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How to use phantom_info method in yandex-tank

Best Python code snippet using yandex-tank

pulseq_jemris_simulator.py

Source:pulseq_jemris_simulator.py

1# Same role as pulseq_bloch_simulator.py except (1) It uses JEMRIS (2) It is run as a function, not a script2# INPUTS: sequence type, geometry parameters, contrast parameters,3#         phantom type (pre-set or custom), coil type (pre-set or custom) (Tx / Rx),4#         k-space trajectory (if noncartesian; flattened version (Nro_total, 3))5import time6import os7from virtualscanner.server.simulation.py2jemris.sim_jemris import sim_jemris8from virtualscanner.server.simulation.py2jemris.recon_jemris import read_jemris_output, recon_jemris9from virtualscanner.server.simulation.py2jemris.coil2xml import coil2xml10from virtualscanner.utils import constants11from virtualscanner.server.simulation.py2jemris.seq2xml import seq2xml12from pypulseq.Sequence.sequence import Sequence13import virtualscanner.server.simulation.bloch.phantom as pht14import numpy as np15import xml.etree.ElementTree as ET16from virtualscanner.server.simulation.bloch.pulseq_library import make_pulseq_se_oblique,\17    make_pulseq_gre_oblique, make_pulseq_irse_oblique18from scipy.io import savemat, loadmat19PY2JEMRIS_PATH = constants.SERVER_SIM_BLOCH_PY2JEMRIS_PATH20def simulate_pulseq_jemris(seq_path, phantom_info, coil_fov,21                           tx='uniform', rx='uniform', # TODO add input that includes sequence info for22                                                       # TODO      dimensioning the RO points into kspace23                           tx_maps=None, rx_maps=None, sim_name=None, env_option="local"):24    """Runs simulation using an already-made .seq file25    Inputs26    ------27    seq_path : str28        Path to seq file29    phantom_info : dict30        Information used to create phantom; input to create_and_save_phantom()31    coil_fov : float32        Field-of-view of coil in mm33    tx : str, optional34        Type of tx coil; default is 'uniform'; the only other option is 'custom'35    rx : str, optional36        Type of rx coil; default is 'uniform'; the only other option is 'custom'37    tx_maps : list, optional38        List of np.ndarray (dtype='complex') maps for all tx channels39        Required for 'custom' type tx40    rx_maps : list, optional41        List of np.ndarray (dtype='complex') maps for all rx channels42        Required for 'custom' type rx43    sim_name : str, optional44        Used as folder name inside sim folder45        Default is None, in which case sim_name will be set to the current timestamp46    Returns47    -------48    sim_output :49        Delivers output from sim_jemris50    """51    if sim_name is None:52        sim_name = time.strftime("%Y%m%d%H%M%S")53    if env_option == 'local':54        target_path = PY2JEMRIS_PATH / 'sim' / sim_name55    elif env_option == 'colab':56        target_path = 'sim/' + sim_name57    # Make target folder58    dir_str = f'{str(PY2JEMRIS_PATH)}\\sim\\{sim_name}'59    if not os.path.isdir(dir_str):60        os.system(f'mkdir {dir_str}')61    # Convert .seq to .xml62    seq = Sequence()63    seq.read(seq_path)64    seq_name = seq_path[seq_path.rfind('/')+1:seq_path.rfind('.seq')]65    seq2xml(seq, seq_name=seq_name, out_folder=str(target_path))66    # Make phantom and save as .h5 file67    pht_name = create_and_save_phantom(phantom_info, out_folder=target_path)68    # Make sure we have the tx/rx files69    tx_filename = tx + '.xml'70    rx_filename = rx + '.xml'71    # Save Tx as xml72    if tx == 'uniform':73        os.system(f'copy sim\\{tx}.xml {str(target_path)}')74    elif tx == 'custom' and tx_maps is not None:75        coil2xml(b1maps=tx_maps, fov=coil_fov, name='custom_tx', out_folder=target_path)76        tx_filename = 'custom_tx.xml'77    else:78        raise ValueError('Tx coil type not found')79    # save Rx as xml80    if rx == 'uniform':81        os.system(f'copy sim\\{rx}.xml sim\\{str(target_path)}')82    elif rx == 'custom' and rx_maps is not None:83        coil2xml(b1maps=rx_maps, fov=coil_fov, name='custom_rx', out_folder=target_path)84        rx_filename = 'custom_rx.xml'85    else:86        raise ValueError('Rx coil type not found')87    # Run simuluation in target folder88    list_sim_files = {'seq_xml': seq_name+'.xml', 'pht_h5': pht_name + '.h5', 'tx_xml': tx_filename,89                       'rx_xml': rx_filename}90    sim_output = sim_jemris(list_sim_files=list_sim_files, working_folder=target_path)91    return sim_output92# TODO93def create_and_save_phantom(phantom_info, out_folder):94    """Generates a phantom and saves it into desired folder as .h5 file for JEMRIS purposes95    Inputs96    ------97    phantom_info : dict98        Info of phantom to be constructed99        REQUIRED100        'fov' : float, field-of-view [meters]101        'N' : int, phantom matrix size (isotropic)102        'type' : str, 'spherical', 'cylindrical' or 'custom'103        'dim' : int, either 3 or 2; 3D or 2D phantom options104        'dir' : str, {'x', 'y', 'z'}; orientation of 2D phantom105        OPTIONAL (only required for 'custom' phantom type)106        'T1' : np.ndarray, T1 map matrix107        'T2' : np.ndarray, T2 map matrix108        'PD' : np.ndarray, PD map matrix109        'dr' : float, voxel size [meters] (isotropic)110        'dBmap' : optional even for 'custom' type. If not provided, dB is set to 0 everywhere.111    out_folder : str or pathlib Path object112        Path to directory where phantom will be saved113    Returns114    -------115    pht_type : str116        phantom_info['pht_type'] (returned for naming purposes)117    """118    out_folder = str(out_folder)119    FOV = phantom_info['fov']120    N = phantom_info['N']121    pht_type = phantom_info['type']122    pht_dim = phantom_info['dim']123    pht_dir = phantom_info['dir']124    sim_phantom = 0125    if pht_type == 'spherical':126        print('Making spherical phantom')127        T1s = [1000]128        T2s = [100]129        PDs = [1]130        R = 0.8*FOV/2131        Rs = [R]132        if pht_dim == 3:133            sim_phantom = pht.makeSphericalPhantom(n=N, fov=FOV, T1s=T1s, T2s=T2s, PDs=PDs, radii=Rs)134        elif pht_dim == 2:135            sim_phantom = pht.makePlanarPhantom(n=N, fov=FOV, T1s=T1s, T2s=T2s, PDs=PDs, radii=Rs,136                                                dir=pht_dir, loc=0)137    elif pht_type == 'cylindrical':138        print("Making cylindrical phantom")139        sim_phantom = pht.makeCylindricalPhantom(dim=pht_dim, n=N, dir=pht_dir, loc=0)140    elif pht_type == 'custom':141        # Use a custom file!142        T1 = phantom_info['T1']143        T2 = phantom_info['T2']144        PD = phantom_info['PD']145        dr = phantom_info['dr']146        if 'dBmap' in phantom_info.keys():147            dBmap = phantom_info['dBmap']148        else:149            dBmap = 0150        sim_phantom = pht.Phantom(T1map=T1, T2map=T2, PDmap=PD, vsize=dr, dBmap=dBmap, loc=(0,0,0))151    else:152        raise ValueError("Phantom type non-existent!")153    # Save as h5154    sim_phantom.output_h5(out_folder, pht_type)155    return pht_type156if __name__ == '__main__':157    # Define the same phantom158    phantom_info = {'fov': 0.256, 'N': 32, 'type': 'cylindrical', 'dim':2, 'dir':'z'}159    sim_names = ['test0413_GRE', 'test0413_SE', 'test0413_IRSE']160    sps = ['gre_fov256mm_Nf15_Np15_TE50ms_TR200ms_FA90deg.seq',161           'se_fov256mm_Nf15_Np15_TE50ms_TR200ms_FA90deg.seq',162           'irse_fov256mm_Nf15_Np15_TI20ms_TE50ms_TR200ms_FA90deg.seq']163    # make_pulseq_irse_oblique(fov=0.256,n=15, thk=0.005, tr=0.2, te=0.05, ti=0.02, fa=90,164    #                          enc='xyz', slice_locs=[0], write=True)165    # make_pulseq_gre_oblique(fov=0.256,n=15, thk=0.005, tr=0.2, te=0.05, fa=90,166    #                          enc='xyz', slice_locs=[0], write=True)167    # make_pulseq_se_oblique(fov=0.256,n=15, thk=0.005, tr=0.2, te=0.05, fa=90,168    #                          enc='xyz', slice_locs=[0], write=True)169    simulate_pulseq_jemris(seq_path=sps[0], phantom_info=phantom_info, sim_name=sim_names[0],170                               coil_fov=0.256)171    kk, im, images = recon_jemris(file='sim/' + sim_names[0] + '/signals.h5', dims=[15,15])...

sim_seq_validation.py

Source:sim_seq_validation.py

1import os2from pulseq_jemris_simulator import simulate_pulseq_jemris, recon_jemris3from scipy.io import savemat, loadmat456# IRSE7n = 328phantom_info = {'fov': 0.25, 'N': n, 'type': 'cylindrical', 'dim': 2, 'dir': 'z', 'loc': 0}9sps = 'sim/seq_validation/irse_32/irse32.seq'10sim_name = 'seq_validation\\irse_32'1112#Simulate13simulate_pulseq_jemris(seq_path=sps, phantom_info=phantom_info, sim_name=sim_name, coil_fov=0.25)14kk, im, images = recon_jemris(file='sim/' + sim_name + '/signals.h5', dims=[n, n])15savemat('sim/' + sim_name + '/utest_pulseq_sim_output.mat', {'images': images, 'kspace': kk, 'imspace': im})161718# #19# # TSE20# n = 3221# phantom_info = {'fov': 0.25, 'N': n, 'type': 'cylindrical', 'dim': 2, 'dir': 'z', 'loc': -0.08}22# sps = 'sim/seq_validation/tse_32/tse32.seq'23# sim_name = 'seq_validation\\tse_32'24# # Make sequence25# simulate_pulseq_jemris(seq_path=sps, phantom_info=phantom_info, sim_name=sim_name, coil_fov=0.25)26# kk, im, images = recon_jemris(file='sim/' + sim_name + '/signals.h5', dims=[n, n])27# savemat('sim/' + sim_name + '/TSE-T2PLANE-utest_pulseq_sim_output.mat', {'images': images, 'kspace': kk, 'imspace': im})28#2930# ## DWI31# n = 3232# phantom_info = {'fov':0.25, 'N':n, 'type': 'cylindrical', 'dim': 2, 'dir': 'z', 'loc': -0.08}33# sps = 'sim/seq_validation/dwi_32/dwi32.seq'34# sim_name = 'seq_validation\\tse_32'35#36# simulate_pulseq_jemris(seq_path=sps, phantom_info=phantom_info, sim_name=sim_name, coil_fov=0.25)37# kk, im, images = recon_jemris(file='sim/'+sim_name+'/signals.h5',dims=[n,n])
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