NAME

       fiign - low-level manipulation of masks associated to FITS images

SYNOPSIS

       fiign [options and operations] [<input>] [-o|--output <output>]

DESCRIPTION

       In  the context of FITS image data processing, "masks" are per pixel associated meta-data,
       representing the state of the given pixel. In general, pixels  considered  to  be  somehow
       "bad"  are  marked  with  these  masks in order to exclude or use only with caution during
       further processing. These masks can either mark the initial  state  of  the  given  pixels
       (e.g.  pixels  can be marked as hot or bad pixels, which describes the detector itself and
       not the individual scientific or calibration frames), or masks can  be  added  during  the
       subsequent steps of the processing (e.g. saturated pixels, "outer" pixels). The purpose of
       the `fiign` program is to give a low-level access to these masks. Although the  operations
       on  the  images  automatically  yields  the respective operations on the masks (e.g. if an
       image is transformed or trimmed, the associated mask will also be transformed  or  trimmed
       with the same geometry), with this program the masks can be manipulated arbitrarily.

OPTIONS

   General options:
       -h, --help
              Gives general summary about the command line options.

       --long-help, --help-long
              Gives a detailed list of command line options.

       --wiki-help, --help-wiki, --mediawiki-help, --help-mediawiki
              Gives a detailed list of command line options in Mediawiki format.

       --version, --version-short, --short-version
              Gives some version information about the program.

       -i, --input <image file>
              Name of the input FITS image file.

       -o, --output <image file>
              Name of the output FITS image file (can be the same as the input image file).

   Generic pixel masking options:
       -n, --ignore-nonpositive
              Mask pixels with non-positive values.

       -g, --ignore-negative
              Mask pixels with negative values.

       -z, --ignore-zero
              Mask pixels with a value of zero.

       --ignore-mask
              Completely ignore mask associated to the input image.

       -M, --input-mask <image file>
              Input mask file to co-add to output image mask.

       -a, --apply-mask
              Apply  the  mask  to  the image, i.e. set the pixel values with non-null mask to be
              zero (by default, or any other value specified by "-m|--mask-value").

       -m, --mask-value <value>
              Override the default pixel value (zero) during explicit marking  of  masked  pixels
              (see also "-a|--apply-mask").

   Marking saturated pixels:
       -s <saturation-level>
              Saturation level.

       -S <image file>
              Image containing saturation level on a per pixel basis.

       --leak-left-right, --leak-lower-upper, --leak-any
              Readout direction, i.e. orientation of "blooming" stripes.

   Mask conversion and expansion:
       --convert <match>:<value>:<reset>:<set>
              Convert  masks:  from  a  mask  which matches to the <match>:<value> pair, i.e. the
              masks with the type of <match> have a value  of  <value>  the  masks  specified  by
              <reset> are cleared and the masks specified by <set> are set. The <match>, <value>,
              <reset> and <set> tags are comma-separated list of mask names (see below).

       -x, --expand <size>
              Expands the mask with the specified size. Applied after all of the  previous  steps
              were performed.

   Additional mask layers:
       -q, --mask-block block:<mask>:<x1>,<y1>:<x2>,<y2>
              Add a rectangular masked area with the specified mask <mask> and with the specified
              coordinates  (<x1>,<y1>:  lower-left   corner,   <x2>,<y2>:   upper-right   corner,
              inclusive).

       -q, --mask-block circle:<mask>:<xc>,<yc>:<radius>
              Add  a  circular  masked area with the specified mask <mask> and with the specified
              cenroid coordinates <xc>,<yc> and radius <radius>.

       -q, --mask-block pixel:<mask>:<x>,<y>
              Add a masked pixel with the specified mask  <mask>  to  the  specified  coordinates
              <x>,<y>.

       -q, --mask-block line:<mask>:<x1>,<y1>:<x2>,<y2>
              Add  a  masked  line with the specified mask <mask> connecting the points <x1>,<y1>
              and <x2>,<y2>.

   Mask names:
       none   no mask at all

       clear  same as "none"

       fault  mask for faulty pixels

       hot    mask for hot pixels

       cosmic mask for marking cosmic pixels

       outer  pixels originating from out of image areas

       oversaturated
              oversaturated pixels

       bloomed
              "bloomed" pixels (i.e. not oversaturated but neighbouring pixel(s) may be so)

       saturated
              oversaturated or bloomed pixels

       interpolated
              pixels having an interpolated value (e.g. hot or cosmic pixels are replaced by  the
              average value of the surrounding pixels).

REPORTING BUGS

       Report bugs to <apal@szofi.net>, see also https://fitsh.net/.

COPYRIGHT

       Copyright © 1996, 2002, 2004-2008, 2010-2016, 2018-2020; Pal, Andras <apal@szofi.net>