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 }