pdf.pdf_insert_table(row_object, addfinalLine=False)
pdf.table.add_hline()
pdf.addTableRow(row_headers, last_row=False, rounddig=2)
pdf.table.add_hline()
# Declare input files
objFolder = resultsFolder / f'{obj}'
results_file = objFolder / f'{obj}_{ext}_measurements.txt'
# Declare output file
table_file = tables_folder / f'{obj}_FadoFitting'
# # Load the data
results_dict = sr.loadConfData(results_file, group_variables=False)
for j, ssp_lib in enumerate(ssp_lib_list):
section_label = f'{ssp_lib}_FADO'
section_results = results_dict[section_label]
row_data = []
for column, param_code in dict_ref.items():
param_value = section_results[param_code]
row_data.append(param_value)
row_data[0] = ssp_lib
pdf.addTableRow(row_data, last_row=False, rounddig=2)
pdf.table.add_hline()
pdf.generate_pdf(table_file)
param_value = (np.mean(trace), np.std(trace))
if param == 'Teff':
param_entry = r'${:.0f}\pm{:.0f}$'.format(param_value[0],
param_value[1])
else:
param_entry = r'${:.2f}\pm{:.2f}$'.format(param_value[0],
param_value[1])
row_data[4] = param_entry
# Bayesian Direct method + HII-CHI-mistry
if outputDirectHIIchemDb.is_file():
model_fit = sr.load_MC_fitting(outputDirectHIIchemDb)
trace = model_fit['trace'][param]
param_value = (np.mean(trace), np.std(trace))
if param == 'Teff':
param_entry = r'${:.0f}\pm{:.0f}$'.format(
param_value[0], param_value[1])
else:
param_entry = r'${:.2f}\pm{:.2f}$'.format(
param_value[0], param_value[1])
row_data[5] = param_entry
pdf.addTableRow(row_data,
color_background='background',
color_font='foreground')
pdf.table.add_hline()
table_file = tables_folder / f'photo-ionization_param_comparison'
pdf.generate_pdf(table_file, clean_tex=False)
wave_rest, flux, header = sr.import_fits_data(fitsFolder/fitsFile, instrument='SDSS')
idx_wave = (wave_rest >= obsData['sample_data']['wmin_array']) & (wave_rest <= obsData['sample_data']['wmax_array'])
# Load line measurer object
lm = sr.LineMesurer(wave_rest[idx_wave], flux[idx_wave], lineLogFolder / lineLogFile, normFlux=flux_norm)
# Measure line fluxes
idcs_lines = ~lm.linesDF.index.str.contains('_b')
obsLines = lm.linesDF.loc[idcs_lines].index.values
# Equivalent width Hbeta
eqw_Hbeta, eqwErr_Hbeta = lm.linesDF.loc['H1_4861A', 'eqw'], lm.linesDF.loc['H1_4861A', 'eqw_err']
eqw_entry = r'${:0.2f}$ $\pm$ ${:0.2f}$'.format(eqw_Hbeta, eqwErr_Hbeta)
# Normalizing flux
flux_Halpha = lm.linesDF.loc['H1_6563A', 'gauss_flux']
flux_Hbeta = lm.linesDF.loc['H1_4861A', 'intg_flux']
halpha_norm = flux_Halpha / flux_Hbeta
halphaRatio_entry = r'${:0.2f}$'.format(halpha_norm)
colorGrade = colorChooser(halpha_norm, 2.86)
RatioComparison = r'\textcolor{{{}}}{{{}}}'.format(colorGrade, halphaRatio_entry)
# Reddening coefficient
rc = pn.RedCorr(R_V=3.4, law='G03 LMC')
rc.setCorr(obs_over_theo=halpha_norm/2.86, wave1=6563., wave2=4861.)
cHbeta_entry = r'${:0.2f}$'.format(rc.cHbeta)
pdf.addTableRow([objName, eqw_entry, cHbeta_entry, RatioComparison], last_row=True if file_address == addressList[-1] else False)
# Generate the table
pdf.generate_pdf(clean_tex=True)
atomic_data_dict = {'T_low': r'$Normal(\mu=15,000K,\sigma=5000K)$',
'T_high': r'$Normal(\mu=15,000K,\sigma=5000K)$',
'n_e': r'$HalfCauchy(\mu=2.0,\sigma=0)$',
'cHbeta': r'$HalfCauchy(\mu=2.0,\sigma=0)$',
'log(X_i+)': r'$Normal(\mu=5,\sigma=5)$',
'log(He1r)': r'$Normal(\mu=0,\sigma=3)$',
'log(He2r)': r'$Normal(\mu=0,\sigma=3)$',
'Teff': r'$Uniform(min=30,000K, max=90,000K)$',
'logU': r'$Uniform(min=-4.0, max=-1.0K)$'}
tables_folder = Path('/home/vital/Dropbox/Astrophysics/Seminars/UniVapo 2021/')
pdf = PdfPrinter()
pdf.create_pdfDoc(pdf_type='table')
pdf.pdfDoc.append(NoEscape('\definecolor{background}{rgb}{0.169, 0.169, 0.169}'))
pdf.pdfDoc.append(NoEscape('\definecolor{foreground}{rgb}{0.702, 0.780, 0.847}'))
pdf.pdfDoc.append(NoEscape(r'\arrayrulecolor{foreground}'))
pdf.pdf_insert_table(['Parameter', 'Prior distribution'],
addfinalLine=True, color_font='foreground', color_background='background')
for ion, params in atomic_data_dict.items():
ion_label = latex_labels[ion]
row = [ion_label, params]
pdf.addTableRow(row, last_row=False, color_font='foreground', color_background='background')
pdf.table.add_hline()
pdf.generate_pdf(tables_folder/'posteriors_table', clean_tex=True)
cHbeta = r'${:0.2f}\,\pm\,{:0.2f}$'.format(cHbeta[0], cHbeta[1])
eqw_Hbeta = r'${}\,\pm\,{}$'.format(f'{eqw:0.0f}', f'{eqw_err:0.0f}')
F_Hbeta = r'${}$'.format(
f'{linesDF_i.loc["H1_4861A", "intg_flux"] / normFlux:0.3f}')
print(linesDF_i.loc["H1_4861A", "intg_flux"], normFlux,
linesDF_i.loc["H1_4861A", "intg_flux"] / normFlux)
# eqw_Hbeta = f'{linesDF_i.loc["H1_4861A", "eqw"]:0.2f}'
# F_Hbeta = f'{linesDF_i.loc["H1_4861A", "intg_flux"]/normFlux:0.2f}'
cHbeta_row[2 + j] = pylatex.MultiColumn(2,
align='c',
data=pylatex.NoEscape(cHbeta))
eqwHbeta_row[2 + j] = pylatex.MultiColumn(2,
align='c',
data=pylatex.NoEscape(eqw_Hbeta))
FHbeta_row[2 + j] = pylatex.MultiColumn(2,
align='c',
data=pylatex.NoEscape(F_Hbeta))
pdf.addTableRow(cHbeta_row)
pdf.addTableRow(eqwHbeta_row)
pdf.addTableRow(FHbeta_row, last_row=True)
# Save the pdf table
print(f'-- Saving table at: {pdfTableFile}')
try:
pdf.generate_pdf(pdfTableFile, clean_tex=False)
except:
print('-- PDF compilation failure')
pdf.pdf_insert_table(table_headers, addfinalLine=True)
for i, obj in enumerate(objList):
if i < 3:
row = ['-'] * len(table_headers)
objData = obsData[obj]
# row[0] = objData['SDSS_label']
row[0] = r'\href{{{}}}{{{}}}'.format(
objData['SDSS_website'].replace('&', '\&'), objData['SDSS_label'])
print(row[0])
row[1] = objRef[i]
row[2] = objData['RA']
row[3] = objData['DEC']
row[4] = objData['z']
row[5] = f'{objData["grism_b"]}, {objData["grism_r"]}'
# row[5] = f'{objData["grism_b"]} (blue), {objData["grism_r"]}(red)'
row[6] = r'${}\times{}s$'.format(objData["exp_number"],
objData["exp_time"])
row[7] = r'$\approx {}$'.format(objData["seeing"])
row[8] = f'{objData["standard_blue"]}, {objData["standard_red"]}'
# row[8] = f'{objData["standard_blue"]} (blue), {objData["standard_red"]}(red)'
# row[9] = f'{objData["night_type"]} night'
pdf.addTableRow(row, last_row=False)
pdf.table.add_hline()
pdf.generate_pdf(tables_folder / 'night_log')
lineInt, lineIntErr = np.array(measurements_dict[section][lineLabel], dtype=float)
lineFlux, lineFluxErr = lineInt / np.power(10, cHbeta[0] * flambda), lineIntErr / np.power(10, cHbeta[0] * flambda)
row_data[3] = r'${:.3f}\pm{:.3f}$'.format(lineFlux, lineFluxErr)
row_data[3] += percent_func(obsFlux, lineFlux)
section = f'HII_Tef_fit_C17_bb_Teff_30-90_pp.dat_{cycle}_sed'
if lineLabel in measurements_dict[section]:
lineInt, lineIntErr = np.array(measurements_dict[section][lineLabel], dtype=float)
lineFlux, lineFluxErr = lineInt / np.power(10, cHbeta[0] * flambda), lineIntErr / np.power(10, cHbeta[0] * flambda)
row_data[4] = r'${:.3f}\pm{:.3f}$'.format(lineFlux, lineFluxErr)
row_data[4] += percent_func(obsFlux, lineFlux)
if lineLabel in flux_tensor_dict:
lineFlux, lineFluxErr = np.mean(flux_tensor_dict[lineLabel]), np.std(flux_tensor_dict[lineLabel])
row_data[5] = r'${:.3f}\pm{:.3f}$'.format(lineFlux, lineFluxErr)
row_data[5] += percent_func(obsFlux, lineFlux)
if lineLabel in srPlus_lineLabels:
i_line = sr_lineLabels.index(lineLabel)
row_data[6] = r'${:.3f}\pm{:.3f}$'.format(mean_plus_line_values[i_line], std_plus_line_values[i_line])
row_data[6] += percent_func(obsFlux, mean_plus_line_values[i_line])
pdf.addTableRow(row_data, last_row=False)
pdf.table.add_hline()
table_file = tables_folder/f'{obj}_lineFlux_fit_comparison'
pdf.generate_pdf(table_file, clean_tex=True)
table_headers = [
'SDSS ID', 'Label', 'R.A', 'DEC', 'z', '$Grisms^{1}$', '$T_{exp}$',
'Seeing', r'Standard stars$^{2}$'
]
pdf = PdfPrinter()
pdf.create_pdfDoc(pdf_type='table')
pdf.pdfDoc.append(
NoEscape('\definecolor{background}{rgb}{0.169, 0.169, 0.169}'))
pdf.pdfDoc.append(
NoEscape('\definecolor{foreground}{rgb}{0.702, 0.780, 0.847}'))
pdf.pdfDoc.append(NoEscape(r'\arrayrulecolor{foreground}'))
pdf.pdf_insert_table(
['Ion', 'Collision Strengths', 'Transition probabilities'],
addfinalLine=True,
color_font='foreground',
color_background='background')
for ion, params in atomic_data_dict.items():
ion_label = latex_labels[ion]
row = [ion_label] + params
pdf.addTableRow(row,
last_row=False,
color_font='foreground',
color_background='background')
pdf.table.add_hline()
pdf.generate_pdf(tables_folder / 'atomic_data', clean_tex=False)
nebCompFile = objFolder / f'{obj}{ext}_NebFlux_{cycle}.txt'
run_ref = f'{obj}{ext}_{cycle}'
objSSP_outputFile = starlight_folder / 'Output' / f'{obj}{ext}_it2.slOutput'
# Starlight wrapper
sw = SSPsynthesizer()
# Data output
results_dict = sr.loadConfData(results_file, group_variables=False)
stellar_fit_dict = results_dict[f'Starlight_run_it2']
stellar_Wave, obj_input_flux, stellar_flux, fit_output = sw.load_starlight_output(
objSSP_outputFile)
if stellar_fit_dict['A_V_stellarr'] == 0:
stellar_fit_dict['A_V_stellarr'] = 0.0
row_data = [
objRefNames[i],
np.round(stellar_fit_dict['Galaxy_mass_Current'], 2),
np.round(stellar_fit_dict['Galaxy_mass_Percentbelow20Myr'], 2),
np.round(stellar_fit_dict['A_V_stellarr'], 2),
np.round(stellar_fit_dict['cHbeta_stellar'], 2),
np.round(stellar_fit_dict['SN'], 2),
np.round(stellar_fit_dict['Chi2'], 2)
]
pdf.addTableRow(row_data, last_row=False, rounddig=2)
pdf.table.add_hline()
pdf.generate_pdf(pdfTableFile)
pdf.pdf_insert_table(table_headers, addfinalLine=True, color_font='foreground')
for i, obj in enumerate(objList):
if i < 3:
row = ['-'] * len(table_headers)
objData = obsData[obj]
# row[0] = objData['SDSS_label']
row[0] = r'\href{{{}}}{{{}}}'.format(
objData['SDSS_website'].replace('&', '\&'), objData['SDSS_label'])
row[1] = objRef[i]
row[2] = objData['RA']
row[3] = objData['DEC']
row[4] = objData['z']
row[5] = f'{objData["grism_b"]}, {objData["grism_r"]}'
# row[5] = f'{objData["grism_b"]} (blue), {objData["grism_r"]}(red)'
row[6] = r'${}\times{}s$'.format(objData["exp_number"],
objData["exp_time"])
row[7] = r'$\approx {}$'.format(objData["seeing"])
row[8] = f'{objData["standard_blue"]}, {objData["standard_red"]}'
# row[8] = f'{objData["standard_blue"]} (blue), {objData["standard_red"]}(red)'
# row[9] = f'{objData["night_type"]} night'
# pdf.addTableRow(NoEscape(r'\rowcolor{background}'), last_row=False)
pdf.addTableRow(row, last_row=False, color_font='foreground')
pdf.table.add_hline()
pdf.generate_pdf(tables_folder / 'night_log_dark', clean_tex=False)