NuMRI/input/mri_input.yaml

#################################################
#
#   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/'