Skip to content

Commit

Permalink
Merge pull request #256 from gafusion/cherry_pick_omas_viewer_dev
Browse files Browse the repository at this point in the history 
Cherry pick omas viewer dev
  • Loading branch information
@torrinba
torrinba authored Mar 28, 2024
2 parents 4ab29a3 + 216cd7e commit e0bd766
Show file tree
Hide file tree
Showing 10 changed files with 794 additions and 362 deletions.
2 changes: 2 additions & 0 deletions omas/machine_mappings/_common.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
from omas.omas_utils import printd
import os
import glob
from omas.omas_setup import omas_dir
from omas.utilities.omas_mds import mdsvalue

__support_files_cache__ = {}

Expand Down
126 changes: 114 additions & 12 deletions omas/machine_mappings/d3d.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -113,32 +113,131 @@
"coils_non_axisymmetric.coil.:.name": {
"PYTHON": "coils_non_axisymmetric_hardware(ods, {pulse})"
},
"core_profiles": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.global_quantities.v_loop": {
"COCOSIO": 11,
"PYTHON": "core_profiles_global_quantities_data(ods, {pulse})"
},
"core_profiles.ids_properties.homogeneous_time": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:": {
"TDI": "size(\\{PROFILES_tree}::TOP.PROFILES.EDENSFIT,1)",
"treename": "{PROFILES_tree}"
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.e_field.radial": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.e_field.radial_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.density_thermal": {
"TDI": "\\{PROFILES_tree}::TOP.PROFILES.EDENSFIT",
"treename": "{PROFILES_tree}"
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.density_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.density_fit.measured": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.density_fit.measured_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.density_fit.psi_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.temperature": {
"TDI": "\\{PROFILES_tree}::TOP.PROFILES.ETEMPFIT",
"treename": "{PROFILES_tree}"
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.temperature_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.temperature_fit.measured": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.temperature_fit.measured_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.electrons.temperature_fit.psi_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.grid.rho_pol_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.grid.rho_tor_norm": {
"eval2TDI": "py2tdi(tile,'dim_of(\\{PROFILES_tree}::TOP.PROFILES.EDENSFIT,0)','size(\\{PROFILES_tree}::TOP.PROFILES.EDENSFIT,1)')",
"treename": "{PROFILES_tree}"
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.density_thermal": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.density_thermal_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.density_thermal_fit.measured": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.density_thermal_fit.measured_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.density_fit.psi_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.time": {
"TDI": "dim_of(\\{PROFILES_tree}::TOP.PROFILES.EDENSFIT,1)/1000.",
"treename": "{PROFILES_tree}"
"core_profiles.profiles_1d.:.ion.:.element.:": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.element.:.a": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.element.:.z_n": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.label": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.temperature": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.temperature_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.temperature_fit.measured": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.temperature_fit.measured_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.temperature_fit.psi_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.velocity.toroidal": {
"COCOSIO": 11,
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_fit.measured": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_fit.measured_error_upper": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_fit.psi_norm": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.j_total": {
"COCOSIO": 11,
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.profiles_1d.:.pressure_perpendicular": {
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"core_profiles.time": {
"PYTHON": "core_profiles_global_quantities_data(ods, {pulse})"
"PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
},
"ec_launchers.beam.:": {
"PYTHON": "ec_launcher_active_hardware(ods, {pulse})"
Expand Down Expand Up @@ -199,6 +298,9 @@
"ec_launchers.beam.:.time": {
"PYTHON": "ec_launcher_active_hardware(ods, {pulse})"
},
"ece": {
"PYTHON": "electron_cyclotron_emission_hardware(ods, {pulse}, {fast_ece!r})"
},
"ece.channel.:": {
"PYTHON": "electron_cyclotron_emission_hardware(ods, {pulse}, {fast_ece!r})"
},
Expand Down
137 changes: 135 additions & 2 deletions omas/machine_mappings/d3d.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,11 @@
from omas import *
from omas.omas_utils import printd, printe, unumpy
from omas.machine_mappings._common import *
from uncertainties import unumpy
from omas.utilities.machine_mapping_decorator import machine_mapping_function
from omas.utilities.omas_mds import mdsvalue
from omas.omas_core import ODS
from omas.omas_structure import add_extra_structures

__all__ = []
__regression_arguments__ = {'__all__': __all__}
Expand Down Expand Up @@ -1353,6 +1358,136 @@ def ip_bt_dflux_data(ods, pulse):
ods['tf.b_field_tor_vacuum_r.data'] *= 1.6955


def add_extra_profile_structures():
extra_structures = {}
extra_structures["core_profiles"] = {}
sh = "core_profiles.profiles_1d"
for quant in ["ion.:.density_fit.psi_norm", "electrons.density_fit.psi_norm",
"ion.:.temperature_fit.psi_norm", "electrons.temperature_fit.psi_norm",
"ion.:.velocity.toroidal_fit.psi_norm"]:
if "velocity" in quant:
psi_struct = {"coordinates": "1- 1...N"}
else:
psi_struct = {"coordinates": sh + ".:." + quant.replace("psi_norm", "rho_tor_norm")}
psi_struct["documentation"] = "Normalized Psi for fit data."
psi_struct["data_type"] = "FLT_1D"
psi_struct["units"] = ""
extra_structures["core_profiles"][f"core_profiles.profiles_1d.:.{quant}"] = psi_struct
velo_struct = {"coordinates": sh + ".:." + "ion.:.velocity.toroidal_fit.psi_norm"}
velo_struct["documentation"] = "Information on the fit used to obtain the toroidal velocity profile [m/s]"
velo_struct["data_type"] = "FLT_1D"
velo_struct["units"] = "m.s^-1"
extra_structures["core_profiles"][f"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_fit.measured"] = velo_struct
extra_structures["core_profiles"][f"core_profiles.profiles_1d.:.ion.:.velocity.toroidal_fit.measured_error_upper"] = velo_struct
add_extra_structures(extra_structures)


@machine_mapping_function(__regression_arguments__, pulse=194842001, PROFILES_tree="OMFIT_PROFS")
def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS"):
add_extra_profile_structures()
ods["core_profiles.ids_properties.homogeneous_time"] = 1
if "OMFIT_PROFS" in PROFILES_tree:
omfit_profiles_node = '\\TOP.'
query = {
"electrons.density_thermal": "N_E",
"electrons.density_fit.measured": "RW_N_E",
"electrons.temperature": "T_E",
"electrons.temperature_fit.measured": "RW_T_E",
"ion[0].density_thermal": "N_D",
"ion[0].temperature": "T_D",
"ion[1].velocity.toroidal": "V_TOR_C",
"ion[1].velocity.toroidal_fit.measured": "RW_V_TOR_C",
"ion[1].density_thermal": "N_C",
"ion[1].density_fit.measured": "RW_N_C",
"ion[1].temperature": "T_C",
"ion[1].temperature_fit.measured": "RW_T_C",
}
uncertain_entries = list(query.keys())
query["electrons.density_fit.psi_norm"] = "PS_N_E"
query["electrons.temperature_fit.psi_norm"] = "PS_T_E"
query["ion[1].density_fit.psi_norm"] = "PS_N_C"
query["ion[1].temperature_fit.psi_norm"] = "PS_T_C"
query["ion[1].velocity.toroidal_fit.psi_norm"]= "PS_V_TOR_C"
#query["j_total"] = "J_TOT"
#query["pressure_perpendicular"] = "P_TOT"
query["e_field.radial"] = "ER_C"
query["grid.rho_tor_norm"] = "rho"
normal_entries = set(query.keys()) - set(uncertain_entries)
for entry in query:
query[entry] = omfit_profiles_node + query[entry]
for entry in uncertain_entries:
query[entry + "_error_upper"] = "error_of(" + query[entry] + ")"
data = mdsvalue('d3d', treename=PROFILES_tree, pulse=pulse, TDI=query).raw()
if data is None:
print("No mds+ data")
raise ValueError(f"Could not find any data in MDS+ for {pulse} and {PROFILES_tree}")
dim_info = mdsvalue('d3d', treename=PROFILES_tree, pulse=pulse, TDI="\\TOP.n_e")
data['time'] = dim_info.dim_of(1) * 1.e-3
psi_n = dim_info.dim_of(0)
data['grid.rho_pol_norm'] = np.zeros((data['time'].shape + psi_n.shape))
data['grid.rho_pol_norm'][:] = np.sqrt(psi_n)
# for density_thermal in densities:
# data[density_thermal] *= 1.e6
for unc in ["", "_error_upper"]:
data[f"ion[0].velocity.toroidal{unc}"] = data[f"ion[1].velocity.toroidal{unc}"]
ods["core_profiles.time"] = data['time']
sh = "core_profiles.profiles_1d"
for i_time, time in enumerate(data["time"]):
ods[f"{sh}[{i_time}].grid.rho_pol_norm"] = data['grid.rho_pol_norm'][i_time]
for entry in uncertain_entries + ["ion[0].velocity.toroidal"]:
if isinstance(data[entry], Exception):
continue
for i_time, time in enumerate(data["time"]):
try:
ods[f"{sh}[{i_time}]." + entry] = data[entry][i_time]
ods[f"{sh}[{i_time}]." + entry + "_error_upper"] = data[entry + "_error_upper"][i_time]
except Exception as e:
print("Uncertain entry", entry)
print("================ DATA =================")
print(data[entry][i_time])
print("================ ERROR =================")
print(data[entry + "_error_upper"][i_time])
print(data[entry][i_time].shape,
data[entry + "_error_upper"][i_time].shape)
print(e)
for entry in normal_entries:
if isinstance(data[entry], Exception):
continue
for i_time, time in enumerate(data["time"]):
try:
ods[f"{sh}[{i_time}]."+entry] = data[entry][i_time]
except:
print("Normal entry", entry)
print("================ DATA =================")
print(data[entry][i_time])
for i_time, time in enumerate(data["time"]):
ods[f"{sh}[{i_time}].ion[0].element[0].z_n"] = 1
ods[f"{sh}[{i_time}].ion[0].element[0].a"] = 2.0141
ods[f"{sh}[{i_time}].ion[1].element[0].z_n"] = 6
ods[f"{sh}[{i_time}].ion[1].element[0].a"] = 12.011
ods[f"{sh}[{i_time}].ion[0].label"] = "D"
ods[f"{sh}[{i_time}].ion[1].label"] = "C"
else:
profiles_node = '\\TOP.PROFILES.'
query = {
"electrons.density_thermal": "EDENSFIT",
"electrons.temperature": "ETEMPFIT"
}
for entry in query:
query[entry] = profiles_node + query[entry]
data = mdsvalue('d3d', treename=PROFILES_tree, pulse=pulse, TDI=query).raw()
dim_info = mdsvalue('d3d', treename=PROFILES_tree, pulse=pulse, TDI="\\TOP.PROFILES.EDENSFIT")
data['time'] = dim_info.dim_of(1) * 1.e-3
rho_tor_norm = dim_info.dim_of(0)
data['grid.rho_tor_norm'] = np.zeros((data['time'].shape + rho_tor_norm.shape))
data['grid.rho_tor_norm'][:] = rho_tor_norm
ods[f"core_profiles.time"] = data['time']
for entry in data:
if isinstance(data[entry], Exception):
continue
for i_time, time in enumerate(data["time"]):
ods[f"core_profiles.profiles_1d[{i_time}]."+entry] = data[entry][i_time]

# ================================
@machine_mapping_function(__regression_arguments__, pulse=133221)
def core_profiles_global_quantities_data(ods, pulse):
Expand All @@ -1375,5 +1510,3 @@ def core_profiles_global_quantities_data(ods, pulse):


# ================================
if __name__ == '__main__':
test_machine_mapping_functions(__all__, globals(), locals())
2 changes: 2 additions & 0 deletions omas/omas_core.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2914,4 +2914,6 @@ def through_omas_pkl(ods):
from .omas_mongo import *
from .omas_symbols import *
from .omas_machine import *
from .utilities.machine_mapping_decorator import *
from .utilities.omas_mds import *
from . import omas_structure
Loading

0 comments on commit e0bd766

Please sign in to comment.