Fix conflicts between feature/composite_indv_detect with develop with…

… temp_metallicity_calc

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')