DOKK / manpages / debian 10 / cpl-plugin-uves-doc / flames_obs_redchain.7.en
FLAMES_OBS_REDCHAIN(7) uves recipes FLAMES_OBS_REDCHAIN(7)

flames_obs_redchain - Runs the full UVES-FIBRE reduction chain

esorex flames_obs_redchain [OPTIONS] FILE.sof

This recipe does a complete science reduction. It runs all necessary calibration recipes depending on the availability of raw/processed calibration frames.

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.

a reference standard star flux table, FLUX_STD_TABLE, 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.

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].
Whether or not to save intermediate results to local directory (bool; default: False). The full name of this option for the EsoRex configuration file is uves.debug [default = False].
Any plots produced by the recipe are redirected to the command specified by this parameter. The 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´. A finer control of the plotting options can be obtained by writing an executable script, e.g. my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options (e.g. set terminal pslatex color). To turn off plotting, set this parameter to ´no´ (str; default: ´no´). The full name of this option for the EsoRex configuration file is uves.plotter [default = no].
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].
If a Guess order table is provided this parameter set 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 (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].
Half X size of median filtering window (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].
Half Y size of median filtering window (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].
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. (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].
Number of grid points (in x- and y-direction) used to estimate the background (mode=poly). (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].
The height (in pixels) of the background sampling window is (2*radiusy + 1). 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.flames_cal_orderpos.preproc.backsubradiusy [default = 2].
The value of kappa in the one-sided kappa-sigma clipping used to estimate the background (mode=poly). (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].
Degree (in x) of polynomial used to estimate the background (mode=poly). (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].
Degree (in y) of polynomial used to estimate the background (mode=poly). (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].
Separation of sample traces (used by Hough transform) in input image (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].
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 (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].
Maximum possible line slope (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].
Resolution (width in pixels) of Hough space (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].
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. (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].
The step size used when tracing the orders (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].
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 (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].
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 (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].
When fitting the orders with straight lines, this is the maximum allowed RMS relative to the median RMS of all orders (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].
The degree of the bivarite fit (cross dispersion direction). If negative, the degree is optimized to give the best fit (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].
The degree of the bivarite fit (order number). If negative, the degree is optimized to give the best fit (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].
Used for kappa-sigma clipping of the final polynomial fit. If negative, no clipping is done (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].
Extraction method (str; default: ´opt´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.ext_method [default = opt].
Bias subtraction method, M for master bias frame, N for no bias subtraction, V to subtract a constant bias level defined by the parameter bias_value (str; default: ´M´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_method [default = M].
Bias value (only if bias_method = V) (int; default: 200). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_value [default = 200].
Filter switch (str; default: ´none´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.filter_switch [default = none].
Saturation threshold (int; default: 55000). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.sat_thr [default = 55000].
Slitff* and Fibreff* file preparation. If fast extraction method is used it should be set to FALSE (bool; default: True). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.fileprep [default = True].
Cubify switch (bool; default: True). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.cubify [default = True].
To be sure to use the flat part of a slit flatsone may need to subtract this bit. The default value -1, is used for automatic setting: if WCEN=520 save_flat_size=0, else save_flat_size=2. Values explicitly set by user overwrite this rule. (int; default: -1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.save_flat_size [default = -1].
Input data format (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.clean_tmp_products [default = False].
Match box X size (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].
Match box Y size (int; default: 40). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.mbox_y [default = 40].
Detector translation along X (float; default: 0.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.trans_x [default = 0.0].
Detector translation along Y (float; default: 0.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.trans_y [default = 0.0].
Offset on echelle angle (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].
Offset on cross disperser angle (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].
Offset on CCD rotation angle (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].
Compute regression? (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].
Polynomial X deg (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].
Polynomial Y deg (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].
Kappa value in kappa sigma clipping on RESIDUAL between YFIT and Y columns (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].
Tolerance in kappa sigma clipping on RESIDUAL between YFIT and Y columns (float; default: 2.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.tol [default = 2.0].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
Method used to build master frame (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].
Background measuring method. If equal to ´median´ the background is sampled using the median of a subwindow. If ´minimum´, the subwindow minimum value is used. If ´no´, no background subtraction is done. (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].
This is the number of columns in interorder space used to sample the background. (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].
The height (in pixels) of the background sampling window is (2*radiusy + 1). 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].
Degree of interpolating splines. Currently only degree = 1 is supported (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].
If spline interpolation is used to measure the background, the x-radius of the post-smoothing window is (smoothx * image_width). Here, ´image_width´ is the image width after binning. If negative, the default values are used: (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].
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 default values are used: (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].
Clean detector traps. If TRUE detector traps are interpolated.The bad pixels are replaced by the average of thenearest 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].
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].
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].
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].
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].
Extraction method (str; default: ´opt´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.ext_method [default = opt].
Find correlation maximum? (str; default: ´Y´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_max_fnd [default = Y].
Correlation range size? (float; default: 6.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_rng [default = 6.0].
Correlation sampling points? (int; default: 25). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_pnt [default = 25].
Correlation center offset? (float; default: 0.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_off [default = 0.0].
Velocity correlation iteration number (SimCal) (int; default: 1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.corvel_iter [default = 1].
Bias subtraction method (str; default: ´M´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bias_method [default = M].
Bias value (only if bias_method = V) (int; default: 200). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bias_value [default = 200].
Cubify switch (str; default: ´N´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cubify_sw [default = N].
Filter switch (str; default: ´none´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.filt_sw [default = none].
Background window number in each full inter order (int; default: 500). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bkg_max_io_win [default = 500].
x maximum size of each background window: (int; default: 6). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_x [default = 6].
y maximum size of each background window: (int; default: 2). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_y [default = 2].
Pixel saturation threshold max (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].
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].
Kappa sigma threshold (float; default: 10.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.drs_k_s_thre [default = 10.0].
Base name for science products (str; default: ´fxb´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.drs_base_name [default = fxb].
Half width of the interval to scan for correlation, when determining y shift (float; default: 3.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.drs_maxyshift [default = 3.0].
Integration window size good: 10 (if fibre deconvolution works fine) (float; default: 10.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.drs_ext_w_siz [default = 10.0].
Order merging method. If ´optimal´, the flux in the overlapping region is set to the (optimally computed, using the uncertainties) average of single order spectra. If ´sum´, the flux in the overlapping region is computed as the sum of the single order spectra. If flat-fielding is done, method ´optimal´ is recommended, otherwise ´sum´. (str; default: ´optimal´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.merge [default = optimal].
Order merging left hand (short wavelength) cut. To reduce the amount of order overlapping regions we allow to cut short and long wavelength ranges. This may reduce the ripple possibly introduced by the order merging. Suggested values are: 10 (W<=390), 12 (390<W<=437, 520<W<=564), 14 (437<W<=520, 564<W<860), 4 (W>=860) (float; default: -1.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.merge_delt1 [default = -1.0].
Order merging right hand (long wavelength) cut. To reduce the amount of order overlapping regions we allow to cut short and long wavelength ranges. This may reduce the ripple possibly introduced by the order merging. Suggested values is 4 for W<860, else 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].
Input data format (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.clean_tmp_products [default = False].
The bin size (in w.l.u.) in wavelength space. 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 [default = -1.0].
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during the rebinning. This option is disabled as default in concordance with the method used in the MIDAS pipeline. This option should be set to true to convert the observed flux (in pixel-space) to a flux per wavelength (in wavelength-space). (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].
Number of extraction windows per trace. The windows will be aligned (i.e. no overlap and no spacing between adjacent windows). Unless an offset is specified, the middle window(s) is centered on the trace (int; default: 1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.nwindows [default = 1].
Length (in pixels) of each extraction window. This parameter is also equal to the seperation of adjacent window centers, causing 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 (float; default: 7.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.length [default = 7.0].
A global offset (in pixels) of all extraction windows (float; default: 0.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.offset [default = 0.0].
Width (pix) of search window is 2*range + 1. This parameter is automatically adjusted according to binning. (int; default: 8). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.search.range [default = 8].
Minimum number of lines to detect. If zero, the default value (1100 for BLUE/REDL chips; 1000 for REDU chip) is used. (int; default: 0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.search.minlines [default = 0].
Maximum number of lines to detect. If zero, the default value (1600 for BLUE/REDL chip; 1400 for REDU chip) is used. (int; default: 0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.search.maxlines [default = 0].
The maximum shift (pix) in either direction compared to guess solution. This parameter is automatically corrected for binning (float; default: 10.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.first.shiftmax [default = 10.0].
The step size (pix) used when searching for the optimum shift. This parameter is automatically corrected for binning (float; default: 0.1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.first.shiftstep [default = 0.1].
Tolerance (pix) when matching shifted lines. This parameter is not adjusted according to binning (float; default: 0.05). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.first.shifttoler [default = 0.05].
The parameter that controls the distance to the nearest neighbours (float; default: 0.1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.identify.alpha [default = 0.1].
This parameter controls the graceful exit of the identification loop. If the RMS of the global fit exceeds this value (pix) the iteration stops (float; default: 20.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.identify.maxerror [default = 20.0].
Degrees of the global 2d dispersion polynomial. If a negative number is specified, the polynomial degrees are automatically selected by starting from (1, 1) and inreasing the degrees as long as the RMS residual decreases significantly (int; default: 4). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.identify.degree [default = 4].
Tolerance of fit. If positive, the tolerance is in pixel units. If negative, abs(tolerance) is in wavelength units. Lines with residuals worse than the tolerance are excluded from the final fit. Unlike in previous versions, this parameter is not corrected for CCD binning. This rejection based on the absolute residual in pixel can be effectively disabled by setting the tolerance to a very large number (e.g. 9999). In that case outliers will be rejected using only kappa sigma clipping. (float; default: 0.6). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.calibrate.tolerance [default = 0.6].
Lines with residuals more then kappa stdev are rejected from the final fit (float; default: 4.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.calibrate.kappa [default = 4.0].
Extraction method. (2d/optimal not supported by uves_cal_wavecal, weighted supported only by uves_cal_wavecal, 2d not supported by uves_cal_response) (str; default: ´average´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.method [default = average].
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. (float; default: 10.0). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.kappa [default = 10.0].
In optimal extraction mode, the chunk size (in pixels) used for fitting the analytical profile (a fit of the analytical profile to single bins would suffer from low statistics). (int; default: 32). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.chunk [default = 32].
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. 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; therefore the order-definition is repeated using the (assumed non-low S/N) science frame (str; default: ´auto´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.profile [default = auto].
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 (str; default: ´optimal´). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.skymethod [default = optimal].
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 (int; default: -1). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.oversample [default = -1].
(optimal extraction only) If false (fastest), the spectrum is extracted only once. If true (best), 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 (bool; default: True). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.extract.best [default = True].
The bin size (in w.l.u.) in wavelength space. 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_cal_wavecal.rebin.wavestep [default = -1.0].
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during the rebinning. This option is disabled as default in concordance with the method used in the MIDAS pipeline. This option should be set to true to convert the observed flux (in pixel-space) to a flux per wavelength (in wavelength-space). (bool; default: False). The full name of this option for the EsoRex configuration file is flames_obs_redchain.flames_cal_wavecal.rebin.scale [default = False].

Note that it is possible to create a configuration file containing these options, along with suitable default values. Please refer to the details provided by the 'esorex --help' command.

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-5.9.1.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.

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)

flames_obs_redchain 5.9.1

Jonas M. Larsen <cpl@eso.org>

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

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

5.9.1 flames_obs_redchain