samples, post_samples,fx_obs,accept,log_likelihood
def plot_para_field(self,i,params, true_permeability, true_pressure,beta,type,exp,model,noise,output_dir):
'''
Plot Markov chain state(log permeability)
'''
pre_permeability = self.prediction.permeability(exp,model,params)
_, pre_pressure = self.prediction.forward(pre_permeability)
if exp=='inversion_16':
pre_permeability = pre_permeability.data.cpu().numpy().reshape(16,16)
if exp=='inversion_64':
pre_permeability = pre_permeability.data.cpu().numpy().reshape(64,64)
samples = [np.log(true_permeability),pre_permeability, true_pressure,pre_pressure]
fig, _ = plt.subplots(2,2, figsize=(6,6))
vmin1 = [np.amin(samples[0]), np.amin(samples[0]),np.amin(samples[2]),np.amin(samples[2])]
vmax1 = [np.amax(samples[0]), np.amax(samples[0]),np.amax(samples[2]),np.amax(samples[2])]
for j, ax in enumerate(fig.axes):
ax.set_aspect('equal')
ax.set_axis_off()
cax = ax.imshow(samples[j], cmap='jet',vmin=vmin1[j],vmax=vmax1[j])
cbar = plt.colorbar(cax, ax=ax, fraction=0.046, pad=0.04,
format=ticker.ScalarFormatter(useMathText=True))
plt.savefig(output_dir+f'/{type}_step_size{beta}_state_{i+1}.pdf')
plt.close()