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 contributions 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 devia-
tions, 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 difference between the image
and its median filtered version, and thresholding 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 command-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 detection. 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 detec-
tion mode, this is an output since the goal of the
detection is to produce a bad pixel map. In clean-
ing 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 following 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
Nicolas Devillard, European Southern Observatory.
Part of eclipse Library