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jeremias 2020-01-17 16:26:16 +01:00
parent 2da253f278
commit b24c48b6e3
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63
input/Graphics_input.yaml Executable file
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#################################################
#
# 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/'
R: [1]
#catheter: '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/Phantom_catheter/cat9mm_Stress/pressure_drop.npz'
catheter: 'None'
#factors: [130,90,1.58,-0.03,0] # 9mm Rest [x0,x1,a,b,theta]
#factors: [52,35,0.9,0.05,0] # 9mm Stress [x0,x1,a,b,theta]
#factors: [162,90,1.67,0.03,0] # 11mm Rest [x0,x1,a,b,theta]
mode: 'cib'
estim: ['PPE','STE','COR']
save: True
name: '/home/yeye/Desktop/11AoCoPhantomRest2_BF.png'
Histograms:
apply: false
outpath: '/home/yeye/Desktop/'
colors:
0: 'orangered'
1: 'lime'
2: 'dodgerblue'
meshnames:
0: 'coaortaH1'
1: 'coaortaRH2'
2: 'coaortaRH3'
paths:
0: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/'
1: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H2/'
2: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H3/'
HistCorrector:
apply: false
errors: '/home/yeye/Desktop/testH/H2/errors.dat'
outpath: '/home/yeye/Desktop/h2_160.png'
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/'
Components:
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/'

80
input/PostCheck_input.yaml Executable file
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#################################################
#
# Input file for the checkpoint postprocessing
#
#################################################
Corrector:
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'
uname: 'u'
dt: 0.03072
Velocity:
apply: false
mesh_path: '/home/yeye/Desktop/Corrector_2019/meshes/NormalAoCoPhantomRest2.h5'
checkpoint: '/home/yeye/Desktop/Corrector_2019/First/meas/NormalAoCo2/'
undersampling: 1
dt: 0.03072
filename: 'u'
Estim_Pressure:
apply: false
filename: 'p_COR_impl_stan'
outpath: '/home/yeye/Desktop/dP/results/11AoCoPhantomRest2/R1/testBF/'
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
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
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/'
filename: ['u','p']
bnds: [3,4,5,6]
out_path: '/home/yeye/NavierStokes/examples/results/aorta/'
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/'
ref_name: 'u'
undersampling: 1
com_check: '/home/yeye/Desktop/Corrector_2019/I/corrector/NormalRest1.4/'
com_name: 'w_COR_impl_stan'
outpath: '/home/yeye/Desktop/Corrector_2019/figures/Errorcurves/Normal/'
Temporal-Average:
apply: false
meshpath: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
original_check: '/home/yeye/Desktop/First/H1/dt5ms/coaorta/'
xdmf: false
dt: 0.005
subsampling_rate: 6
out_check: '/home/yeye/Desktop/First/H1/test/'
Temporal-Interpolation:
apply: false
meshpath: '/home/yeye/Desktop/Corrector_2019/meshes/11AoCoPhantomRest1.4.h5'
original_check: '/home/yeye/Desktop/Corrector_2019/I/meas/11mmRest1.4/R1/'
xdmf: true
dt: 0.03072
dt_new: 0.015
out_check: '/home/yeye/Desktop/Corrector_2019/I/meas/11mmRest1.4/dt15ms/'

138
input/aorta.yaml Executable file
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# Set of default parameters for steady Navier-Stokes
mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
density: 1.119
dynamic_viscosity: 0.0483
stokes: False
io:
write_hdf5: True
write_hdf5_timeseries: False
write_xdmf: True
write_path: '/home/yeye/Desktop/coaorta'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_checkpoints: true
write_velocity: 'update' # tentative
log: False
boundary_conditions:
- id: 2
type: 'dirichlet'
value: ['0','0','U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))']
degree: 3
parameters:
U: -30 # 60 original
Th: 0.35 # 0.35 original
t: 0
- id: 1
type: 'dirichlet'
value: ['0','0','0']
degree: 2
- id: 3
type: 'windkessel'
value: [10,0.01,1000]
p0: [47,1333.223874]
- id: 4
type: 'windkessel'
value: [250,0.0001,8000] # [R,C,R_d]
p0: [47,1333.223874]
- id: 5
type: 'windkessel'
value: [250,0.0001,8000] # [R,C,R_d]
p0: [47,1333.223874]
- id: 6
type: 'windkessel'
value: [250,0.0001,8000] # [R,C,R_d]
p0: [47,1333.223874]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
monolithic:
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
nonlinear:
method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
maxit: 20
init_steps: 30
use_aitken: 1 # 0: False, 1: Picard only, 2: all
report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
atol: 1.e-6 # note: dot required!!
rtol: 1.e-16
stol: 0.0
fractionalstep:
scheme: 'CT' # CT, IPCS
coupled_velocity: False # False faster, True needed if robin_bc implicit
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.005
write_dt: 0.05
checkpoint_dt: 0.05 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
#estimation:
# boundary_conditions:
# - id: 2
# type: 'dirichlet'
# initial_stddev: [0.2]
# parameters: [U]
#
# measurements:
# -
# mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
# fe_degree: 0
# xdmf_file: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements/meas.xmf'
# #file_root: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements2/meas2.h5'
# file_root: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements/u{i}.h5'
# indices: [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20] #,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45] # indices of checkpoints to be processed. 0 == all
# noise_stddev: 1 # standard deviation of Gaussian noise
#
# roukf:
# particles: 'simplex'
# observation_operator: 'postprocessing'
# reparameterize: True
#observations:
# mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
# timeseries: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements'
# stddev: 10. # noiselevel x VENC
# solver setup
fem:
velocity_space: p1 # p1 p1b/p1+ p2
pressure_space: p1 # p1 p0/dg0 dg1
strain_symmetric: 0
convection_skew_symmetric: 1 # aka Temam term
stabilization:
forced_normal:
enabled: false
boundaries: [4,5,6]
gamma: 10
backflow_boundaries: [3,4,5,6]
streamline_diffusion:
enabled: False
parameter: 'shakib' # standard, shakib, codina, klr
length_scale: 'metric' # average, max, metric
consistent: False # deprecated
Cinv: ~
monolithic:
infsup: False # pspg, pressure-stabilization
graddiv: False
consistent: False
pressure_stab_constant: 1.
fix_pressure: False
fix_pressure_point: [0., 0. , 0.]
linear_solver:
method: 'lu'
# inputfile: './projects/nse_coa3d/input/pc/MUMPS_default.yaml'
# inputfile: './input/pc/fgmres_gamg_rtol1e-6.yaml'

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input/aorta_roukf.yaml Executable file
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# Set of default parameters for steady Navier-Stokes
mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
density: 1.2
dynamic_viscosity: 0.035
stokes: False
io:
write_hdf5: True
write_hdf5_timeseries: False
write_xdmf: True
write_path: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/roukf'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_checkpoints: True
write_velocity: 'update' # tentative
log: False
write_outlets: False
outlets_path: '/home/yeye/Desktop/PhD/AORTA/outlets/'
boundary_conditions:
- id: 2
type: 'dirichlet'
value: ['0','0','-0.5*U*(fabs( sin(2*DOLFIN_PI*t/Th)) + sin(2*DOLFIN_PI*t/Th) )*(t<0.7)']
degree: 3
parameters:
U: 60 # 60 original
Th: 0.7 # 0.7 original
t: 0
- id: 1
type: 'dirichlet'
value: ['0','0','0']
degree: 2
- id: 3
type: 'windkessel'
value: [100,0.01,1000]
- id: 4
type: 'windkessel'
value: [250,0.0001,8000] # [R,C,R_d]
- id: 5
type: 'windkessel'
value: [250,0.00001,8000] # [R,C,R_d]
- id: 6
type: 'windkessel'
value: [250,0.0001,8000] # [R,C,R_d]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
monolithic:
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
nonlinear:
method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
maxit: 20
init_steps: 30
use_aitken: 1 # 0: False, 1: Picard only, 2: all
report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
atol: 1.e-6 # note: dot required!!
rtol: 1.e-16
stol: 0.0
fractionalstep:
scheme: 'CT' # CT, IPCS
coupled_velocity: False # False faster, True needed if robin_bc implicit
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 0.9 # end time
dt: 0.01
write_dt: 0.01
checkpoint_dt: 0.01 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
estimation:
boundary_conditions:
- id: 2
type: 'dirichlet'
initial_stddev: [10]
parameters: [U]
measurements:
-
mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
fe_degree: 1
xdmf_file: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/measurements/meas.xdmf'
file_root: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/measurements/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
noise_stddev: 20 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'state' #state or postprocessing
reparameterize: False
#observations:
# mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
# timeseries: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements'
# stddev: 10. # noiselevel x VENC
# solver setup
fem:
velocity_space: p1 # p1 p1b/p1+ p2
pressure_space: p1 # p1 p0/dg0 dg1
strain_symmetric: 0
convection_skew_symmetric: 1 # aka Temam term
stabilization:
backflow_boundaries: [2,3,4,5,6]
streamline_diffusion:
enabled: False
parameter: 'shakib' # standard, shakib, codina, klr
length_scale: 'metric' # average, max, metric
consistent: False # deprecated
Cinv: ~
monolithic:
infsup: False # pspg, pressure-stabilization
graddiv: False
consistent: False
pressure_stab_constant: 1.
fix_pressure: False
fix_pressure_point: [0., 0. , 0.]
linear_solver:
method: 'lu'
# inputfile: './projects/nse_coa3d/input/pc/MUMPS_default.yaml'
# inputfile: './input/pc/fgmres_gamg_rtol1e-6.yaml'

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input/cfd_input.yaml Executable file
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#################################################
#
# 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}

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input/mri_input.yaml Executable file
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#################################################
#
# Input file for 4D flow
#
#################################################
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'
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'
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'
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'
sequence:
apply: False
checkpoint_path: '/home/yeye/Desktop/First/H1/dt5ms/coaorta/'
meshpath: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.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'
cs:
apply: false
short: false
seqpath: '/home/yeye/Desktop/Corrector_2019/Second/Vol3/dicom/u_R1.mat'
Mpath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG.npz'
VENC: 160 # cm/s
noise: false
R: [2,4,8] # Acceleration factors
savepath: '/home/yeye/Desktop/Corrector_2019/Second/Vol3/dicom/'
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'
reference:
apply : False
#checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_ffine/dt0.0005/checkpoint/'
checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/undersampling/MAG_2.5/R1/checkpoint/'
#meshpath : '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_ffine/aorta_ffine_marked.h5'
meshpath : '/home/yeye/Desktop/PhD/AORTA/MESH/structured/aoreal_2.5_marked.h5'
under_rate : 1
fix_const : 0 # 0: false, 1: substract zero_point
zero_point : [12.79353, 14.32866, 6.51101]
savepath : '/home/yeye/Desktop/dP/results/MAG_2.5/'
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/'
seqname: 'u'
extension: '.mat'
mesh_into: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod/aorta.h5'
boxtype: 'box_zeros'
boxsize: [80,80,80]
resol: [0.14,0.14,0.14]
ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
masked: False
masked_seq: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/Uffine/aoreal_2.5.npz'
dt: 0.0343 #vol 1,2,4
#dt: 0.03 #vol3
under_rate: 1
Rseq: [1]
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/'
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/'
xdmf: True
SENSE:
apply: False
R: [2]
VENC: 250
Mpath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG.npz'
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/MG_sR2.npz'
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]
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'
outpath: '/home/yeye/Desktop/PhD/PROGRAMS/LEO_matlab/LEO_files/'
kspace_cib:
apply : False
kspace : '/home/yeye/Desktop/Kspaces/9mmRest_2.5/k_space.mat'
VENC : 320
output : '/home/yeye/Desktop/FFE_PCA.mat'
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/'