# plt.show()
# az.plot_posterior(trace)
# plt.show()
# -------------------------------------- Test 2 --------------------------------------------------
# Load synthetic observation
linesLogAddress = user_folder / f'Teff_LogU_epmGrids_linesLog.txt'
simulationData_file = user_folder / f'Teff_LogU_epmGrids_config.txt'
# Load simulation parameters
objParams = sr.loadConfData(simulationData_file, group_variables=False)
# Load emission lines
merged_lines = {'O2_3726A_m': 'O2_3726A-O2_3729A', 'O2_7319A_m': 'O2_7319A-O2_7330A'}
objLinesDF = sr.import_emission_line_data(linesLogAddress, include_lines=objParams['inference_model_configuration']['input_lines'], exclude_lines=['S3_9069A'])
# Establish lines used in photo-ionization model
lineLabels = objLinesDF.index.values
lines_Grid = np.array(list(gridLineDict.keys()))
idx_analysis_lines = np.in1d(lineLabels, lines_Grid)
lineFluxes = objLinesDF.obsFlux.values
lineErr = objLinesDF.obsFluxErr.values
lineWaves = objLinesDF.wavelength.values
# Extinction parameters
objRed = sr.ExtinctionModel(Rv=objParams['simulation_properties']['R_v'],
red_curve=objParams['simulation_properties']['reddenig_curve'],
data_folder=objParams['data_location']['external_data_folder'])
lineFlambdas = objRed.gasExtincParams(wave=lineWaves)
print(f'- Treating object ({i}): {obj}')
objFolder = resultsFolder / f'{obj}'
fits_file = dataFolder / f'{obj}_{ext}.fits'
objMask = dataFolder / f'{obj}_{ext}_mask.txt'
results_file = objFolder / f'{obj}_{ext}_measurements.txt'
lineLog_file = objFolder / f'{obj}_{ext}_linesLog_{cycle}.txt'
# Declare output files
outputDb = objFolder / f'{obj}_{ext}_fitting_{cycle}.db'
outputTxt = objFolder / f'{obj}_{ext}_fitting_{cycle}.txt'
simConf = dataFolder / f'{obj}_config.txt'
# Load data
objParams = sr.loadConfData(simConf, group_variables=False)
results_dict = sr.loadConfData(results_file, group_variables=False)
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'])
objFolder = resultsFolder / f'{obj}'
results_file = objFolder / f'{obj}_{ext}_measurements.txt'
lineLog_file = objFolder / f'{obj}_{ext}_linesLog_{cycle}.txt'
outputDb = objFolder / f'{obj}_{ext}_fitting_{cycle}.db'
outputTxt = objFolder / f'{obj}_{ext}_fitting_{cycle}.txt'
outputPiDb = objFolder / f'{obj}_{ext}_pI_fitting_{cycle}.db'
outputPiTxt = objFolder / f'{obj}_{ext}_pI_fitting_{cycle}.txt'
outputDirectHIIchemDb = objFolder / f'{obj}_{ext}_Direct-Teff-logU_{cycle}.db'
outputDirectHIIchemTxt = objFolder / f'{obj}_{ext}_Direct-Teff-logU_{cycle}.txt'
obj1_model = sr.SpectraSynthesizer()
measurements_dict = sr.loadConfData(results_file,
group_variables=False)
objLinesDF = sr.import_emission_line_data(lineLog_file)
fit_pickle = sr.load_MC_fitting(outputDb)
pI_pickle = sr.load_MC_fitting(outputPiDb)
bayes_plus_PI_pickle = sr.load_MC_fitting(outputDirectHIIchemDb)
fit_inputs_dict = sr.loadConfData(outputTxt)
pI_inputs_dict = sr.loadConfData(outputPiTxt)
bayes_inputs_dict = sr.loadConfData(outputDirectHIIchemTxt)
# Recover Direct method Bayesian fitting
sr_lineLabels = fit_inputs_dict['Input_data']['lineLabels_list']
inFlux = fit_inputs_dict['Input_data']['inputFlux_array']
inErr = fit_inputs_dict['Input_data']['inputErr_array']
flux_matrix = fit_pickle['trace']['calcFluxes_Op']
mean_line_values = flux_matrix.mean(axis=0)
# Results folder
output_folder = Path(r'D:\Dropbox\Astrophysics\Data\CGCG0707_mike')
# Conf file
chem_conf = output_folder / f'MIKE_CGCG007_chemical_fitting.txt'
objParams = load_cfg(chem_conf)
for i_night in nights_range:
# Declare sampler
obj1_model = sr.SpectraSynthesizer()
input_lines = objParams['inference_model_configuration']['input_lines']
lines_log_address = output_folder / f'MIKE_CGCG007_linelog_night{i_night}.txt'
objLinesDF = sr.import_emission_line_data(lines_log_address,
include_lines=input_lines)
output_db = output_folder / f'MIKE_CGCG007_db{i_night}'
lineLabels = objLinesDF.index.values
lineIons = objLinesDF['ion'].values
lineFluxes = objLinesDF['intg_flux'].values
lineErr = objLinesDF['intg_err'].values
# Declare simulation physical 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'])
objIons = sr.IonEmissivity(
tempGrid=objParams['simulation_properties']['temp_grid'],
# linesDF.rename(columns={'wavelength': 'obsWave'}, inplace=True)
if ('O2_7319A' in linesDF.index) and ('O2_7330A'
in linesDF.index):
flux_comb = linesDF.loc[
'O2_7319A', 'obsFlux'] + linesDF.loc['O2_7330A',
'obsFlux']
err_comb = np.sqrt(
linesDF.loc['O2_7319A', 'obsFluxErr']**2 +
linesDF.loc['O2_7330A', 'obsFluxErr']**2)
linesDF.loc['O2_7319A_b'] = None
linesDF.loc['O2_7319A_b',
['wavelength', 'obsFlux', 'obsFluxErr'
]] = 7325, flux_comb, err_comb
linesDF.loc['O2_7319A_b', 'ion'] = 'O2'
objLinesDF = sr.import_emission_line_data(
linesDF=linesDF, include_lines=input_lines)
normLine = 'H1_4861A'
idcs_lines = (objLinesDF.index != normLine)
lineLabels = objLinesDF.loc[idcs_lines].index
lineIons = objLinesDF.loc[idcs_lines, 'ion'].values
lineFluxes = objLinesDF.loc[idcs_lines, 'obsFlux'].values
lineErr = objLinesDF.loc[idcs_lines, 'obsFluxErr'].values
# Declare simulation physical properties
objRed = sr.ExtinctionModel(
Rv=chem_conf['simulation_properties']['R_v'],
red_curve=chem_conf['simulation_properties']
['reddenig_curve'],
data_folder=chem_conf['data_location']
['external_data_folder'])
for idx_obj in range(n_objs):
# State the objects to study
linesLogAddress = user_folder / f'GridEmiss_region{idx_obj+1}of{n_objs}_linesLog.txt'
simulationData_file = user_folder / f'GridEmiss_region{idx_obj+1}of{n_objs}_config.txt'
# Load simulation parameters
objParams = sr.loadConfData(simulationData_file, group_variables=False)
# Load emission lines
merged_lines = {
'O2_3726A_m': 'O2_3726A-O2_3729A',
'O2_7319A_m': 'O2_7319A-O2_7330A'
}
default_lines = objParams['inference_model_configuration']['input_lines']
objLinesDF = sr.import_emission_line_data(linesLogAddress,
include_lines=default_lines)
normLine = 'H1_4861A'
idcs_lines = (objLinesDF.index != normLine)
lineLabels = objLinesDF.loc[idcs_lines].index
lineIons = objLinesDF.loc[idcs_lines, 'ion'].values
lineFluxes = objLinesDF.loc[idcs_lines, 'intg_flux'].values
lineErr = objLinesDF.loc[idcs_lines, 'intg_err'].values
# Declare simulation physical 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'])
objIons = sr.IonEmissivity(
'obsFlux'] = lm.linesDF.loc[idcs_blended,
'gauss_flux'] / flux_Hbeta
lm.linesDF.loc[idcs_blended,
'obsFluxErr'] = lm.linesDF.loc[idcs_blended,
'gauss_err'] / flux_Hbeta
lm.linesDF.loc[~idcs_blended,
'obsFlux'] = lm.linesDF.loc[~idcs_blended,
'intg_flux'] / flux_Hbeta
lm.linesDF.loc[~idcs_blended,
'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,
linesDF['obsFlux'] = linesDF['intg_flux']/flux_Hbeta
linesDF['obsFluxErr'] = linesDF['intg_err']/flux_Hbeta
linesDF.rename(columns={'wavelength': 'obsWave'}, inplace=True)
for ion in ['H1', 'He1', 'He2']:
idcs_ions = linesDF.ion == ion
linesDF.loc[idcs_ions, 'ion'] = ion + 'r'
if ('O2_7319A' in linesDF.index) and ('O2_7330A' in linesDF.index):
flux_comb = linesDF.loc['O2_7319A', 'intg_flux'] + linesDF.loc['O2_7330A', 'intg_flux']
err_comb = np.sqrt(linesDF.loc['O2_7319A', 'intg_err']**2 + linesDF.loc['O2_7330A', 'intg_err']**2)
linesDF.loc['O2_7319A_b'] = None
linesDF.loc['O2_7319A_b', ['obsWave', 'obsFlux', 'obsFluxErr']] = 7325, flux_comb/flux_Hbeta, err_comb/flux_Hbeta
linesDF.loc['O2_7319A_b', 'ion'] = 'O2'
sr.save_lineslog(linesDF, inputLinesLog)
# Load emission lines
objLinesDF = sr.import_emission_line_data(inputLinesLog,
include_lines=chem_conf['inference_model_configuration']['input_lines'])
# Declare simulation physical properties
objRed = sr.ExtinctionModel(Rv=chem_conf['simulation_properties']['R_v'],
red_curve=chem_conf['simulation_properties']['reddenig_curve'],
data_folder=chem_conf['data_location']['external_data_folder'])
objIons = sr.IonEmissivity(tempGrid=chem_conf['simulation_properties']['temp_grid'],
denGrid=chem_conf['simulation_properties']['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_7319A_b': 'O2_7319A-O2_7330A'})
'Ar4': 5.06,
'err_lines': 0.02}
# Declare lines to simulate
objParams['input_lines'] = ['H1_4341A', 'H1_6563A',
'O3_4363A', 'O3_4959A', 'O3_5007A', 'N2_6548A', 'N2_6584A',
'S2_6716A', 'S2_6731A', 'S3_6312A', 'S3_9069A', 'S3_9531A']
# We use the default simulation configuration for the remaining settings
objParams.update(ss._default_cfg)
# We use the default lines database to generate the synthetic emission lines log for this simulation
linesLogPath = os.path.join(ss._literatureDataFolder, ss._default_cfg['lines_data_file'])
# 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'])
user_folder = Path('D:/AstroModels')
output_db = user_folder/f'Teff_LogU_epmGrids_db'
# Declare sampler
obj1_model = sr.SpectraSynthesizer()
# State the objects to study
linesLogAddress = user_folder/f'Teff_LogU_epmGrids_linesLog.txt'
simulationData_file = user_folder/f'Teff_LogU_epmGrids_config.txt'
# Load simulation parameters
objParams = sr.loadConfData(simulationData_file, group_variables=False)
# Load emission lines
inputLines = objParams['inference_model_configuration']['input_lines']
objLinesDF = sr.import_emission_line_data(linesLogAddress, include_lines=inputLines)
# Declare simulation physical 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 region physical model
obj1_model.define_region(objLinesDF, extinction_model=objRed)
# Declare sampling properties
obj1_model.simulation_configuration(objParams['inference_model_configuration']['parameter_list'],
prior_conf_dict=objParams['priors_configuration'],
photo_ionization_grid=True)
# Declare simulation inference model
