objLinesDF = sr.import_emission_line_data(
lineLog_file, include_lines=objParams[obj]['input_lines'])
# Load previous measurements to compare
true_values = check_previous_measurements(
obj, objParams['inference_model_configuration']['parameter_list'],
results_dict, obsData)
# Declare extinction properties
objRed = sr.ExtinctionModel(
Rv=objParams['simulation_properties']['R_v'],
red_curve=objParams['simulation_properties']['reddenig_curve'],
data_folder=objParams['data_location']['external_data_folder'])
# Declare ion properties
objIons = sr.IonEmissivity(
tempGrid=objParams['simulation_properties']['temp_grid'],
denGrid=objParams['simulation_properties']['den_grid'])
# Generate interpolator from the emissivity grids
ionDict = objIons.get_ions_dict(np.unique(objLinesDF.ion.values))
objIons.computeEmissivityGrids(objLinesDF,
ionDict,
combined_dict=combined_line_dict)
# Declare chemical model
objChem = sr.DirectMethod(
linesDF=objLinesDF,
highTempIons=objParams['simulation_properties']
['high_temp_ions_list'])
# Declare region physical model
'obsFluxErr'] = lm.linesDF.loc[~idcs_blended,
'intg_err'] / flux_Hbeta
lm.linesDF.rename(columns={'wavelength': 'obsWave'}, inplace=True)
lm.save_lineslog(lm.linesDF, simFolder / inputLinesLog)
# Load emission lines
objLinesDF = sr.import_emission_line_data(
simFolder / inputLinesLog, include_lines=objParams['input_lines'])
# Declare simulation physical properties
objRed = sr.ExtinctionModel(
Rv=objParams['R_v'],
red_curve=objParams['reddenig_curve'],
data_folder=objParams['external_data_folder'])
objIons = sr.IonEmissivity(tempGrid=objParams['temp_grid'],
denGrid=objParams['den_grid'])
# Generate interpolator from the emissivity grids
ionDict = objIons.get_ions_dict(np.unique(objLinesDF.ion.values))
objIons.computeEmissivityGrids(
objLinesDF,
ionDict,
linesDb=sr._linesDb,
combined_dict={'O2_3726A': 'O2_3726A-O2_3729A'})
# Declare chemical model
objChem = sr.DirectMethod(
linesDF=objLinesDF, highTempIons=objParams['high_temp_ions_list'])
# Declare region physical model
obj1_model.define_region(objLinesDF, objIons, objRed, objChem)
n_voxels = idcs_voxels.shape[0]
print(
f'\nTreating {region_label} consisting of {n_voxels}. The estimated time is {(n_voxels*1.85)/60:0.1f} hrs'
)
# Region chemical configuration
chem_conf_file = dataFolder / f'{obj}_chemical_model_region_{idx_region}.txt'
chem_conf = sr.loadConfData(chem_conf_file, group_variables=False)
# Load emission lines
input_lines = chem_conf['inference_model_configuration']['input_lines']
ion_array, wave_array, latex_array = lime.label_decomposition(
input_lines)
objIons = sr.IonEmissivity(
tempGrid=chem_conf['simulation_properties']['temp_grid'],
denGrid=chem_conf['simulation_properties']['den_grid'])
ionDict = objIons.get_ions_dict(ion_array)
# Generate interpolator from the emissivity grids
objIons.computeEmissivityGrids(input_lines,
ionDict,
combined_dict=merge_dict)
for idx_voxel, idx_pair in enumerate(idcs_voxels):
idx_j, idx_i = idx_pair
print(
f'\nTreating voxel {idx_j}-{idx_i}: ({idx_voxel}/{n_voxels})')
# Prepare dataframe with the observed lines labeled
objLinesDF = ss.import_emission_line_data(linesLogPath, include_lines=objParams['input_lines'])
# Declare extinction properties
objRed = ss.ExtinctionModel(Rv=objParams['R_v'],
red_curve=objParams['reddenig_curve'],
data_folder=objParams['external_data_folder'])
# Compute the flambda value for the input emission lines
lineFlambdas = objRed.gasExtincParams(wave=objLinesDF.obsWave.values)
lineWaves = objLinesDF.pynebCode.values
# Establish atomic data references
ftau_file_path = os.path.join(ss._literatureDataFolder, objParams['ftau_file'])
objIons = ss.IonEmissivity(ftau_file_path=ftau_file_path, tempGrid=objParams['temp_grid'],
denGrid=objParams['den_grid'])
# Define the dictionary with the pyneb ion objects
ionDict = objIons.get_ions_dict(np.unique(objLinesDF.ion.values))
# Compute the emissivity surfaces for the observed emission lines # TODO this database is not necesary since we duplicate the logs
objIons.computeEmissivityGrid(objLinesDF, ionDict, linesDb=ss._linesDb)
# Declare the paradigm for the chemical composition measurement
objChem = ss.DirectMethod()
# Tag the emission features for the chemical model implementation
objChem.label_ion_features(linesDF=objLinesDF, highTempIons=objParams['high_temp_ions_list'])
# Declare a dictionary with the synthetic abundances
abundDict = {}