This commit is contained in:
J.E. Garay Labra 2020-06-29 12:38:24 +02:00
parent 2d3873605d
commit b7d7695faf
11 changed files with 1297 additions and 1438 deletions

File diff suppressed because it is too large Load Diff

View File

@ -586,25 +586,15 @@ def CenterComparison(A,B,C,R,center):
def VelocityChannel(M,repeat,recorder):
[row,col,numt2] = M.shape
[X,Y] = np.meshgrid(np.linspace(0,col,col),np.linspace(0,row,row))
plt.ion()
rown = row*6/row
coln = col*6/row
fig = plt.figure()#figsize=(4, 6) , dpi=200)
ax = fig.add_subplot(111, projection='3d')
for rr in range(-1,repeat):
for t in range(numt2):
V = M[:,:,t]
#ax.plot_surface(X, Y, V, cmap=plt.cm.magma, vmin=-30, vmax=50, linewidth=0, antialiased=False)
#ax.plot_wireframe(X, Y, V,rcount=20,ccount=20,linewidth=0.5)
ax.plot_surface(X, Y, V,cmap='magma',vmin=-30, vmax=100, linewidth=0, antialiased=False)
@ -615,7 +605,6 @@ def VelocityChannel(M,repeat,recorder):
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
ax.set_zlabel('$v(r)$')
ax.set_title('phase ' + str(t))
plt.pause(0.001)
plt.draw()
@ -633,115 +622,6 @@ def PlotTri(tri,pos,p):
ax = fig.add_subplot(1, 1, 1, projection='3d')
#ax.plot_trisurf(pos[:,0], pos[:,1], pos[:,2], triangles=tri.simplices, cmap=plt.cm.Spectral,linewidth=0.1,edgecolors='k')
#ax.tripcolor(pos[:,0], pos[:,1], pos[:,2], triangles=tri.simplices, facecolors=p2.T, edgecolor='black')
plt.show()
def PlotPressureDrop(mode):
barye2mmHg = 1/1333.22387415
CT = np.loadtxt('Pressure/DROPS/pd_NS_coarse.txt')
CT2 = np.loadtxt('Pressure/DROPS/pd_NS_coarse2.txt')
ref_ao = np.loadtxt('Pressure/DROPS2/refPPE1_coarse.txt')
ref = np.loadtxt('Pressure/DROPS2/refPPE1_coarse_leo1.txt')
CS2 = np.loadtxt('Pressure/DROPS2/CSPPE2_coarse_leo1.txt')
PPE_CT = np.loadtxt('Pressure/DROPS/pd_PPE_NS_coarse.txt')
PPE_CT_leo = np.loadtxt('Pressure/DROPS/pd_PPE_NS_coarse_leo1.txt')
STE_CT = np.loadtxt('Pressure/DROPS/test_STE_R1_coarse.txt')
test_STE_CT = np.loadtxt('Pressure/DROPS/test2_STE_R1_coarse_leo1.txt')
STEint_CT = np.loadtxt('Pressure/DROPS/test_STEint_R1_coarse.txt')
test_STEint_CT = np.loadtxt('Pressure/DROPS/test2_STEint_R1_coarse_leo1.txt')
# UNDERSAMPLING
PPE_R1_leo1 = np.loadtxt('Pressure/DROPS/test_PPE_R1_coarse_leo1.txt')
PPE_KT_R2_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R2_coarse_leo1.txt')
PPE_KT_R4_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R4_coarse_leo1.txt')
PPE_KT_R8_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R8_coarse_leo1.txt')
PPE_KT_R12_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R12_coarse_leo1.txt')
PPE_KT_R20_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R20_coarse_leo1.txt')
PPE_CS_R2_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R2_coarse_leo1.txt')
PPE_CS_R4_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R4_coarse_leo1.txt')
PPE_CS_R8_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R8_coarse_leo1.txt')
PPE_CS_R12_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R12_coarse_leo1.txt')
PPE_CS_R20_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R20_coarse_leo1.txt')
#CT_fine = np.loadtxt('Pressure/DROPS/pd_NS_fine.txt')
#CT_fine_T = np.loadtxt('Pressure/DROPS/pd_NS_fine_T.txt')
#PPE_CT_fine = np.loadtxt('Pressure/DROPS/pd_PPE_NS_fine.txt')
#PPE_CT_fine_leo3 = np.loadtxt('Pressure/DROPS/pd_PPE_NS_fine_leo3.txt')
tvec2 = np.linspace(0, 2.5 ,PPE_CT_leo.size)
tvec = np.linspace(tvec2[1]*0.5 ,2.5+tvec2[1]*0.5 , CT.size)
#tvec_T = np.linspace(0,2.5,CT_fine_T.size)
fig = plt.figure()
if mode=='KT':
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
plt.plot(tvec2,PPE_R1_leo1,'xkcd:red',linewidth=2,linestyle='-' , label='$R = 1$')
plt.plot(tvec2,PPE_KT_R2_leo1,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
plt.plot(tvec2,PPE_KT_R4_leo1,'xkcd:green',linewidth=2,linestyle='-',label='$R = 4$')
plt.plot(tvec2,PPE_KT_R8_leo1,'xkcd:orange',linewidth=2,linestyle='-',label='$R = 8$')
plt.plot(tvec2,PPE_KT_R20_leo1,'xkcd:magenta',linewidth=2,linestyle='-', label='$R = 20$')
plt.title('$kt-BLAST$',fontsize=20)
if mode=='CS':
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
plt.plot(tvec2,ref_ao,'xkcd:red',linewidth=2,linestyle='--' , label='$aorta$')
plt.plot(tvec2,ref,'xkcd:red',linewidth=2,linestyle='-' , label='$leo$')
plt.plot(tvec2,CS2,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
#plt.plot(tvec2,PPE_R1_leo1,'xkcd:red',linewidth=2,linestyle='-' , label='$R = 1$')
#plt.plot(tvec2,PPE_CS_R2_leo1,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
#plt.plot(tvec2,PPE_CS_R4_leo1,'xkcd:green',linewidth=2,linestyle='-',label='$R = 4$')
#plt.plot(tvec2,PPE_CS_R8_leo1,'xkcd:orange',linewidth=2,linestyle='-',label='$R = 8$')
#plt.plot(tvec2,PPE_CS_R20_leo1,'xkcd:magenta',linewidth=2,linestyle='-', label='$R = 20$')
plt.title('$Compressed \ \ Sensing$',fontsize=20)
if mode=='STE':
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
plt.plot(tvec2,STE_CT , 'xkcd:purple' , label='STE-CT aorta')
plt.plot(tvec2,test_STE_CT , 'xkcd:purple' , linestyle='--', marker='o', label='STE-CT leo')
if mode=='STEint':
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
plt.plot(tvec2,STEint_CT, 'xkcd:aquamarine', label='STEint-CT aorta')
plt.plot(tvec2,test_STEint_CT, 'xkcd:aquamarine', linestyle='--', marker='o',label='STEint-CT aorta')
plt.ylim([-2,7])
plt.xlabel(r'$time \ \ \ (s)$',fontsize=20)
plt.ylabel(r'$\delta p \ \ \ (mmHg) $',fontsize=20)
plt.legend(fontsize=16)
##############################################################################################################################
#fig = plt.figure()
#plt.plot(tvec2,CT_fine,'-ok',label='CT')
##plt.plot(tvec_T,CT_fine_T,'--k',label='CT T')
#plt.plot(tvec2 ,PPE_CT_fine ,'-om',label='PPE-CT aorta')
#plt.plot(tvec2 ,PPE_CT_fine_leo3,'-oc',label='PPE-CT leo3')
#plt.title('aorta fine')
#plt.xlabel(r'$time \ \ (s) $',fontsize=20)
#plt.ylabel(r'$\delta p \ \ \ (mmHg) $',fontsize=20)
#plt.legend(fontsize=14)
plt.show()
def Plot_flux(masterpath,meshpath,options,mode,R):
@ -1091,7 +971,6 @@ def Plot_dP(masterpath,options,mode,R):
tcat = tcat+shift_t
ax.plot(tcat[cstar[0]:tcat.size-cstar[1]],catheter[cstar[0]:tcat.size-cstar[1]],'white',linewidth=linesize,linestyle='--',label='$catheter$')
tm = np.linspace(0,Dt*tend,tend)
ax.set_xlim([-0.05,0.81])
@ -1132,225 +1011,6 @@ def Plot_dP(masterpath,options,mode,R):
plt.show()
def Plot_peaksystole(datapath,options,meshes,dt,R):
import pickle
barye2mmHg = 1/1333.22387415
for mesh_size in meshes:
t_star = 6
PPE_MEAN = np.zeros([len(R)])
PPE_STD = np.zeros([len(R)])
STE_MEAN = np.zeros([len(R)])
STE_STD = np.zeros([len(R)])
V_MEAN = np.zeros([len(R)])
V_STD = np.zeros([len(R)])
ref_P = 0
ref_V = 0
if mesh_size=='Ucoarse':
ref_V = 326.95828118309191
if mesh_size=='Ufine':
ref_V = 232.95021682714497
if mesh_size=='Uffine':
ref_V = 234.66445211879045
for l in range(len(R)):
if R[l]==0:
ref = np.loadtxt('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/ref_'+mesh_size+'.txt')
PPE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_PPE_impl_stan.dat','rb')
STE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_STE_impl_stan.dat','rb')
PPE0 = pickle.load(PPE0_raw)['pdrop']*(-barye2mmHg)
STE0 = pickle.load(STE0_raw)['pdrop']*(-barye2mmHg)
curpath = datapath + 'sequences/aorta_'+mesh_size+'.npz'
p = np.load(curpath)
px = p['x']
py = p['y']
pz = p['z']
v = np.sqrt(px[:,:,:,t_star]**2 + py[:,:,:,t_star]**2 + pz[:,:,:,t_star]**2)
max0 = np.where(v==np.max(v))
ref_P = ref[6]
V_MEAN[l] = ref_V
V_STD[l] = 0
PPE_MEAN[l] = PPE0[6]
PPE_STD[l] = 0
STE_MEAN[l] = STE0[6]
STE_STD[l] = 0
else:
PPE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppemean_R'+ str(R[l]) +'.txt')
PPE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppestd_R'+ str(R[l]) +'.txt')
STE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stemean_R'+ str(R[l]) +'.txt')
STE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stestd_R'+ str(R[l]) +'.txt')
V_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vmean_R'+ str(R[l]) +'.txt')
V_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vstd_R'+ str(R[l]) +'.txt')
plt.figure(figsize=(10, 6), dpi=100)
Rvec = np.linspace(-10,R[-1]+5,100)
hline = Rvec*0+ref_P
plt.subplot(1,2,1)
plt.plot([0],[ref_P],color='k',marker='o',label= '$ref$')
plt.plot(Rvec,hline,color='k',linestyle='--')
plt.errorbar(R,PPE_MEAN, yerr=PPE_STD,color=options['ppecol'],marker='o',label= '$PPE$')
plt.errorbar(R,STE_MEAN, yerr=STE_STD,color=options['stecol'],marker='o',label= '$STE$')
plt.xlim([-2,R[-1]+5])
plt.ylim([-7,18])
plt.xlabel(r'$R$',fontsize=20)
plt.title('$Peak \ Systole \ pressure$',fontsize=18)
plt.ylabel(r'$ max \ \big ( \delta P \big ) \ \ mmHg$',fontsize=16)
plt.subplot(1,2,2)
#plt.plot([0],[ref_V],color='k',marker='o',label= '$ref$')
Rvec = np.linspace(-10,R[-1]+5,100)
hline = Rvec*0+ref_V
plt.plot(Rvec,hline,color='k',linestyle='--')
plt.errorbar(R,V_MEAN, yerr=V_STD,color='royalblue',marker='o',label= '$' + mesh_size + '$')
plt.xlim([-2,R[-1]+5])
plt.ylim([0,350])
plt.xlabel(r'$R$',fontsize=20)
plt.ylabel(r'$ max \ \big ( v \big ) \ \ cm/s$',fontsize=16)
plt.title('$Peak \ Systole \ velocity$',fontsize=18)
#plt.legend(fontsize=15)
plt.annotate('$'+mesh_size+'$', xy=(-0.2, 1.1), xycoords='axes fraction',fontsize=15)
plt.show()
def Plot_peaksystole_flux(datapath,options,meshes,dt,R):
import pickle
barye2mmHg = 1/1333.22387415
for mesh_size in meshes:
t_star = 6
PPE_MEAN = np.zeros([len(R)])
PPE_STD = np.zeros([len(R)])
STE_MEAN = np.zeros([len(R)])
STE_STD = np.zeros([len(R)])
V_MEAN = np.zeros([len(R)])
V_STD = np.zeros([len(R)])
Q_MEAN = np.zeros([len(R)])
Q_STD = np.zeros([len(R)])
ref_V = 0
if mesh_size=='Ucoarse':
ref_V = 326.95828118309191
if mesh_size=='Ufine':
ref_V = 232.95021682714497
if 'Uffine' in mesh_size:
ref_V = 226.93523675462458
maxv1 = 184.05091675316763
ref_Q = 454.77517472437495
maxq1 = 429.01393994253556
for l in range(len(R)):
if R[l]==0:
ref = np.loadtxt('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/ref_'+mesh_size+'.txt')
PPE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_PPE_impl_stan.dat','rb')
STE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_STE_impl_stan.dat','rb')
PPE0 = pickle.load(PPE0_raw)['pdrop']*(-barye2mmHg)
STE0 = pickle.load(STE0_raw)['pdrop']*(-barye2mmHg)
curpath = datapath + 'sequences/aorta_'+mesh_size+'.npz'
p = np.load(curpath)
px = p['x']
py = p['y']
pz = p['z']
v = np.sqrt(px[:,:,:,t_star]**2 + py[:,:,:,t_star]**2 + pz[:,:,:,t_star]**2)
max0 = np.where(v==np.max(v))
V_MEAN[l] = ref_V
V_STD[l] = 0
PPE_MEAN[l] = PPE0[6]
PPE_STD[l] = 0
STE_MEAN[l] = STE0[6]
STE_STD[l] = 0
elif R[l]==1:
PPE_MEAN[l] = 0
PPE_STD[l] = 0
STE_MEAN[l] = 0
STE_STD[l] = 0
V_MEAN[l] = maxv1
V_STD[l] = 0
Q_MEAN[l] = maxq1
Q_STD[l] = 0
else:
PPE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppemean_R'+ str(R[l]) +'.txt')
PPE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppestd_R'+ str(R[l]) +'.txt')
STE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stemean_R'+ str(R[l]) +'.txt')
STE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stestd_R'+ str(R[l]) +'.txt')
V_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vmean_R'+ str(R[l]) +'.txt')
V_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vstd_R'+ str(R[l]) +'.txt')
Q_MEAN[l] = -np.loadtxt(datapath + 'maxpv/'+mesh_size + '/Q2_R'+ str(R[l]) +'.txt')
Q_STD[l] = -np.loadtxt(datapath + 'maxpv/'+mesh_size + '/Qstd2_R'+ str(R[l]) +'.txt')
plt.figure(figsize=(15, 5), dpi=100)
plt.annotate('$'+mesh_size+'$', xy=(-0.2, 1.1), xycoords='axes fraction',fontsize=15)
Rvec = np.linspace(-10,R[-1]+5,100)
plt.subplot(1,3,1)
#plt.plot(Rvec,hline,color='k',linestyle='--')
plt.errorbar(R,PPE_MEAN, yerr=PPE_STD,color=options['ppecol'],marker='o',label= '$PPE$')
plt.errorbar(R,STE_MEAN, yerr=STE_STD,color=options['stecol'],marker='o',label= '$STE$')
plt.xlim([-2,R[-1]+5])
plt.ylim([-0.1,2.0])
plt.xlabel(r'$R$',fontsize=20)
plt.legend(fontsize=12,loc=2)
plt.title('$ l_2 \ error \ in \ Peak \ pressure$',fontsize=16)
plt.xticks(R)
plt.ylabel(r'$ || p - p^{ref} ||/|| p^{ref} ||_{l2} $',fontsize=16)
plt.subplot(1,3,2)
#plt.plot([0],[ref_V],color='k',marker='o',label= '$ref$')
Rvec = np.linspace(-10,R[-1]+7,100)
hline = Rvec*0+ref_V
plt.plot(Rvec,hline,color='royalblue',linestyle='--')
plt.errorbar(R,V_MEAN, yerr=V_STD,color='royalblue',marker='o',label= '$' + mesh_size + '$')
plt.xlim([-2,R[-1]+5])
plt.ylim([0,350])
plt.xlabel(r'$R$',fontsize=20)
plt.ylabel(r'$ v \ \ cm/s$',fontsize=16)
plt.xticks(R)
plt.title('$Peak \ velocity$',fontsize=16)
#plt.legend(fontsize=15)
plt.subplot(1,3,3)
Rvec = np.linspace(-10,R[-1]+7,100)
hline = Rvec*0+ref_Q
plt.plot(Rvec,hline,color='mediumvioletred',linestyle='--')
plt.errorbar(R,Q_MEAN, yerr=Q_STD,color='mediumvioletred',marker='o',label= '$' + mesh_size + '$')
plt.xlim([-2,R[-1]+5])
plt.xlabel(r'$R$',fontsize=20)
plt.ylabel(r'$ Q \ \ ml/s$',fontsize=16)
plt.xticks(R)
plt.ylim([150,550])
plt.title('$Peak \ Flux $',fontsize=16)
plt.show()
def CLOCK(t1, t2):
tot_time = np.round(t2 - t1, 2)
if tot_time < 60:
@ -1411,6 +1071,9 @@ def ROUTINE(options):
if options['Error-curves']['apply']:
print('--- Error-curves analysis ---')
ratio = False
fac=1
if '11mm' in options['Error-curves']['subfolders']:
fac=100
for types in options['Error-curves']['type']:
if types=='mean_ratio':
types = 'mean'
@ -1418,6 +1081,9 @@ def ROUTINE(options):
if types=='max_ratio':
types = 'max'
ratio = True
if types=='norm2_m':
types='norm2'
meas=True
nc = 0
if len(options['Error-curves']['subfolders'])==0:
ucomp = []
@ -1445,45 +1111,261 @@ def ROUTINE(options):
for subf in options['Error-curves']['subfolders']:
ucomp = []
wcomp = []
colorset = options['Error-curves']['colors']
if 'colors' in options['Error-curves']:
print('colors setted...')
colorset = options['Error-curves']['colors']
colorsetted = True
else:
colorsetted = False
styles = options['Error-curves']['styles']
labelset = options['Error-curves']['labels']
path = options['Error-curves']['folder'] + subf + '/'
try:
ucomp = np.loadtxt(path + '/u'+types+'.txt')
wcomp = np.loadtxt(path + '/w'+types+'.txt')
times = np.loadtxt(path + '/times.txt')
except IOError:
print('no cError-curves for ' + subf)
wcomp = np.loadtxt(path + 'w'+types+'.txt')
times = np.loadtxt(path + 'times.txt')
if types != 'grad':
ucomp = np.loadtxt(path + 'u'+types+'.txt')
if not ratio:
plt.plot(
times, ucomp, color=colorset[nc], linestyle='-', label= '$u'+ subf +'$' )
plt.plot(
times, wcomp, color=colorset[nc], linestyle='--', label='$w'+subf+'$')
if colorsetted:
if not ratio:
if types not in ['grad']:
if meas:
plt.plot(times, fac*ucomp, color=colorset[nc], linestyle='--', label= '$ u \ '+ labelset[nc] +'$',linewidth=2.5 )
plt.plot(times, fac*wcomp, color=colorset[nc], linestyle=styles[nc], label= '$ w \ '+ labelset[nc] +'$',linewidth=2.5)
else:
wu = wcomp/ucomp
plt.plot(
times, wu, color=colorset[nc], linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
nc +=1
else:
wu = wcomp/ucomp
plt.plot(
times, wu, color=colorset[nc], linestyle='-', label= '$'+ labelset[nc] +'$' )
nc +=1
if not ratio:
if types not in ['grad']:
if meas:
plt.plot(times, fac*ucomp, linestyle='--', label= '$'+ labelset[nc] +'$' )
else:
plt.plot(times, fac*ucomp, linestyle='--', label= '$'+ labelset[nc] +'$' )
plt.plot(
times, fac*wcomp, linestyle=styles[nc], label= '$'+ labelset[nc] +'$')
else:
wu = wcomp/ucomp
plt.plot(
times, wu, linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
nc +=1
#plt.ylim([0, 170])
plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=16)
plt.legend(fontsize=14)
if options['Error-curves']['title']:
plt.title(options['Error-curves']['title'], fontsize=18)
if not ratio:
plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
if types == 'grad':
plt.ylim([0, 230])
plt.ylabel('$ |grad(w)|_2 \ \ (1/s)$', fontsize=18)
elif types == 'norm2':
plt.ylim([0, 52])
plt.ylabel('$ |w|_2 \ \ (cm/s)$', fontsize=18)
else:
plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
plt.savefig(options['Error-curves']['outpath'] + types + '.png', dpi=500, bbox_inches='tight')
else:
plt.ylabel('$w/u$', fontsize=18)
if 'max' in types:
plt.ylim([0, 1.8])
plt.ylabel('$|w/u|$', fontsize=18)
#if 'max' in types:
#plt.ylim([0, 1.8])
plt.savefig(options['Error-curves']['outpath'] + types + '_ratio.png', dpi=500, bbox_inches='tight')
plt.show()
if 'Histograms_checkpoint' in options:
if options['Histograms_checkpoint']['apply']:
print('--- Histograms ---')
path = options['Histograms_checkpoint']['path']
freq = np.loadtxt(path + 'hist_freq.txt')
edges = np.loadtxt(path + 'hist_edges.txt')
fig, ax = plt.subplots()
#ax.bar(edges[:-1], freq, width=np.diff(edges), edgecolor="black", align="edge")
ax.bar(edges[:-1], freq, width=np.diff(edges), align="edge")
plt.title(options['Histograms_checkpoint']['title'], fontsize=18)
plt.xlim([0 , 50])
plt.ylim([0 , 1.8])
plt.savefig(path + 'hist.png', dpi=500, bbox_inches='tight')
plt.show()
if 'Pressure_drops' in options:
if options['Pressure_drops']['apply']:
print('--- Pressure_drops ---')
import pickle
nc = 0
tommhg = options['Pressure_drops']['convertor']
for subf in options['Pressure_drops']['subfolders']:
ucomp = []
wcomp = []
if 'colors' in options['Pressure_drops']:
colorset = options['Pressure_drops']['colors']
colorsetted = True
else:
colorsetted = False
styles = options['Pressure_drops']['styles']
labelset = options['Pressure_drops']['labels']
path = options['Pressure_drops']['folder'] + subf + '/'
dataname = 'pdrop_COR_impl_stan.dat'
if 'STE' in path:
dataname = 'pdrop_STE_impl_stan.dat'
if labelset[nc]=='ref':
dataname = 'pdrop.dat'
data = open(path+dataname, 'rb')
p_drop = pickle.load(data)['pdrop']/tommhg
data = open(path+dataname, 'rb')
times = pickle.load(data)['time']
if labelset[nc] == 'ref':
plt.plot(times, p_drop,color='black', linestyle='-', label= '$ref$' )
else:
if colorsetted:
plt.plot(
times, p_drop, color=colorset[nc], linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
else:
plt.plot(times, p_drop, linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
if options['Pressure_drops']['catheter']:
c_path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/catheter_data/catheter_'+ labelset[nc]+'_rest_stats.csv'
with open(c_path, 'r') as csvfile:
mylist = [row[0] for row in csv.reader(csvfile, delimiter=';')]
Values = np.array(mylist)
catheter = np.zeros([len(Values)-2])
tcat = np.zeros([len(Values)-2])
for l in range(2,len(Values)):
row = Values[l].split(',')
catheter[l-2] = float(row[5])
tcat[l-2] = float(row[0])
if '11mm' in subf:
tdelay = 0.015
elif '9mm' in subf:
tdelay = -0.12
elif '13mm' in subf:
tdelay = 0.1
elif 'Normal' in subf:
tdelay = -0.01
plt.plot(tcat+tdelay,catheter,color=colorset[nc],linestyle='--')# ,label='$cat' + subf + '$')
nc +=1
#plt.ylim([0, 170])
plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=14)
if options['Pressure_drops']['title']:
plt.title(options['Pressure_drops']['title'], fontsize=18)
plt.ylabel('$ \delta P \ \ (mmHg)$', fontsize=18)
plt.savefig(options['Pressure_drops']['outpath'] + 'pressure_drops.png', dpi=500, bbox_inches='tight')
plt.show()
if 'l2_comp' in options:
if options['l2_comp']['apply']:
print('--- L2 component analysis ---')
fig, ax = plt.subplots()
for subf in options['l2_comp']['subfolder']:
path = options['l2_comp']['folder'] + subf + '/'
colors = options['l2_comp']['colors']
mode = options['l2_comp']['mode']['type']
if mode in ['gain','gain_compressed']:
gain = True
path_to_comp = options['l2_comp']['mode']['comp']
wx = np.loadtxt(path_to_comp + '/wx.txt')
wy = np.loadtxt(path_to_comp + '/wy.txt')
wz = np.loadtxt(path_to_comp + '/wz.txt')
else:
gain = False
wx = np.loadtxt(path + '/wx.txt')
wy = np.loadtxt(path + '/wy.txt')
wz = np.loadtxt(path + '/wz.txt')
times = np.loadtxt(path + '/times.txt')
if subf != 'SNRinfV120' and gain:
varux = np.loadtxt(path + '/varux.txt')
varuy = np.loadtxt(path + '/varuy.txt')
varuz = np.loadtxt(path + '/varuz.txt')
if 'SNRinfV120' in subf:
lsty = '--'
labels = ['','','','','']
else:
lsty = '-'
lsty2 = '--'
labels = ['$wx$','$wy$','$wz$','$div$']
labels2 = ['$\delta u_x$','$\delta u_y$','$\delta u_z$']
labels3 = ['$x$','$y$','$z$']
if mode == 'gain':
plt.plot(times, varux, color = colors[0], linestyle=lsty2 , label= labels2[0] )
plt.plot(times, varuy, color = colors[1], linestyle=lsty2 , label= labels2[1] )
plt.plot(times, varuz, color = colors[2], linestyle=lsty2 , label= labels2[2] )
plt.plot(times, wx, color = colors[0], linestyle=lsty, label= labels[0] )
plt.plot(times, wy, color = colors[1], linestyle=lsty, label= labels[1] )
plt.plot(times, wz, color = colors[2], linestyle=lsty, label= labels[2] )
elif mode == 'gain_compressed':
plt.plot(times, varux-wx, color = colors[0], linestyle=lsty, label= labels3[0] )
plt.plot(times, varuy-wy, color = colors[1], linestyle=lsty, label= labels3[1] )
plt.plot(times, varuz-wz, color = colors[2], linestyle=lsty, label= labels3[2] )
else:
plt.plot(times, wx, color = colors[0], linestyle=lsty, label= labels[0] )
plt.plot(times, wy, color = colors[1], linestyle=lsty, label= labels[1] )
plt.plot(times, wz, color = colors[2], linestyle=lsty, label= labels[2] )
plt.xlabel('$time \ \ (s)$', fontsize=18)
if options['l2_comp']['div']:
div = np.loadtxt(path + 'div.txt')
div_rescaled = div*0.01
div_rescaled = div_rescaled + 0.1
plt.plot(times, div_rescaled, color = 'indigo', linestyle=lsty, label= labels[3] )
if 'title' in options['l2_comp']:
if options['l2_comp']['title']:
plt.title(options['l2_comp']['title'], fontsize=18)
if options['l2_comp']['aliasing']:
if 'Poiseuille' in options['l2_comp']['folder']:
print('adding alaising color in Poiseuille')
import matplotlib.transforms as mtransforms
trans = mtransforms.blended_transform_factory(ax.transData, ax.transAxes)
if 'SNR10' in subf:
time_al = [0.15,0.78]
elif 'SNRinf' in subf:
time_al = [0.21,0.78]
pm_al = 0.5*(time_al[1] + time_al[0])
r_al = 0.5*(time_al[1] - time_al[0])
ax.fill_between(times, 0, 1, where=np.abs(times -pm_al)<= r_al ,facecolor='gold', alpha=0.4, transform=trans)
if mode == 'gain_compressed':
ax.text(pm_al/times[-1], 0.55, '$aliasing$', horizontalalignment='center',verticalalignment='center', transform=ax.transAxes,fontsize=17)
else:
ax.text(pm_al/times[-1], 0.82, '$aliasing$', horizontalalignment='center',verticalalignment='center', transform=ax.transAxes,fontsize=17)
leg = plt.legend(fancybox=True,fontsize=16)
leg.get_frame().set_linewidth(0.0)
ax.tick_params(axis='both', which='major', labelsize=14)
#plt.ylim([-0.005 , 0.235])
if mode == 'gain_compressed':
plt.ylim([-0.25 , 1.75])
plt.ylabel('$|| \delta u ||_{L2} - || w ||_{L2}$', fontsize=18)
if not gain:
plt.ylim([-0.005 , 0.5])
plt.ylabel('$ \sqrt{\int w^2 dx /| \Omega|}/ venc$', fontsize=18)
plt.savefig(options['l2_comp']['folder'] + options['l2_comp']['name'] + '.png', dpi=500, bbox_inches='tight')
plt.show()

View File

@ -3,13 +3,10 @@
# Workspace for MRI analysis of the 4Dflow data
#
# written by Jeremias Garay L: j.e.garay.labra@rug.nl
# Fernanda te amo
# for autoreload in ipython3
# %load_ext autoreload
# %autoreload 2
################################################################
import h5py
from dPdirectestim.dPdirectestim import *
from dolfin import *
import dolfin
import numpy as np
@ -999,14 +996,8 @@ def CLOCK(rank,t1,t2):
print('Total time: ' + str(time_hour) + ' hrs, ' + str(time_min) + ' min, ' + str(time_sec) + ' s')
def SCANNER(options):
########################################
#
# Basic Tools
#
########################################
if 'kspace_cib' in options:
if options['kspace_cib']['apply']:
print('--- kspace from CIB data ---')
@ -1416,24 +1407,18 @@ def SCANNER(options):
else:
CIBtoH5(path_to_cib,times,dt,outpath,flip=flip)
########################################
#
# Undersampling
#
########################################
if 'cs' in options:
if options['cs']['apply']:
if rank==0:
print('Applying Compressed Sensing')
[Sqx, Sqy, Sqz] = LOADsequences(options['cs']['seqpath'])
import CS
if options['cs']['short']:
[Mx,My,Mz] = LOADsequences(options['cs']['Mpath'])
CS.undersampling_short(Mx,My,Mz,options)
if 'short' in options['cs']:
if options['cs']['short']:
[Mx,My,Mz] = LOADsequences(options['cs']['Mpath'])
CS.undersampling_short(Mx,My,Mz,options)
else:
CS.undersampling(Sqx,Sqy,Sqz,options,options['cs']['savepath'])
@ -1457,12 +1442,6 @@ def SCANNER(options):
print('saving the sequences' + options['SENSE']['savepath'])
np.savez_compressed(options['SENSE']['savepath'], x=MxS,y=MyS,z=MzS)
########################################
#
# Writing Checkpoint from Sequence
#
########################################
if 'create_checkpoint' in options:
if options['create_checkpoint']['apply']:
print('--- Create Checkpoint ---')
@ -1529,7 +1508,7 @@ def SCANNER(options):
comm = MESH['mesh'].mpi_comm()
dt = options['create_checkpoint']['dt']
if options['create_checkpoint']['xdmf']:
xdmf_u = XDMFFile(options['create_checkpoint']['savepath']+'u.xdmf')
xdmf_u = XDMFFile(options['create_checkpoint']['savepath']+ 'R' + str(r) + '/u.xdmf')
for l in range(len(vel_seq)):
if rank == 0:
@ -1545,11 +1524,6 @@ def SCANNER(options):
inout.write_HDF5_data(
comm, path + '/u.h5', vel_seq[l], '/u', t=l*dt)
########################################
#
# Relative Pressure Estimators
#
########################################
if 'reference' in options:
if options['reference']['apply']:
if rank == 0:
@ -1688,157 +1662,6 @@ def SCANNER(options):
if rank==0:
print(' ')
if 'peak_pv' in options:
if options['peak_pv']['apply']:
import CS
import pickle
import sys
import logging
# DPestim
logging.getLogger().setLevel(logging.INFO)
parameters['form_compiler']['optimize'] = True
parameters['form_compiler']['cpp_optimize'] = True
parameters['form_compiler']['cpp_optimize_flags'] = '-O3 -ffast-math -march=native'
infile_dp = options['peak_pv']['infile_dp']
estimator = DPDirectEstim(infile_dp)
barye2mmHg = 1/1333.22387415
t_star = 0.185
if rank==0:
print('Computing Velocity and Pressure at Peak Systole')
print('The inlet max occurs at ' + str(t_star) + ' sec')
[BOX,AORTA,LEO] = CREATEmeshes(options)
if options['peak_pv']['mesh_into']=='leo':
MESH = LEO
del AORTA
if options['peak_pv']['mesh_into']=='aorta':
MESH = AORTA
del LEO
if options['peak_pv']['p_comp']=='error':
if rank==0:
print('Reading Pressure Reference')
P0_PPE = READcheckpoint(MESH,'p',options,options['checkpoint_path'],'p_PPE_impl_stan')
P0_STE = READcheckpoint(MESH,'p',options,options['checkpoint_path'],'p_STE_impl_stan')
[Sqx,Sqy,Sqz] = LOADsequences(options['peak_pv']['orig_seq'])
Nite = options['peak_pv']['N_CS']
[row,col,dep,numt] = Sqz.shape
frms_num = 3
peakslice = options['peak_pv']['peak_slice']
R = options['peak_pv']['R']
v0 = np.sqrt(Sqx[:,:,:,peakslice]**2 + Sqy[:,:,:,peakslice]**2 + Sqz[:,:,:,peakslice]**2)
max0 = np.where(v0==np.max(v0))
qqvec = {}
for ss in options['peak_pv']['flux_bnd']:
qqvec[ss] = np.zeros([Nite])
ppemax = np.zeros([Nite])
stemax = np.zeros([Nite])
vmax = np.zeros([Nite])
slrdmax = peakslice
# Selecting around the max only
slrdmax = 1
Sqx = Sqx[:,:,:,peakslice-1:peakslice+2]
Sqy = Sqy[:,:,:,peakslice-1:peakslice+2]
Sqz = Sqz[:,:,:,peakslice-1:peakslice+2]
for l in range(len(R)):
if rank==0:
print('Peak Systole velocity and pressure at R = ' + str(R[l]))
sx_cs = np.zeros([row,col,dep,frms_num,Nite])
sy_cs = np.zeros([row,col,dep,frms_num,Nite])
sz_cs = np.zeros([row,col,dep,frms_num,Nite])
for k in range(Nite):
if rank==0:
print('CS iteration number ' + str(k+1))
[xcs,ycs,zcs] = CS.undersampling_peakpv(Sqx,Sqy,Sqz,options,R[l])
sx_cs[:,:,:,:,k] = xcs
sy_cs[:,:,:,:,k] = ycs
sz_cs[:,:,:,:,k] = zcs
vk = np.sqrt(sx_cs[:,:,:,1,k]**2 + sy_cs[:,:,:,1,k]**2 + sz_cs[:,:,:,1,k]**2)
vmax[k] = vk[max0]
if rank==0:
print('\n CS done')
# To write the checkpoints
vel_seq = SqtoH5(BOX,MESH,sx_cs[:,:,:,:,k],sy_cs[:,:,:,:,k],sz_cs[:,:,:,:,k])
comm = MESH['mesh'].mpi_comm()
# Computing the Fluxes
if rank==0:
print('\n Computing the Flux')
QQ = Fluxes(MESH,vel_seq,options,options['peak_pv']['flux_bnd'])
for ss in options['peak_pv']['flux_bnd']:
qqvec[ss][k] = QQ[ss][slrdmax]
if rank==0:
print('\n Writing checkpoints')
for ns in range(len(vel_seq)):
pathss = options['peak_pv']['savepath'] + 'H5/checkpoint/{i}/'.format(i=ns)
if l<10 and l>0:
pathss = options['peak_pv']['savepath'] + 'H5/checkpoint/0{i}/'.format(i=ns)
inout.write_HDF5_data(comm, pathss + '/u.h5', vel_seq[ns], '/u', t=0)
if rank==0:
print('\n The checkpoints were wrote')
# Computing the Pressure Drop
estimator.estimate()
# Reading the results
if options['peak_pv']['p_comp']=='peak':
ppe_raw = open(options['peak_pv']['savepath'] + '/H5/pdrop_PPE_impl_stan.dat','rb')
ste_raw = open(options['peak_pv']['savepath'] + '/H5/pdrop_STE_impl_stan.dat','rb')
ppe = pickle.load(ppe_raw)['pdrop']*(-barye2mmHg)
ste = pickle.load(ste_raw)['pdrop']*(-barye2mmHg)
p1max[k] = ppe[slrdmax]
p2max[k] = ste[slrdmax]
elif options['peak_pv']['p_comp']=='error':
PPE = READcheckpoint(MESH,'p',options,options['peak_pv']['savepath']+'H5/checkpoint/','p_PPE_impl_stan')
STE = READcheckpoint(MESH,'p',options,options['peak_pv']['savepath']+'H5/checkpoint/','p_STE_impl_stan')
ppe_vec_0 = P0_PPE[peakslice].vector().get_local() - P0_PPE[peakslice].vector().get_local()[0]
ppe_vec = PPE[slrdmax].vector().get_local() - PPE[slrdmax].vector().get_local()[0]
ste_vec_0 = P0_STE[peakslice].vector().get_local() - P0_STE[peakslice].vector().get_local()[0]
ste_vec = STE[slrdmax].vector().get_local() - STE[slrdmax].vector().get_local()[0]
ppemax[k] = np.linalg.norm(ppe_vec_0 - ppe_vec)/np.linalg.norm(ppe_vec_0)
stemax[k] = np.linalg.norm(ste_vec_0 - ste_vec)/np.linalg.norm(ste_vec_0)
else:
raise Exception('Pressure computation not recognize!')
# VELOCITIES
vmean = np.mean(vmax)
vstd = np.std(vmax)
# PRESSURES
ppemean = np.mean(ppemax)
stemean = np.mean(stemax)
ppestd = np.std(ppemax)
stestd = np.std(stemax)
if options['peak_pv']['save']:
if rank==0:
print('\n saving the files in ' + options['peak_pv']['savepath'])
for ss in options['peak_pv']['flux_bnd']:
np.savetxt( options['peak_pv']['savepath'] + 'Q'+str(ss) +'_R'+str(R[l])+'.txt', [np.mean(qqvec[ss])])
np.savetxt( options['peak_pv']['savepath'] + 'Qstd'+str(ss) +'_R'+str(R[l])+'.txt', [np.std(qqvec[ss])])
np.savetxt( options['peak_pv']['savepath'] + 'ppemean_R'+str(R[l])+'.txt', [ppemean] )
np.savetxt( options['peak_pv']['savepath'] + 'stemean_R'+str(R[l])+'.txt', [stemean] )
np.savetxt( options['peak_pv']['savepath'] + 'vmean_R'+str(R[l])+'.txt', [vmean] )
np.savetxt( options['peak_pv']['savepath'] + 'ppestd_R'+str(R[l])+'.txt', [ppestd] )
np.savetxt( options['peak_pv']['savepath'] + 'stestd_R'+str(R[l])+'.txt', [stestd] )
np.savetxt( options['peak_pv']['savepath'] + 'vstd_R'+str(R[l])+'.txt', [vstd] )
if 'change_mesh' in options:
if options['change_mesh']['apply']:
if rank == 0:
@ -1861,9 +1684,9 @@ def SCANNER(options):
changed = {}
#W = LEO['FEM'].sub(0).collapse()
comm = MESH_out['mesh'].mpi_comm()
v2 = Function(MESH_out['FEM'])
for k in range(len(list(origin))):
v2 = Function(MESH_out['FEM'])
if rank == 0:
print('CHANGING: index', k)
LagrangeInterpolator.interpolate(v2, origin[k])
@ -1878,7 +1701,7 @@ def SCANNER(options):
if rank == 0:
print('saving checkpoint', l)
path = options['change_mesh']['savepath'] + \
'R1/checkpoint/{i}/'.format(i=l)
'checkpoint/{i}/'.format(i=l)
writepath = path + '/'+options['change_mesh']['mode']+'.h5'
inout.write_HDF5_data(
comm, writepath, changed[l] ,'/'+options['change_mesh']['mode'], t=l*dt)

View File

@ -109,14 +109,10 @@ def WORKcheck(MESH, mode, output_path, checkpoint_path, filename, outname, optio
if mode == 'p' or mode == 'p_cib':
xdmf_p = XDMFFile(output_path+outname+'.xdmf')
for k in range(0, len(indexes), 1):
dt = options['Pressure']['dt']
for k in range(0, len(indexes), options['Pressure']['undersampling']):
te = k*dt
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
if filename == 'p':
if k < 10 and k > 0:
path = checkpoint_path + '0' + \
str(indexes[k]) + '/'+filename+'.h5'
p = Function(W)
if mode == 'p':
barye2mmHg = 1/1333.22387415
@ -126,36 +122,10 @@ def WORKcheck(MESH, mode, output_path, checkpoint_path, filename, outname, optio
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
hdf.read(p, 'p/vector_0')
hdf.close()
p1vec = p.vector().get_local()
p1vec = p1vec - np.mean(p1vec)
#p1vec = p1vec - np.mean(p1vec)
p.vector()[:] = p1vec*barye2mmHg
xdmf_p.write(p, te)
te = te + dt
numt = numt + 1
if mode == 'divu':
xdmf_u = XDMFFile(output_path+outname+'.xdmf')
for k in range(0, len(indexes), 1):
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
if indexes[k] < 10 and indexes[k] > 0:
path = checkpoint_path + '0' + \
str(indexes[k]) + '/'+filename+'.h5'
v = Function(V)
dv = Function(W)
dv.rename('div', outname)
comm = MPI.COMM_WORLD
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
hdf.read(v, 'u/vector_0')
hdf.close()
dv.assign(project(div(v), W))
xdmf_u.write(dv, te)
te = te + dt
numt = numt + 1
def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname, options, flow=False, bnds=None):
@ -203,7 +173,7 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
freq,edges = np.histogram(ValuesPeak, bins=80, density=True)
#Saving the histogram
print('Saving at ' + output_path)
np.savetxt(output_path + 'hist_frew.txt', freq)
np.savetxt(output_path + 'hist_freq.txt', freq)
np.savetxt(output_path + 'hist_edges.txt', edges)
if mode == 'perturbation':
@ -235,6 +205,20 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
noise_in_coil = options['Perturbation']['type']['coil']
umaxima = []
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()
umaxima.append(np.max(uvec))
ufactor = options['Perturbation']['type']['phase_contrast']/100
VENC = np.floor(np.ceil(np.max(umaxima))*ufactor)
print('VENC chosen = ',VENC)
for k in indexes:
path = checkpoint_path + str(k) + '/'+filename+'.h5'
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
@ -244,9 +228,7 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
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
#gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
B0 = 1.5 # Tesla Magnetic Field Strenght
TE = 5e-3 # Echo-time
Phi1 = 1*B0*TE + 0*uvec
@ -474,7 +456,11 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
from dolfin import HDF5File
V = MESH['FEM']
V1 = MESH['FEM'].sub(1).collapse()
W = MESH['FEM'].sub(0).collapse()
DGs = FunctionSpace( MESH['mesh'], 'DG',0)
cellv = CellVolume(MESH['mesh'])
h = CellDiameter(MESH['mesh'])
unsort_indexes = os.listdir(checkpoint_path)
indexes = [int(x) for x in unsort_indexes]
indexes.sort()
@ -486,6 +472,80 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
if len(indexes)!=len(indexes0):
raise Exception('The lengh of the checkpoints are not the same!')
if mode == 'algebra':
outname = options['Algebra']['outname']
output = XDMFFile(outpath+outname+'.xdmf')
checkpoint = options['Algebra']['checkpoint']
v1 = Function(W)
v2 = Function(W)
vout = Function(W)
vout.rename('velocity','velocity')
vout_vec = np.zeros(vout.vector().get_local().size)
times_vec = np.zeros(len(indexes0))
vdict1 = {}
vdict2 = {}
if options['Algebra']['mode'] == 'aliasing':
print('Assuming the corrector in the second path entered')
# Reading all the timestamps first
for k in range(len(indexes)):
path_v1 = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
path_v2 = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
hdf_v1 = HDF5File(MESH['mesh'].mpi_comm(), path_v1, 'r')
if 'w' in refname:
hdf_v1.read(v1, 'w/vector_0')
time = hdf_v1.attributes('w/vector_0').to_dict()['timestamp']
else:
hdf_v1.read(v1, 'u/vector_0')
time = hdf_v1.attributes('u/vector_0').to_dict()['timestamp']
times_vec[k] = time
hdf_v2 = HDF5File(MESH['mesh'].mpi_comm(), path_v2, 'r')
if 'w' in comname:
hdf_v2.read(v2, 'w/vector_0')
else:
hdf_v2.read(v2, 'u/vector_0')
print('computing algebra for the time',time)
hdf_v1.close()
hdf_v2.close()
vdict1[k] = v1.vector().get_local()
vdict2[k] = v2.vector().get_local()
for k in range(len(indexes)):
if options['Algebra']['mode'] == '+':
vout.vector()[:] = vdict1[k] + vdict2[k]
elif options['Algebra']['mode'] == '-':
vout.vector()[:] = vdict1[k] - vdict2[k]
elif options['Algebra']['mode'] == 'aliasing':
VENC = options['Algebra']['VENC']
aliasing = False
for l in range(len(vout_vec)):
if k>0:
#mean1 = abs(np.mean(vdict2[0][:]))
#mean2 = abs(np.mean(vdict2[1][:]))
#mean3 = abs(np.mean(vdict2[2][:]))
#treshold = 10*max(mean1,mean2,mean3)
#if abs(np.mean(vdict2[k][:]))>treshold:
# vout_vec[l] = 0
if vdict1[k][l]-vdict1[k-1][l] < -VENC:
vdict1[k][l] = vdict1[k][l] + 2*VENC
vout_vec[l] = vdict1[k][l]
else:
vout_vec[l] = vdict1[k][l]
else:
vout_vec[l] = vdict1[k][l] # first case is suppouse to be aliasing-free
vout.vector()[:] = vout_vec
else:
raise Exception('Not supported operation between vectors!')
output.write(vout, times_vec[k])
if checkpoint:
path = outpath + 'checkpoint/' + str(indexes[k]) + '/' + 'u.h5'
inout.write_HDF5_data(MESH['mesh'].mpi_comm(), path , vout, '/u', t=times_vec[k])
if mode =='curves':
if options['Error-curves']['undersampling']>1:
@ -495,27 +555,54 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
u = Function(W)
w = Function(W)
ones = interpolate(Constant(1), V.sub(1).collapse())
L_sys = assemble(ones*dx)
VENC = options['Error-curves']['VENC']
for typs in options['Error-curves']['type']:
ucomp = []
wcomp = []
div_array = []
varu = []
times = []
dt = options['Error-curves']['dt']
for k in range(1,len(indexes)):
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
if typs == 'l2_comp':
wy = Function(V1)
wz = Function(V1)
comname2 = comname
wx_array = []
wy_array = []
wz_array = []
if typs == 'utrue-uobs':
u_path = options['Error-curves']['true_check'] + 'checkpoint/'
w_path = options['Error-curves']['ref_check'] + 'checkpoint/'
comname2 = 'u'
varux_array = []
varuy_array = []
varuz_array = []
else:
u_path = reference_path
w_path = checkpoint_path
dt = options['Error-curves']['dt']
for k in range(1,len(indexes)):
path_w = w_path + str(indexes[k]) + '/'+comname2+'.h5'
path_u = u_path + str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
w.rename('w', 'w')
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
if 'w' in comname:
if 'w' in comname2:
hdf_w.read(w, 'w/vector_0')
else:
hdf_w.read(w, 'u/vector_0')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
hdf_u.close()
if typs != 'l2_comp':
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
hdf_u.close()
u_vec = u.vector().get_local()
hdf_w.close()
u_vec = u.vector().get_local()
w_vec = w.vector().get_local()
print('computing error in timestep numer',k)
@ -525,59 +612,53 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
elif typs == 'max':
ucomp.append(np.max(abs(u_vec)))
wcomp.append(np.max(abs(w_vec)))
elif typs == 'norm2':
ucomp.append(np.sqrt(assemble(dot(u,u)*dx)/L_sys))
wcomp.append(np.sqrt(assemble(dot(w,w)*dx)/L_sys))
elif typs == 'grad':
wcomp.append(np.sqrt(assemble(inner(grad(w),grad(w))*dx)/L_sys))
elif typs == 'l2_comp':
wx = w.sub(0,deepcopy=True)
wy = w.sub(1,deepcopy=True)
wz = w.sub(2,deepcopy=True)
wx_array.append(np.sqrt(assemble(wx*wx*dx)/L_sys)/VENC)
wy_array.append(np.sqrt(assemble(wy*wy*dx)/L_sys)/VENC)
wz_array.append(np.sqrt(assemble(wz*wz*dx)/L_sys)/VENC)
elif typs == 'div':
div_array.append(np.sqrt(assemble(div(u)**2/h*dx)/L_sys)/VENC)
elif typs == 'utrue-uobs':
wx = w.sub(0,deepcopy=True)
wy = w.sub(1,deepcopy=True)
wz = w.sub(2,deepcopy=True)
ux = u.sub(0,deepcopy=True)
uy = u.sub(1,deepcopy=True)
uz = u.sub(2,deepcopy=True)
varux_array.append(np.sqrt(assemble((ux-wx)**2*dx)/L_sys)/VENC)
varuy_array.append(np.sqrt(assemble((uy-wy)**2*dx)/L_sys)/VENC)
varuz_array.append(np.sqrt(assemble((uz-wz)**2*dx)/L_sys)/VENC)
else:
raise Exception('No defined type for curve printing!')
times.append(k*dt)
np.savetxt(outpath+'u' +typs+'.txt',ucomp)
np.savetxt(outpath+'w' +typs+'.txt',wcomp)
if typs == 'grad':
np.savetxt(outpath+'w' +typs+'.txt',wcomp)
elif typs == 'l2_comp':
np.savetxt(outpath+'wx.txt',wx_array)
np.savetxt(outpath+'wy.txt',wy_array)
np.savetxt(outpath+'wz.txt',wz_array)
elif typs == 'div':
np.savetxt(outpath+'div.txt',div_array)
elif typs == 'utrue-uobs':
np.savetxt(outpath+'varux.txt',varux_array)
np.savetxt(outpath+'varuy.txt',varuy_array)
np.savetxt(outpath+'varuz.txt',varuz_array)
else:
np.savetxt(outpath+'u' +typs+'.txt',ucomp)
np.savetxt(outpath+'w' +typs+'.txt',wcomp)
np.savetxt(outpath+'times.txt',times)
if mode == 'histogram':
from pathlib import Path
import pickle
u = Function(V)
w = Function(V)
errors = {}
for k in range(len(indexes)):
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
if indexes0[k] < 10:
path_u = reference_path + '0' + \
str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
w.rename('w', 'w')
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
hdf_w.read(w, 'w/vector_0')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
hdf_u.close()
hdf_w.close()
u_vec = u.vector().get_local()
w_vec = w.vector().get_local()
errors[k] = np.zeros(u_vec.size)
for l in range(len(errors[k])):
#errors[k][l] = np.nan
if u_vec[l]<1e-9:
errors[k][l] = -1
else:
eta = np.abs(w_vec[l]/u_vec[l])
if np.abs(eta)>50:
errors[k][l] = -1
else:
errors[k][l] = eta
write_path = Path(outpath)
fpath = write_path.joinpath('errors.dat')
pickle.dump(errors, fpath.open('wb'))
if mode == 'h5':
xdmf_u = XDMFFile(outpath+'meas.xdmf')
#xdmf_ucor = XDMFFile(output_path+'ucor.xdmf')
@ -592,10 +673,6 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
if indexes0[k] < 10:
path_u = reference_path + '0' + \
str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
w.rename('w', 'w')
#ucor.rename('ucor', 'ucor')
@ -612,34 +689,173 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
#ucor.vector()[:] = u_vec + w_vec
xdmf_u.write(u, k)
#xdmf_ucor.write(ucor, k)
xdmf_w.write(w, k)
if mode == 'colormap':
colormap = XDMFFile(outpath+'colormap.xdmf')
if mode == 'u':
colormap = XDMFFile(outpath+'u.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
u = Function(W)
#P2 = FunctionSpace( MESH['mesh'], 'P',1)
cm = Function(DGs)
vs = TestFunction(DGs)
for k in range(len(indexes)):
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
cm.rename('vel','vel')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_u.close()
r = assemble(dot(u,u)*vs/cellv*dx).get_local()
cm.vector()[:] = np.sqrt(np.abs(r))
#cm.vector()[:] = np.sqrt(r)
colormap.write(cm, time)
if mode == 'w':
colormap = XDMFFile(outpath+'w.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
w = Function(W)
#P2 = FunctionSpace( MESH['mesh'], 'P',2)
cm = Function(DGs)
vs = TestFunction(DGs)
for k in range(len(indexes)):
path_w = checkpoint_path + str(indexes0[k]) + '/'+comname+'.h5'
w.rename('cor', 'cor')
cm.rename('w','w')
hdf_w = HDF5File(MESH['mesh'].mpi_comm(), path_w, 'r')
hdf_w.read(w, 'w/vector_0')
time = hdf_w.attributes('w/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_w.close()
r = assemble(dot(w,w)*vs/cellv*dx).get_local()
cm.vector()[:] = np.sqrt(np.abs(r))
colormap.write(cm, time)
if mode == 'w/u':
colormap = XDMFFile(outpath+'w_u.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
u = Function(W)
w = Function(W)
cm = Function(W)
dt = options['Corrector']['dt']
cm = Function(DGs)
vs = TestFunction(DGs)
for k in range(len(indexes)):
print('making the colormap in the time',np.round(k*dt,2))
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
w.rename('w', 'w')
cm.rename('color','color')
cm.rename('w_u','w_u')
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
hdf_w.read(w, 'w/vector_0')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_u.close()
hdf_w.close()
uvec = u.vector().get_local()
wvec = w.vector().get_local()
cm.vector()[:] = np.sqrt((uvec - wvec)**2)
colormap.write(cm, k*dt)
rw = assemble(dot(w,w)*vs/cellv*dx).get_local()
ru = assemble(dot(u,u)*vs/cellv*dx).get_local()
cm.vector()[:] = np.sqrt(rw)/np.sqrt(ru)
colormap.write(cm, time)
if mode == 'dot':
colormap = XDMFFile(outpath+'dot.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
u = Function(W)
w = Function(W)
cm = Function(V1)
u.rename('meas', 'meas')
w.rename('w', 'w')
for k in range(len(indexes)):
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
hdf_w.read(w, 'w/vector_0')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_u.close()
hdf_w.close()
cm = project(inner(u,w),V1)
cm.rename('dot','dot')
colormap.write(cm, time)
if mode == 'div(u)':
colormap = XDMFFile(outpath+'divu.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
u = Function(W)
cm = Function(DGs)
vs = TestFunction(DGs)
for k in range(len(indexes)):
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
cm.rename('divu','divu')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_u.close()
r = assemble(div(u)**2*vs/cellv*dx).get_local()
cm.vector()[:] = np.sqrt(r)
colormap.write(cm, time)
if mode == 'div(u)/u':
colormap = XDMFFile(outpath+'divu_u.xdmf')
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
u = Function(W)
cm = Function(DGs)
vs = TestFunction(DGs)
surface = np.zeros(cm.vector().get_local().size)
volume = np.zeros(cm.vector().get_local().size)
Cells = MESH['mesh'].cells()
Points = MESH['mesh'].coordinates()
for k in range(MESH['mesh'].num_cells()):
A = Points[Cells[k]][0]
B = Points[Cells[k]][1]
C = Points[Cells[k]][2]
D = Points[Cells[k]][3]
# volume
Vol = 1/6*np.abs(np.inner(A-D, np.cross(B-D, C-D)))
volume[k] = Vol
# surface area
SA = 0
for l in range(4):
if l == 0:
[P1, P2, P3, P4] = [A, B, C, D]
if l == 1:
[P1, P2, P3, P4] = [D, A, B, C]
if l == 2:
[P1, P2, P3, P4] = [C, D, A, B]
if l == 3:
[P1, P2, P3, P4] = [B, C, D, A]
SA += 0.5*np.linalg.norm(np.cross(P2-P1, P3-P1))
surface[k] = SA
for k in range(len(indexes)):
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
u.rename('meas', 'meas')
cm.rename('divu','divu')
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0')
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
print('making the colormap in the time',time)
hdf_u.close()
rdiv = assemble(div(u)**2*vs*dx).get_local()
ru = assemble(dot(u,u)*vs*dx).get_local()
cm.vector()[:] = np.sqrt(rdiv)/np.sqrt(ru)*volume/surface/np.sqrt(120)
colormap.write(cm, time)
if mode == 'error_u':
xdmf_u = XDMFFile(output_path+'error_u.xdmf')
@ -874,6 +1090,11 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
#from dolfin import HDF5File
V = MESH['FEM']
W = MESH['FEM'].sub(1).collapse()
p = Function(W)
one_mesh = interpolate(Constant(1), W)
dt = options['Estim_Pressure']['dt']
p_drop_lst = []
time_ = []
# Checkpoints folders
unsort_indexes = os.listdir(checkpoint_path)
indexes = [int(x) for x in unsort_indexes]
@ -897,22 +1118,25 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
sphere1 = mshr.Sphere(x1, radius1)
mesh_s1 = mshr.generate_mesh(sphere0, Npts0)
mesh_s2 = mshr.generate_mesh(sphere1, Npts1)
# New elements
VS1 = FunctionSpace(mesh_s1, FiniteElement('P', mesh_s1.ufl_cell(), 1))
VS2 = FunctionSpace(mesh_s2, FiniteElement('P', mesh_s2.ufl_cell(), 1))
s1 = Function(VS1)
s2 = Function(VS2)
LagrangeInterpolator.interpolate(s1, one_mesh)
LagrangeInterpolator.interpolate(s2, one_mesh)
vol1 = assemble(s1*dx)
vol2 = assemble(s1*dx)
VS1 = FunctionSpace(mesh_s1, FiniteElement('P', mesh_s1.ufl_cell(), 1))
VS2 = FunctionSpace(mesh_s2, FiniteElement('P', mesh_s2.ufl_cell(), 1))
s1 = Function(VS1)
s2 = Function(VS2)
p = Function(W)
if options['Estim_Pressure']['method'] == 'boundaries':
boundaries = MESH['boundaries']
ds = Measure("ds", subdomain_data=boundaries)
bnd1 = options['Estim_Pressure']['boundaries'][0]
bnd2 = options['Estim_Pressure']['boundaries'][1]
area1 = assemble(one_mesh*ds(bnd1))
area2 = assemble(one_mesh*ds(bnd2))
one_mesh = interpolate(Constant(1), W)
LagrangeInterpolator.interpolate(s1, one_mesh)
LagrangeInterpolator.interpolate(s2, one_mesh)
vol1 = assemble(s1*dx)
vol2 = assemble(s1*dx)
dt = options['Estim_Pressure']['dt']
p_drop_lst = []
time_ = []
for k in range(0, len(indexes)):
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
@ -920,11 +1144,14 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
hdf.read(p, 'p/vector_0')
hdf.close()
LagrangeInterpolator.interpolate(s1, p)
LagrangeInterpolator.interpolate(s2, p)
P1 = assemble(s1*dx)/vol1
P2 = assemble(s2*dx)/vol2
if options['Estim_Pressure']['method'] == 'spheres':
LagrangeInterpolator.interpolate(s1, p)
LagrangeInterpolator.interpolate(s2, p)
P1 = assemble(s1*dx)/vol1
P2 = assemble(s2*dx)/vol2
if options['Estim_Pressure']['method'] == 'boundaries':
P1 = assemble(p*ds(bnd1))/area1
P2 = assemble(p*ds(bnd2))/area2
p_drop_lst.append(P2-P1)
time_.append(k*dt)
@ -1012,41 +1239,60 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
def ROUTINE(options):
if 'Algebra' in options:
if options['Algebra']['apply']:
if rank == 0:
print('Applying Algebra')
print('Choosen mode: ' + options['Algebra']['mode'])
MESH = LOADmesh(options['Algebra']['meshpath'])
v1path = options['Algebra']['v1']['path'] + 'checkpoint/'
v1name = options['Algebra']['v1']['name']
v2path = options['Algebra']['v2']['path'] + 'checkpoint/'
v2name = options['Algebra']['v2']['name']
outpath = options['Algebra']['outpath']
ERRORmap(MESH, 'algebra', outpath, v1path,
v2path, v1name, v2name, options)
if 'Outlet_Wind' in options:
if options['Outlet_Wind']['apply']:
if rank == 0:
print('--- Outlet Windkessel ---')
mesh_path = options['Outlet_Wind']['mesh_path']
meshpath = options['Outlet_Wind']['meshpath']
out_path = options['Outlet_Wind']['out_path']
filename = options['Outlet_Wind']['filename']
checkpoint = options['Outlet_Wind']['checkpoint'] + 'checkpoint/'
bnds = options['Outlet_Wind']['bnds']
MESH = LOADmesh(mesh_path)
MESH = LOADmesh(meshpath)
OUTLETwind(MESH, out_path, checkpoint, filename, bnds)
if 'Corrector' in options:
if options['Corrector']['apply']:
if rank == 0:
print('Applying Corrector')
if 'Colormap' in options:
if options['Colormap']['apply']:
MESH = LOADmesh(options['Corrector']['mesh_path'])
u_path = options['Corrector']['u_path'] + 'checkpoint/'
w_path = options['Corrector']['w_path'] + 'checkpoint/'
wname = options['Corrector']['wname']
uname = options['Corrector']['uname']
mode = options['Corrector']['mode']
outpath = options['Corrector']['outpath']
for mode in options['Colormap']['mode']:
if rank == 0:
print('Applying Colormap')
print('Choosen mode: ' + mode)
ERRORmap(MESH, mode, outpath, u_path,
w_path, uname, wname, options)
MESH = LOADmesh(options['Colormap']['meshpath'])
upath = options['Colormap']['upath'] + 'checkpoint/'
wpath = options['Colormap']['wpath'] + 'checkpoint/'
wname = options['Colormap']['wname']
uname = options['Colormap']['uname']
outpath = options['Colormap']['outpath']
ERRORmap(MESH, mode, outpath, upath,
wpath, uname, wname, options)
if 'Velocity' in options:
if options['Velocity']['apply']:
if rank == 0:
print('--- Reading Velocity ---')
MESH = LOADmesh(options['Velocity']['mesh_path'])
MESH = LOADmesh(options['Velocity']['meshpath'])
filename = options['Velocity']['filename']
checkpoint_path = options['Velocity']['checkpoint'] + 'checkpoint/'
outpath = options['Velocity']['checkpoint']
@ -1067,7 +1313,7 @@ def ROUTINE(options):
if options['W_map']['apply']:
if rank == 0:
print('Applying W--MAP')
MESH = LOADmesh(options['mesh_path'])
MESH = LOADmesh(options['meshpath'])
filename = options['W_map']['filename']
outname = options['W_map']['out_name']
mode = 'w'
@ -1078,7 +1324,7 @@ def ROUTINE(options):
if options['GradW_map']['apply']:
if rank == 0:
print('Applying Grad W--MAP')
MESH = LOADmesh(options['mesh_path'])
MESH = LOADmesh(options['meshpath'])
filename = options['GradW_map']['filename']
outname = options['GradW_map']['out_name']
mode = 'gradw'
@ -1088,21 +1334,21 @@ def ROUTINE(options):
if 'Pressure' in options:
if options['Pressure']['apply']:
if rank == 0:
print('Applying Pressure-MAP')
print('---Applying Pressure---')
MESH = LOADmesh(options['mesh_path'])
MESH = LOADmesh(options['meshpath'])
outpath = options['Pressure']['checkpoint']
checkpoint_path = options['Pressure']['checkpoint'] + 'checkpoint/'
filename = options['Pressure']['filename']
outname = options['Pressure']['out_name']
mode = 'p'
WORKcheck(MESH, mode, output_path, checkpoint_path,
filename, outname, options)
WORKcheck(MESH, 'p', outpath, checkpoint_path,
filename, filename, options)
if 'Error_P' in options:
if options['Error_P']['apply']:
if rank == 0:
print('Applying L2 error to Pressure')
MESH = LOADmesh(options['mesh_path'])
MESH = LOADmesh(options['meshpath'])
refname = options['Error_P']['refname']
reference_path = options['Error_P']['refpath']
filename = options['Error_P']['filename']
@ -1115,10 +1361,13 @@ def ROUTINE(options):
if options['Estim_Pressure']['apply']:
if rank == 0:
print('Applying Pressure Estimator')
print('Method choosed: '+options['Estim_Pressure']['method'])
MESH = LOADmesh(options['mesh_path'])
MESH = LOADmesh(options['Estim_Pressure']['meshpath'])
filename = options['Estim_Pressure']['filename']
outpath = options['Estim_Pressure']['outpath']
outpath = options['Estim_Pressure']['checkpath']
checkpoint_path = options['Estim_Pressure']['checkpath'] + 'checkpoint/'
ESTIMpressure(MESH, outpath, checkpoint_path, filename, options)
if 'Error-curves' in options:
@ -1162,7 +1411,11 @@ def ROUTINE(options):
MESH = LOADmesh(options['Perturbation']['meshpath'])
checkpath = options['Perturbation']['checkpath'] + 'checkpoint/'
name_folder = 'SNR' +options['Perturbation']['type']['SNR'] + 'V' + str(options['Perturbation']['type']['phase_contrast'])
if type(options['Perturbation']['type']['SNR'])=='str':
name_folder = 'SNR' +options['Perturbation']['type']['SNR'] + 'V' + str(options['Perturbation']['type']['phase_contrast'])
else:
name_folder = 'SNR' +str(options['Perturbation']['type']['SNR']) + 'V' + str(options['Perturbation']['type']['phase_contrast'])
out_check = options['Perturbation']['checkpath'] + name_folder + '/'
READcheckpoint(MESH,'perturbation', out_check,checkpath,'u','u',options)

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@ -1,5 +1,4 @@
from dolfin import *
import matplotlib.pyplot as plt
import numpy as np
from common import inout
from mpi4py import MPI
@ -23,7 +22,6 @@ def solv_NavierStokes(options):
theta = Constant(options['theta'])
Tf = options['Tf']
dt = options['dt']
dt_w = options['dt_write']
# CREATING THE FILES
xdmf_u = XDMFFile(options['savepath']+'u.xdmf')
@ -53,7 +51,6 @@ def solv_NavierStokes(options):
BCS = []
bc = options['boundary_conditions']
# For Windkessel implementation
flows = {}
pii0 = {}
pii = {}
press = {}
@ -63,6 +60,23 @@ def solv_NavierStokes(options):
Windkvar = {}
windkessel = False
u, p = TrialFunctions(W)
w = Function(W)
h = CellDiameter(mesh)
u0, p0 = w.split()
u_ = theta*u + otheta*u0
p_ = theta*p + otheta*p0
# The variational formulation
# Mass matrix
F = (
(rho/dt)*dot(u - u0, v)*dx
+ mu*inner(grad(u_), grad(v))*dx
- p_*div(v)*dx + q*div(u)*dx
+ rho*dot(grad(u_)*u0, v)*dx
)
for nbc in range(len(bc)):
nid = bc[nbc]['id']
if bc[nbc]['type'] == 'dirichlet':
@ -82,43 +96,27 @@ def solv_NavierStokes(options):
windkessel = True
if rank==0:
print('Adding Windkessel BC at boundary ',nid)
[R_p,C,R_d] = bc[nbc]['value']
[R_p,R_d,C] = bc[nbc]['value']
# coeficients
alpha[nid] = R_d*C/(R_d*C + dt)
beta[nid] = R_d*(1-alpha[nid])
gamma[nid] = R_p + beta[nid]
# dynamical terms
if C ==0:
flows[nid] = Constant(0)
press[nid] = Constant(R_p*0)
print('no capacitance C for boundary',nid)
press[nid] = Constant(0)
else:
flows[nid] = Constant(0)
pii0[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
pii[nid] = Constant(alpha[nid]*pii0[nid] + beta[nid]*flows[nid])
press[nid] = Constant(gamma[nid]*flows[nid] + alpha[nid]*pii0[nid])
pii[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
press[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
Windkvar[nid] = dt*press[nid]*dot(v,n)*ds(nid)
Windkvar[nid] = press[nid]*dot(v,n)*ds(nid)
u, p = TrialFunctions(W)
w = Function(W)
h = CellDiameter(mesh)
u0, p0 = w.split()
u_ = theta*u + otheta*u0
p_ = theta*p + otheta*p0
# The variational formulation
# Mass matrix
F = (
(rho/dt)*dot(u - u0, v)*dx
+ mu*inner(grad(u_), grad(v))*dx
- p_*div(v)*dx + q*div(u)*dx
+ rho*dot(grad(u_)*u0, v)*dx
)
# Stabilization Terms
if options['stabilization']['temam']:
if rank==0:
print('Addint Temam stabilization term')
print('Adding Temam stabilization term')
F += 0.5*rho*div(u0)*dot(u_, v)*dx
if pspg:
@ -132,7 +130,7 @@ def solv_NavierStokes(options):
for nid in options['stabilization']['forced_normal']['boundaries']:
if rank==0:
print('Forcing normal velocity in border ', nid)
ut = u - n*dot(u,n)
ut = u - n*dot(u0,n)
vt = v - n*dot(v,n)
F += gparam*dot(ut,vt)*ds(nid)
@ -145,52 +143,67 @@ def solv_NavierStokes(options):
print('adding backflow stabilization in border number:' + str(nk))
F -= 0.5*rho*abs_n(dot(u0, n))*dot(u_, v)*ds(nk)
a = lhs(F)
L = rhs(F)
if windkessel:
for nid in Windkvar.keys():
L = L - Windkvar[nid]
F += Windkvar[nid]
a = lhs(F)
L = rhs(F)
# The static part of the matrix
A = assemble(a)
u, p = w.split()
uwrite = Function(W.sub(0).collapse())
pwrite = Function(W.sub(1).collapse())
uwrite.rename('velocity', 'u')
pwrite.rename('pressure', 'p')
u.rename('velocity', 'u')
p.rename('pressure', 'p')
ind = 0
t = dt
checkcicle = int(options['checkpoint_dt']/options['dt'])
writecicle = int(options['checkpoint_dt']/options['dt_write'])
writecicle = int(options['xdmf_dt']/options['dt'])
while t<=Tf+dt:
if windkessel:
for k in flows.keys():
flows[k].assign(assemble(dot(u0,n)*ds(k)))
pii0[k].assign(pii[k])
pii[k].assign(alpha[k]*pii0[k] + beta[k]*flows[k])
press[k].assign(gamma[k]*flows[k] + alpha[k]*pii0[k])
# To solve
assemble(a, tensor=A)
b = assemble(L)
[bcs.apply(A, b) for bcs in BCS]
solve(A, w.vector(), b , 'lu')
print('solving for t = ' + str(np.round(t,4)))
solve(A, w.vector(), b )
ind += 1
if options['write_xdmf']:
if np.mod(ind,writecicle)<0.1 or ind==1:
xdmf_u.write(u, t)
xdmf_p.write(p, t)
assign(uwrite, w.sub(0))
assign(pwrite, w.sub(1))
if np.mod(ind,checkcicle)<0.1 or ind==1:
if options['write_checkpoint']:
checkpath = options['savepath'] +'checkpoint/{i}/'.format(i=ind)
comm = u.function_space().mesh().mpi_comm()
inout.write_HDF5_data(comm, checkpath + '/u.h5', u, '/u', t=t)
inout.write_HDF5_data(comm, checkpath + '/p.h5', p, '/p', t=t)
comm = uwrite.function_space().mesh().mpi_comm()
inout.write_HDF5_data(comm, checkpath + '/u.h5', uwrite, '/u', t=t)
inout.write_HDF5_data(comm, checkpath + '/p.h5', pwrite, '/p', t=t)
inflow.t = t
t += dt
inflow.t = t
assign(u0, w.sub(0))
if windkessel:
for nid in Windkvar.keys():
qq = assemble(dot(u0,n)*ds(nid))
pii0[nid].assign(pii[nid])
pii[nid].assign(Constant(alpha[nid]*float(pii0[nid]) + beta[nid]*qq))
pp = Constant(gamma[nid]*qq + alpha[nid]*float(pii0[nid]))
press[nid].assign(pp)
if __name__ == '__main__':

View File

@ -3,12 +3,6 @@
# Input file for Graphics
#
#################################################
ppecol: 'coral'
stecol: 'yellowgreen'
daecol: 'cyan'
corcol: 'indigo'
refcol: 'black'
dP:
apply: false
data: '/home/yeye/Desktop/dP/results/11AoCoPhantomRest2/R1/testBF/'
@ -23,7 +17,7 @@ dP:
save: True
name: '/home/yeye/Desktop/11AoCoPhantomRest2_BF.png'
Histograms:
Histograms_meshes:
apply: false
outpath: '/home/yeye/Desktop/'
colors:
@ -44,20 +38,45 @@ HistCorrector:
errors: '/home/yeye/Desktop/testH/H2/errors.dat'
outpath: '/home/yeye/Desktop/h2_160.png'
Histograms_checkpoint:
apply: false
path: '/home/yeye/Desktop/Corrector_2019/mono2/dt10ms_SUPGcon/'
title: '$dt = 10 \ ms$'
Error-curves:
apply: false
norm: 2
folder: '/home/yeye/Desktop/First/'
resol: ['H2']
mode: ['meas','corrs']
times: ['30ms']
colors: ['orangered','lime','dodgerblue']
outpath: '/home/yeye/Desktop/'
folder: '/home/yeye/Desktop/Corrector_2019/Perturbation/'
type: ['norm2_m']
subfolders: ['SNRinfV120','SNR10V120','SNRinfV80','SNR10V80']
labels: ['SNRinfV120','SNR10V120','SNRinfV80','SNR10V80']
#subfolders: ['BA_p2p1','BAA','BBA']
#labels: ['BA_{P2P1}','BAA','BBA']
colors: ['indigo','limegreen','dodgerblue','orangered','yellow']
styles: ['-','-','-','-','-','-','-','-']
title: '$leo2.0$'
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/'
Components:
Pressure_drops:
apply: false
folder: '/home/yeye/Desktop/Corrector_2019/Perturbation/STE/'
convertor: -1333.22387415
#convertor: -133.322
catheter: false
subfolders: ['SNRinfV120','SNR15V120','SNRinfV80','SNR15V80','dt10ms']
labels: ['SNRinfV120','SNR15V120','SNRinfV80','SNR15V80','ref']
colors: ['indigo','limegreen','dodgerblue','orangered','yellow']
styles: ['-','-','-','-','-','-','-','-','-','-']
title: '$STE \ leo2.0$'
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/STE/'
l2_comp:
apply: True
folder: '/home/yeye/Desktop/Corrector_2019/figures/Errorcurves/'
subfolders: ['11mm','13mm','Normal']
type: ['mean','max']
colors: ['orangered','lime','dodgerblue']
outpath: '/home/yeye/Desktop/'
colors: ['dodgerblue','orangered','limegreen']
div: false
aliasing: false
folder: '/home/yeye/Desktop/Poiseuille/curves/'
subfolder: ['SNR10V80']
name: 'SNR10V120_gain'
mode:
type: 'gain_compressed'
comp: '/home/yeye/Desktop/Poiseuille/curves/SNR10V120/'

View File

@ -3,63 +3,95 @@
# Input file for the checkpoint postprocessing
#
#################################################
Corrector:
Algebra:
apply: false
mode: 'colormap' # h5 , histogram, colormap
outpath: '/home/yeye/Desktop/Corrector_2019/figure3/11mm/'
mesh_path: '/home/yeye/Desktop/Corrector_2019/meshes/11AoCoPhantomRest2.h5'
u_path: '/home/yeye/Desktop/Corrector_2019/First/meas/11mmAoCo2/'
w_path: '/home/yeye/Desktop/Corrector_2019/First/corrector/11mmAoCo2/'
wname: 'w_COR_impl_stan'
mode: '+'
VENC: 97
outname: 'ucor'
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/gain/SNR10V60/'
checkpoint: true
#meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/leoH3_2.0.h5'
v1:
name: 'u'
path: '/home/yeye/Desktop/Corrector_2019/Perturbation/Meas/SNR10V60/'
v2:
name: 'w_COR_impl_stan'
path: '/home/yeye/Desktop/Corrector_2019/Perturbation/COR/SNR10V60/'
Colormap:
apply: false
#mode: ['u','w','w/u','div(u)','div(u)/u']
mode: ['dot']
outpath: '/home/yeye/Desktop/Poiseuille/H5/leo2mm/SNRinfV80/'
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
upath: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNRinfV80/'
wpath: '/home/yeye/Desktop/Poiseuille/Corrector/leo2mm/SNRinfV80/'
uname: 'u'
dt: 0.03072
wname: 'w_COR_impl_stan'
Velocity:
apply: false
mesh_path: '/home/yeye/Desktop/Corrector_2019/meshes/NormalAoCoPhantomRest2.h5'
checkpoint: '/home/yeye/Desktop/Corrector_2019/First/meas/NormalAoCo2/'
meshpath: '/home/yeye/Desktop/Corrector_2019/Poiseuille/poiseuille.h5'
checkpoint: '/home/yeye/Desktop/Corrector_2019/Poiseuille/COR/SNR15V120/'
undersampling: 1
dt: 0.03072
filename: 'u'
dt: 0.03
filename: 'w_COR_impl_stan'
Estim_Pressure:
apply: false
meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/9mmRest2.0.h5'
filename: 'p_COR_impl_stan'
outpath: '/home/yeye/Desktop/dP/results/11AoCoPhantomRest2/R1/testBF/'
checkpath: '/home/yeye/Desktop/Corrector_2019/AoCo/9mm_pspg/'
method: spheres # slices, boundaries, spheres
dt: 0.03072
boundaries: [2,3]
spheres:
- center: [0.09, 0.093, 0.08] # 11mm
#- center : [0.08, 0.09, 0.08]
#- center : [0.093, 0.09, 0.085] # Normal
- center: [0.0980092, 0.0909768, 0.0802258] # 9mm
#- center: [0.110266, 0.086805, 0.0794744] # 11mm
#- center : [0.0940797, 0.0766444, 0.080433] #13mm
#- center: [0.0870168, 0.0901715, 0.0883529] # Normal
radius: 0.005
Npts: 32
- center: [0.134, 0.135, 0.026] # 11mm
#- center : [0.125, 0.135, 0.025] # 13 mm
#- center : [0.13, 0.14, 0.03] # Normal
- center: [0.0980092, 0.135047, 0.0252659] # 9mm
#- center: [0.110266, 0.133002, 0.0263899] # 11mm
#- center : [0.0940573, 0.123321, 0.0260755] # 13 mm
#- center: [0.0869949, 0.12838, 0.0269889] # Normal
radius: 0.005
Npts: 32
Outlet_Wind:
apply: false
mesh_path: '/home/yeye/NavierStokes/examples/meshes/aorta.h5'
checkpoint: '/home/yeye/NavierStokes/examples/results/aorta/'
mesh_path: '/home/yeye/Desktop/aorta/mesh/aorta_coarse_marked.h5'
checkpoint: '/home/yeye/Desktop/aorta/results/mono/'
filename: ['u','p']
bnds: [3,4,5,6]
out_path: '/home/yeye/NavierStokes/examples/results/aorta/'
out_path: '/home/yeye/Desktop/aorta/results/mono/'
Error-curves:
apply: true
dt: 0.03072
type: ['mean','max']
meshpath: '/home/yeye/Desktop/Corrector_2019/meshes/NormalAoCoPhantomRest1.4.h5'
ref_check: '/home/yeye/Desktop/Corrector_2019/I/meas/NormalRest1.4/R1/'
dt: 0.03
VENC: 204 #194/129/113/97 for aorta(120,80,70,60)/ 204/136
type: ['utrue-uobs']
#type: ['l2_comp','div']
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
#meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/leoH3_2.0.h5'
true_check: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNRinfV120/'
true_name: 'u'
ref_check: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNR10V120/'
ref_name: 'u'
undersampling: 1
com_check: '/home/yeye/Desktop/Corrector_2019/I/corrector/NormalRest1.4/'
com_check: '/home/yeye/Desktop/Poiseuille/Corrector/leo2mm/SNR10V120/'
com_name: 'w_COR_impl_stan'
outpath: '/home/yeye/Desktop/Corrector_2019/figures/Errorcurves/Normal/'
outpath: '/home/yeye/Desktop/Poiseuille/curves/SNR10V120/'
Histograms:
apply: false
type: ['normal','grad']
meshpath: '/home/yeye/Desktop/Corrector_2019/meshes/11AoCoPhantomRest1.4.h5'
checkpath: '/home/yeye/Desktop/Corrector_2019/I/corrector/11mmRest1.4/'
field_name: 'w_COR_impl_stan'
outpath: '/home/yeye/Desktop/Corrector_2019/I/corrector/11mmRest1.4/'
Temporal-Average:
apply: false
@ -78,3 +110,14 @@ Temporal-Interpolation:
dt: 0.03072
dt_new: 0.015
out_check: '/home/yeye/Desktop/Corrector_2019/I/meas/11mmRest1.4/dt15ms/'
Perturbation:
apply: false
undersampling: 1
type:
SNR: 10 # dB signal to noise ratio
coil: true
phase_contrast: 80 # venc % respect u max
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
checkpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/original/'
xdmf: true

View File

@ -1,50 +0,0 @@
#################################################
#
# Input file for CFD Monolithic Solver
#
#################################################
mesh_path : '/home/p283370/Desktop/PhD/AORTA/MESH/aorta_fine/aorta_fine_marked.h5'
write_xdmf : False
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/'
write_checkpoint : False
checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/checkpoint/'
write_outlets : False
outlets_path : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/outlets/'
Tf : 0.9 # seg
density : 1.2 # gr/cm3
dynamic_viscosity : 0.035
dt : 0.005
dt_write : 0.01
checkpoint_dt : 0.02
stab:
pspg : 1
epsilon : 0.01
backflow : 1
back_id : [3,4,5,6]
temam : 1
supg : 0
pssu : 0
param:
U : 60
period : 0.7
Nvel : 1
Npress : 1
theta : 1
windkessel:
id : [3,4,5,6]
R_p : {'3':100 , '4':250, '5':250 , '6':250 }
R_d : {'3':1000, '4':8000, '5':8000 , '6':8000}
C : {'3':0.01, '4':0.0001, '5':0.00001, '6':0.0001}
alpha : {'3':0 , '4':0 , '5':0 , '6':0}
beta : {'3':0 , '4':0 , '5':0 , '6':0}
gamma : {'3':0 , '4':0 , '5':0 , '6':0}

View File

@ -5,42 +5,43 @@
#################################################
phase_contrast:
apply : False
dealiased : True
VENC : 400
meas0 : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.90.npz'
measG : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9G.npz'
output : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/u_R1.npz'
apply: False
dealiased: True
VENC: 400
meas0: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.90.npz'
measG: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9G.npz'
output: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/u_R1.npz'
resize:
apply : False
dim : [120,120,84]
loadseq : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
save : True
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal_rs.npz'
apply: False
dim: [120,120,84]
loadseq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
save: True
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal_rs.npz'
magnetization_CIB:
apply : False
loadpath : '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/'
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9.npz'
apply: False
loadpath: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/'
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantom0.9/Mag9AoCo0.9.npz'
magnetization:
apply : False
loadseq : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
VENC : 250
save : True
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/Mag9AoCoE1.npz'
apply: False
loadseq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal.npz'
VENC: 250
save: True
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/Mag9AoCoE1.npz'
sequence:
apply: False
checkpoint_path: '/home/yeye/Desktop/First/H1/dt5ms/coaorta/'
meshpath: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
apply: false
checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/'
meshpath: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
sampling_rate: 1
boxtype: 'fix_resolution'
ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
resol: [0.14,0.14,0.14]
boxsize: [80,80,80]
name: 'SH1_5ms'
#ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
ranges: {'x': [-1,1] , 'y': [-1,1] , 'z': [0,6] }
resol: [0.2,0.2,0.2]
boxsize: [100,100,100]
name: 'seq'
cs:
apply: false
@ -54,14 +55,14 @@ cs:
name: 'ucs'
kt-BLAST:
apply : False
VENC : 3.5 # cm/s
mode : 'kxky'
R : [4] # Acceleration factors
noise : False
save : True
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantomRest2E1/'
name : 'KT_kxky'
apply: False
VENC: 3.5 # cm/s
mode: 'kxky'
R: [4] # Acceleration factors
noise: False
save: True
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/9AoCoPhantomRest2E1/'
name: 'KT_kxky'
reference:
apply : False
@ -76,11 +77,6 @@ reference:
save : True
name : 'ref'
norms:
apply : False
field_path : '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/'
plot : True
create_checkpoint:
apply: false
loadseq: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod/'
@ -100,28 +96,15 @@ create_checkpoint:
savepath: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/'
xdmf: true
peak_pv:
apply : False
orig_seq : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/aorta_Ucoarse.npz'
peak_slice : 6
R : [1,2]
p_comp : 'error' # 'peak' or 'error'
flux_bnd : [2]
N_CS : 1
mesh_into : 'leo'
save : True
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/maxpv/Ucoarse_test/'
infile_dp : '/home/yeye/Desktop/dP/input/all_points.yaml'
change_mesh:
apply: false
mode: 'u'
dt: 0.005
checkpoint_path: '/home/yeye/Desktop/R1/checkpoint/'
dt: 0.03
checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/checkpoint/'
under_rate: 1
mesh_in: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
mesh_out: '/home/yeye/Desktop/meshes/leo_1.42.h5'
savepath: '/home/yeye/Desktop/test/'
mesh_in: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
mesh_out: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
savepath: '/home/yeye/Desktop/Poiseuille/Meas_leo/'
xdmf: True
SENSE:
@ -133,8 +116,9 @@ SENSE:
create_leo:
apply: false
velseq: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod_nocoro/u_R1.mat'
resol: [0.09,0.09,0.09]
velseq: '/home/yeye/Desktop/Corrector_2019/Meshes/SH3_2.0_R1.npz'
resol: [0.2,0.2,0.2]
#ranges: {'x': [-1.2,1.2] , 'y': [-1.2,1.2] , 'z': [-0.2,6.2] }
ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
masked: false
segmentation: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/Segmented_Aorta.mat'
@ -148,13 +132,13 @@ kspace_cib:
CIBtoH5:
apply: false
data_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/AoCo/9AoCoPhantomRest0.9/'
interpolate: true
flip: false
dt: 0.03072
mesh_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/AoCo/9AoCoPhantomRest1.4/'
times: [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25]
outpath: '/home/yeye/Desktop/9mmRest1.4/R1/'
data_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
interpolate: false
flip: false # Set it True for AoCo = 13mm
dt: 0.03831417624521074
mesh_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
times: [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]
outpath: '/home/yeye/Desktop/Patient_GM/'