apero_extract_nirps_ha¶
Contents¶
1. Description¶
SHORTNAME: EXT
No description set
2. Schematic¶
No schematic set
3. Usage¶
apero_extract_nirps_ha.py {obs_dir}[STRING] [FILE:DRS_PP] {options}
{obs_dir}[STRING] // [STRING] The directory to find the data files in. Most of the time this is organised by nightly observation directory
[FILE:DRS_PP] // [STRING/STRINGS] A list of fits files to use separated by spaces. Current accepts all preprocessed filetypes. All files used will be combined into a single frame.
4. Optional Arguments¶
--quicklook[True/False] // [BOOLEAN] Sets whether extraction done in quick look mode
--badpixfile[FILE:BADPIX] // [STRING] Define a custom file to use for bad pixel correction. Checks for an absolute path and then checks 'directory'
--badcorr[True/False] // [BOOLEAN] Whether to correct for the bad pixel file
--backsub[True/False] // [BOOLEAN] Whether to do background subtraction
--blazefile[FILE:FF_BLAZE] // [STRING] Define a custom file to use for blaze correction. If unset uses closest file from calibDB. Checks for an absolute path and then checks 'directory' (CALIBDB=BADPIX)
--combine[True/False] // [BOOLEAN] Whether to combine fits files in file list or to process them separately
--combine_method[STRING] // Method to combine files (if --combine=True)
--objname[STRING] // Sets the object name to extract (filters input files)
--dprtype[STRING] // [STRING] Sets the DPRTYPE to extract (filters input files)
--darkfile[FILE:DARKREF] // [STRING] The Dark file to use (CALIBDB=DARKM)
--darkcorr[True/False] // [BOOLEAN] Whether to correct for the dark file
--fiber[ALL,A,B] // [STRING] Define which fibers to extract
--flipimage[None,x,y,both] // [BOOLEAN] Whether to flip fits image
--fluxunits[ADU/s,e-] // [STRING] Output units for flux
--flatfile[FILE:FF_FLAT] // [STRING] Define a custom file to use for flat correction. If unset uses closest file from calibDB. Checks for an absolute path and then checks 'directory'
--locofile[FILE:LOC_LOCO] // [STRING] Sets the LOCO file used to get the coefficients (CALIBDB=LOC_{fiber})
--orderpfile[FILE:LOC_ORDERP] // [STRING] Sets the Order Profile file used to get the coefficients (CALIBDB=ORDER_PROFILE_{fiber}
--plot[0>INT>4] // [INTEGER] Plot level. 0 = off, 1 = interactively, 2 = save to file
--resize[True/False] // [BOOLEAN] Whether to resize image
--shapex[FILE:SHAPE_X] // [STRING] Sets the SHAPE DXMAP file used to get the dx correction map (CALIBDB=SHAPEX)
--shapey[FILE:SHAPE_Y] // [STRING] Sets the SHAPE DYMAP file used to get the dy correction map (CALIBDB=SHAPEY)
--shapel[FILE:SHAPEL] // [STRING] Sets the SHAPE local file used to get the local transforms (CALIBDB = SHAPEL)
--leakcorr[True/False] // [BOOLEAN] Sets whether to do the leak correction (else defaults to CORRECT_LEAKAGE value in constants)
--wavefile[FILE:WAVESOL_REF,WAVE_NIGHT,WAVESOL_DEFAULT] // [STRING] Define a custom file to use for the wave solution. If unset uses closest file from header or calibDB (depending on setup). Checks for an absolute path and then checks 'directory'
--force_ref_wave // Force using the reference wave solution
--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 |
fibers |
input file |
|---|---|---|---|---|---|---|
EXT_E2DS |
Extracted 2D spectrum |
EXT_E2DS |
.fits |
_e2ds |
A, B |
DRS_PP |
EXT_E2DS_FF |
Extracted + flat-fielded 2D spectrum |
EXT_E2DS_FF |
.fits |
_e2dsff |
A, B |
DRS_PP |
EXT_E2DS_LL |
Pre-extracted straighted stacked spectrum |
EXT_E2DS_LL |
.fits |
_e2dsll |
A, B |
DRS_PP, FLAT_FLAT |
EXT_S1D_W |
1D stitched spectrum (constant wavelength binning) |
EXT_S1D_W |
.fits |
_s1d_w |
A, B |
DRS_PP |
EXT_S1D_V |
1D stitched spectrum (constant velocity binning) |
EXT_S1D_V |
.fits |
_s1d_v |
A, B |
DRS_PP |
ORDERP_STRAIGHT |
Straightened order profile for an individual image |
ORDERP_STRAIGHT |
.fits |
_orderps |
A, B |
SHAPEL |
DEBUG_BACK |
Individual file background map |
DEBUG_BACK |
.fits |
_background.fits |
– |
DRS_PP |
EXT_FPLIST |
FP lines identified from extracted FP fiber |
EXT_FPLIST |
.fits |
_ext_fplines |
A, B |
EXT_E2DS, EXT_E2DS_FF |
QL_E2DS |
Extracted 2D spectrum (quick output) |
QL_E2DS |
.fits |
_q2ds |
A, B |
DRS_PP |
QL_E2DS_FF |
Extracted + flat-fielded 2D spectrum (quick output) |
QL_E2DS_FF |
.fits |
_q2dsff |
A, B |
DRS_PP |
8. Debug plots¶
FLAT_ORDER_FIT_EDGES1
FLAT_ORDER_FIT_EDGES2
FLAT_BLAZE_ORDER1
FLAT_BLAZE_ORDER2
THERMAL_BACKGROUND
EXTRACT_SPECTRAL_ORDER1
EXTRACT_SPECTRAL_ORDER2
EXTRACT_S1D
EXTRACT_S1D_WEIGHT
WAVEREF_EXPECTED
9. Summary plots¶
SUM_FLAT_ORDER_FIT_EDGES
SUM_EXTRACT_SP_ORDER
SUM_EXTRACT_S1D