import numpy as np
from lib.inferenceModel import SpectraSynthesizer
# Declare synthesizer object
specS = SpectraSynthesizer()
# Object data to prepare a synthetic observation
synth_data = {
'spectra_components': ['emission', 'nebular', 'stellar'],
'wavelengh_limits': [4000, 6900],
'resample_inc': 1,
'norm_interval': [5100, 5150],
'output_folder':
'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/testing_output/',
'obs_name': 'ObsHIIgalaxySynth',
'obj_lines_file':
'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objlines.txt',
'obj_properties_file':
'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objProperties.txt',
'ssp_lib_type': 'starlight', # TODO In here we will add "test" for the pip
'data_folder': '/home/vital/Starlight/Bases/',
'data_file': '/home/vital/Starlight/Bases/Dani_Bases_Extra_short.txt',
'obj_ssp_coeffs_file':
'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_stellarPop.txt',
'error_stellarContinuum': 0.01,
'error_lines': 0.02
}
#
# # Generate the synthetic data
specS.gen_synth_obs(**synth_data)
import numpy as np
from collections import OrderedDict
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
from lib.Astro_Libraries.spectrum_fitting.import_functions import make_folder
# Import functions
dz = Dazer()
specS = SpectraSynthesizer()
# Declare data location
root_folder = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\bayesianModel\\'
whtSpreadSheet = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\WHT_Galaxies_properties.xlsx'
# 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)
# Sample objects
excludeObjects = [
'SHOC579', 'SHOC575_n2', '11', 'SHOC588', 'SDSS3', 'SDSS1', 'SHOC36'
# headers_dic['n_e'] = r'$n_{e}[SII](cm^{-3})$'
# headers_dic['T_low'] = r'$T_{e}[SIII](K)$'
# headers_dic['T_high'] = r'$T_{e}[OIII](K)$'
# headers_dic['cHbeta'] = r'$c(H\beta)$'
headers_dic['n_e'] = r'$n_{e}[SII]$'
headers_dic['T_low'] = r'$T_{e}[SIII]$'
headers_dic['T_high'] = r'$T_{e}[OIII]$'
headers_dic['cHbeta'] = ''
# headers_dic['tau'] = r'$\tau$'
varsNum = len(headers_dic)
headers_format = [''] + headers_dic.values()
# 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/'
article_folder = 'E:\\Dropbox\\Astrophysics\\Papers\\Yp_BayesianMethodology\\source files\\tables\\'
whtSpreadSheet = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\WHT_Galaxies_properties.xlsx' # whtSpreadSheet = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/WHT_Galaxies_properties.xlsx'
# Import data
catalogue_dict = dz.import_catalogue()
catalogue_df = dz.load_excel_DF(whtSpreadSheet)
# Quick indexing
dz.quick_indexing(catalogue_df)
# Sample objects
excludeObjects = [
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
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'
]
import numpy as np
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
import matplotlib.pyplot as plt
# Declare synthesizer object
specS = SpectraSynthesizer()
#Import library object
dz = Dazer()
# Object database
dataFolder = '/home/vital/SpecSynthesizer_data/'
whtSpreadSheet = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/WHT_Galaxies_properties.xlsx'
catalogue_dict = dz.import_catalogue()
catalogue_df = dz.load_excel_DF(whtSpreadSheet)
dz.quick_indexing(catalogue_df)
# Data root folder
root_folder = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/bayesianModel/'
# Import stellar library data
starlight_ssp = {
'ssp_lib_type': 'starlight',
'data_folder': '/home/vital/Starlight/Bases/',
'data_file': '/home/vital/Starlight/Bases/Dani_Bases_Extra.txt',
'wavelengh_limits': [3600, 6900],
'resample_inc': 1,
'norm_interval': [5100, 5150]
}
stats_dict[parameter]['mean'] = np.mean(trace_i)
stats_dict[parameter]['median'] = np.median(trace_i)
stats_dict[parameter]['standard deviation'] = np.std(trace_i)
stats_dict[parameter]['n'] = trace_i.size
stats_dict[parameter]['16th_p'] = np.percentile(trace_i, 16)
stats_dict[parameter]['84th_p'] = np.percentile(trace_i, 84)
stats_dict[parameter]['95% HPD interval'] = (
stats_dict[parameter]['16th_p'], stats_dict[parameter]['84th_p'])
stats_dict[parameter]['trace'] = trace_i
return stats_dict
# Declare synthesizer object
specS = SpectraSynthesizer()
specS.synth_coefs = dict(He1_3889A = np.array([0.904, 1.5e-6, -0.173, -0.00054]),
He1_4026A = np.array([-8.12509670e-02, 1.78807195e-04, 4.31012092e+00, -1.95511656e-04]),
He1_4471A = np.array([-1.19176501e-01, 2.67353941e-04, 2.04665573e+00, -1.37697881e-04]),
He1_5876A = np.array([-2.07460883e-01, 6.03088917e-04, 7.37037512e-01, -1.13466418e-04]),
He1_6678A = np.array([-2.18639788e-01, 6.40026064e-04, 2.59194623e+00, -4.07583592e-04]),
He1_7065A = np.array([4.329, -0.0024, -0.368, -0.0017]),
H1_6563A = np.array([10.35, -3.254, 0.3457]),
H1_4341A = np.array([0.0254, 0.1922, -0.0204]),
He2_4686A = np.array([12.309698048256134, -0.06407094]))
def H1_linesEmis(xy_space, a, b, c):
temp_range, den_range = xy_space
return a + b * np.log10(temp_range) + c * np.log10(temp_range) * np.log10(temp_range)
import numpy as np
import pandas as pd
import ConfigParser
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
from lib.Astro_Libraries.spectrum_fitting.import_functions import parseObjData
# Declare synthesizer object
specS = SpectraSynthesizer()
#Import library object
dz = Dazer()
# Object database
dataFolder = '/home/vital/SpecSynthesizer_data/'
whtSpreadSheet = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/WHT_Galaxies_properties.xlsx'
catalogue_dict = dz.import_catalogue()
catalogue_df = dz.load_excel_DF(whtSpreadSheet)
dz.quick_indexing(catalogue_df)
# Data root folder
root_folder = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/bayesianModel/'
# Import stellar library data
starlight_ssp = {
'ssp_lib_type': 'starlight', # TODO In here we will add "test" for the pip
'data_folder': '/home/vital/Starlight/Bases/',
'data_file': '/home/vital/Starlight/Bases/Dani_Bases_Extra.txt',
'wavelengh_limits': [3600, 6900],
'resample_inc': 1,
'norm_interval': [5100, 5150]
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
from lib.Astro_Libraries.spectrum_fitting.import_functions import make_folder
# Import functions
dz = Dazer()
specS = SpectraSynthesizer()
# Declare data location
root_folder = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\bayesianModel\\'
whtSpreadSheet = 'E:\\Dropbox\\Astrophysics\\Data\\WHT_observations\\WHT_Galaxies_properties.xlsx'
# 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)
# Sample objects
excludeObjects = ['SHOC579', 'SHOC575_n2', '11', 'SHOC588', 'SDSS3', 'SDSS1', 'SHOC36'] # SHOC579, SHOC575, SHOC220, SHOC588, SHOC592, SHOC036
sampleObjects = catalogue_df.loc[dz.idx_include & ~catalogue_df.index.isin(excludeObjects)].index.values
# Failing objects
listFails = []
from os import environ
environ["MKL_THREADING_LAYER"] = "GNU"
import theano
import theano.tensor as tt
import pymc3 as pm
import numpy as np
import matplotlib.pyplot as plt
from lib.inferenceModel import SpectraSynthesizer
import pymc as pm2
specS = SpectraSynthesizer()
# synth_data = {'spectra_components' :['emission', 'nebular', 'stellar'],
# 'wavelengh_limits' :[4200,6900],
# 'resample_inc' :1,
# 'norm_interval' :[5100,5150],
# 'input_ions' :['H1r','He1r','He2r','O2','O3','Ar3','Ar4','S2','S3','N2'],
# 'output_folder' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/testing_output/',
# 'obs_name' :'ObsHIIgalaxySynth',
# 'obj_lines_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objlines.txt',
# 'obj_properties_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objProperties.txt',
# 'ssp_lib_type' :'starlight', # TODO In here we will add "test" for the pip
# 'data_folder' :'/home/vital/Starlight/Bases/',
# 'data_file' :'/home/vital/Starlight/Bases/Dani_Bases_Extra_short.txt',
# 'obj_ssp_coeffs_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_stellarPop.txt',
# 'error_stellarContinuum' :0.01,
# 'error_lines' :0.02}
#
# specS.gen_synth_obs(**synth_data)
import numpy as np
from lib.inferenceModel import SpectraSynthesizer
# Declare synthesizer object
specS = SpectraSynthesizer()
# Object data to prepare a synthetic observation
synth_data = {
'obs_name': 'synthTestHIIgalaxy',
'output_folder':
'E:\\Research\\article_YpBayesian\\', #'/home/vital/article_YpBayesian/',#
'obj_properties_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_TestObjProperties.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_TestObjProperties.txt',
'obj_lines_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_TestObjLines.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_TestObjLines.txt',
'wavelengh_limits': [4000, 6900],
'resample_inc': 1,
'norm_interval': [5100, 5150],
'ssp_lib_type': 'starlight',
'ssp_folder':
'E:\\Research\\Starlight\\Bases\\', #'/home/vital/Starlight/Bases/', #
'ssp_file':
'E:\\Research\\Starlight\\Bases\\Dani_Bases_Extra_short.txt', #'/home/vital/Starlight/Bases/Dani_Bases_Extra_short.txt',
'obj_ssp_coeffs_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_StellarPop.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_StellarPop.txt', # ,
'error_stellarContinuum': 0.01,
'error_lines': 0.02,
'atomic_data': None,
'ftau_coeffs': None
}
import numpy as np
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
import matplotlib.pyplot as plt
# Import library object
dz = Dazer()
specS = SpectraSynthesizer()
# Data root folder
specS.normContants = {'He1r': 0.1, 'He2r': 0.001}
root_folder = '/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/'
# HII galaxy
model_name = 'testSimu'
outputFolder = root_folder + 'testing_output/'
specS.objName = 'ObsHIIgalaxySynth_objParams'
specS.configFile = '{}/{}_objParams.txt'.format(outputFolder, specS.objName)
# # Load the results
db_address = outputFolder + model_name + '.db' #
inferenceTrace, db_dict = specS.load_pymc_database_manual(db_address,
sampler='pymc3')
params_list = np.array(db_dict.keys())
params_list = np.array(['T_low', 'n_e', 'He1r', 'S2'])
# Corner plot
print '--Scatter plot matrix'
trueValues = {'T_low': 12500.0, 'n_e': 125.0, 'He1r': 0.869, 'S2': 5.48}
specS.corner_plot(params_list,
from os import environ
environ["MKL_THREADING_LAYER"] = "GNU"
import theano
import theano.tensor as tt
import pymc3 as pm
import numpy as np
import matplotlib.pyplot as plt
from lib.inferenceModel import SpectraSynthesizer
import pymc as pm2
specS = SpectraSynthesizer()
# synth_data = {'spectra_components' :['emission', 'nebular', 'stellar'],
# 'wavelengh_limits' :[4200,6900],
# 'resample_inc' :1,
# 'norm_interval' :[5100,5150],
# 'input_ions' :['H1r','He1r','He2r','O2','O3','Ar3','Ar4','S2','S3','N2'],
# 'output_folder' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/testing_output/',
# 'obs_name' :'ObsHIIgalaxySynth',
# 'obj_lines_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objlines.txt',
# 'obj_properties_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_objProperties.txt',
# 'ssp_lib_type' :'starlight', # TODO In here we will add "test" for the pip
# 'data_folder' :'/home/vital/Starlight/Bases/',
# 'data_file' :'/home/vital/Starlight/Bases/Dani_Bases_Extra_short.txt',
# 'obj_ssp_coeffs_file' :'/home/vital/PycharmProjects/thesis_pipeline/spectrum_fitting/synth_stellarPop.txt',
# 'error_stellarContinuum' :0.01,
# 'error_lines' :0.02}
#
# specS.gen_synth_obs(**synth_data)
# Import observation
return
# Ar vs S ionisation fractions relation
m_SIV_correction = un.ufloat(1.1628, 0.00559)
n_SIV_correction = un.ufloat(0.0470, 0.0097)
# Ohrs 2016 relation for the OI_SI gradient
logSI_OI_Gradient = un.ufloat(-1.53, 0.05)
OI_SI_un = umath_pow(10, -logSI_OI_Gradient)
# Constants
normContants = {'He1r': 0.1, 'He2r': 0.001}
# Declare synthesizer object
specS = SpectraSynthesizer()
#Import library object
dz = Dazer()
# Object database
dataFolder = '/home/vital/SpecSynthesizer_data/'
whtSpreadSheet = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/WHT_Galaxies_properties.xlsx'
catalogue_dict = dz.import_catalogue()
catalogue_df = dz.load_excel_DF(whtSpreadSheet)
dz.quick_indexing(catalogue_df)
# Data root folder
root_folder = '/home/vital/Dropbox/Astrophysics/Data/WHT_observations/bayesianModel/'
rawData = OrderedDict([
import numpy as np
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
#Generate dazer object
dz = Dazer()
specS = SpectraSynthesizer()
#Define plot frame and colors
size_dict = {
'axes.labelsize': 28,
'legend.fontsize': 24,
'font.family': 'Times New Roman',
'mathtext.default': 'regular',
'xtick.labelsize': 24,
'ytick.labelsize': 24
}
dz.FigConf(plotSize=size_dict)
Te = 10000.0
wave = np.arange(600, 10000, 1)
HeII_HII = 0.1
HeIII_HII = 0.001
H_He_frac = 1 + HeII_HII * 4 + HeIII_HII * 4
# Bound bound continuum
gamma_2q = specS.twoPhotonGammaCont(wave, Te)
# Free-Free continuum
gamma_ff = H_He_frac * specS.freefreeGammaCont(wave, Te, Z_ion=1.0)
from dazer_methods import Dazer
from lib.inferenceModel import SpectraSynthesizer
# Import functions
dz = Dazer()
specS = SpectraSynthesizer()
# Object data to prepare a synthetic observation
synth_data = {
'obs_name': 'synthTestHIIgalaxy',
'output_folder':
'E:\\Research\\article_YpBayesian\\', #'/home/vital/article_YpBayesian/',#
'obj_properties_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_TestObjProperties.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_TestObjProperties.txt',
'obj_lines_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_TestObjLines.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_TestObjLines.txt',
'wavelengh_limits': [4000, 6900],
'resample_inc': 1,
'norm_interval': [5100, 5150],
'ssp_lib_type': 'starlight',
'ssp_folder':
'E:\\Research\\Starlight\\Bases\\', #'/home/vital/Starlight/Bases/', #
'ssp_file':
'E:\\Research\\Starlight\\Bases\\Dani_Bases_Extra_short.txt', #'/home/vital/Starlight/Bases/Dani_Bases_Extra_short.txt',
'obj_ssp_coeffs_file':
'C:\\Users\\Vital\\PycharmProjects\\thesis_pipeline\\article2_material\\synth_StellarPop.txt', #'/home/vital/PycharmProjects/thesis_pipeline/article2_material/synth_StellarPop.txt', # ,
'error_stellarContinuum': 0.01,
'error_lines': 0.02,
'atomic_data': None,
'ftau_coeffs': None
}