#################################################
#
#   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/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] }
    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
    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'
    
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

change_mesh:
    apply: false
    mode: 'u'
    dt: 0.03
    checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/checkpoint/'
    under_rate: 1
    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:
    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/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'   
    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/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/'