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jeremias
2020-02-17 11:00:29 +01:00
parent 49e6de207b
commit 66b0e7a8e6
9 changed files with 354 additions and 381 deletions
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92
codes/PostCheck.py
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@ -175,6 +175,86 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
for bb in bnds:
QQ[bb] = []
if mode == 'perturbation':
u = Function(W)
unew = Function(W)
u.rename('velocity', outname)
unew.rename('velocity', outname)
if options['Perturbation']['xdmf']:
xdmf_u = XDMFFile(output_path+'u.xdmf')
if not options['Perturbation']['type']['SNR']=='inf':
Noise = True
def Add_Noise(signal,SNR):
Psignal = signal**2
Psignal_av = np.mean(Psignal)
Psignal_av_db = 10*np.log10(Psignal_av)
Pnoise_av_db = Psignal_av_db - SNR
Pnoise_av = 10**(Pnoise_av_db/10)
noise_std = np.sqrt(Pnoise_av)
noise = np.random.normal(0,noise_std,len(signal))
return signal + noise
else:
Noise = False
if not options['Perturbation']['type']['phase_contrast']==0:
Phase_Contrast = True
else:
Phase_Contrast = False
noise_in_coil = options['Perturbation']['type']['coil']
for k in indexes:
path = checkpoint_path + str(k) + '/'+filename+'.h5'
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
hdf.read(u, 'u/vector_0')
time = hdf.attributes('u/vector_0').to_dict()['timestamp']
hdf.close()
uvec = u.vector().get_local()
if Phase_Contrast:
ufactor = options['Perturbation']['type']['phase_contrast']/100
VENC = np.max(np.abs(uvec))*ufactor
gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
#B0 = 1.5 # Tesla Magnetic Field Strenght
TE = 5e-3 # Echo-time
Phi1 = gamma*10*TE + 0*uvec
Phi2 = gamma*10*TE + np.pi*uvec/VENC
M1 = np.cos(Phi1) + 1j*np.sin(Phi1)
M2 = np.cos(Phi2) + 1j*np.sin(Phi2)
if noise_in_coil:
SNR = options['Perturbation']['type']['SNR']
m1x_new = Add_Noise(np.real(M1),SNR)
m1y_new = Add_Noise(np.imag(M1),SNR)
m2x_new = Add_Noise(np.real(M2),SNR)
m2y_new = Add_Noise(np.imag(M2),SNR)
M1_new = m1x_new + 1j*m1y_new
M2_new = m2x_new + 1j*m2y_new
uvec = (np.angle(M2_new) - np.angle(M1_new))*VENC/np.pi
unew.vector()[:] = uvec
else:
uvec = (np.angle(M2) - np.angle(M1))*VENC/np.pi
else:
if noise_in_coil:
raise Exception('In order to perturb in coils some PC should be selected')
if not noise_in_coil:
if Noise:
SNR = options['Perturbation']['type']['SNR']
unew.vector()[:] = Add_Noise(uvec,SNR)
else:
unew.vector()[:] = uvec
print('Writing checkpoint number ',k)
write_path = output_path + 'checkpoint/{i}/'.format(i=k)
hdf2 = HDF5File(MESH['mesh'].mpi_comm(), write_path + 'u.h5', 'w')
hdf2.write(unew, '/u', time)
hdf2.close()
if options['Perturbation']['xdmf']:
xdmf_u.write(unew, time)
if mode == 'interpolation':
dt_new = options['Temporal-Interpolation']['dt_new']
@ -239,7 +319,6 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
if options['Temporal-Interpolation']['xdmf']:
xdmf_u.write(unew, (k-1)*dt_new)
if mode == 'average':
N_av = options['Temporal-Average']['subsampling_rate']
dt = options['Temporal-Average']['dt']
@ -1047,7 +1126,16 @@ def ROUTINE(options):
ref_check = options['Temporal-Interpolation']['original_check'] + 'checkpoint/'
out_check = options['Temporal-Interpolation']['out_check']
READcheckpoint(MESH,'interpolation', out_check,ref_check,'u','u',options)
if 'Perturbation' in options:
if options['Perturbation']['apply']:
if rank==0:
print('--- Perturbation in measurements ---')
MESH = LOADmesh(options['Perturbation']['meshpath'])
checkpath = options['Perturbation']['checkpath'] + 'checkpoint/'
out_check = options['Perturbation']['checkpath'] + 'Perturbation/'
READcheckpoint(MESH,'perturbation', out_check,checkpath,'u','u',options)