Machine mappings profilesdb ccfe

[TimSlendebroek]

Attempt at gathering tokamak profile data from 'tokamak-profiledb.ccfe.ac.uk:8000' using machine mappings.

I tested the function profile_db_to_ODS() in an OMFIT session with success:

def profile_db_to_ODS(ods, pulse,tok,db,ngrid):
    print(pulse,tok,db,ngrid)
    ods['dataset_description.ids_properties.comment'] = f'Comment for {tok}'

    if ods is None:
        ods = ODS()
    if tok == 'DIII-D':
        tok = 'd3d'

    available_in_database = {'d3d':[69627, 69648, 71378, 71384, 77557, 77559, 78106, 78109, 78281, 78283, 78316, 78328, 81321, 81329, 81499, 81507, 82183, 82188, 82205, 82788, 84682, 87031, 89943, 90105, 90108, 90117, 90118, 92664, 95989, 98549, 98775, 98777, 99251, 99411, 99696, 103818, 104276, 106919, 106956, 111203, 111221, 111239, 118334, 118341, 118348, 118446]
    }

    if tok not in available_in_database:
        print(f"tokamak not in database see: {available_in_database.keys()}")
    if pulse not in available_in_database[tok]:
        print(f"Shot {pulse} not in {tok} database, available pulses = {available_in_database[tok]}")

    zero_d_ods_locations = {'R': 'summary.boundary.geometric_axis_r.value','a': 'summary.boundary.minor_radius.value','dwdt':'summary.global_quantities.denergy_thermal_dt.value','hl_mode':'summary.global_quantities.h_mode.value','Ip':'summary.global_quantities.ip.value','zeff':'summary.volume_average.zeff.value','tau_exp':'summary.global_quantities.tau_energy.value','Bt':'summary.global_quantities.b0.value', 'kappa':'summary.boundary.elongation.value', 'delta_u':'summary.boundary.triangularity_upper.value','delta_l':'summary.boundary.triangularity_lower.value', 'nel':'summary.line_average.n_e.value', 'power_nbi':'summary.heating_current_drive.power_launched_nbi.value', 'power_ec':'summary.heating_current_drive.power_launched_ec.value','power_ohm':'summary.global_quantities.power_ohm.value', 'power_ic':'summary.heating_current_drive.power_launched_ic.value' ,'power_loss':'summary.global_quantities.power_loss.value','stored_energy':'summary.global_quantities.energy_thermal.value'}
    zero_d_profiles_locations = {'a':"['ZEROD']['AMIN']",'R':"['ZEROD']['RGEO']",'dwdt':"['ZEROD']['DWDIA']",'Ip':"['ZEROD']['IP']",'zeff':"['ZEROD']['ZEFF']",'tau_exp':"['ZEROD']['TAUTH']",'Bt':"['ZEROD']['BT']", 'kappa':"['ZEROD']['KAPPA']",'delta_l':"['ZEROD']['DELTA']", 'delta_u':"['ZEROD']['DELTA']", 'nel':"['ZEROD']['NEL']", 'power_nbi':"['ZEROD']['PINJ']", 'power_ec':"['ZEROD']['PECH']",'power_ohm':"['ZEROD']['POHM']", 'power_ic':"['ZEROD']['PECH']",'power_loss':"['ZEROD']['PLTH']",'stored_energy':"['ZEROD']['WTH']"}

    one_d_ods_locations = {'zeff':'core_profiles.profiles_1d[0].zeff','volume':'core_profiles.profiles_1d[0].grid.volume','omega':'core_profiles.profiles_1d[0].rotation_frequency_tor_sonic','q':'core_profiles.profiles_1d[0].q','Ti':'core_profiles.profiles_1d[0].t_i_average','Te':'core_profiles.profiles_1d[0].electrons.temperature','ne':'core_profiles.profiles_1d[0].electrons.density_thermal','jtot':'core_profiles.profiles_1d[0].j_tor'}
    one_d_profiles_locations = {'volume':"['TWOD']['VOLUME']",'omega':"['TWOD']['VROT']",'q':"['TWOD']['Q']",'Ti':"['TWOD']['TI']",'Te':"['TWOD']['TE']",'ne':"['TWOD']['NE']",'q_nbi_i':"['TWOD']['QNBII']",'q_nbi_e':"['TWOD']['QNBIE']",'s_nbi_se':"['TWOD']['SNBII']",'q_ohm_e':"['TWOD']['QOHM']",'jtot':"['TWOD']['CURTOT']"}

    mds_tree = mdstree(server='tokamak-profiledb.ccfe.ac.uk:8000', pulse=int(pulse), treename=f'pr{db}_{tok}')

    ods['summary.global_quantities.h_mode.value'] = [True]
    ods['dataset_description.data_entry.machine'] = tok
    ods['dataset_description.data_entry.pulse'] = int(mds_tree['ZEROD']['SHOT'].data())
    ods['summary.time'] = mds_tree['ZEROD']['TIME'].data()
    for key, location in zero_d_profiles_locations.items():
        try:
            if key in zero_d_ods_locations:
                print(location,eval(f"mds_tree{location}").data()[-1])
                ods[zero_d_ods_locations[key]] = np.array(eval(f"mds_tree{location}").data())

        except Exception as e:
            print(repr(e))
            print(key, "not in db")
            if key in zero_d_ods_locations:
                ods[zero_d_ods_locations[key]] = [0.0]

    heating_idx_dict = {'nbi':2 , 'ec': 3, 'lh':4, 'ic':5, 'fusion':6, 'ohm':7}
    source_index = 0
    ion_elec = {'i':'total_ion_energy', 'e':'electrons.energy','se':'electrons.particles'}

    for key, location in one_d_profiles_locations.items():
        rho_tor_norm = np.linspace(0,1,ngrid)
        rho_init = np.linspace(0,1,len(mds_tree['TWOD']['VOLUME'].data()[0]))

        try:
            if 'q_' in key or 's_' in key:
                name = key.split(sep='_')[1]
                ods[f'core_sources.source[{source_index}].identifier.index'] = heating_idx_dict[name]
                ods[f'core_sources.source[{source_index}].identifier.name'] = name
                ods[f'core_sources.source[{source_index}].profiles_1d[0].grid.rho_tor_norm'] = rho_tor_norm
                ods[f'core_sources.source[{source_index}].profiles_1d[0].grid.volume'] = np.interp(x=rho_tor_norm,xp=rho_init,fp=mds_tree['TWOD']['VOLUME'].data()[0])
                ods[f"core_sources.source[{source_index}].profiles_1d[0].{ion_elec[key.split(sep='_')[-1]]}"] = np.interp(x=rho_tor_norm,xp=rho_init,fp=eval(f"mds_tree{location}").data()[0])

                source_index += 1

            elif key in one_d_ods_locations:
                ods[one_d_ods_locations[key]] = np.interp(x=rho_tor_norm,xp=rho_init,fp=eval(f"mds_tree{location}").data()[0])

                if key == 'omega':
                    ods[one_d_ods_locations[key]] /= 2*np.pi

        except Exception as e:
            print(repr(e))
            print(key, "not in db")
            if key in zero_d_ods_locations:
                ods[one_d_ods_locations[key]] = np.zeros(ngrid)

but seem to get into trouble when running this through (after reloading machine mappings):

ods = ODS()
ods.open('profiles_db_ccfe',pulse=81499)

with mappings script (/home/slendebroekt/GIT_projects/omas/omas/machine_mappings/profiles_db_ccfe.py):

import os
import numpy as np
from inspect import unwrap
from omas import *
from omas.omas_utils import printd, unumpy
from omas.machine_mappings._common import *

__all__ = []
__regression_arguments__ = {'__all__': __all__}

# Use the @machine_mapping_function to automatically fill out the .json mapping file
# All these functions must accept `ods` as their first argument
# All other arguments should have a default value defined, as this serves two purposes:
#  1. run the run_machine_mapping_functions
#  2. automatically fill the __options__ entry in the .json mapping file

@machine_mapping_function(__regression_arguments__,pulse=77557, tok="d3d", db='98', ngrid=201)
def profile_db_to_ODS(ods, pulse,tok,db,ngrid):
    print(pulse,tok,db,ngrid)
    ods['dataset_description.ids_properties.comment'] = f'Comment for {tok}'

    if ods is None:
        ods = ODS()
    if tok == 'DIII-D':
        tok = 'd3d'

    available_in_database = {'d3d':[69627, 69648, 71378, 71384, 77557, 77559, 78106, 78109, 78281, 78283, 78316, 78328, 81321, 81329, 81499, 81507, 82183, 82188, 82205, 82788, 84682, 87031, 89943, 90105, 90108, 90117, 90118, 92664, 95989, 98549, 98775, 98777, 99251, 99411, 99696, 103818, 104276, 106919, 106956, 111203, 111221, 111239, 118334, 118341, 118348, 118446]
    }

    if tok not in available_in_database:
        print(f"tokamak not in database see: {available_in_database.keys()}")
    if pulse not in available_in_database[tok]:
        print(f"Shot {pulse} not in {tok} database, available pulses = {available_in_database[tok]}")

    zero_d_ods_locations = {'R': 'summary.boundary.geometric_axis_r.value','a': 'summary.boundary.minor_radius.value','dwdt':'summary.global_quantities.denergy_thermal_dt.value','hl_mode':'summary.global_quantities.h_mode.value','Ip':'summary.global_quantities.ip.value','zeff':'summary.volume_average.zeff.value','tau_exp':'summary.global_quantities.tau_energy.value','Bt':'summary.global_quantities.b0.value', 'kappa':'summary.boundary.elongation.value', 'delta_u':'summary.boundary.triangularity_upper.value','delta_l':'summary.boundary.triangularity_lower.value', 'nel':'summary.line_average.n_e.value', 'power_nbi':'summary.heating_current_drive.power_launched_nbi.value', 'power_ec':'summary.heating_current_drive.power_launched_ec.value','power_ohm':'summary.global_quantities.power_ohm.value', 'power_ic':'summary.heating_current_drive.power_launched_ic.value' ,'power_loss':'summary.global_quantities.power_loss.value','stored_energy':'summary.global_quantities.energy_thermal.value'}
    zero_d_profiles_locations = {'a':"['ZEROD']['AMIN']",'R':"['ZEROD']['RGEO']",'dwdt':"['ZEROD']['DWDIA']",'Ip':"['ZEROD']['IP']",'zeff':"['ZEROD']['ZEFF']",'tau_exp':"['ZEROD']['TAUTH']",'Bt':"['ZEROD']['BT']", 'kappa':"['ZEROD']['KAPPA']",'delta_l':"['ZEROD']['DELTA']", 'delta_u':"['ZEROD']['DELTA']", 'nel':"['ZEROD']['NEL']", 'power_nbi':"['ZEROD']['PINJ']", 'power_ec':"['ZEROD']['PECH']",'power_ohm':"['ZEROD']['POHM']", 'power_ic':"['ZEROD']['PECH']",'power_loss':"['ZEROD']['PLTH']",'stored_energy':"['ZEROD']['WTH']"}

    one_d_ods_locations = {'zeff':'core_profiles.profiles_1d[0].zeff','volume':'core_profiles.profiles_1d[0].grid.volume','omega':'core_profiles.profiles_1d[0].rotation_frequency_tor_sonic','q':'core_profiles.profiles_1d[0].q','Ti':'core_profiles.profiles_1d[0].t_i_average','Te':'core_profiles.profiles_1d[0].electrons.temperature','ne':'core_profiles.profiles_1d[0].electrons.density_thermal','jtot':'core_profiles.profiles_1d[0].j_tor'}
    one_d_profiles_locations = {'volume':"['TWOD']['VOLUME']",'omega':"['TWOD']['VROT']",'q':"['TWOD']['Q']",'Ti':"['TWOD']['TI']",'Te':"['TWOD']['TE']",'ne':"['TWOD']['NE']",'q_nbi_i':"['TWOD']['QNBII']",'q_nbi_e':"['TWOD']['QNBIE']",'s_nbi_se':"['TWOD']['SNBII']",'q_ohm_e':"['TWOD']['QOHM']",'jtot':"['TWOD']['CURTOT']"}

    mds_tree = mdstree(server='tokamak-profiledb.ccfe.ac.uk:8000', pulse=int(pulse), treename=f'pr{db}_{tok}')

    ods['summary.global_quantities.h_mode.value'] = [True]
    ods['dataset_description.data_entry.machine'] = tok
    ods['dataset_description.data_entry.pulse'] = int(mds_tree['ZEROD']['SHOT'].data())
    ods['summary.time'] = mds_tree['ZEROD']['TIME'].data()
    for key, location in zero_d_profiles_locations.items():
        try:
            if key in zero_d_ods_locations:
                print(location,eval(f"mds_tree{location}").data()[-1])
                ods[zero_d_ods_locations[key]] = np.array(eval(f"mds_tree{location}").data())

        except Exception as e:
            print(repr(e))
            print(key, "not in db")
            if key in zero_d_ods_locations:
                ods[zero_d_ods_locations[key]] = [0.0]

    heating_idx_dict = {'nbi':2 , 'ec': 3, 'lh':4, 'ic':5, 'fusion':6, 'ohm':7}
    source_index = 0
    ion_elec = {'i':'total_ion_energy', 'e':'electrons.energy','se':'electrons.particles'}

    for key, location in one_d_profiles_locations.items():
        rho_tor_norm = np.linspace(0,1,ngrid)
        rho_init = np.linspace(0,1,len(mds_tree['TWOD']['VOLUME'].data()[0]))

        try:
            if 'q_' in key or 's_' in key:
                name = key.split(sep='_')[1]
                ods[f'core_sources.source[{source_index}].identifier.index'] = heating_idx_dict[name]
                ods[f'core_sources.source[{source_index}].identifier.name'] = name
                ods[f'core_sources.source[{source_index}].profiles_1d[0].grid.rho_tor_norm'] = rho_tor_norm
                ods[f'core_sources.source[{source_index}].profiles_1d[0].grid.volume'] = np.interp(x=rho_tor_norm,xp=rho_init,fp=mds_tree['TWOD']['VOLUME'].data()[0])
                ods[f"core_sources.source[{source_index}].profiles_1d[0].{ion_elec[key.split(sep='_')[-1]]}"] = np.interp(x=rho_tor_norm,xp=rho_init,fp=eval(f"mds_tree{location}").data()[0])

                source_index += 1

            elif key in one_d_ods_locations:
                ods[one_d_ods_locations[key]] = np.interp(x=rho_tor_norm,xp=rho_init,fp=eval(f"mds_tree{location}").data()[0])

                if key == 'omega':
                    ods[one_d_ods_locations[key]] /= 2*np.pi

        except Exception as e:
            print(repr(e))
            print(key, "not in db")
            if key in zero_d_ods_locations:
                ods[one_d_ods_locations[key]] = np.zeros(ngrid)

# =====================
if __name__ == '__main__':
    test_machine_mapping_functions(__all__, globals(), locals())

[orso82]

@TimSlendebroek I think you had it right, just you need to pass the options:

ods = ODS()
ods.open('profiles_db_ccfe', pulse=81499, options={'tok':'d3d', 'db':'08'})

Notice that I modified your function so that by default it returns the same number of points as the original database

[orso82]

@TimSlendebroek can you please add a proper docstring to the profile_db_to_ODS function?

Nice job, by the way :)