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NuMRI
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This commit is contained in:
jeremias 2020-03-18 14:09:22 +01:00
parent 0dd4e01188
commit 2d3873605d
2 changed files with 112 additions and 124 deletions
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171
codes/Graphics.py
View File

@ -132,7 +132,6 @@ def Plot_Histogram(meshnames,paths,colors,outpath):
ind = 0 ind = 0
for nm in range(len(meshnames)): for nm in range(len(meshnames)):
if 'box' in meshnames[nm]: if 'box' in meshnames[nm]:
# VOXEL SEQUENCE SIZE # VOXEL SEQUENCE SIZE
Lx = 64 Lx = 64
@ -167,13 +166,11 @@ def Plot_Histogram(meshnames,paths,colors,outpath):
heights_method = False heights_method = False
for k in range(mesh.num_cells()): for k in range(mesh.num_cells()):
# Coordinates of each cell (A,B,C,D) # Coordinates of each cell (A,B,C,D)
A = Points[Cells[k]][0] A = Points[Cells[k]][0]
B = Points[Cells[k]][1] B = Points[Cells[k]][1]
C = Points[Cells[k]][2] C = Points[Cells[k]][2]
D = Points[Cells[k]][3] D = Points[Cells[k]][3]
if heights_method: if heights_method:
hs = np.zeros([4]) hs = np.zeros([4])
for l in range(4): for l in range(4):
@ -1412,127 +1409,79 @@ def ROUTINE(options):
if 'Error-curves' in options: if 'Error-curves' in options:
if options['Error-curves']['apply']: if options['Error-curves']['apply']:
print('--- Error curves ---') print('--- Error-curves analysis ---')
ratio = False
meas = {} for types in options['Error-curves']['type']:
corrs = {} if types=='mean_ratio':
times = {} types = 'mean'
norm = options['Error-curves']['norm'] ratio = True
colorset = options['Error-curves']['colors'] if types=='max_ratio':
types = 'max'
for resol in options['Error-curves']['resol']: ratio = True
meas[resol] = {}
corrs[resol] = {}
times[resol] = {}
for dts in options['Error-curves']['times']:
path = options['Error-curves']['folder'] + \
resol + '/dt' + dts
try:
corrs[resol][dts] = np.loadtxt(
path + '/w_' + str(norm) + 'norm.txt')
except IOError:
print('no curve for ' + resol + '/' + dts)
try:
meas[resol][dts] = np.loadtxt(
path + '/u_' + str(norm) + 'norm.txt')
times[resol][dts] = np.loadtxt(
path + '/times_' + str(norm) + 'norm.txt')
except IOError:
print('no meas for ' + resol + '/' + dts)
if 'meas' in options['Error-curves']['mode']:
for resol in options['Error-curves']['resol']:
for dts in meas[resol].keys():
if resol == 'H1':
nc = 0
elif resol == 'H2':
nc = 1
elif resol == 'H3':
nc = 2
plt.plot(times[resol][dts], meas[resol]
[dts], color=colorset[nc], label='$' + resol + '/' + dts + '$')
#plt.ylim([0, 1.1])
plt.ylabel('$||u||_2$', fontsize=18)
plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=16)
plt.savefig(options['Error-curves']['outpath'] + 'meas_' +dts + '.png',
dpi=500, bbox_inches='tight')
plt.show()
if 'corrs' in options['Error-curves']['mode']:
for resol in options['Error-curves']['resol']:
for dts in corrs[resol].keys():
if resol == 'H1':
nc = 0
elif resol == 'H2':
nc = 1
elif resol == 'H3':
nc = 2
plt.plot(times[resol][dts], corrs[resol]
[dts], color = colorset[nc],label='$' + resol + '/' + dts + '$')
plt.ylim([0, 16.2])
plt.ylabel('$||w||_2$', fontsize=18)
plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=16)
plt.savefig(options['Error-curves']['outpath'] + 'corrs_' +dts + '.png',
dpi=500, bbox_inches='tight')
plt.show()
if 'fracs' in options['Error-curves']['mode']:
for resol in options['Error-curves']['resol']:
for dts in corrs[resol].keys():
if resol == 'H1':
nc = 0
elif resol == 'H2':
nc = 1
elif resol == 'H3':
nc = 2
plt.plot(times[resol][dts], corrs[resol][dts]/meas[resol][dts],
color=colorset[nc], label='$' + resol + '/' + dts + '$')
plt.ylim([0, 1])
plt.ylabel('$||w||_2/||u||_2$', fontsize=18)
plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=16)
plt.savefig(options['Error-curves']['outpath'] + 'fracs_' +dts + '.png',
dpi=500, bbox_inches='tight')
plt.show()
if 'Components' in options:
if options['Components']['apply']:
print('--- Components analysis ---')
for types in options['Components']['type']:
nc = 0 nc = 0
for subf in options['Components']['subfolders']: if len(options['Error-curves']['subfolders'])==0:
ucomp = [] ucomp = []
wcomp = [] wcomp = []
colorset = options['Components']['colors'] colorset = options['Error-curves']['colors']
path = options['Components']['folder'] + subf + '/' path = options['Error-curves']['folder']
try: try:
ucomp = np.loadtxt(path + '/u'+types+'.txt') ucomp = np.loadtxt(path + '/u'+types+'.txt')
wcomp = np.loadtxt(path + '/w'+types+'.txt') wcomp = np.loadtxt(path + '/w'+types+'.txt')
times = np.loadtxt(path + '/times.txt') times = np.loadtxt(path + '/times.txt')
except IOError: except IOError:
print('no components for ' + subf) print('no Error-curves for ' + subf)
if not ratio:
plt.plot(
plt.plot( times, ucomp, color=colorset[nc], linestyle='-', label= '$u$' )
times, ucomp, color=colorset[nc], linestyle='-', label= '$u'+ subf +'$' ) plt.plot(
times, wcomp, color=colorset[nc], linestyle='--', label='$w$')
plt.plot( else:
times, wcomp, color=colorset[nc], linestyle='--', label='$w'+subf+'$') plt.plot(
times, ucomp, color=colorset[nc], linestyle='-', label= '$u$' )
plt.plot(
times, wcomp, color=colorset[nc], linestyle='--', label='$w$')
nc +=1 nc +=1
else:
for subf in options['Error-curves']['subfolders']:
ucomp = []
wcomp = []
colorset = options['Error-curves']['colors']
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)
if not ratio:
plt.plot(
times, ucomp, color=colorset[nc], linestyle='-', label= '$u'+ subf +'$' )
plt.plot(
times, wcomp, color=colorset[nc], linestyle='--', label='$w'+subf+'$')
else:
wu = wcomp/ucomp
plt.plot(
times, wu, color=colorset[nc], linestyle='-', label= '$'+ labelset[nc] +'$' )
nc +=1
#plt.ylim([0, 170]) #plt.ylim([0, 170])
plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
plt.xlabel('$time \ \ (s)$', fontsize=18) plt.xlabel('$time \ \ (s)$', fontsize=18)
plt.legend(fontsize=16) plt.legend(fontsize=16)
plt.savefig(options['Components']['outpath'] + types + '.png', dpi=500, bbox_inches='tight') if options['Error-curves']['title']:
plt.title(options['Error-curves']['title'], fontsize=18)
if not ratio:
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.savefig(options['Error-curves']['outpath'] + types + '_ratio.png', dpi=500, bbox_inches='tight')
plt.show() plt.show()

65
codes/PostCheck.py
View File

@ -175,6 +175,37 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
for bb in bnds: for bb in bnds:
QQ[bb] = [] QQ[bb] = []
if mode == 'Histograms':
u = Function(W)
if 'w_COR' in filename:
h5name = 'w/vector_0'
else:
h5name = 'u/vector_0'
ValuesTime = np.zeros([len(indexes),len(u.vector().get_local())])
ValuesPeak = np.zeros([len(u.vector().get_local())])
ix = int(0)
for k in indexes:
path = checkpoint_path + str(k) + '/'+filename+'.h5'
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
print('Reading checkpoint ',indexes[k])
hdf.read(u, h5name)
time = hdf.attributes(h5name).to_dict()['timestamp']
hdf.close()
uvec = u.vector().get_local()
ValuesTime[ix,:] = np.abs(uvec)
ix +=1
CoordPeak = np.where(ValuesTime==np.max(ValuesTime))
ValuesPeak = np.abs(ValuesTime[CoordPeak[0],:])
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_edges.txt', edges)
if mode == 'perturbation': if mode == 'perturbation':
u = Function(W) u = Function(W)
unew = Function(W) unew = Function(W)
@ -216,10 +247,10 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
ufactor = options['Perturbation']['type']['phase_contrast']/100 ufactor = options['Perturbation']['type']['phase_contrast']/100
VENC = np.max(np.abs(uvec))*ufactor 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 B0 = 1.5 # Tesla Magnetic Field Strenght
TE = 5e-3 # Echo-time TE = 5e-3 # Echo-time
Phi1 = gamma*10*TE + 0*uvec Phi1 = 1*B0*TE + 0*uvec
Phi2 = gamma*10*TE + np.pi*uvec/VENC Phi2 = 1*B0*TE + np.pi*uvec/VENC
M1 = np.cos(Phi1) + 1j*np.sin(Phi1) M1 = np.cos(Phi1) + 1j*np.sin(Phi1)
M2 = np.cos(Phi2) + 1j*np.sin(Phi2) M2 = np.cos(Phi2) + 1j*np.sin(Phi2)
@ -476,7 +507,10 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
u.rename('meas', 'meas') u.rename('meas', 'meas')
w.rename('w', 'w') w.rename('w', 'w')
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r') hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
hdf_w.read(w, 'w/vector_0') if 'w' in comname:
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 = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
hdf_u.read(u, 'u/vector_0') hdf_u.read(u, 'u/vector_0')
hdf_u.close() hdf_u.close()
@ -917,7 +951,6 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
unsort_indexes = os.listdir(checkpoint_path) unsort_indexes = os.listdir(checkpoint_path)
indexes = [int(x) for x in unsort_indexes] indexes = [int(x) for x in unsort_indexes]
indexes.sort() indexes.sort()
QQ = {} QQ = {}
PP = {} PP = {}
ds = Measure('ds', domain=MESH['mesh'], subdomain_data=MESH['boundaries']) ds = Measure('ds', domain=MESH['mesh'], subdomain_data=MESH['boundaries'])
@ -930,11 +963,6 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
for k in range(0, len(indexes)): for k in range(0, len(indexes)):
path_u = checkpoint_path + str(indexes[k]) + '/'+filename[0]+'.h5' path_u = checkpoint_path + str(indexes[k]) + '/'+filename[0]+'.h5'
path_p = checkpoint_path + str(indexes[k]) + '/'+filename[1]+'.h5' path_p = checkpoint_path + str(indexes[k]) + '/'+filename[1]+'.h5'
if indexes[k] < 10:
path_u = checkpoint_path + '0' + \
str(indexes[k]) + '/'+filename[0]+'.h5'
path_p = checkpoint_path + '0' + \
str(indexes[k]) + '/'+filename[1]+'.h5'
u = Function(V) u = Function(V)
p = Function(W) p = Function(W)
@ -946,7 +974,7 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
hdf_p.read(p, 'p/vector_0') hdf_p.read(p, 'p/vector_0')
hdf_p.close() hdf_p.close()
print('Computing flows and pressures at timestep number ' + str(k)) print('Computing flows and pressures at timestep number ' + str(indexes[k]))
for bb in bnds: for bb in bnds:
if bb == 2: if bb == 2:
QQ[bb].append(-assemble(dot(u, n)*ds(bb))) QQ[bb].append(-assemble(dot(u, n)*ds(bb)))
@ -1134,10 +1162,21 @@ def ROUTINE(options):
MESH = LOADmesh(options['Perturbation']['meshpath']) MESH = LOADmesh(options['Perturbation']['meshpath'])
checkpath = options['Perturbation']['checkpath'] + 'checkpoint/' checkpath = options['Perturbation']['checkpath'] + 'checkpoint/'
out_check = options['Perturbation']['checkpath'] + 'Perturbation/' name_folder = 'SNR' +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) READcheckpoint(MESH,'perturbation', out_check,checkpath,'u','u',options)
if 'Histograms' in options:
if options['Histograms']['apply']:
if rank==0:
print('--- Histograms in measurements ---')
MESH = LOADmesh(options['Histograms']['meshpath'])
checkpath = options['Histograms']['checkpath'] + 'checkpoint/'
outpath = options['Histograms']['checkpath']
field_name = options['Histograms']['field_name']
READcheckpoint(MESH,'Histograms', outpath, checkpath,field_name,field_name,options)
if __name__ == '__main__': if __name__ == '__main__':