feature/composite_indv_detect -> develop

Metallicity_Stack_Commons/analysis/composite_indv_detect.py

@@ -0,0 +1,122 @@
+from os.path import join
+from os.path import exists
+
+import numpy as np
+from astropy.io import ascii as asc
+from astropy.table import Table
+
+from ..temp_metallicity_calc import metallicity_calculation
+from .. import OIII_r
+from ..column_names import bin_names0, indv_names0, temp_metal_names0
+from ..column_names import filename_dict
+
+ID_name = indv_names0[0]
+bin_ID_name = bin_names0[0]
+
+
+def main(fitspath, dataset, revised=False, det3=True):
+    """
+    Purpose:
+      Reads in composite table(s) containing bin information to
+      determine temperature-based metallicity from composite average
+      T_e and individual line ratios ([OII]/H-beta, [OIII]/H-beta)
+
+    :param fitspath: str containing folder path
+    :param dataset: str containing sub-folder (specific to stacking approach)
+    :param revised: Bool indicates whether to use revised bin properties
+                    (e.g., *.revised.tbl files)
+    :param det3: Bool indicates whether individual galaxy files is limited to
+                 those satisfying emission-line det3 requirement
+                 Default: True
+
+    Files identified by default
+    composite_file: str containing filename of composite data
+      e.g., '[dataset]/bin_derived_properties.tbl' or
+            '[dataset]/bin_derived_properties.revised.tbl'
+    indv_em_line_file: str containing filename that contains
+                     emission-line information for each galaxy
+      e.g., 'individual_properties.tbl'
+    indv_bin_file: str containing filename tha contains bin information
+                   for each galaxy
+      e.g., '[dataset]/individual_bin_info.tbl'
+    outfile: str containing filename of output file
+      e.g., '[dataset]/individual_derived_properties.tbl'
+    """
+
+    # Define [composite_file]
+    t_comp = filename_dict['bin_derived_prop'] if not revised else \
+        filename_dict['bin_derived_prop']
+    composite_file = join(fitspath, dataset, t_comp)
+    if not exists(composite_file):
+        print("ERROR: File not found! "+composite_file)
+        return
+
+    # Read in composite table
+    composite_table = asc.read(composite_file)
+
+    bin_id = composite_table['bin_ID'].data
+    bin_temp = composite_table['T_e'].data
+
+    # Define [indv_em_line_file]
+    indv_em_line_file = join(fitspath, dataset, filename_dict['indv_prop'])
+    if not exists(indv_em_line_file):
+        print("ERROR: File not found! "+indv_em_line_file)
+        return
+
+    # Read in tables containing line ratios, etc.
+    indv_em_line_table = asc.read(indv_em_line_file)
+
+    # Define [indv_bin_file]
+    indv_bin_file = join(fitspath, dataset, filename_dict['indv_bin_info'])
+    if not exists(indv_bin_file):
+        print("ERROR: File not found! "+indv_bin_file)
+        return
+
+    # Read in tables containing bin info for individual
+    indv_bin_info_table = asc.read(indv_bin_file)
+
+    # Populate composite temperature for individual galaxies
+    adopted_temp = np.zeros(len(indv_em_line_table))
+    bin_id_indv = np.zeros(len(indv_em_line_table))
+    for comp_bin, comp_temp in zip(bin_id, bin_temp):
+        bin_idx = np.where(indv_bin_info_table['bin_ID'].data == comp_bin)[0]
+        adopted_temp[bin_idx] = comp_temp
+        bin_id_indv[bin_idx]  = comp_bin
+
+    O2 = indv_em_line_table['OII_3727_Flux_Gaussian'].data            # [OII]3726,3728 fluxes
+    O3 = indv_em_line_table['OIII_5007_Flux_Gaussian'].data * OIII_r  # [OIII]4959,5007 fluxes (Assume 3.1:1 ratio)
+    Hb = indv_em_line_table['HBETA_Flux_Gaussian'].data               # H-beta fluxes
+
+    if det3:
+        com_O_log, metal_dict = metallicity_calculation(adopted_temp, O2/Hb, O3/Hb)
+    else:
+        det3 = np.where((indv_bin_info_table['Detection'] == 1.0) | (indv_bin_info_table['Detection'] == 0.5))[0]
+        temp_com_O_log, temp_metal_dict = \
+            metallicity_calculation(adopted_temp[det3], O2[det3]/Hb[det3],
+                                    O3[det3]/Hb[det3])
+        com_O_log = np.zeros(len(indv_em_line_table))
+        com_O_log[det3] = temp_com_O_log
+
+        metal_dict = dict()
+        for key0 in temp_metal_dict.keys():
+            metal_dict[key0] = np.zeros(len(indv_em_line_table))
+            metal_dict[key0][det3] = temp_metal_dict[key0]
+
+    # Define [indv_derived_prop_table] to include ID, bin_ID, composite T_e,
+    # and 12+log(O/H)
+    arr0 = [indv_em_line_table[ID_name], bin_id_indv, adopted_temp, com_O_log]
+    names0 = [ID_name, bin_ID_name] + temp_metal_names0[:2]
+
+    # Include other metallicities
+    arr0 += list(metal_dict.values())
+    names0 += metal_dict.keys()
+    indv_derived_prop_table = Table(arr0, names=names0)
+
+    outfile = join(fitspath, dataset, filename_dict['indv_derived_prop'])
+
+    # Write Astropy ASCII table containing composite T_e and derived metallicity
+    if exists(outfile):
+        print("File exists! Overwriting : ", outfile)
+    else:
+        print("Writing : ", outfile)
+    indv_derived_prop_table.write(outfile, overwrite=True, format='ascii.fixed_width_two_line')

Metallicity_Stack_Commons/column_names.py

@@ -0,0 +1,136 @@
+from . import line_name, line_type
+
+
+# Need to define here
+def line_fit_suffix_add(line_name0, line_type0):
+    """
+    Purpose:
+      Simple list comprehension combining emission line fit suffixes with
+      the emission line.  This works for individual lines
+
+    :param line_name0: str containing the line name
+    :param line_type0: str containing the emisison-line type (e.g., 'Balmer')
+    :return: gauss_lines_names: list with str formatted as [LINE]_[SUFFIX]
+    """
+
+    gauss_lines_names = ['{}_{}'.format(line_name0, suffix) for suffix in gauss_names0]
+    if line_type0 == 'Balmer':
+        gauss_lines_names += ['{}_{}'.format(line_name0, suffix) for suffix in balmer_names0]
+
+    return gauss_lines_names
+
+
+# These are common/general column names
+
+# Column names for bin information
+bin_names0 = ['bin_ID', 'N_stack', 'Detection']
+
+# Column names for individual galaxies/spectra
+indv_names0 = ['ID', 'logR23', 'logO32', 'logM', 'logLHb', 'two_beta', 'three_beta']
+
+# Dust attenuation
+dust0 = ['E(B-V)', 'HgHb', 'HdHb']
+
+# Column names for bin information in stellar mass and H-beta luminosity
+bin_mzevolve_names0 = ['logM_min', 'logM_max', 'logM_avg', 'logM_median',
+                       'logLHb_min', 'logLHb_max', 'logLHb_avg', 'logLHb_median']
+
+# Column names for bin information in R23 and O32 line ratios
+bin_zcalbase_names0 = ['logR23_min', 'logR23_max', 'logR23_avg', 'logR23_median',
+                       'logO32_min', 'logO32_max', 'logO32_avg', 'logO32_median']
+
+# Column names for composite line ratios
+bin_ratios0 = ['logR23_composite', 'logO32_composite',
+               'two_beta_composite', 'three_beta_composite']
+
+# Column names for Gaussian fitting
+# This is just the suffix
+gauss_names0 = ['Flux_Gaussian', 'Flux_Observed', 'S/N', 'Center', 'Norm',
+                'Median', 'Sigma']
+balmer_names0 = ['Abs_Norm', 'Abs_Sigma']
+
+# Emission-line fit column names with [LINE] prefix
+gauss_lines_names0 = []
+for line0, type0 in zip(line_name, line_type):
+    gauss_lines_names0 += line_fit_suffix_add(line0, type0)
+
+
+# Temperature and metallicity properties
+temp_metal_names0 = ['T_e', '12+log(O/H)', 'log(O+/H)', 'log(O++/H)', 'O+/H', 'O++/H']
+
+# Dictionary containing filenames
+filename_dict = dict()
+
+# Bin-related files
+filename_dict['bin_info'] = 'bin_info.tbl'
+filename_dict['bin_valid'] = 'bin_validation.tbl'
+filename_dict['bin_fit'] = 'bin_emission_line_fit.tbl'
+filename_dict['bin_fit_rev'] = filename_dict['bin_fit'].replace('.tbl', '.revised.tbl')
+filename_dict['bin_derived_prop'] = 'bin_derived_properties.tbl'
+filename_dict['bin_derived_prop_rev'] = filename_dict['bin_derived_prop'].replace('.tbl', '.revised.tbl')
+
+# Individual galaxy/spectra-related files
+filename_dict['indv_prop'] = 'individual_properties.tbl'
+filename_dict['indv_bin_info'] = 'individual_bin_info.tbl'
+filename_dict['indv_derived_prop'] = 'individual_derived_properties.tbl'
+
+
+def merge_column_names(*args):
+    """
+    Purpose:
+      Merges multiple lists containing column names.
+
+    Usage:
+      column_names = merge_column_names(bin_names0, indv_names0)
+
+    :param args: An undefined number of lists
+    :return merge_list:
+    """
+
+    merge_list = list()
+
+    arg_count = len(args)
+    if arg_count > 0:
+        for elem in args:
+            merge_list += elem
+
+    return merge_list
+
+
+def remove_from_list(list0, remove_entries):
+    """
+    Purpose:
+      Remove entries from list
+
+    :param list0: list of column names
+    :param remove_entries: list of column names to remove
+    """
+
+    dup_list0 = list0.copy()
+
+    for entry in remove_entries:
+        dup_list0.remove(entry)
+
+    return dup_list0
+
+
+def indv_R23_O32():
+    """
+    Purpose:
+      Use remove_from_list() to provide simplified list that contains ID, logR23 and logO32
+
+    :return: list containing just ID, logR23, logO32
+    """
+
+    return remove_from_list(indv_names0, ['logM', 'logLHb'])
+
+
+def indv_M_LHb():
+    """
+    Purpose:
+      Use remove_from_list() to provide simplified list that contains ID, logM and logLHb
+
+    :return: list containing just ID, logM, logLHb
+    """
+
+    return remove_from_list(indv_names0, ['logR23', 'logO32'])

Metallicity_Stack_Commons/temp_metallicity_calc.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from . import k_dict
+from .column_names import temp_metal_names0
 
 k_4363 = k_dict['OIII_4363']
 k_5007 = k_dict['OIII_5007']
@@ -73,7 +74,8 @@ def metallicity_calculation(T_e, TWO_BETA, THREE_BETA):
     com_O = O_s_ion + O_d_ion
     com_O_log = np.log10(com_O) + 12
 
-    metal_dict = dict(O_s_ion=O_s_ion, O_d_ion=O_d_ion,
-                      O_s_ion_log=O_s_ion_log, O_d_ion_log=O_d_ion_log)
+    keys = temp_metal_names0[2:]
+    arr0 = [O_s_ion, O_d_ion, O_s_ion_log, O_d_ion_log]
+    metal_dict = dict(zip(keys, arr0))
 
     return com_O_log, metal_dict