Name
deadpix - bad pixel map handling
Synopsis
deadpix [parameters]
Description
deadpix is a tool to generate bad pixel maps from images of the sky
background in infrared. It can also be used to remove bad pixel contri-
butions in a frame by applying a bad pixel map on it.
Methods offered by this tool for bad pixel detection are not the best
ones, statistical studies of a twilight data set usually brings a more
reliable information about pixel quality (see flat command). However,
these methods are still of some use when no other data are available
for calibration.
The skyvar method needs a sky cube, preferrably with many planes (>20)
to observe meaningful statistical behaviours.
The median method detects spikes in an image, it needs in input a small
number (<10) of flat frames.
The cleaning algorithm only requires a valid pixel map and a cube to
clean out.
Detection Algorithms
Two methods are implemented for bad pixel detection. They both make use
of sky images.
First method : sky variations statistics (skyvar method)
Let’s compute for each pixel its standard deviation along time. If we
plot a histogram of these standard deviations, we see a gaussian-shaped
function that represents the response to the sky signal. We decide to
throw away all pixels which response is too low (dead) or too high
(noisy) by rejecting all pixels out of a central +/- sigma_width/2
interval on the histogram. Default sigma_width is 3, it can be changed
by feeding a new sigma width through the -s option.
example:
> deadpix -d --skyvar --sigma 4 --sky skycube.fits
Second method : median filter detection (median method)
This method does not make use of temporal information, by merely
observes each image independently. If we assume that the signal is
smooth enough, bad pixels are spikes easily found by computing the dif-
ference between the image and its median filtered version, and thresh-
olding it. All spikes are then detected. This is not as strong as using
the temporal information, but this is the only way when not enough
images are present. Default threshold is fixed to 10.0, it can be
changed by using the -m option. This threshold is given directly in
pixel values.
example:
> deadpix -d --median --threshold 15 --sky skyplanes.fits
Cleaning Algorithm
The algorithm used to clean out a plane from bad pixels is simple. It
just replaces bad pixel positions by an average of the valid pixels out
of the 8 closest neighbours. If no value is available, the pixel is set
to null.
example:
> deadpix --clean --in toclean.fits --pixmap badpixmap
Parameters
First, choose between dead pixel detection and dead pixel cleaning
mode. This is done by activating either --detect/-d or --clean/-c com-
mand-line options.
Detection mode: --detect or -d
--skyvar or -m skyvar
This forces the use of the sky variation method for bad pixel
detection. An expected parameter is then --sigma.
--sigma value or -s value
This specifies the sigma threshold for the sky variation method.
Default value is 3.0.
--median or -m median
This forces the use of the median method for bad pixel detec-
tion. An expected parameter is then --threshold.
--threshold thr or -t thr
This specifies the median threshold for the median method.
Default value is thr=10.
--sky name or -S name
Specifies the name of the file which contains the sky planes to
work with. This is used by both detection methods.
Cleaning mode: --clean or -c
--in name or -i name
Specifies the name of the input file to clean out.
--out name or -o name
Specifies the name of the output file to create. This is
optional, default naming scheme for input files named *.fits is
*.cln.fits.
Parameters common to both modes
--pixmap name or -p name
This specifies the name of a pixel map. In detection mode, this
is an output since the goal of the detection is to produce a bad
pixel map. In cleaning mode, this is an input which is used to
clean out other files.
Files
Input files shall all comply with FITS format. Pixel maps are in 8 bit
FITS format.
In a bad pixel map, good pixels are set to 1, bad pixels are set to 0.
This can also be found in bad pixel map FITS headers, where the follow-
ing keywords are written:
GOODPIX = 1
BADPIX = 0
Notice
Pixel maps are in 8 bits signed FITS format. They can be easily viewed
that way.
See Also
flat
Author
N. Devillard -- ESO