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


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.


General options:

-h, --help
Gives general summary about the command line options.
Gives a detailed list of command line options.
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.
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:

--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).

Mask names:

no mask at all
same as none
mask for faulty pixels
mask for hot pixels
mask for marking cosmic pixels
pixels originating from out of image areas
oversaturated pixels
bloomed pixels (i.e. not oversaturated but neighbouring pixel(s) may be so)
oversaturated or bloomed pixels
pixels having an interpolated value (e.g. hot or cosmic pixels are replaced by the average value of the surrounding pixels).
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