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 qual- ity (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 pix- els 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 varia- tion 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 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 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 N. Devillard -- ESO