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>

fiign 0.9.4 (2021.01.24)                          January 2021                                          FIIGN(1)