# Step 3: Subtracting the Sky

This step measures, subtracts and/or equalizes the sky from each input image while recording the subtracted value in the image header.

Authors: | Christopher Hanley, Megan Sosey, Mihai Cara
License: | http://www.stsci.edu/resources/software_hardware/pyraf/LICENSE

`drizzlepac.sky.``sky`(input=None, outExt=None, configObj=None, group=None, editpars=False, **inputDict)

  Function for computing and subtracting (or equalizing/matching) the backgroud in input images. The algorithm for sky subtraction can be selected through the `skymethod` parameter. This function will update the `MDRIZSKY` keyword in the headers of the input files.

  Sky subtraction is generally recommended for optimal flagging and removal of CR’s when the sky background is more than a few electrons. However, some science applications may require the sky to not be removed, allowing for the final drizzle step to be performed with no sky subtraction. If you turn off sky subtraction, you should also set drizzle.pixfrac to 1, otherwise variations in sky between images will add noise to your data.

  In addition to the “pure” sky computation, this task can be used for sky “equalization”, that is, it can match sky values in the images that are part of a mosaic.

  For cameras with multiple detectors (such as ACS/WFC, WFPC2, or WFC3), the sky values in each exposure are first measured separately for the different detectors. These different values are then compared, and the lowest measured sky value is used as the estimate for all of the detectors for that exposure. This is based on the premise that for large extended or bright targets, the pixel intensity distribution in one or more of the detectors may be significantly skewed toward the bright end by the target itself, thereby overestimating the sky on that detector. If the other detector is less affected by such a target, then its sky value will be lower, and can therefore also be substituted as the sky value for the detector with the bright source.

  For more information on the science applications of the sky task, see the DrizzlePac Handbook:.

  > Parameters: | input : str or list of str (Default = None) A python list of image filenames, or just a single filename. outExt : str (Default = None) The extension of the output image. If the output already exists then the input image is overwritten. configObj : configObject (Default = None) An instance of `configObject` group : int (Default = None) The group of the input image. editpars : bool (Default = False) A parameter that allows user to edit input parameters by hand in the GUI. inputDict : dict, optional An optional list of parameters specified by the user. Note These are parameters that `configObj` should contain by default. These parameters can be altered on the fly using the `inputDict`. If `configObj` is set to None and there is no `inputDict` information, then the values for the parameters will be pulled from the default configuration files for the task. These are the same configuration files that are referenced in the TEAL parameter interface GUI. If you wish to edit these parameters by hand in the GUI, simply set editpars=True. Table of optional parameters that should be in `configobj` and can also be specified in `inputDict`.
  > Name | Definition
  > --- | ---
  > `skyuser` | ‘KEYWORD in header which indicates a sky subtraction value to use’.
  > `skymethod` | ‘Sky computation method’
  > `skysub` | ‘Perform sky subtraction?’
  > `skywidth` | ‘Bin width of histogram for sampling sky statistics (in sigma)’
  > `skystat` | ‘Sky correction statistics parameter’
  > `skylower` | ‘Lower limit of usable data for sky (always in electrons)’
  > `skyupper` | ‘Upper limit of usable data for sky (always in electrons)’
  > `skyclip` | ‘Number of clipping iterations’
  > `skylsigma` | ‘Lower side clipping factor (in sigma)’
  > `skyusigma` | ‘Upper side clipping factor (in sigma)’
  > `skymask_cat` | ‘Catalog file listing image masks’
  > `use_static` | ‘Use static mask for skymatch computations?’
  > `sky_bits` | ‘Bit flags for identifying bad pixels in DQ array’
  > `skyuser` | ‘KEYWORD indicating a sky subtraction value if done by user’
  > `skyfile` | ‘Name of file with user-computed sky values’
  > `in_memory` | ‘Optimize for speed or for memory use’
  These optional parameters are described in more detail below in the “Other Parameters” section.
  Returns: | None : The input file’s primary headers is updated with the computed sky value.
  Other Parameters:
  | skysub : bool (Default = Yes) Turn on or off sky subtraction on the input data. When `skysub` is set to `no`, then `skyuser` field will be enabled and if user specifies a header keyword showing the sky value in the image, then that value will be used for CR-rejection but it will not be subtracted from the (drizzled) image data. If user sets `skysub` to `yes` then `skyuser` field will be disabled (and if it is not empty - it will be ignored) and user can use one of the methods available through the `skymethod` parameter to compute the sky or provide a file (see `skyfile` parameter) with values that should be subtracted from (single) drizzled images. skymethod : {‘localmin’, ‘globalmin+match’, ‘globalmin’, ‘match’}, optional (Default = ‘localmin’) Select the algorithm for sky computation: ‘localmin’: compute a common sky for all members of an exposure (see NOTES below). For a typical use, it will compute sky values for each chip/image extension (marked for sky subtraction in the `input` parameter) in an input image, and it will subtract the previously found minimum sky value from all chips (marked for sky subtraction) in that image. This process is repeated for each input image. Note This setting is recommended when regions of overlap between images are dominated by “pure” sky (as opposite to extended, diffuse sources). Note This is similar to the “skysub” algorithm used in previous versions of astrodrizzle. ‘globalmin’: compute a common sky value for all members of all exposures (see NOTES below). It will compute sky values for each chip/image extension (marked for sky subtraction in the `input` parameter) in all input images, find the minimum sky value, and then it will subtract the same minimum sky value from all chips (marked for sky subtraction) in all images. This method may useful when input images already have matched background values. ‘match’: compute differences in sky values between images in common (pair-wise) sky regions. In this case computed sky values will be relative (delta) to the sky computed in one of the input images whose sky value will be set to (reported to be) 0. This setting will “equalize” sky values between the images in large mosaics. However, this method is not recommended when used in conjunction with astrodrizzle because it computes relative sky values while `astrodrizzle` needs “measured” sky values for median image generation and CR rejection. ‘globalmin+match’: first find a minimum “global” sky value in all input images and then use ‘match’ method to equalize sky values between images. Note This is the recommended setting for images containing diffuse sources (e.g., galaxies, nebulae) covering significant parts of the image. skywidth : float, optional (Default Value = 0.1) Bin width, in sigma, used to sample the distribution of pixel flux values in order to compute the sky background statistics. skystat : {‘median’, ‘mode’, ‘mean’}, optional (Default Value = ‘median’) Statistical method for determining the sky value from the image pixel values. skylower : float, optional (Default Value = INDEF) Lower limit of usable pixel values for computing the sky. This value should be specified in the units of the input image. skyupper : float, optional (Default Value = INDEF) Upper limit of usable pixel values for computing the sky. This value should be specified in the units of the input image. skyclip : int, optional (Default Value = 5) Number of clipping iterations to use when computing the sky value. skylsigma : float, optional (Default Value = 4.0) Lower clipping limit, in sigma, used when computing the sky value. skyusigma : float, optional (Default Value = 4.0) Upper clipping limit, in sigma, used when computing the sky value. skymask_cat : str, optional (Default Value = ‘’) File name of a catalog file listing user masks to be used with images. use_static : bool, optional (Default Value = True) Specifies whether or not to use static mask to exclude masked image pixels from sky computations. sky_bits : int, None, optional (Default = 0) Integer sum of all the DQ bit values from the input image’s DQ array that should be considered “good” when building masks for sky computations. For example, if pixels in the DQ array can be combinations of 1, 2, 4, and 8 flags and one wants to consider DQ “defects” having flags 2 and 4 as being acceptable for sky computations, then `sky_bits` should be set to 2+4=6. Then a DQ pixel having values 2,4, or 6 will be considered a good pixel, while a DQ pixel with a value, e.g., 1+2=3, 4+8=12, etc. will be flagged as a “bad” pixel. Default value (0) will make all non-zero pixels in the DQ mask to be considered “bad” pixels, and the corresponding image pixels will not be used for sky computations. Set `sky_bits` to `None` to turn off the use of image’s DQ array for sky computations. Note DQ masks (if used), will be combined with user masks specified in the input @-file. skyfile : str, optional (Default Value = ‘’) Name of file containing user-computed sky values to be used with each input image. This ASCII file should only contain 2 columns: image filename in column 1 and sky value in column 2. The sky value should be provided in units that match the units of the input image and for multi-chip images, the same value will be applied to all chips. skyuser : str (Default = ‘’) Name of header keyword which records the sky value already subtracted from the image by the user. The `skyuser` parameter is ignored when `skysub` is set to `yes`. Note When `skysub`=`no` and `skyuser` field is empty, then `AstroDrizzle` will assume that sky background is 0.0 for the purpose of cosmic-ray rejection. in_memory : bool, optional (Default Value = False) Specifies whether to optimize execution for speed (maximum memory usage) or use a balanced approach in which a minimal amount of image data is kept in memory and retrieved from disk as needed. The default setting is recommended for most systems.

  Notes

  `sky` provides new algorithms for sky value computations and enhances previously available algorithms used by, e.g., Astrodrizzle.

  First, the standard sky computation algorithm (see `skymethod` = `'localmin'`) was upgraded to be able to use DQ flags and user supplied masks to remove “bad” pixels from being used for sky statistics computations.

  Second, two new methods have been introduced: `'globalmin'` and `'match'`, as well as a combination of the two – `'globalmin+match'`.

  - The `'globalmin'` method computes the minimum sky value across all chips in all input images. That sky value is then considered to be the background in all input images.

  - The `'match'` algorithm is somewhat similar to the traditional sky subtraction method (`skymethod`=`'localmin'`) in the sense that it measures the sky indipendently in input images (or detector chips). The major differences are that, unlike the traditional method,

    > 1. `'match'` algorithm computes relative sky values with regard to the sky in a reference image chosen from the input list of images; and
    > 2. Sky statistics is computed only in the part of the image that intersects other images.

    This makes `'match'` sky computation algorithm particularly useful for “equalizing” sky values in large mosaics in which one may have only (at least) pair-wise intersection of images without having a common intersection region (on the sky) in all images.

    The `'match'` method works in the following way: for each pair of intersecting images, an equation is written that requires that average surface brightness in the overlapping part of the sky be equal in both images. The final system of equations is then solved for unknown background levels.

    Warning

    Current algorithm is not capable of detecting cases when some groups of intersecting images (from the input list of images) do not intersect at all other groups of intersecting images (except for the simple case when single images do not intersect any other images). In these cases the algorithm will find equalizing sky values for each group. However since these groups of images do not intersect each other, sky will be matched only within each group and the “inter-group” sky mismatch could be significant.

    Users are responsible for detecting such cases and adjusting processing accordingly.

    Warning

    Because this method computes relative sky values compared to a reference image (which will have its sky value set to 0), the sky values computed with this method usually are smaller than the “absolute” sky values computed, e.g., with the `'localmin'` algorithm. Since astrodrizzle expects “true” (as opposite to relative) sky values in order to correctly compute the median image or to perform cosmic-ray detection, this algorithm in not recommended to be used alone for sky computations to be used with `astrodrizzle`.

    For the same reason, IVM weighting in `astrodrizzle` should not be used with `'match'` method: sky values reported in `MDRIZSKY` header keyword will be relative sky values (sky offsets) and derived weights will be incorrect.

  - The `'globalmin+match'` algorithm combines `'match'` and `'globalmin'` methods in order to overcome the limitation of the `'match'` method described in the note above: it uses `'globalmin'` algorithm to find a baseline sky value common to all input images and the `'match'` algorithm to “equalize” sky values in the mosaic. Thus, the sky value of the “reference” image will be equal to the baseline sky value (instead of 0 in `'match'` algorithm alone) making this method acceptable for use in conjunction with `astrodrizzle`.

  Glossary:

    Exposure – a subset of FITS image extensions in an input image that correspond to different chips in the detector used to acquire the image. The subset of image extensions that form an exposure is defined by specifying extensions to be used with input images (see parameter `input`).

    See help for `skypac.parseat.parse_at_line` for details on how to specify image extensions.

    Footprint – the outline (edge) of the projection of a chip or of an exposure on the celestial sphere.

    Note

    - Footprints are managed by the `SphericalPolygon` class.
    - Both footprints and associated exposures (image data, WCS information, and other header information) are managed by the `SkyLine` class.
    - Each `SkyLine` object contains one or more `SkyLineMember` objects that manage both footprints and associated chip data that form an exposure.
  Remarks:

    - `sky` works directly on geometrically distorted flat-fielded images thus avoiding the need to perform an additional drizzle step to perform distortion correction of input images.

      Initially, the footprint of a chip in an image is aproximated by a 2D planar rectangle representing the borders of chip’s distorted image. After applying distortion model to this rectangle and progecting it onto the celestial sphere, it is approximated by spherical polygons. Footprints of exposures and mosaics are computed as unions of such spherical polygons while overlaps of image pairs are found by intersecting these spherical polygons.

  Limitations and Discussions:

    Primary reason for introducing “sky match” algorithm was to try to equalize the sky in large mosaics in which computation of the “absolute” sky is difficult due to the presence of large diffuse sources in the image. As discussed above, `sky` accomplishes this by comparing “sky values” in a pair of images in the overlap region (that is common to both images). Quite obviously the quality of sky “matching” will depend on how well these “sky values” can be estimated. We use quotation marks around sky values because for some image “true” background may not be present at all and the measured sky may be the surface brightness of large galaxy, nebula, etc.

    Here is a brief list of possible limitations/factors that can affect the outcome of the matching (sky subtraction in general) algorithm:

    - Since sky subtraction is performed on flat-fielded but not distortion corrected images, it is important to keep in mind that flat-fielding is performed to obtain uniform surface brightness and not flux. This distinction is important for images that have not been distortion corrected. As a consequence, it is advisable that point-like sources be masked through the user-supplied mask files. Alternatively, one can use `upper` parameter to limit the use of bright objects in sky computations.
    - Normally, distorted flat-fielded images contain cosmic rays. This algorithm does not perform CR cleaning. A possible way of minimizing the effect of the cosmic rays on sky computations is to use clipping (`nclip` > 0) and/or set `upper` parameter to a value larger than most of the sky background (or extended source) but lower than the values of most CR pixels.
    - In general, clipping is a good way of eliminating “bad” pixels: pixels affected by CR, hot/dead pixels, etc. However, for images with complicated backgrounds (extended galaxies, nebulae, etc.), affected by CR and noise, clipping process may mask different pixels in different images. If variations in the background are too strong, clipping may converge to different sky values in different images even when factoring in the “true” difference in the sky background between the two images.
    - In general images can have different “true” background values (we could measure it if images were not affected by large diffuse sources). However, arguments such as `lower` and `upper` will apply to all images regardless of the intrinsic differences in sky levels.
  How to use the tasks stand alone interface in your own scripts:
    These tasks are designed to work together seemlessly when run in the full `AstroDrizzle` interface. More advanced users may wish to create specialized scripts for their own datasets, making use of only a subset of the predefined `AstroDrizzle` tasks, or add additional processing, which may be usefull for their particular data. In these cases, individual access to the tasks is important.

  Something to keep in mind is that the full `AstroDrizzle` interface will make backup copies of your original files and place them in the `OrIg/` directory of your current working directory. If you are working with the stand alone interfaces, it is assumed that the user has already taken care of backing up their original datafiles as the input file with be directly altered.

  Examples

  Basic example of how to call sky yourself from a python command line, this example will use the default parameter settings and subtract a sky value from each `*flt.fits` image in the current directory, saving the output file with the extension of “mysky”:

      >>> from drizzlepac import sky
      >>> sky.sky('*flt.fits',outExt='mysky')

`drizzlepac.sky.``help`(file=None)

  Print out syntax help for running astrodrizzle

  Parameters: | file : str (Default = None) If given, write out help to the filename specified by this parameter Any previously existing file with this name will be deleted before writing out the help.