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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
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59
input/Graphics_input.yaml
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@@ -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/'

101
input/PostCheck_input.yaml
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@@ -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
@@ -77,4 +109,15 @@ Temporal-Interpolation:
xdmf: true
dt: 0.03072
dt_new: 0.015
out_check: '/home/yeye/Desktop/Corrector_2019/I/meas/11mmRest1.4/dt15ms/'
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

50
input/cfd_input.yaml
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@@ -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}

116
input/mri_input.yaml
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@@ -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/'