Merge branch 'master' into JP-809-support-jsonschema-3.x

CHANGES.rst

@@ -10,12 +10,11 @@ datamodels
 0.13.8 (Unreleased)
 ===================
 
-flatfield
----------
-
-- Three new unit tests were added, and two existing ones were split into
-  multiple functions. [#3704]
+extract_1d
+----------
 
+- Parameters were added to ExtractBase.__init__, and most of the initialization
+  is done there rather than in the subclasses. [#3714]
 
 0.13.7 (2019-06-21)
 ===================
@@ -25,6 +24,12 @@ datamodels
 
 - Reverted #3680 and #3709. [#3717, #3718]
 
+flatfield
+---------
+
+- Three new unit tests were added.  Two existing files were modified to
+  split the tests into separate functions. [#3704]
+
 0.13.6 (2019-06-20)
 ===================
 
@@ -36,7 +41,7 @@ associations
 datamodels
 ----------
 
-- Fixed corruption of FITS tables wiht unsigned int columns. [#3680]
+- Fixed corruption of FITS tables with unsigned int columns. [#3680]
 
 
 0.13.5 (2019-06-19)

docs/jwst/extract_1d/description.rst

@@ -19,7 +19,8 @@ optionally including background subtraction using a circular annulus.
 For an extended source, rectangular aperture photometry will be used, with
 the entire image being extracted, and no background subtraction, regardless
 of what was specified in the reference file or command-line arguments.
-The photometry makes use of astropy photutils.
+For either point source or extended, the photometry makes use of
+astropy photutils.
 The region of overlap between an aperture and a pixel can be calculated by
 one of three different methods:  "exact", limited only by finite precision
 arithmetic; "center", i.e. the full value in a pixel will be included if its
@@ -37,23 +38,42 @@ have keyword SLTNAME to specify which slit was extracted, though if there
 is only one slit (e.g. full-frame data), the slit name can be taken from
 the JSON reference file instead.
 
+The input data should be in units of surface brightness, megajanskys per
+steradian.  The photom step reads data in units of count rate and writes
+data in units of surface brightness.
+
 Output
 ======
 The output will be in MultiSpecModel format; for each input slit there will
 be an output table extension with the name EXTRACT1D.  This extension will
-have columns WAVELENGTH, FLUX, ERROR, DQ, NET, NERROR, BACKGROUND, BERROR
-and NPIXELS.
+have columns WAVELENGTH, FLUX, ERROR, SURF_BRIGHT, SB_ERROR, DQ,
+BACKGROUND, BERROR and NPIXELS.
+
 WAVELENGTH was copied from the wavelength attribute of the input 2-D data,
 if that attribute exists and was populated, or it was calculated from the
 WCS otherwise.
-NET is the count rate minus background, in counts/second (per pixel in the
-dispersion direction), obtained by summing along the direction perpendicular
-to the dispersion.  Currently only a simple summation is done, with
-no weighting.
+FLUX is the flux density in janskys (or mJy for IFU data); see keyword
+TUNIT2, if the data are in a FITS BINTABLE.  ERROR is the error estimate
+for FLUX, and it has the same units as FLUX.
+SURF_BRIGHT is the surface brightness in MJy / sr.  SB_ERROR is the error
+estimate for SURF_BRIGHT.
+While it was expected that a user would make use of the FLUX column for
+point-source data or the SURF_BRIGHT column for an extended source,
+both columns will be populated regardless of the target.
+The extract_1d step collapses the input data from 2-D to 1-D by summing
+one or more rows (or columns, depending on the dispersion direction).
+A background may optionally be subtracted by the extract_1d step, but
+there are also other options for background subtraction prior to extract_1d.
+Since the input data are in units of MJy / sr, the SURF_BRIGHT column will be
+populated by dividing the sum by the number of pixels (see the NPIXELS column,
+described below) that were added together.  The FLUX column will be populated
+by multiplying the sum by the solid angle of a pixel, and then multiplying
+by 10^6 to convert from MJy to Jy.
+
 NPIXELS is the number of pixels that were added together for the source
-extraction region.
+extraction region.  Note that this is not necessarily a constant, and
+the value is not necessarily an integer (the data type is float).
 BACKGROUND is the measured background, scaled to the extraction width used
-for the NET.  BACKGROUND will be zero if no background was subtracted.
-FLUX will be computed from NET if there is a RELSENS table
-for the input slit; otherwise, FLUX will be zero.
-ERROR, DQ, NERROR, and BERROR are not populated with useful values yet.
+for FLUX and SURF_BRIGHT.  BACKGROUND will be zero if no background was
+subtracted in the extract_1d step.
+ERROR, SB_ERROR, BERROR, and DQ are not populated with useful values yet.