diff --git a/CHANGES.rst b/CHANGES.rst index 2c05d9c5f7..4b7c096009 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -253,6 +253,10 @@ 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 -------- diff --git a/docs/jwst/outlier_detection/arguments.rst b/docs/jwst/outlier_detection/arguments.rst index a2900bcbd6..b2acf485d4 100644 --- a/docs/jwst/outlier_detection/arguments.rst +++ b/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. diff --git a/docs/jwst/outlier_detection/outlier_detection_imaging.rst b/docs/jwst/outlier_detection/outlier_detection_imaging.rst index c4cf5eceba..d1b86b28f8 100644 --- a/docs/jwst/outlier_detection/outlier_detection_imaging.rst +++ b/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. diff --git a/docs/jwst/outlier_detection/outlier_detection_tso.rst b/docs/jwst/outlier_detection/outlier_detection_tso.rst index 2f74611e32..0df852ea00 100644 --- a/docs/jwst/outlier_detection/outlier_detection_tso.rst +++ b/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 \ No newline at end of file +.. automodapi:: jwst.outlier_detection.outlier_detection_tso diff --git a/jwst/outlier_detection/outlier_detection_step.py b/jwst/outlier_detection/outlier_detection_step.py index 8add2f32a9..cd633a42c2 100644 --- a/jwst/outlier_detection/outlier_detection_step.py +++ b/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')