apero_badpix_spirou¶
Contents¶
1. Description¶
SHORTNAME: BAD
Bad pixel calibration¶
The bad pixel recipe takes preprocessed DARK_DARK and FLAT_FLAT files (as many as given by the user or as many as occur on the nights being used via pre-processing). It combines all DARK_DARK files and all FLAT_FLAT files into a single DARK_DARK and a single FLAT_FLAT (via a median combination of the images). Bad pixels are then identified in the FLAT_FLAT by using Equation:
where \(FLAT_{i,j}\) is the flux in ith row jth column of the FLAT_FLAT image; \(FLAT_{\text{med }}\) is the median filtered flat image (using a filtering width of 7 pixels) and \(M_{\text{flat } i,j}\) is 1 to flag a bad pixel or 0 otherwise, cut_ratio is 0.5 (flagging pixels with a response less than 50 percent of their neighbors or unphysically brighter than neighbors) and illum_cut is 0.05 (flagging pixels at the edge of the blaze response). FLAT and \(FLAT_{\text{med }}\) have first been normalized by the $90^{rm th}$ percentile of flux in the median filtered flat image. Thus \(M_{\text{flat}}\) is a Boolean flag map of bad pixels on the flat image. For the DARK_DARK image, bad pixels are identified using Equation:
where \(DARK_{i,j}\) is the flux in the ith row jth column of the dark image. Thus \(M_{\text{dark}}\) is a Boolean flag map of bad pixels on the dark image. We choose a value of 5.0 ADU/s as it is representative of the pixel flux of a typical science target. Including pixels with a brighter level of dark current than this leads to a loss in SNR rather than a gain. We note that this threshold could be target-dependent but for simplicity we use a single value.
In addition to this bad pixels in a full detector engineering flat (FULLFLAT taken during commissioning) are also identified using Equation:
where \(FULLFLAT_{i,j}\) is the flux in ith row jth column of the full detector engineering flat. Thus \(M_{\text{full-flat}}\) is a Boolean flag map of bad pixels on the full detector engineering flat image. We chose 0.3 as this flagged the defective regions identified manually on the detector. The \(1 \sigma\) dispersion of the full detector engineering flat image is 2 percent.
These three bad pixel maps are then combined into a single bad pixel map.
2. Schematic¶
3. Usage¶
apero_badpix_spirou.py {obs_dir}[STRING] --flatfiles[FILE:FLAT_FLAT] --darkfiles[FILE:DARK_DARK_TEL,DARK_DARK_INT] {options}
{obs_dir}[STRING] // [STRING] The directory to find the data files in. Most of the time this is organised by nightly observation directory
--flatfiles[FILE:FLAT_FLAT] // Current allowed types: FLAT_FLAT
--darkfiles[FILE:DARK_DARK_TEL,DARK_DARK_INT] // Current allowed types: DARK_DARK
4. Optional Arguments¶
--database[True/False] // [BOOLEAN] Whether to add outputs to calibration database
--combine[True/False] // [BOOLEAN] Whether to combine fits files in file list or to process them separately
--flipimage[None,x,y,both] // [BOOLEAN] Whether to flip fits image
--fluxunits[ADU/s,e-] // [STRING] Output units for flux
--plot[0>INT>4] // [INTEGER] Plot level. 0 = off, 1 = interactively, 2 = save to file
--resize[True/False] // [BOOLEAN] Whether to resize image
--no_in_qc // Disable checking the quality control of input files
5. Special Arguments¶
--xhelp[STRING] // Extended help menu (with all advanced arguments)
--debug[STRING] // Activates debug mode (Advanced mode [INTEGER] value must be an integer greater than 0, setting the debug level)
--listing[STRING] // Lists the night name directories in the input directory if used without a 'directory' argument or lists the files in the given 'directory' (if defined). Only lists up to 15 files/directories
--listingall[STRING] // Lists ALL the night name directories in the input directory if used without a 'directory' argument or lists the files in the given 'directory' (if defined)
--version[STRING] // Displays the current version of this recipe.
--info[STRING] // Displays the short version of the help menu
--program[STRING] // [STRING] The name of the program to display and use (mostly for logging purpose) log becomes date | {THIS STRING} | Message
--recipe_kind[STRING] // [STRING] The recipe kind for this recipe run (normally only used in apero_processing.py)
--parallel[STRING] // [BOOL] If True this is a run in parellel - disable some features (normally only used in apero_processing.py)
--shortname[STRING] // [STRING] Set a shortname for a recipe to distinguish it from other runs - this is mainly for use with apero processing but will appear in the log database
--idebug[STRING] // [BOOLEAN] If True always returns to ipython (or python) at end (via ipdb or pdb)
--ref[STRING] // If set then recipe is a reference recipe (e.g. reference recipes write to calibration database as reference calibrations)
--crunfile[STRING] // Set a run file to override default arguments
--quiet[STRING] // Run recipe without start up text
--nosave // Do not save any outputs (debug/information run). Note some recipes require other recipesto be run. Only use --nosave after previous recipe runs have been run successfully at least once.
--force_indir[STRING] // [STRING] Force the default input directory (Normally set by recipe)
--force_outdir[STRING] // [STRING] Force the default output directory (Normally set by recipe)
6. Output directory¶
DRS_DATA_REDUC // Default: "red" directory
7. Output files¶
name |
description |
HDR[DRSOUTID] |
file type |
suffix |
dbname |
dbkey |
input file |
|---|---|---|---|---|---|---|---|
BADPIX |
Bad pixel map |
BADPIX |
.fits |
_badpixel |
calibration |
BADPIX |
FLAT_FLAT |
BKGRD_MAP |
Bad pixel background map |
BKGRD_MAP |
.fits |
_bmap.fits |
calibration |
BKGRDMAP |
FLAT_FLAT |
8. Debug plots¶
BADPIX_MAP
9. Summary plots¶
SUM_BADPIX_MAP