obj_AssignLines['FTDTR-9'] = helium1Lines + helium2Lines + sulfurLines + oxygen3Lines + oxygen2Lines + nitrogenLines + argon3Lines
obj_AssignLines['FTDTR-10'] = helium1Lines + helium2Lines + sulfurLines + oxygen3Lines + oxygen2Lines + nitrogenLines + argon3Lines
#Loop throught the objects
failing_objects = []
for objName in catalogue_df.loc[dz.idx_include].index:
# Article reference
quick_reference = catalogue_df.loc[objName].quick_index
print objName, (quick_reference)
# Object folder
oldFolder = '{}{}/'.format(catalogue_dict['Obj_Folder'], objName)
objectNewFolder = root_folder + objName + '/'
make_folder(objectNewFolder)
# Get fits data
fits_file = catalogue_df.loc[objName].reduction_fits
wave, flux, etraData = dz.get_spectra_data(fits_file)
# Get lines log data
lineslog_address = '{}{}{}'.format(oldFolder,objName,lineslog_ext)
linesLogDf = dz.load_lineslog_frame(lineslog_address)
linesLogDf.rename(columns=lineslogDfNewHeaders, inplace=True)
linesLogDf.rename(index=lineslogDfNewIndeces, inplace=True)
# Generate a grid plot and add continuum contribution in recombination lines
lineFluxes = linesLogDf['line_Flux'].values
linesLogDf['obs_flux'], linesLogDf['obs_fluxErr'] = nominal_values(lineFluxes), std_devs(lineFluxes)
plotFolder = '{}/input_data/'.format(objectNewFolder)
from lib.Astro_Libraries.spectrum_fitting.import_functions import make_folder
import shutil
# Import functions
dz = Dazer()
specS = SpectraSynthesizer()
# Declare data location
root_folder = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\bayesianModel\\' # root_folder = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/bayesianModel/'
whtSpreadSheet = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\WHT_Galaxies_properties.xlsx' # whtSpreadSheet = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/WHT_Galaxies_properties.xlsx'
article_supplementary_folder = 'E:\\Dropbox\\Astrophysics\\Papers\\Yp_BayesianMethodology\\supplementary material online\\'
fluxes_folder = article_supplementary_folder + 'emission_line_fluxes\\'
results_folder = article_supplementary_folder + 'model_parameters\\'
# Make new folder
make_folder(fluxes_folder)
make_folder(results_folder)
# Import data
catalogue_dict = dz.import_catalogue()
catalogue_df = dz.load_excel_DF(whtSpreadSheet)
default_lines = [
'H1_4341A', 'H1_6563A', 'He1_4471A', 'He1_5876A', 'He1_6678A', 'He2_4686A',
'O2_7319A', 'O2_7319A_b', 'O2_7330A', 'O3_4363A', 'O3_4959A', 'O3_5007A',
'N2_6548A', 'N2_6584A', 'S2_6716A', 'S2_6731A', 'S3_6312A', 'S3_9069A',
'S3_9531A', 'Ar3_7136A', 'Ar4_4740A'
]
# Quick indexing
dz.quick_indexing(catalogue_df)
def prepareSimulation(self,
obs_data,
ssp_data=None,
output_folder=None,
storage_folder=None,
spectra_components=None,
input_lines='all',
normalized_by_Hbeta=True,
excludeReddening=False,
T_high_prior=False,
prefit_ssp=True,
wavelengh_limits=None,
resample_inc=None,
norm_interval=None):
# Store components fit
self.spectraComponents = spectra_components
# Folders to store inputs and outputs
self.input_folder = output_folder + 'input_data/' # TODO sure?
self.output_folder = output_folder + 'output_data/'
self.dataFolder = self.output_folder if storage_folder is None else storage_folder # TODO sure?
self.configFile = obs_data[
'obsFile'] #TODO this one has to go into the configuration
self.objName = str(obs_data['objName'])
self.prefit_db = '{}{}_sspPrefitDB'.format(self.dataFolder,
self.objName)
self.sspCoeffsPrefit_file = '{}{}_prefitSSPpopulations.txt'.format(
self.input_folder, self.objName)
self.sspCoeffs_file = '{}{}_SSPpopulations.txt'.format(
self.input_folder, self.objName)
# Create them if not available
make_folder(self.input_folder)
make_folder(self.output_folder)
# Prepare spectrum components for fitting
self.emissionCheck, self.stellarCheck, self.emissionCheck = False, False, False
# Pre-analysis emission spectrum
if 'emission' in self.spectraComponents:
# Get emission data from input files
self.ready_simulation(output_folder,
obs_data,
ssp_data,
spectra_components,
input_lines=input_lines,
wavelengh_limits=wavelengh_limits,
resample_inc=resample_inc,
norm_interval=norm_interval)
# Declare gas sampler variables
self.gasSamplerVariables(
self.obj_data['lineIons'], self.config['high_temp_ions'],
self.obj_data['lineFluxes'], self.obj_data['lineErr'],
self.obj_data['lineLabels'], self.obj_data['lineFlambda'],
normalized_by_Hbeta, self.config['linesMinimumError'])
# Prios definition # TODO this must go to the a special section
self.priorsDict = {
'T_low': self.obj_data['Te_prior'],
'n_e': self.obj_data['ne_prior']
}
# Confirm inputs are valid
self.emissionCheck = True
# Prefit stellar continua
if 'stellar' in self.spectraComponents:
self.stellarCheck = True
# Perform a new SPP synthesis otherwise use available data
if prefit_ssp:
# Compute nebular continuum using normalise Halpha and standard conditions
self.computeDefaultNeb(
self.nebDefault['Te_neb'], self.obj_data['nebFlambda'],
self.nebDefault['cHbeta_neb'], self.nebDefault['He1_neb'],
self.nebDefault['He2_neb'],
self.nebDefault['flux_halpha'] /
self.obj_data['normFlux_coeff'], self.nebDefault['z_neb'])
# Ready continuum data
self.prepareContinuaData(
self.ssp_lib['wave_resam'],
self.ssp_lib['flux_norm'],
self.ssp_lib['normFlux_coeff'],
self.obj_data['wave_resam'],
self.obj_data['flux_norm'],
self.obj_data['continuum_sigma'],
self.int_mask,
nebularFlux=self.nebDefault['synth_neb_flux'])
# Select model
self.select_inference_model('stelar_prefit')
# Plot input simulation data
self.plotInputSSPsynthesis()
# Run stellar continua prefit and store/print the results
#self.run_pymc(self.prefit_db, iterations=8000, variables_list=['Av_star', 'sigma_star'], prefit = True)
self.savePrefitData(self.sspCoeffsPrefit_file, self.prefit_db)
# Compute nebular continuum using prior physical data
self.computeDefaultNeb(
self.nebDefault['Te_neb'], self.obj_data['nebFlambda'],
self.nebDefault['cHbeta_neb'], self.nebDefault['He1_neb'],
self.nebDefault['He2_neb'],
self.obj_data['flux_halpha'] / self.obj_data['normFlux_coeff'],
self.nebDefault['z_neb'])
# Compute nebular continuum using normalise Halpha and standard conditions
# TODO I think I need to remove nebular continuum here if I want to add it later
self.prepareContinuaData(
self.ssp_lib['wave_resam'],
self.ssp_lib['flux_norm'],
self.ssp_lib['normFlux_coeff'],
self.obj_data['wave_resam'],
self.obj_data['flux_norm'],
self.obj_data['continuum_sigma'],
self.int_mask,
nebularFlux=None, #self.nebDefault['synth_neb_flux'],
mainPopulationsFile=self.sspCoeffsPrefit_file)
return