Merge branch 'main' into multi_int_jump_detection

CHANGES.rst

@@ -32,6 +32,8 @@ jump
   when the number of groups is above a threshold use single pass
   outlier flagging rather than the iterative flagging. [#242]
 
+=======
+
 Other
 -----
 

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