From b24c48b6e386a1fbf3bb3f1976face4fae26699e Mon Sep 17 00:00:00 2001
From: jeremias <jeremias.garay.l@gmail.com>
Date: Fri, 17 Jan 2020 16:26:16 +0100
Subject: [PATCH] inputs

---
 input/Graphics_input.yaml  |  63 ++++++++++++++
 input/PostCheck_input.yaml |  80 ++++++++++++++++++
 input/aorta.yaml           | 138 +++++++++++++++++++++++++++++++
 input/aorta_roukf.yaml     | 131 +++++++++++++++++++++++++++++
 input/cfd_input.yaml       |  50 ++++++++++++
 input/mri_input.yaml       | 163 +++++++++++++++++++++++++++++++++++++
 6 files changed, 625 insertions(+)
 create mode 100755 input/Graphics_input.yaml
 create mode 100755 input/PostCheck_input.yaml
 create mode 100755 input/aorta.yaml
 create mode 100755 input/aorta_roukf.yaml
 create mode 100755 input/cfd_input.yaml
 create mode 100755 input/mri_input.yaml

diff --git a/input/Graphics_input.yaml b/input/Graphics_input.yaml
new file mode 100755
index 0000000..a57b9da
--- /dev/null
+++ b/input/Graphics_input.yaml
@@ -0,0 +1,63 @@
+#################################################
+#
+#   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/'
\ No newline at end of file
diff --git a/input/PostCheck_input.yaml b/input/PostCheck_input.yaml
new file mode 100755
index 0000000..5efb529
--- /dev/null
+++ b/input/PostCheck_input.yaml
@@ -0,0 +1,80 @@
+#################################################
+#
+#   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/'
\ No newline at end of file
diff --git a/input/aorta.yaml b/input/aorta.yaml
new file mode 100755
index 0000000..71314ed
--- /dev/null
+++ b/input/aorta.yaml
@@ -0,0 +1,138 @@
+# 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'
diff --git a/input/aorta_roukf.yaml b/input/aorta_roukf.yaml
new file mode 100755
index 0000000..c2f5add
--- /dev/null
+++ b/input/aorta_roukf.yaml
@@ -0,0 +1,131 @@
+# 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'
diff --git a/input/cfd_input.yaml b/input/cfd_input.yaml
new file mode 100755
index 0000000..c7ef27c
--- /dev/null
+++ b/input/cfd_input.yaml
@@ -0,0 +1,50 @@
+#################################################
+#
+#   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}
+
+
+
+
+
diff --git a/input/mri_input.yaml b/input/mri_input.yaml
new file mode 100755
index 0000000..ffbb89b
--- /dev/null
+++ b/input/mri_input.yaml
@@ -0,0 +1,163 @@
+#################################################
+#
+#   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/'
+
+
+
+
+
+