Merge branch 'main' into shower_flagging_enhancement

CHANGES.rst

@@ -1,7 +1,64 @@
-1.5.3 (unreleased)
+1.6.2 (unreleased)
 ==================
 
-- 
+Changes to API
+--------------
+
+Bug Fixes
+---------
+
+Other
+-----
+
+1.6.1 (2024-02-29)
+==================
+
+Changes to API
+--------------
+
+ramp_fitting
+~~~~~~~~~~~~
+
+- Add ``average_dark_current`` to calculations of poisson variance. [#243]
+
+1.6.0 (2024-02-15)
+==================
+
+Changes to API
+--------------
+
+jump
+~~~~
+
+- Add in the flagging of groups in the integration after a snowball
+  occurs. The saturated core of the snowball gets flagged as jump
+  for a number of groups passed in as a parameter [#238]
+
+Bug Fixes
+---------
+
+jump
+~~~~
+
+- Fixed the computation of the number of rows per slice for multiprocessing, which
+  was causing different results when running the step with multiprocess [#239]
+
+- Fix the code to at least always flag the group with the shower and the requested
+  groups after the primary shower. [#237]
+
+Other
+-----
+
+jump
+~~~~
+
+- Reorganize jump docs between the jwst and stcal repos. [#240]
+
+ramp_fitting
+~~~~~~~~~~~~
+
+- Reorganize ramp_fitting docs between the jwst and stcal repos. [#240]
+
 
 1.5.2 (2023-12-13)
 ==================
@@ -24,7 +81,7 @@ Other
 - Enable automatic linting and code style checks [#187]
 
 ramp_fitting
-------------
+~~~~~~~~~~~~
 
 - Refactor Casertano, et.al, 2022 uneven ramp fitting and incorporate the matching
   jump detection algorithm into it. [#215]
@@ -84,13 +141,16 @@ jump
   within a group. [#207]
 
 - Added more allowable selections for the number of cores to use for
-  multiprocessing [#183].
+  multiprocessing [#183]
+
+- Fixed the computation of the number of rows per slice for multiprocessing,
+  which caused different results when running the step with multiprocess [#239]
 
 ramp_fitting
 ~~~~~~~~~~~~
 
 - Added more allowable selections for the number of cores to use for
-  multiprocessing [#183].
+  multiprocessing [#183]
 
 - Updating variance computation for invalid integrations, as well as
   updating the median rate computation by excluding groups marked as

docs/stcal/jump/description.rst

@@ -1,6 +1,8 @@
+.. _jump_algorithm:
+
 Algorithm
 ---------
-This routine detects jumps in an exposure by looking for outliers
+This routine detects jumps by looking for outliers
 in the up-the-ramp signal for each pixel in each integration within
 an input exposure. On output, the GROUPDQ array is updated with the DQ flag
 "JUMP_DET" to indicate the location of each jump that was found.
@@ -10,34 +12,39 @@ output PIXELDQ array.
 The SCI and ERR arrays of the input data are not modified.
 
 The current implementation uses the two-point difference method described
-in Anderson&Gordon2011_.
+in `Anderson & Gordon (2011) <https://ui.adsabs.harvard.edu/abs/2011PASP..123.1237A>`_.
 
 Two-Point Difference Method
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 The two-point difference method is applied to each integration as follows:
 
-* Compute the first differences for each pixel (the difference between
-  adjacent groups)
-* Compute the clipped (dropping the largest difference) median of the first differences for each pixel.
-* Use the median to estimate the Poisson noise for each group and combine it
-  with the read noise to arrive at an estimate of the total expected noise for
-  each difference.
-* Compute the "difference ratio" as the difference between the first differences
-  of each group and the median, divided by the expected noise.
-* If the largest "difference ratio" is greater than the rejection threshold,
-  flag the group corresponding to that ratio as having a jump.
-* If a jump is found in a given pixel, iterate the above steps with the
-  jump-impacted group excluded, looking for additional lower-level jumps
-  that still exceed the rejection threshold.
-* Stop iterating on a given pixel when no new jumps are found or only one
-  difference remains.
-* If the there are only three differences (four groups), the standard median
-  is used rather than the clipped median.
-* If there are only two differences (three groups), the smallest one is compared to the larger
-  one and if the larger one is above a threshold, it is flagged as a jump.
+#. Compute the first differences for each pixel (the difference between
+   adjacent groups)
+#. Compute the clipped median (dropping the largest difference) of the first differences for each pixel.
+   If there are only three first difference values (four groups), no clipping is
+   performed when computing the median.
+#. Use the median to estimate the Poisson noise for each group and combine it
+   with the read noise to arrive at an estimate of the total expected noise for
+   each difference.
+#. Compute the "difference ratio" as the difference between the first differences
+   of each group and the median, divided by the expected noise.
+#. If the largest "difference ratio" is greater than the rejection threshold,
+   flag the group corresponding to that ratio as having a jump.
+#. If a jump is found in a given pixel, iterate the above steps with the
+   jump-impacted group excluded, looking for additional lower-level jumps
+   that still exceed the rejection threshold.
+#. Stop iterating on a given pixel when no new jumps are found or only one
+   difference remains.
+#. If there are only two differences (three groups), the smallest one is compared to the larger
+   one and if the larger one is above a threshold, it is flagged as a jump.
+#. If flagging of the 4 neighbors is requested, then the 4 adjacent pixels will
+   have ramp jumps flagged in the same group as the central pixel as long as it has
+   a jump between the min and max requested levels for this option.
+#. If flagging of groups after a ramp jump is requested, then the groups in the
+   requested time since a detected ramp jump will be flagged as ramp jumps if
+   the ramp jump is above the requested threshold.  Two thresholds and times are
+   possible for this option.
 
-Note that any ramp values flagged as SATURATED in the input GROUPDQ array
+Note that any ramp groups flagged as SATURATED in the input GROUPDQ array
 are not used in any of the above calculations and hence will never be
 marked as containing a jump.
-
-.. _Anderson&Gordon2011: https://ui.adsabs.harvard.edu/abs/2011PASP..123.1237A