From 83c0a4287dced8a81e4ab97d58acc6c632ccb42a Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 31 Mar 2020 22:43:28 -0700 Subject: [PATCH 1/9] Move fitting module into analysis subpackage; Update code to fix relative imports (iss #39) --- Metallicity_Stack_Commons/{ => analysis}/fitting.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename Metallicity_Stack_Commons/{ => analysis}/fitting.py (99%) diff --git a/Metallicity_Stack_Commons/fitting.py b/Metallicity_Stack_Commons/analysis/fitting.py similarity index 99% rename from Metallicity_Stack_Commons/fitting.py rename to Metallicity_Stack_Commons/analysis/fitting.py index fcd701f..98e4487 100644 --- a/Metallicity_Stack_Commons/fitting.py +++ b/Metallicity_Stack_Commons/analysis/fitting.py @@ -2,7 +2,7 @@ from astropy.convolution import Box1DKernel, convolve from astropy.io import ascii as asc -from . import scalefact, wavelength_dict +from .. import scalefact, wavelength_dict con1 = wavelength_dict['OII_3729'] / wavelength_dict['OII_3726'] # Ratio of OII doublet line From 6ad3e701c852bb31dbb7cf3512388825af1f221d Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 31 Mar 2020 22:46:27 -0700 Subject: [PATCH 2/9] plotting.balmer: Update to use relative imports for analysis.fitting (iss #39) --- Metallicity_Stack_Commons/plotting/balmer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metallicity_Stack_Commons/plotting/balmer.py b/Metallicity_Stack_Commons/plotting/balmer.py index e042313..7addc0e 100644 --- a/Metallicity_Stack_Commons/plotting/balmer.py +++ b/Metallicity_Stack_Commons/plotting/balmer.py @@ -14,7 +14,7 @@ from astropy.io import ascii as asc from matplotlib.backends.backend_pdf import PdfPages -from ..fitting import gauss, double_gauss +from ..analysis.fitting import gauss, double_gauss from .. import scalefact, wavelength_dict From 02def692a2c00957c0224618f212d0ddbbb27857 Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 31 Mar 2020 22:54:41 -0700 Subject: [PATCH 3/9] Move attenuation module into analysis subpackage; Update to fix relative imports (iss #39) --- Metallicity_Stack_Commons/{ => analysis}/attenuation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename Metallicity_Stack_Commons/{ => analysis}/attenuation.py (98%) diff --git a/Metallicity_Stack_Commons/attenuation.py b/Metallicity_Stack_Commons/analysis/attenuation.py similarity index 98% rename from Metallicity_Stack_Commons/attenuation.py rename to Metallicity_Stack_Commons/analysis/attenuation.py index 9b7dd37..ebb857b 100644 --- a/Metallicity_Stack_Commons/attenuation.py +++ b/Metallicity_Stack_Commons/analysis/attenuation.py @@ -2,7 +2,7 @@ from astropy.table import Table import numpy as np -from . import k_dict +from .. import k_dict HgHb_CaseB = 0.468 # Hg/Hb ratio for zero reddening From b233f49ac2bc1cbaeaaa8ec2f90815d2f01bff9c Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 7 Apr 2020 21:08:41 -0700 Subject: [PATCH 4/9] Update temp_metallicity_calc to include hotfix/v0.6.2 fix (iss #39) --- .../temp_metallicity_calc.py | 28 +++++++++++++------ 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/Metallicity_Stack_Commons/temp_metallicity_calc.py b/Metallicity_Stack_Commons/temp_metallicity_calc.py index b953054..1194d65 100644 --- a/Metallicity_Stack_Commons/temp_metallicity_calc.py +++ b/Metallicity_Stack_Commons/temp_metallicity_calc.py @@ -48,7 +48,7 @@ def temp_calculation(R): return T_e -def metallicity_calculation(T_e, TWO_BETA, THREE_BETA): +def metallicity_calculation(T_e, TWO_BETA, THREE_BETA, det3=None): """ Determines 12+log(O/H) from electron temperature and [OII]/Hb and [OIII]/Hb flux ratio @@ -59,15 +59,27 @@ def metallicity_calculation(T_e, TWO_BETA, THREE_BETA): :return metal_dict: dictionary containing 12+log(O/H), O+/H, O++/H, log(O+/H), log(O++/H) """ - t_3 = T_e * 1e-4 - t_2 = 0.7 * t_3 + 0.17 - x2 = 1e-4 * 1e3 * t_2 ** (-0.5) + n_sample = len(T_e) + t_3 = np.zeros(n_sample) + t_2 = np.zeros(n_sample) + x2 = np.zeros(n_sample) + + if det3 is None: + det3 = np.arange(n_sample) + + t_3[det3] = T_e[det3] * 1e-4 + t_2[det3] = 0.7 * t_3[det3] + 0.17 + x2[det3] = 1e-4 * 1e3 * t_2[det3] ** (-0.5) + + O_s_ion_log = np.zeros(n_sample) + O_d_ion_log = np.zeros(n_sample) # Equations from Izotov et al. (2006) - O_s_ion_log = np.log10(TWO_BETA) + 5.961 + 1.676 / t_2 - 0.4 * np.log10(t_2) \ - - 0.034 * t_2 + np.log10(1 + 1.35 * x2) - 12 - O_d_ion_log = np.log10(THREE_BETA) + 6.200 + 1.251 / t_3 \ - - 0.55 * np.log10(t_3) - 0.014 * (t_3) - 12 + O_s_ion_log[det3] = np.log10(TWO_BETA[det3]) + 5.961 + 1.676 / t_2[det3] \ + - 0.4 * np.log10(t_2[det3]) - 0.034 * t_2[det3] + \ + np.log10(1 + 1.35 * x2[det3]) - 12 + O_d_ion_log[det3] = np.log10(THREE_BETA[det3]) + 6.200 + 1.251 / t_3[det3] \ + - 0.55 * np.log10(t_3[det3]) - 0.014 * (t_3[det3]) - 12 O_s_ion = 10 ** O_s_ion_log O_d_ion = 10 ** O_d_ion_log From 5d2587f648013e5de36970573e77243a09e18d64 Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 7 Apr 2020 21:14:53 -0700 Subject: [PATCH 5/9] Move error_prop, ratios, and temp_metallicity_calc into analysis sub-package (iss #39) --- Metallicity_Stack_Commons/{ => analysis}/error_prop.py | 2 +- Metallicity_Stack_Commons/{ => analysis}/ratios.py | 0 .../{ => analysis}/temp_metallicity_calc.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename Metallicity_Stack_Commons/{ => analysis}/error_prop.py (98%) rename Metallicity_Stack_Commons/{ => analysis}/ratios.py (100%) rename Metallicity_Stack_Commons/{ => analysis}/temp_metallicity_calc.py (97%) diff --git a/Metallicity_Stack_Commons/error_prop.py b/Metallicity_Stack_Commons/analysis/error_prop.py similarity index 98% rename from Metallicity_Stack_Commons/error_prop.py rename to Metallicity_Stack_Commons/analysis/error_prop.py index f300b5c..69a020f 100644 --- a/Metallicity_Stack_Commons/error_prop.py +++ b/Metallicity_Stack_Commons/analysis/error_prop.py @@ -5,7 +5,7 @@ from astropy.io import ascii as asc import numpy as np -from .column_names import filename_dict, temp_metal_names0, npz_filename_dict +from ..column_names import filename_dict, temp_metal_names0, npz_filename_dict from .ratios import error_prop_flux_ratios from .temp_metallicity_calc import temp_calculation, metallicity_calculation diff --git a/Metallicity_Stack_Commons/ratios.py b/Metallicity_Stack_Commons/analysis/ratios.py similarity index 100% rename from Metallicity_Stack_Commons/ratios.py rename to Metallicity_Stack_Commons/analysis/ratios.py diff --git a/Metallicity_Stack_Commons/temp_metallicity_calc.py b/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py similarity index 97% rename from Metallicity_Stack_Commons/temp_metallicity_calc.py rename to Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py index 1194d65..b4312a1 100644 --- a/Metallicity_Stack_Commons/temp_metallicity_calc.py +++ b/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py @@ -2,7 +2,7 @@ from . import k_dict -from .column_names import temp_metal_names0, remove_from_list +from ..column_names import temp_metal_names0, remove_from_list k_4363 = k_dict['OIII_4363'] k_5007 = k_dict['OIII_5007'] From b35661d389735a06f97e30105e0f25f5882fb4ce Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Tue, 7 Apr 2020 21:15:35 -0700 Subject: [PATCH 6/9] analysis.composite_indv_detect: Update to use correct relative imports for temp_metallicity_calc (iss #39) --- Metallicity_Stack_Commons/analysis/composite_indv_detect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metallicity_Stack_Commons/analysis/composite_indv_detect.py b/Metallicity_Stack_Commons/analysis/composite_indv_detect.py index a3c51f3..eec20f5 100644 --- a/Metallicity_Stack_Commons/analysis/composite_indv_detect.py +++ b/Metallicity_Stack_Commons/analysis/composite_indv_detect.py @@ -5,7 +5,7 @@ from astropy.io import ascii as asc from astropy.table import Table -from ..temp_metallicity_calc import metallicity_calculation +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 From 4f3d6775f28eedf68ce15e30aa5e5ccc90f3fd08 Mon Sep 17 00:00:00 2001 From: Reagen Leimbach Date: Sat, 11 Apr 2020 18:14:55 -0700 Subject: [PATCH 7/9] Fixed import k_dict call because it is now in the directory above --- Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py b/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py index b4312a1..1302b7f 100644 --- a/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py +++ b/Metallicity_Stack_Commons/analysis/temp_metallicity_calc.py @@ -1,6 +1,6 @@ import numpy as np -from . import k_dict +from .. import k_dict from ..column_names import temp_metal_names0, remove_from_list From 857525d43d471be36c33fda0b90c41f59217cbd9 Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Sat, 11 Apr 2020 22:51:15 -0700 Subject: [PATCH 8/9] analysis.error_prop: Fix relative import for line_name (iss #39) --- Metallicity_Stack_Commons/analysis/error_prop.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metallicity_Stack_Commons/analysis/error_prop.py b/Metallicity_Stack_Commons/analysis/error_prop.py index 69a020f..8fa1b8b 100644 --- a/Metallicity_Stack_Commons/analysis/error_prop.py +++ b/Metallicity_Stack_Commons/analysis/error_prop.py @@ -1,7 +1,7 @@ from os.path import join, exists from chun_codes import random_pdf, compute_onesig_pdf -from . import line_name +from .. import line_name from astropy.io import ascii as asc import numpy as np From fdac1484f249533d666e85c95ebf80f2a5d21973 Mon Sep 17 00:00:00 2001 From: Chun Ly Date: Sat, 11 Apr 2020 22:51:44 -0700 Subject: [PATCH 9/9] analysis.ratios: Fix relative import for line_name_short, OIII_r (iss #39) --- Metallicity_Stack_Commons/analysis/ratios.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Metallicity_Stack_Commons/analysis/ratios.py b/Metallicity_Stack_Commons/analysis/ratios.py index 227b64e..9e40dc1 100644 --- a/Metallicity_Stack_Commons/analysis/ratios.py +++ b/Metallicity_Stack_Commons/analysis/ratios.py @@ -1,6 +1,6 @@ import numpy as np -from . import line_name_short, OIII_r +from .. import line_name_short, OIII_r from .temp_metallicity_calc import R_calculation