Merge branch 'master' of https://github.com/sdss/marvin into dev

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.2.4dev
+current_version = 2.2.5dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?P<release>[a-z]+)?

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Marvin's Change Log
 ===================
 
+
+[2.2.4] - 2018/04/04
+--------------------
+
+Fixed
+^^^^^
+- Issue `#400 <https://github.com/sdss/marvin/issues/400>`: SII in BPT diagram should use sum of 6717 and 6732.
+
+
 [2.2.3] - 2018/03/20
 --------------------
 

python/marvin/__init__.py

@@ -14,7 +14,7 @@
 from collections import OrderedDict
 
 # Set the Marvin version
-__version__ = '2.2.4dev'
+__version__ = '2.2.5dev'
 # try:
 #     from marvin.version import get_version
 # except ImportError as e:

python/marvin/data/sdssMaskbits.par

@@ -621,6 +621,9 @@ maskbits EBOSS_TARGET2 2 SPIDERS_ERASS_AGN         "ERASS AGN sources"
 maskbits EBOSS_TARGET2 3 SPIDERS_ERASS_CLUS            "ERASS Cluster sources"
 maskbits EBOSS_TARGET2 4 SPIDERS_XMMSL_AGN         "XMM Slew survey"
 maskbits EBOSS_TARGET2 5 SPIDERS_XCLASS_CLUS       "XMM serendipitous clusters"
+maskbits EBOSS_TARGET2 6 SPIDERS_CODEX_CLUS_CFHT       "CODEX clusters, CFHT photometry"
+maskbits EBOSS_TARGET2 7 SPIDERS_CODEX_CLUS_PS1       "CODEX clusters, PS1 photometry"
+maskbits EBOSS_TARGET2 8 SPIDERS_CODEX_CLUS_DECALS       "CODEX clusters, DECALS photometry"
 maskbits EBOSS_TARGET2 20 TDSS_A                "Main PanSTARRS selection for TDSS"
 maskbits EBOSS_TARGET2 21 TDSS_FES_DE               "QSOs with disk emitter broad line profiles"
 maskbits EBOSS_TARGET2 22 TDSS_FES_DWARFC           "dwarf carbon stars"
@@ -1002,9 +1005,23 @@ maskbits MANGA_DRP3QUAL  7 BADSET " One or more sets are bad"
 maskbits MANGA_DRP3QUAL  8 BADFLUX " Bad flux calibration"
 maskbits MANGA_DRP3QUAL  9 BADPSF " PSF estimate may be bad"
 maskbits MANGA_DRP3QUAL 10 MANYDEAD " Many dead fibers"
-maskbits MANGA_DRP3QUAL 11 BADHELIORV " MASTAR: High variance between stellar RVs"
+maskbits MANGA_DRP3QUAL 11 RETIRED2 " Bit retired, moved into MASTAR_QUAL instead"
 maskbits MANGA_DRP3QUAL 30 CRITICAL " Critical failure in one or more frames"
 
+# MaStar quality flag bitmask
+masktype MASTAR_QUAL 64 "Mask bits for MaStar spectra quality flags"
+maskbits MASTAR_QUAL  0 NODATA " No Data"
+maskbits MASTAR_QUAL  1 SKYSUBBAD " Bad sky subtraction in one or more frames"
+maskbits MASTAR_QUAL  2 HIGHSCAT " High scattered light in one or more frames"
+maskbits MASTAR_QUAL  3 BADFLUX " Bad flux calibration"
+maskbits MASTAR_QUAL  4 LOWCOV " PSF-covering fraction by fiber is too small (<10%)"
+maskbits MASTAR_QUAL  5 POORCAL " Poor throughput"
+maskbits MASTAR_QUAL  6 BADHELIORV " High variance between stellar RVs"
+maskbits MASTAR_QUAL  7 MANUAL " Flagged as problematic by visual inspection"
+maskbits MASTAR_QUAL  8 EMLINE " Spectrum contain emission lines"
+maskbits MASTAR_QUAL  9 LOWSN  " Per-MJD Spectrum has median S/N <= 15"
+maskbits MASTAR_QUAL 30 CRITICAL " Critical failure in one or more frames"
+
 # The following mask bits are for the 2D MANGA pipeline
 # 0-13 refer to each fiber, 15-30 refer to each pixel in a spectrum."
 # The following mask bits are for fibers
@@ -1089,13 +1106,6 @@ maskbits MANGA_DAPPIXMASK  9 NOCORRECTION "Appropriate correction not available"
 maskbits MANGA_DAPPIXMASK 10 MULTICOMP "Multi-component velocity features present"
 maskbits MANGA_DAPPIXMASK 30 DONOTUSE "Do not use this spaxel for science"
 
-# MaStar quality flag bitmask
-masktype MASTAR_QUAL 64 "Mask bits for MaStar spectra"
-maskbits MASTAR_QUAL  0 NODATA "No Data"
-maskbits MASTAR_QUAL  1 POORCAL "Poor flux calibration"
-maskbits MASTAR_QUAL  2 LOWCOV "PSF-covering fraction by fiber is too small (<10%)"
-maskbits MASTAR_QUAL  3 MANUAL "flagged as problematic by visual inspection"
-
 # MaNGA targeting bitmask for galaxy targets
 masktype MANGA_TARGET1     64 "Mask bits identifying galaxy samples."
 maskbits MANGA_TARGET1     0  NONE " "

python/marvin/utils/dap/bpt.py

@@ -212,7 +212,8 @@ def bpt_kewley06(maps, snr_min=3, return_figure=True, use_oi=True, **kwargs):
             the lines. Alternatively, a dictionary of signal-to-noise values, with the
             emission line channels as keys, can be used.
             E.g., ``snr_min={'ha': 5, 'nii': 3, 'oi': 1}``. If some values are not provided,
-            they will default to ``SNR>=3``.
+            they will default to ``SNR>=3``. Note that the value ``sii`` will be applied to both
+            ``[SII 6718]`` and ``[SII 6732]``.
         return_figure (bool):
             If ``True``, it also returns the matplotlib figure_ of the BPT diagram plot,
             which can be used to modify the style of the plot.
@@ -268,9 +269,12 @@ def bpt_kewley06(maps, snr_min=3, return_figure=True, use_oi=True, **kwargs):
     nii = get_masked(maps, 'nii_6585', snr=get_snr(snr_min, 'nii'))
     ha = get_masked(maps, 'ha_6564', snr=get_snr(snr_min, 'ha'))
     hb = get_masked(maps, 'hb_4862', snr=get_snr(snr_min, 'hb'))
-    sii = get_masked(maps, 'sii_6718', snr=get_snr(snr_min, 'sii'))
     oi = get_masked(maps, 'oi_6302', snr=get_snr(snr_min, 'oi'))
 
+    sii_6718 = get_masked(maps, 'sii_6718', snr=get_snr(snr_min, 'sii'))
+    sii_6732 = get_masked(maps, 'sii_6732', snr=get_snr(snr_min, 'sii'))
+    sii = sii_6718 + sii_6732
+
     # Calculate masked logarithms
     log_oiii_hb = np.ma.log10(oiii / hb)
     log_nii_ha = np.ma.log10(nii / ha)

setup.py

@@ -75,7 +75,7 @@ def remove_args(parser):
 
 NAME = 'sdss-marvin'
 # do not use x.x.x-dev.  things complain.  instead use x.x.xdev
-VERSION = '2.2.4dev'
+VERSION = '2.2.5dev'
 RELEASE = 'dev' not in VERSION