Merge branch 'master' into JP-3631

CHANGES.rst

@@ -259,6 +259,10 @@ outlier_detection
 - Fixed a bug that led to small total flux offsets between input and blotted
   images if the nominal and actual wcs-computed pixel areas were different. [#8553]
 
+- Deprecate ``nlow`` and ``nhigh`` parameters, which no longer have an effect. [#8603]
+
+- Fix errors in documentation describing arguments. [#8603]
+
 pathloss
 --------
 

docs/jwst/outlier_detection/arguments.rst

@@ -1,80 +1,81 @@
 .. _outlier_detection_step_args:
 
+For more details about step arguments (including datatypes, possible values
+and defaults) see :py:obj:`jwst.outlier_detection.OutlierDetectionStep.spec`.
+
 Step Arguments for Non-IFU data
 ===============================
 The `outlier_detection` step for non-IFU data has the following optional arguments
 that control the behavior of the processing:
 
-``--weight_type`` (string, default='exptime')
-  The type of data weighting to use during resampling;
-  options are 'exptime', 'error', and 'None'.
+``--weight_type``
+  The type of data weighting to use during resampling.
 
-``--pixfrac`` (float, default=1.0)
+``--pixfrac``
   The pixel fraction used during resampling;
   valid values go from 0.0 to 1.0.
 
-``--kernel`` (string, default='square')
+``--kernel``
   The form of the kernel function used to distribute flux onto a
-  resampled image. Options are 'square', 'turbo', 'point', and
-  'lanczos'.
+  resampled image.
 
-``--fillval`` (string, default='INDEF')
+``--fillval``
   The value to assign to resampled image pixels that have zero weight or
   do not receive any flux from any input pixels during drizzling.
   Any floating-point value, given as a string, is valid.
   A value of 'INDEF' will use the last zero weight flux.
 
-``--nlow`` (integer, default=0)
-  The number of low values in each pixel stack to ignore
-  when computing the median value.
+``--nlow``
+  Deprecated and has no effect. This parameter will be removed
+  in a future version.
 
-``--nhigh`` (integer, default=0)
-  The number of high values in each pixel stack to ignore
-  when computing the median value.
+``--nhigh``
+  Deprecated and has no effect. This parameter will be removed
+  in a future version.
 
-``--maskpt`` (float, default=0.7)
+``--maskpt``
   The percent of maximum weight to use as lower-limit for valid data;
   valid values go from 0.0 to 1.0.
 
-``--snr`` (string, default='4.0 3.0')
+``--snr``
   The signal-to-noise values to use for bad pixel identification.
   Since cosmic rays often extend across several pixels the user
   must specify two cut-off values for determining whether a pixel should
   be masked: the first for detecting the primary cosmic ray, and the
   second (typically lower threshold) for masking lower-level bad pixels
   adjacent to those found in the first pass.  Valid values are a pair of
-  floating-point values in a single string.
+  floating-point values in a single string (for example "5.0 4.0").
 
-``--scale`` (string, default='0.5 0.4')
+``--scale``
   The scaling factor applied to derivative used to identify bad pixels.
   Since cosmic rays often extend across several pixels the user
   must specify two cut-off values for determining whether a pixel should
   be masked: the first for detecting the primary cosmic ray, and the
   second (typically lower threshold) for masking lower-level bad pixels
   adjacent to those found in the first pass.  Valid values are a pair of
-  floating-point values in a single string.
+  floating-point values in a single string (for example "1.2 0.7").
 
-``--backg`` (float, default=0.0)
+``--backg``
   User-specified background value to apply to the median image.
 
-``--rolling_window_width`` (int, default=25)
+``--rolling_window_width``
   Number of integrations over which to take the median when using rolling-window
   median for TSO observations.
 
-``--save_intermediate_results`` (boolean, default=False)
+``--save_intermediate_results``
   Specifies whether or not to save any intermediate products created
   during step processing.
 
-``--resample_data`` (boolean, default=True)
+``--resample_data``
   Specifies whether or not to resample the input images when
   performing outlier detection.
 
-``--good_bits`` (string, default="~DO_NOT_USE")
+``--good_bits``
   The DQ bit values from the input image DQ arrays
   that should be considered 'good' when building the weight mask. See
   DQ flag :ref:`dq_parameter_specification` for details.
 
-``--allowed_memory`` (float, default=None)
+``--allowed_memory``
   Specifies the fractional amount of
   free memory to allow when creating the resampled image. If ``None``, the
   environment variable ``DMODEL_ALLOWED_MEMORY`` is used. If not defined, no
@@ -84,7 +85,7 @@ that control the behavior of the processing:
   For example, if set to ``0.5``, only resampled images that use less than half
   the available memory can be created.
 
-``--in_memory`` (boolean, default=False)
+``--in_memory``
   Specifies whether or not to load and create all images that are used during
   processing into memory. If ``False``, input files are loaded from disk when
   needed and all intermediate files are stored on disk, rather than in memory.
@@ -94,19 +95,20 @@ Step Arguments for IFU data
 The `outlier_detection` step for IFU data has the following optional arguments
 that control the behavior of the processing:
 
-``--kernel_size`` (string, default='7 7')
+``--kernel_size``
   The size of the kernel to use to normalize the pixel differences. The kernel size
-  must only contain odd values.
+  must only contain odd values. Valid values are a pair of ints in a single string
+  (for example "7 7").
 
-``--threshold_percent`` (float, default=99.8)
+``--threshold_percent``
   The threshold (in percent) of the normalized minimum pixel difference used to identify bad pixels.
   Pixels with   a normalized minimum pixel difference above this percentage are flagged as a outlier.
 
-``--save_intermediate_results`` (boolean, default=False)
+``--save_intermediate_results``
   Specifies whether or not to save any intermediate products created
   during step processing.
 
-``--in_memory`` (boolean, default=False)
+``--in_memory``
   Specifies whether or not to load and create all images that are used during
   processing into memory. If ``False``, input files are loaded from disk when
   needed and all intermediate files are stored on disk, rather than in memory.

docs/jwst/outlier_detection/outlier_detection_imaging.rst

@@ -69,8 +69,6 @@ Specifically, this routine performs the following operations:
 
    * The median image is created by combining all grouped mosaic images or
      non-resampled input data (as planes in a ModelContainer) pixel-by-pixel.
-   * The ``nlow`` and ``nhigh`` parameters specify how many low and high values
-     to ignore when computing the median for any given pixel.
    * The ``maskpt`` parameter sets the percentage of the weight image values to
      use, and any pixel with a weight below this value gets flagged as "bad" and
      ignored when resampled.

docs/jwst/outlier_detection/outlier_detection_tso.rst

@@ -21,8 +21,6 @@ a few variations to accomodate the nature of these 3D data.
    * The ``rolling_window_width`` parameter specifies the number of integrations over
      which to compute the median. The default is 25. If the number of integrations
      is less than or equal to ``rolling_window_width``, a simple median is used instead.
-   * The ``nlow`` and ``nhigh`` parameters specify how many low and high values
-     to ignore when computing the median for any given pixel.
    * The ``maskpt`` parameter sets the percentage of the weight image values to
      use, and any pixel with a weight below this value gets flagged as "bad" and
      ignored when the median is taken.
@@ -38,4 +36,4 @@ a few variations to accomodate the nature of these 3D data.
 #. The input data model DQ arrays are updated with the mask of detected outliers.
 
 
-.. automodapi:: jwst.outlier_detection.outlier_detection_tso
+.. automodapi:: jwst.outlier_detection.outlier_detection_tso

jwst/outlier_detection/outlier_detection_step.py

@@ -55,8 +55,8 @@ class OutlierDetectionStep(Step):
         pixfrac = float(default=1.0)
         kernel = string(default='square') # drizzle kernel
         fillval = string(default='INDEF')
-        nlow = integer(default=0)
-        nhigh = integer(default=0)
+        nlow = integer(default=0)  # DEPRECATED this setting has no effect and will be removed
+        nhigh = integer(default=0)  # DEPRECATED this setting has no effect and will be removed
         maskpt = float(default=0.7)
         snr = string(default='5.0 4.0')
         scale = string(default='1.2 0.7')