FLAMES_OBS_REDCHAIN(7)

📦
version 6.1.8 · 2 versions
, in debian bookworm, ubuntu noble

💖 FLAMES_OBS_REDCHAIN(7) 💖

okay bestie, welcome to the uves recipes manual page for flames_obs_redchain ✨ this is part 1 of 5, so we are not signing off, we are just getting started. Grab a snack 🍓 and let's get into the lore.

✨ NAME ✨

flames_obs_redchain — runs the full UVES-FIBRE reduction chain 💅

🦋 SYNOPSIS 🦋

esorex flames_obs_redchain [OPTIONS] FILE.sof

🌈 DESCRIPTION 🌈

okay so this recipe does a complete science reduction 🔥. It runs all the necessary calibration recipes depending on the availability of raw/processed calibration frames, periodt.

Input frames are all UVES-FIBER raw and reference frames: formatchecks, FIB_ARC_LAMP_FORM_RED, order definition frames, FIB_ORDER_FLAT_RED, biases, BIAS_RED, darks, DARK_RED, flats, SFLAT_RED, arc lamps, FIB_ARC_LAMP_RED, standard stars, FIB_STANDARD_RED, a wavelength catalogue table, LINE_REFER_TABLE, and optionally a wavelength table of bright lines, LINE_INTMON_TABLE, used only for computing Quality Control parameters.

Also a reference standard star flux table, FLUX_STD_TABLE, and a table describing the atmospheric extintion, EXTCOEFF_TABLE 🌸.

Optionally, science frames: SCIENCE_xxx, or UVES_SCI_POINT_xxx, or UVES_SCI_EXTND_xxx, or UVES_SCI_SLICER_xxx ✨.

For further details on the data reduction and the input frame types, refer to the man page of the individual recipes, bestie 🫶.

👑 OPTIONS 👑

  • --debug <bool> — whether or not to save intermediate results to local directory. It's a bool; default: False. The full name of this option for the EsoRex configuration file is uves.debug [default = False]. 💾
  • --flames_cal_orderpos.backsubdegx <int> — degree (in x) of polynomial used to estimate the background (mode=poly). It's an int; default: 2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubdegx [default = 2]. ✨
  • --flames_cal_orderpos.backsubdegy <int> — degree (in y) of polynomial used to estimate the background (mode=poly). It's an int; default: 2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubdegy [default = 2]. ✨
  • --flames_cal_orderpos.backsubgrid <int> — number of grid points (in x- and y-direction) used to estimate the background (mode=poly). It's an int; default: 50. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubgrid [default = 50]. 🎀
  • --flames_cal_orderpos.backsubkappa <float> — the value of kappa in the one-sided kappa-sigma clipping used to estimate the background (mode=poly). It's a float; default: 4.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubkappa [default = 4.0]. 🧚
  • --flames_cal_orderpos.backsubradiusy <int> — the height (in pixels) of the background sampling window is (2*radiusy + 1). This parameter is not corrected for binning. It's an int; default: 2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubradiusy [default = 2]. 📏
  • --flames_cal_orderpos.defpol1 <int> — the degree of the bivarite fit (cross dispersion direction). If negative, the degree is optimized to give the best fit. It's an int; default: -1. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.reject.defpol1 [default = -1]. 🦋
  • --flames_cal_orderpos.defpol2 <int> — the degree of the bivarite fit (order number). If negative, the degree is optimized to give the best fit. It's an int; default: -1. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.reject.defpol2 [default = -1]. 🦋
  • --flames_cal_orderpos.kappa <float> — used for kappa-sigma clipping of the final polynomial fit. If negative, no clipping is done. It's a float; default: 4.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.reject.kappa [default = 4.0]. ✂️
  • --flames_cal_orderpos.maxgap <float> — if the order line drops below detection threshold, the order tracing algorithm will try to jump a gap of maximum size ´maxgap´ multiplied by the image width. It's a float; default: 0.2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.trace.maxgap [default = 0.2]. 🕳️
  • --flames_cal_orderpos.maxrms <float> — when fitting the orders with straight lines, this is the maximum allowed RMS relative to the median RMS of all orders. It's a float; default: 100.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.reject.maxrms [default = 100.0]. 📈
  • --flames_cal_orderpos.maxslope <float> — maximum possible line slope. It's a float; default: 0.2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.hough.maxslope [default = 0.2]. 📐
  • --flames_cal_orderpos.minslope <float> — minimum possible line slope. This should be the ´physical´ slope on the chip, i.e. not taking binning factors into account, which is handled by the recipe. It's a float; default: 0.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.hough.minslope [default = 0.0]. 📐
  • --flames_cal_orderpos.minthresh <float> — the minimum threshold value is (min + minthres*(max - min)). Here ´min´ and ´max´ are the lowest and highest pixel values in the central bin of the order. It's a float; default: 0.2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.trace.minthresh [default = 0.2]. 🍓
  • --flames_cal_orderpos.mmethod <str> — background subtraction method. If equal to ´median´, the background is sampled using the median of a sub-window. If ´minimum´, the minimum sub-window value is used. If ´no´, no background subtraction is done. It's a str; default: ´median´. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.mmethod [default = median]. 🧼
  • --flames_cal_orderpos.pthres <float> — in automatic mode, or if the number of orders to detect is read from a guess table, the detection of new lines stops when the intensity of a candidate line drops to less than ´pthres´ times the intensity of the previous detection. It's a float; default: 0.2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.hough.pthres [default = 0.2]. 🛑
  • --flames_cal_orderpos.radx <int> — half X size of median filtering window. It's an int; default: 2. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.radx [default = 2]. 🌸
  • --flames_cal_orderpos.rady <int> — half Y size of median filtering window. It's an int; default: 1. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.rady [default = 1]. 🌸
  • --flames_cal_orderpos.samplewidth <int> — separation of sample traces (used by Hough transform) in input image. It's an int; default: 50. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.hough.samplewidth [default = 50]. 🎀
  • --flames_cal_orderpos.sloperes <int> — resolution (width in pixels) of Hough space. It's an int; default: 120. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.hough.sloperes [default = 120]. ✨
  • --flames_cal_orderpos.tracestep <int> — the step size used when tracing the orders. It's an int; default: 10. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.trace.tracestep [default = 10]. 👣
  • --flames_cal_orderpos.use_guess_tab <int> — if a Guess order table is provided, this parameter sets how it is used: 0: No usage, 1: use it to set lower/upper Y raws where order are searched, 2: the order table try to fully match the guess. It's an int; default: 1. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.use_guess_tab [default = 1]. 🔮
  • --flames_cal_predict.ccd_rot_angle_off <float> — offset on CCD rotation angle. It's a float; default: 0.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.ccd_rot_angle_off [default = 0.0]. 🔄
  • --flames_cal_predict.cd_angle_off <float> — offset on cross disperser angle. It's a float; default: 0.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.cd_angle_off [default = 0.0]. 🔄
  • --flames_cal_predict.compute_regression_sw <bool> — compute regression? It's a bool; default: True. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.compute_regression_sw [default = True]. 📊
  • --flames_cal_predict.def_pol1 <int> — polynomial X deg. It's an int; default: 4. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.def_pol1 [default = 4]. 🧮
  • --flames_cal_predict.def_pol2 <int> — polynomial Y deg. It's an int; default: 5. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.def_pol2 [default = 5]. 🧮
  • --flames_cal_predict.ech_angle_off <float> — offset on echelle angle. It's a float; default: 0.0. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.ech_angle_off [default = 0.0]. 📐
  • --flames_cal_predict.kappa <float> — kappa value in kappa sigma clipping on RESIDUAL between YFIT and Y columns. It's a float; default: 4.5. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.kappa [default = 4.5]. ✂️
  • --flames_cal_predict.mbox_x <int> — match box X size. It's an int; default: 40. The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.mbox_x [default = 40]. 📦
okay bestie we're still in the options, stay with me, we're almost through the flames_cal_predict and flames_cal_prep_sff_ofpos chunks and then it's wavecal hours ✨
  • --flames_cal_predict.mbox_y <int> — the match box Y size, so like how tall the little box is that we go matching in. Takes an int, default is 40. EsoRex config file full name: flames_obs_redchain.flames_cal_predict.mbox_y [default = 40].
  • --flames_cal_predict.tol <float> — the tolerance for kappa sigma clipping on the RESIDUAL between the YFIT and Y columns. Takes a float, default is 2.0. EsoRex config file full name: flames_obs_redchain.flames_cal_predict.tol [default = 2.0].
  • --flames_cal_predict.trans_x <float> — detector translation along X, literally just nudging the detector sideways. Takes a float, default is 0.0. EsoRex config file full name: flames_obs_redchain.flames_cal_predict.trans_x [default = 0.0].
  • --flames_cal_predict.trans_y <float> — same energy but along Y, detector translation up/down. Takes a float, default is 0.0. EsoRex config file full name: flames_obs_redchain.flames_cal_predict.trans_y [default = 0.0].

🧼 the flames_cal_prep_sff_ofpos era 🧼

  • --flames_cal_prep_sff_ofpos.bias_method <str> — which bias subtraction method we're doing. M for master bias frame, N for no bias subtraction at all, V to subtract a constant bias level defined by the bias_value parameter. Takes a str, default is M. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_method [default = M].
  • --flames_cal_prep_sff_ofpos.bias_value <int> — the bias value, and heads up, this one only applies if bias_method = V. Takes an int, default is 200. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_value [default = 200].
  • --flames_cal_prep_sff_ofpos.clean_tmp_products <bool> — described as "Input data format", which is a whole vibe, but that's what it says. Takes a bool, default is False. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.clean_tmp_products [default = False].
  • --flames_cal_prep_sff_ofpos.cubify <bool> — the cubify switch. Flip it, cubes happen. Takes a bool, default is True. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.cubify [default = True].
  • --flames_cal_prep_sff_ofpos.ext_method <str> — the extraction method. Takes a str, default is opt. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.ext_method [default = opt].
  • --flames_cal_prep_sff_ofpos.fileprep <bool> — Slitff* and Fibreff* file preparation. ⚠️ bestie listen: if the fast extraction method is used, this should be set to FALSE. Takes a bool, default is True. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.fileprep [default = True].
  • --flames_cal_prep_sff_ofpos.filter_switch <str> — the filter switch. Takes a str, default is none. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.filter_switch [default = none].
  • --flames_cal_prep_sff_ofpos.sat_thr <int> — saturation threshold, i.e. the number where we're like "ok that pixel is cooked". Takes an int, default is 55000. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.sat_thr [default = 55000].
  • --flames_cal_prep_sff_ofpos.save_flat_size <int> — to be sure you use the flat part of a slit flat, you may need to subtract this bit. The default value -1 is used for automatic setting: if WCEN=520 then save_flat_size=0, else save_flat_size=2. And values explicitly set by the user overwrite this rule. Takes an int, default is -1. EsoRex config file full name: flames_obs_redchain.flames_cal_prep_sff_ofpos.save_flat_size [default = -1].

🌈 the flames_cal_wavecal chapter, aka the main character 🌈

  • --flames_cal_wavecal.alpha <float> — the parameter that controls the distance to the nearest neighbours. Takes a float, default is 0.1. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.identify.alpha [default = 0.1].
  • --flames_cal_wavecal.degree <int> — degrees of the global 2d dispersion polynomial. And ooh, if you specify a negative number, the polynomial degrees get auto-selected by starting from (1, 1) and increasing the degrees as long as the RMS residual decreases significantly. Takes an int, default is 4. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.identify.degree [default = 4].
  • --flames_cal_wavecal.extract.best <bool> — optimal extraction only, bestie. If false (the fastest option), the spectrum is extracted only once. If true (the best option), the spectrum is extracted twice, the second time using improved variance estimates based on the first iteration. Better variance estimates slightly improve the obtained signal to noise, but at the cost of increased execution time. Takes a bool, default is True. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.best [default = True].
  • --flames_cal_wavecal.extract.chunk <int> — in optimal extraction mode, the chunk size (in pixels) used for fitting the analytical profile, because apparently fitting the analytical profile to single bins would suffer from low statistics. Takes an int, default is 32. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.chunk [default = 32].
  • --flames_cal_wavecal.extract.kappa <float> — in optimal extraction mode, this is the threshold for bad (i.e. hot/cold) pixel rejection. If a pixel deviates more than kappa*sigma (where sigma is the uncertainty of the pixel flux) from the inferred spatial profile, its weight is set to zero. Range: [-1,100]. If this parameter is negative, no rejection is performed. Takes a float, default is 10.0. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.kappa [default = 10.0].
  • --flames_cal_wavecal.extract.method <str> — the extraction method. Important receipts here: 2d/optimal are not supported by uves_cal_wavecal, weighted is supported only by uves_cal_wavecal, and 2d is not supported by uves_cal_response. Takes a str, default is average. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.method [default = average].
  • --flames_cal_wavecal.extract.oversample <int> — the oversampling factor used for the virtual resampling algorithm. If negative, the value 5 is used for S/N <=200, and the value 10 is used if the estimated S/N is > 200. Takes an int, default is -1. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.oversample [default = -1].
  • --flames_cal_wavecal.extract.profile <str> — in optimal extraction mode, the kind of profile to use. gauss gives a Gaussian profile. moffat gives a Moffat profile with beta=4 and a possible linear sky contribution. virtual uses a virtual resampling algorithm (i.e. it measures and uses the actual object profile). constant assumes a constant spatial profile and allows optimal extraction of wavelength calibration frames. auto will automatically select the best method based on the estimated S/N of the object. For low S/N, moffat or gauss are recommended (for robustness). For high S/N, virtual is recommended (for accuracy). In the case of virtual resampling, a precise determination of the order positions is required, so the order-definition is repeated using the (assumed non-low S/N) science frame. Takes a str, default is auto. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.profile [default = auto].
  • --flames_cal_wavecal.extract.skymethod <str> — in optimal extraction mode, the sky subtraction method to use. median estimates the sky as the median of pixels along the slit (ignoring pixels close to the object), whereas optimal does a chi square minimization along the slit to obtain the best combined object and sky levels. The optimal method gives the most accurate sky determination but is also a bit slower than the median method. Takes a str, default is optimal. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.extract.skymethod [default = optimal].
  • --flames_cal_wavecal.kappa <float> — lines with residuals more than kappa stdev get rejected from the final fit. bye felicia 💅 Takes a float, default is 4.0. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.calibrate.kappa [default = 4.0].
  • --flames_cal_wavecal.length <float> — length (in pixels) of each extraction window. This parameter is also equal to the separation of adjacent window centers, which causes the extraction windows to always be aligned. The parameter is automatically adjusted according to the binning of the input raw frame. If negative, the extraction window length is determined automatically to cover the full slit. Takes a float, default is 7.0. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.length [default = 7.0].
  • --flames_cal_wavecal.maxerror <float> — this parameter controls the graceful exit of the identification loop. If the RMS of the global fit exceeds this value (in pix), the iteration stops. Takes a float, default is 20.0. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.identify.maxerror [default = 20.0].
  • --flames_cal_wavecal.maxlines <int> — maximum number of lines to detect. If zero, the default value is used, and those defaults are 1600 for the BLUE/REDL chip and 1400 for the REDU chip. Takes an int, default is 0. EsoRex config file full name: flames_obs_redchain.flames_cal_wavecal.search.maxlines [default = 0].
  • --flames_cal_wavecal.minlines <int> — bestie, this is the minimum number of lines we're willing to accept for detection. If you set it to zero, we just fall back to the default: 1100 for BLUE/REDL chips, and 1000 for the REDU chip. It's an int, default 0. EsoRex config file name, full and unhinged: flames_obs_redchain.flames_cal_wavecal.search.minlines [default = 0].
  • --flames_cal_wavecal.nwindows <int> — how many extraction windows per trace, queen. And the windows are aligned — no overlap, no gaps between neighbours, they're all sitting shoulder to shoulder 💅. Unless you hand over an offset, the middle window(s) gets centered right on the trace. It's an int, default 1. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.nwindows [default = 1].
  • --flames_cal_wavecal.offset <float> — a global offset, in pixels, applied to all the extraction windows. It's a float, default 0.0. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.offset [default = 0.0].
  • --flames_cal_wavecal.range <int> — the width of the search window in pixels is 2*range + 1. And heads up, this one gets auto-adjusted according to binning, it's not just gonna sit there static. It's an int, default 8. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.search.range [default = 8].
  • --flames_cal_wavecal.rebin.scale <bool> — okay so this is a yes/no: do we multiply by the factor dx/dlambda (pixels per wavelength) while rebinning, to conserve flux? And the answer by default is no, because applying the flat field correction already conserves flux for us — no cap 🫶. So this parameter should only be TRUE (for response and science data, bestie) if reduce.ffmethd = no. It's a bool, default False. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.rebin.scale [default = False].
  • --flames_cal_wavecal.rebin.wavestep <float> — the bin size used for BLUE/REDL data, measured in w.l.u. in wavelength space ✨. If it's negative, a step size of 2/3 * ( average pixel size ) gets used instead. It's a float, default -1.0. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.rebin.wavestep [default = -1.0].
  • --flames_cal_wavecal.rebin.wavestep_redu <float> — literally the same energy as the one above, except this bin size (in w.l.u., in wavelength space) is the one used for REDU data 🦋. If negative, 2/3 * ( average pixel size ) steps in. It's a float, default -1.0. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.rebin.wavestep_redu [default = -1.0].
  • --flames_cal_wavecal.shiftmax <float> — the maximum shift, in pixels, in either direction compared to the guess solution. Auto-corrected for binning, because of course it is. It's a float, default 10.0. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.first.shiftmax [default = 10.0].
  • --flames_cal_wavecal.shiftstep <float> — the step size, in pixels, used when hunting for the optimum shift 🔍. Also auto-corrected for binning. It's a float, default 0.1. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.first.shiftstep [default = 0.1].
  • --flames_cal_wavecal.shifttoler <float> — the tolerance, in pixels, for matching shifted lines. And plot twist: this one is not adjusted according to binning, unlike its little friends above. It's a float, default 0.05. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.first.shifttoler [default = 0.05].
  • --flames_cal_wavecal.tolerance <float> — the tolerance of the fit, and here's the vibe: if it's positive, the tolerance is in pixel units. If it's negative, then abs(tolerance) is in wavelength units. Lines whose residuals are worse than the tolerance get yeeted from the final fit 🙈. And not like the previous versions, this parameter is not corrected for CCD binning. If you wanna effectively disable this whole absolute-residual-in-pixel rejection situation, set the tolerance to a very large number (like 9999) — then outliers only get rejected using kappa sigma clipping. It's a float, default 0.6. EsoRex config name: flames_obs_redchain.flames_cal_wavecal.calibrate.tolerance [default = 0.6].

okay and now we pivot into a whole different prefix, flames_obs_scired, stay with me bestie 💜

  • --flames_obs_scired.bias_method <str> — the bias subtraction method. It's a str, default ´M´. EsoRex config name: flames_obs_redchain.flames_obs_scired.bias_method [default = M].
  • --flames_obs_scired.bias_value <int> — the bias value, and heads up, this only matters if bias_method = V. It's an int, default 200. EsoRex config name: flames_obs_redchain.flames_obs_scired.bias_value [default = 200].
  • --flames_obs_scired.bkg_max_io_win <int> — background window number in each full inter order. It's an int, default 500. EsoRex config name: flames_obs_redchain.flames_obs_scired.bkg_max_io_win [default = 500].
  • --flames_obs_scired.bkg_xy_win_sz_x <int> — the x maximum size of each background window. It's an int, default 6. EsoRex config name: flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_x [default = 6].
  • --flames_obs_scired.bkg_xy_win_sz_y <int> — the y maximum size of each background window. It's an int, default 2. EsoRex config name: flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_y [default = 2].
  • --flames_obs_scired.clean_tmp_products <bool> — the description literally just says "Input data format" (iconic of it tbh), and it's a bool, default False. EsoRex config name: flames_obs_redchain.flames_obs_scired.clean_tmp_products [default = False].
  • --flames_obs_scired.cor_def_off <float> — correlation center offset? (the question mark is the original's, I'm just the messenger 🎀). It's a float, default 0.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.cor_def_off [default = 0.0].
  • --flames_obs_scired.cor_def_pnt <int> — correlation sampling points? Again, question mark is theirs. It's an int, default 25. EsoRex config name: flames_obs_redchain.flames_obs_scired.cor_def_pnt [default = 25].
  • --flames_obs_scired.cor_def_rng <float> — correlation range size? Yes bestie, question mark. It's a float, default 6.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.cor_def_rng [default = 6.0].
  • --flames_obs_scired.cor_max_fnd <str> — find correlation maximum? It's a str, default ´Y´. EsoRex config name: flames_obs_redchain.flames_obs_scired.cor_max_fnd [default = Y].
  • --flames_obs_scired.corvel_iter <int> — velocity correlation iteration number (SimCal). It's an int, default 1. EsoRex config name: flames_obs_redchain.flames_obs_scired.corvel_iter [default = 1].
  • --flames_obs_scired.cubify_sw <str> — the cubify switch. It's a str, default ´N´. EsoRex config name: flames_obs_redchain.flames_obs_scired.cubify_sw [default = N].
  • --flames_obs_scired.drs_base_name <str> — base name for science products. It's a str, default ´fxb´. EsoRex config name: flames_obs_redchain.flames_obs_scired.drs_base_name [default = fxb].
  • --flames_obs_scired.drs_ext_w_siz <float> — integration window size, and the original says good: 10, that's the value if fibre deconvolution works fine. It's a float, default 10.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.drs_ext_w_siz [default = 10.0].
  • --flames_obs_scired.drs_k_s_thre <float> — the kappa sigma threshold. It's a float, default 10.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.drs_k_s_thre [default = 10.0].
  • --flames_obs_scired.drs_maxyshift <float> — the half width of the interval to scan for correlation, used when determining the y shift. It's a float, default 3.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.drs_maxyshift [default = 3.0].
  • --flames_obs_scired.ext_method <str> — the extraction method. It's a str, default ´opt´. EsoRex config name: flames_obs_redchain.flames_obs_scired.ext_method [default = opt].
  • --flames_obs_scired.filt_sw <str> — the filter switch. It's a str, default ´none´. EsoRex config name: flames_obs_redchain.flames_obs_scired.filt_sw [default = none].
  • --flames_obs_scired.merge <str> — the order merging method, and this one actually has lore 📖. If it's ´optimal´, the flux in the overlapping region gets set to the (optimally computed, using the uncertainties) average of single order spectra. If it's ´sum´, the flux in that overlapping region is just computed as the sum of the single order spectra. And the tea: if flat-fielding is done, method ´optimal´ is the recommended one — otherwise go ´sum´. It's a str, default ´optimal´. EsoRex config name: flames_obs_redchain.flames_obs_scired.merge [default = optimal].
  • --flames_obs_scired.merge_delt1 <float> — the order merging left hand (short wavelength) cut. So basically, to reduce the amount of order overlapping regions, we're allowed to cut short and long wavelength ranges — and that may reduce the ripple that order merging possibly introduces. The suggested values are: 10 (W<=390), 12 (390<W<=437, 520<W<=564), 14 (437<W<=520, 564<W<860), 4 (W>=860). It's a float, default -1.0. EsoRex config name: flames_obs_redchain.flames_obs_scired.merge_delt1 [default = -1.0].
  • --flames_obs_scired.merge_delt2 <float> — this is the order-merging right hand (long wavelength) cut. The way it works is we're allowed to chop the short and long wavelength ranges short, and that shrinks the amount of order-overlapping regions, which lowkey might tone down the ripple that order merging can sneak in. Suggested value is 4 for W<860, otherwise 0. (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.merge_delt2 [default = -1.0].
  • --flames_obs_scired.pixel_thresh_max <int> — pixel saturation threshold max, no cap. (int; default: 55000). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.pixel_thresh_max [default = 55000].
  • --flames_obs_scired.pixel_thresh_min <int> — pixel saturation threshold min. (int; default: -20). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.pixel_thresh_min [default = -20].
  • --flames_obs_scired.rebin.scale <bool> — do we multiply by the factor dx/dlambda (that's pixels per wavelength) during the rebinning to conserve the flux, or not 💭. This one is disabled by default bc applying the flat field correction already handles flux conservation, so honestly it's covered. Which means this parameter should be TRUE (for response and science data) only if reduce.ffmethd = no. (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.rebin.scale [default = False].
  • --flames_obs_scired.rebin.wavestep <float> — the bin size used for BLUE/REDL data (in w.l.u.) in wavelength space ✨. If it's negative, a step size of 2/3 * ( average pixel size ) gets used. (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.rebin.wavestep [default = -1.0].
  • --flames_obs_scired.rebin.wavestep_redu <float> — same energy but for REDU data: the bin size in wavelength space (in w.l.u.). If negative, a step size of 2/3 * ( average pixel size ) is used. (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.rebin.wavestep_redu [default = -1.0].
  • --plotter <str> — any plots the recipe makes get redirected to whatever command you put here 🎨. Your plotting command must contain the substring gnuplot and must be able to parse gnuplot syntax on its standard input. Valid examples of such a command may include gnuplot -persist and cat > mygnuplot$$.gp. Want finer control over the plotting options? Write an executable script, e.g. my_gnuplot.pl, that executes gnuplot after setting the gnuplot options you want (e.g. set terminal pslatex color). To turn plotting off entirely, set this parameter to no. (str; default: no). The full name of this option for the EsoRex configuration file is uves.plotter [default = no].
  • --process_chip <str> — for RED arm data, process the redl, redu, or both chip(s). (str; default: both). The full name of this option for the EsoRex configuration file is uves.process_chip [default = both].
  • --scired <bool> — whether or not to do science reduction 🧪. If false, only master calibration frames are created. If false, either zero or all necessary calibration frames must be provided for each arm. (bool; default: True). The full name of this option for the EsoRex configuration file is flames_obs_redchain.scired [default = True].
  • --uves_cal_mbias.clean_traps <bool> — clean detector traps. If TRUE, detector traps are interpolated. The bad pixels are replaced by the average of the nearest good pixels in the same column, or simply marked as bad. The positions of bad pixels are hard-coded (as function of UVES chip). (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.clean_traps [default = False].
  • --uves_cal_mbias.dc_mask_x <int> — x-size (pixel) of the mask starting at (x,y) = (1,1). (int; default: 1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.dc_mask_x [default = 1].
  • --uves_cal_mbias.dc_mask_y <int> — y-size (pixel) of the mask starting at (x,y) = (1,1). (int; default: 1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.dc_mask_y [default = 1].
  • --uves_cal_mbias.khigh <float> — kappa used to clip high level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.khigh [default = 5.0].
  • --uves_cal_mbias.klow <float> — kappa used to clip low level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.klow [default = 5.0].
  • --uves_cal_mbias.niter <int> — number of kappa sigma iterations, when method is set to mean. (int; default: 5). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.niter [default = 5].
  • --uves_cal_mbias.pd_compute <bool> — determine Fixed Pattern Noise 🕵️. If TRUE, the Fixed Patter Noise power spectrum is determined (as function of UVES chip). (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.pd_compute [default = False].
  • --uves_cal_mbias.stack_method <str> — method used to build master frame. (str; default: median). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mbias.stack_method [default = median].
  • --uves_cal_mdark.khigh <float> — kappa used to clip high level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.khigh [default = 5.0].
  • --uves_cal_mdark.khigh <float> — okay bestie yes, it's listed again, and I'm not about to edit the manpage for it 💀 same deal: kappa used to clip high level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.khigh [default = 5.0].
  • --uves_cal_mdark.klow <float> — kappa used to clip low level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.klow [default = 5.0].
  • --uves_cal_mdark.klow <float> — and here it is again, same twin energy: kappa used to clip low level values, when method is set to mean. (float; default: 5.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.klow [default = 5.0].
  • --uves_cal_mdark.niter <int> — number of kappa sigma iterations, when method is set to mean. (int; default: 5). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.niter [default = 5].
  • --uves_cal_mdark.niter <int> — the sequel 🎬 number of kappa sigma iterations, when method is set to mean. (int; default: 5). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.niter [default = 5].
  • --uves_cal_mdark.qc_dark.reg.border_x <int> — X distance between the left hand side of the detector and the left hand side of the region [pix]. (int; default: 100). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.border_x [default = 100].
  • --uves_cal_mdark.qc_dark.reg.border_y <int> — X distance between the left hand side of the detector and the left hand side of the region [pix]. (int; default: 100). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.border_y [default = 100].
  • --uves_cal_mdark.qc_dark.reg.box_sx <int> — region X size [pix]. (int; default: 100). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.box_sx [default = 100].
  • --uves_cal_mdark.qc_dark.reg.box_sy <int> — region Y size [pix]. (int; default: 100). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.box_sy [default = 100].
  • --uves_cal_mdark.qc_dark.reg.num_x <int> — number of regions along the X axis (where mean/med/rms are computed). (int; default: 4). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.num_x [default = 4].
  • --uves_cal_mdark.qc_dark.reg.num_y <int> — number of regions along the Y axis (where mean/med/rms are computed). (int; default: 4). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.num_y [default = 4].
  • --uves_cal_mdark.qc_dark.reg.when <int> — when QC analysis is performed. 0: on each raw frame, or 1: on the master frame. (int; default: 0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.when [default = 0].
  • --uves_cal_mdark.stack_method <str> — method used to build master frame. (str; default: median). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.stack_method [default = median].
  • --uves_cal_mdark.stack_method <str> — and one more time for the people in the back 📣 method used to build master frame. (str; default: median). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.stack_method [default = median].
  • --uves_cal_mflat.backsub.mmethod <str> — the whole entire vibe for how we measure the background, bestie. Set it to median and we sample the background using the median of a subwindow. Set it to minimum and we grab the subwindow's minimum value instead. Set it to no and… we do absolutely no background subtraction at all, it's giving raw. (str; default: median). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.mmethod [default = median].
  • --uves_cal_mflat.backsub.npoints <int> — how many columns in interorder space we use to sample the background. That's it, that's the whole job. (int; default: 82). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.npoints [default = 82].
  • --uves_cal_mflat.backsub.radiusy <int> — the height (in pixels) of the background sampling window, and the way that math works is literally (2*radiusy + 1). 🎀 Heads up though: this parameter is not corrected for binning. (int; default: 2). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.radiusy [default = 2].
  • --uves_cal_mflat.backsub.sdegree <int> — the degree of the interpolating splines. And here's the tea: currently only degree = 1 is supported. Just the one. (int; default: 1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.sdegree [default = 1].
  • --uves_cal_mflat.backsub.smoothx <float> — if spline interpolation is used to measure the background, the x-radius of the post-smoothing window is (smoothx * image_width). And image_width here means the image width after binning, okay, don't forget that part. If it's negative, we fall back to the default values, which are: (25.0/4096) for blue flat-field frames, (50.0/4096) for red flat-field frames, (300.0/4096) for blue science frames, and (300.0/4096) for red science frames. (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.smoothx [default = -1.0].
  • --uves_cal_mflat.backsub.smoothy <float> — same energy as smoothx but for y, bestie. If spline interpolation is used to measure the background, the y-radius of the post-smoothing window is (smoothy * image_height). Here image_height is the image height after binning. If negative, the defaults kick in: (100.0/2048) for blue flat-field frames, (300.0/2048) for red flat-field frames, (200.0/2048) for blue science frames, and (500.0/2048) for red science frames. (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.backsub.smoothy [default = -1.0].
  • --uves_cal_mflat.norm_method <str> — the method used to build the master frame. Periodt. (str; default: explevel). The full name of this option for the EsoRex configuration file is flames_obs_redchain.uves_cal_mflat.norm_method [default = explevel].

okay so quick lil PSA 🫶 — it is possible to create a configuration file containing these options, along with suitable default values. Just go check out the details provided by the 'esorex --help' command, she'll tell you everything.

🌈 SEE ALSO 🌈

The full documentation for the uves pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/uves/uves-pipeline-manual-6.1.8.pdf

An overview over the existing ESO pipelines can be found on the web page https://www.eso.org/sci/software/pipelines/.

Basic documentation about the EsoRex program can be found at the esorex (1) man page. Iconic.

It is possible to call the pipelines from python using the python-cpl package. See https://packages.python.org/python-cpl/index.html for further information. 💅

The other recipes of the uves pipeline are flames_cal_mkmaster(7), flames_cal_orderpos(7), flames_cal_predict(7), flames_cal_prep_sff_ofpos(7), flames_cal_wavecal(7), flames_obs_scired(7), flames_utl_unpack(7), uves_cal_cd_align(7), uves_cal_mbias(7), uves_cal_mdark(7), uves_cal_mflat(7), uves_cal_mflat_combine(7), uves_cal_mkmaster(7), uves_cal_orderpos(7), uves_cal_predict(7), uves_cal_response(7), uves_cal_tflat(7), uves_cal_wavecal(7), uves_obs_redchain(7), uves_obs_scired(7), uves_utl_ima_arith(7), uves_utl_remove_crh_single(7)

⭐ VERSION ⭐

flames_obs_redchain 6.1.8

👑 AUTHOR 👑

Jonas M. Larsen <cpl@eso.org>

💖 BUG REPORTS 💖

Please report any problems to cpl@eso.org. Alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>.

📜 LICENSE 📜

This file is part of the FLAMES/UVES Pipeline Copyright (C) 2004, 2005, 2006, 2007 European Southern Observatory

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA

and that's the whole page, bestie, we did it 🎉💅✨ This lil masterpiece is flames_obs_redchain version 6.1.8, living its best life as FLAMES_OBS_REDCHAIN(7) — go forth and reduce that red chain, you absolute icon 🦋💜

📦 where this page comes from