Merge branch 'feature/validation_tables' into develop (PR #34)

Metallicity_Stack_Commons/column_names.py

@@ -62,12 +62,17 @@ def line_fit_suffix_add(line_name0, line_type0):
 # Temperature and metallicity properties
 temp_metal_names0 = ['T_e', '12+log(O/H)', 'log(O+/H)', 'log(O++/H)', 'O+/H', 'O++/H']
 
+# Validation Table
+valid_table_names0 = ['bin_ID','N_stack','Detection', 'OIII_4363_Flux_Observed', 'OIII_4363_S/N']
+
 # 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_valid_rev'] = 'bin_validation_revised.tbl'
+filename_dict['bin_valid_rev'] = filename_dict['bin_valid'].replace('.tbl', '.revised.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'

Metallicity_Stack_Commons/valid_table.py

@@ -0,0 +1,178 @@
+from os.path import exists
+import numpy as np
+from astropy.io import ascii as asc
+from astropy.table import Table, Column
+
+from .column_names import filename_dict, valid_table_names0  # , bin_names0, remove_from_list
+
+
+def make_validation_table(fitspath):
+    """
+    Purpose:
+        This function creates a validation table for a given binning set. The validation table
+        contains a OIII4363 detection column where 1.0 means detection, 0.5 means non-detection with
+        reliable OIII5007, and 0.0 means unreliable non-detection.
+        This function will be run every time the analysis is completed and will create a validation
+        table for every analysis.
+
+    Usage:
+        valid_table.make_validation_table(fitspath, bin_type_str)
+
+    Params:
+        fitspath --> a string of the file path where the input file is and where the output file
+            will be placed.
+        not in use:
+        bin_type_str --> a string describing the binning type. (e.g. 'massLHbetabin' or 'massbin')
+                     --> This is dataset for Zcalbase_gal analysis
+
+    Returns:
+        None
+
+    Outputs:
+        fitspath + 'bin_validation.tbl' --> a validation table containing bin IDs;
+                                        number of galaxies in each bin; and
+                                        column indicating  OIII4363 detection/non-detection
+                                        OIII4363_Flux_Observed
+                                        OIII4363_S/N
+    """
+
+    bin_table = asc.read(fitspath + filename_dict['bin_info'])
+    em_table = asc.read(fitspath + filename_dict['bin_fit']) 
+
+    bin_ID = em_table['bin_ID'].data
+    raw_OIII4363 = em_table['OIII_4363_Flux_Observed'].data
+    O_4363_SN = em_table['OIII_4363_S/N'].data
+    O_4363_sigma = em_table['OIII_4363_Sigma'].data
+    O_5007_SN = em_table['OIII_5007_S/N'].data
+
+    N_stack = bin_table['N_stack'].data
+    Hgamma_SN = em_table['HGAMMA_S/N'].data
+    Hgamma = em_table['HGAMMA_Flux_Observed'].data
+
+    detection  = np.zeros(len(bin_ID))
+    OIII4363 = np.zeros(len(bin_ID))
+    up_limit = (Hgamma/Hgamma_SN) * 3
+
+    valid_stacks_idx = np.where((O_4363_SN >= 3) & (O_5007_SN > 100) & (O_4363_sigma < 1.6))[0] 
+    reliable_5007_stacks = np.where((O_4363_SN < 3) & (O_5007_SN > 100))[0]
+    wide_lines_valid = np.where((O_4363_SN >= 3) & (O_5007_SN > 100) & (O_4363_sigma >= 1.6))[0]
+    detection[valid_stacks_idx] = 1
+    detection[reliable_5007_stacks] = 0.5
+    detection[wide_lines_valid] = 0.5
+    print(detection)
+
+    for ii in range(len(OIII4363)):
+        if detection[ii] == 1:
+            OIII4363[ii] = raw_OIII4363[ii]
+        if detection[ii] == 0.5:
+            OIII4363[ii] = up_limit[ii]
+        if detection[ii] == 0:
+            OIII4363[ii] = up_limit[ii]
+
+    ver_tab = fitspath + filename_dict['bin_valid']
+    tab1 = Table([bin_ID, N_stack, detection, OIII4363, O_4363_SN], names=valid_table_names0)
+    asc.write(tab1, ver_tab, format='fixed_width_two_line')
+    '''
+    # Write revised file for human editing
+    ver_tab_revised = fitspath + filename_dict['bin_valid_rev']
+    if not exists(ver_tab_revised):
+        asc.write(tab1, ver_tab_revised, format='fixed_width_two_line')
+        print("   ")
+        print("URGENT!!! HUMAN EDITING OF FILE NEEDED : "+ver_tab_revised)
+        print("   ")
+    else:
+        print("   ")
+        print("ERROR!!! FILE EXISTS!!!  WILL NOT OVERWRITE !!!")
+        print("ERROR!!! PLEASE RENAME/DELETE FILE TO REGENERATE !!!")
+        print("   ")
+    '''
+
+
+def compare_to_by_eye(fitspath, dataset):
+    """
+    Purpose -> This function takes the automated validation table and checks it against
+               inputted measurement that are determined by eye. These inputted measurements
+               are in the np.where statements. It outputs a revised validation table based
+               on the inputted measurements.
+
+    Usage -> valid_table.make_validation_table(fitspath, dataset)
+
+    Params:
+        fitspath --> a string of the file path where the input file is and where the output file
+            will be placed
+        dataset  --> a string that is used to determine which eye measurements to use
+
+    Returns:
+        None
+
+    Outputs:
+        fitspath + 'bin_validation_revised.tbl' and '.csv' -->
+                                        a validation table containing bin IDs;
+                                        number of galaxies in each bin; and
+                                        column indicating  OIII4363 detection/non-detection
+                                        OIII4363_Flux_Observed
+                                        OIII4363_S/N
+                                        Notes
+
+    """
+    ver_table = fitspath + filename_dict['bin_valid']
+    ver_tab = asc.read(ver_table)
+    indicate = ver_tab['Detection']
+    ID = ver_tab['bin_ID']
+
+    # Detections By Eye
+    if dataset == 'Voronoi20':
+        det_4363 = np.where((ID == 0) | (ID == 2) | (ID == 3) | (ID == 5) | (ID == 6))[0]
+    if dataset == 'Voronoi14':
+        det_4363 = np.where((ID == 0) | (ID == 7) | (ID == 10) | (ID == 11) | (ID == 12))[0]
+    if dataset == 'Voronoi10':
+        det_4363 = np.where((ID == 1) | (ID == 9) | (ID == 18) | (ID == 21))[0]
+    if dataset == 'Grid':
+        det_4363 = np.where((ID == 11) | (ID == 13) | (ID == 19) | (ID == 20) | (ID == 21))[0]
+    if dataset == 'R23_Grid':
+        det_4363 = np.where((ID == 0) | (ID == 4) | (ID == 5) | (ID == 6))[0]
+    if dataset == 'O32_Grid':
+        det_4363 = np.where((ID == 6))[0]
+    if dataset == 'Double_Bin':
+        det_4363 = np.where((ID == 0) | (ID == 1) | (ID == 2) | (ID == 7) | (ID == 9) |
+                            (ID == 10) | (ID == 11) | (ID == 13))[0]
+    if dataset == 'n_Bins':
+        det_4363 = np.where((ID == 10) | (ID == 11) | (ID == 14) | (ID == 15) | (ID == 20) |
+                            (ID == 23) | (ID == 26))[0]
+        rlimit = np.where((ID == 5) | (ID == 7) | (ID == 8) | (ID == 13) | (ID == 16) |
+                          (ID == 17) | (ID == 19) | (ID == 22))[0]
+
+    # Caroline: Add you conditions here
+
+    check_ID = np.zeros(len(ID))
+
+    check_ID[det_4363] = 1
+    if dataset == 'n_Bins':
+        check_ID[rlimit] = 0.5
+
+    for ii in range(len(ID)):
+        if check_ID[ii] == indicate[ii]:
+            print(ID[ii], 'matches with by eye validation')
+        else:
+            print('*****', ID[ii], 'does not match calculated values. Please check!')
+
+    # This is where I need to add the column for notes
+    if dataset == 'n_Bins':
+        notes = ['N/A', 'N/A', 'N/A', 'N/A', 'N/A',
+                 'N/A', 'N/A', 'Broad features, but reliable OIII5007 and HGAMMA',
+                 'Bad fit, but good OIII5007', 'N/A',
+                 'N/A', 'N/A', 'N/A', 'N/A', 'N/A',
+                 'High Temperature', 'not fit well, but reliable OIII5007 and HGAMMA',
+                 'N/A', 'N/A', 'N/A', 'N/A', 'N/A', 'N/A', 'N/A', 'N/A', 'N/A', 'N/A']
+        note_add = Column(name='Notes', data=notes)
+        ver_tab.add_column(note_add, 5)
+
+    # Caroline: Add your notes column here and copy the note_add and ver_tab.add_column lines to your if statement
+
+    ver_tab.remove_column('Detection')
+
+    detect_add = Column(name='Detection', data=check_ID)
+    ver_tab.add_column(detect_add, 2)
+
+    asc.write(ver_tab, fitspath + filename_dict['bin_valid_rev'], format='fixed_width_two_line')
+    asc.write(ver_tab, fitspath + 'bin_validation_revised.csv', format='csv')