Scroll to navigation

SINFO_REC_DISTORTION(7) sinfo recipes SINFO_REC_DISTORTION(7)

NAME

sinfo_rec_distortion - Finds optical distortions and slitlets distances

SYNOPSIS

esorex sinfo_rec_distortion [OPTIONS] FILE.sof

DESCRIPTION

This recipe determines the optical distortions and the slitlets distances.

Necessary input are: Several (usually 75) raw frames classified as FIBRE_NS Standard (an ´ON´ and an ´OFF´) flat frames having classified as FLAT_NS Standard (an ´ON´ and an ´OFF´) arc lamp frames having classified as WAVE_NS A corresponding (band) reference arc line list classified as REF_LINE_ARC A reference table with data reduction parameters classified as DRS_SETUP_WAVE.

Default output are (with their PRO.CATG) A master flat: MASTER_FLAT_LAMP A Bad pixel map: BP_MAP_DI A fake-off fibre stacked frame: FIBRE_NS_STACKED_OFF A fake-on fibre stacked frame: FIBRE_NS_STACKED_ON A fake on-off fibre stacked frame: FIBRE_NS_STACKED A table with optical distortion coefficients: DISTORTION A distortion corrected frame: FIBRE_NS_STACKED_DIST A temporary frame: MASTER_SLIT A table with the slitlets distances: SLITLETS_DISTANCE

OPTIONS

Overwrite DRS ini parameters: (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.general.overwrite_parameters [default = True].
Correct for bad lines introduced by instrument software: (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.general.lc_sw [default = False].
Kappa sigma value (int; default: 18). The full name of this option for the EsoRex configuration file is sinfoni.general.lc_kappa [default = 18].
Filtering radii applied during median filter. Should be small (int; default: 3). The full name of this option for the EsoRex configuration file is sinfoni.general.lc_filt_rad [default = 3].
Density of pipeline products: 0 (low), 1 (low+skycor), 2 (med-QC), 3 (high-debug+skycor) (int; default: 2). The full name of this option for the EsoRex configuration file is sinfoni.product.density [default = 2].
lower rejection: percentage of rejected low intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.low_rejection [default = 0.1].
high rejection: percentage of rejected high intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.high_rejection [default = 0.1].
Interpolation index switch: indicator if the bad pixels of the flatfield should be interpolated (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.interpol_index [default = False].
Max Rad: maximal pixel distance from bad pixel to take valid pixels (int; default: 4). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.max_rad [default = 4].
indicator if a bad pixel mask should be generated or not (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.bad_ind [default = False].
Sigma Factor: factor of the sigma noise limit; to remove the column intensity tilt only pixels which lie within a defined noise limit are used to fit a straight line (float; default: 5.0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.sigma_factor [default = 5.0].
Factor: if |pixel - median| > factor * standard deviation -> then the pixel value is replaced by the median of the 8 nearest neighbors (float; default: 3.0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.factor [default = 3.0].
Iterations: number of iterations to of median filtering to find bad pixel clusters (int; default: 8). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.iterations [default = 8].
low rejection: Percentage for bad pixel low rejection (float; default: 10.0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.bad_low_rejection [default = 10.0].
high rejection: Percentage for bad pixel high rejection (float; default: 10.0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.bad_high_rejection [default = 10.0].
Lower Lext X corner (int; default: 1350). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.llx [default = 1350].
Lower Lext Y corner (int; default: 1000). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.lly [default = 1000].
Upper right X corner (int; default: 1390). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.urx [default = 1390].
Upper right Y corner (int; default: 1200). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.ury [default = 1200].
Treshold index: (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.thresh_ind [default = False].
Mean Factor: factor to the clean standard deviation to define the threshold deviation from the clean mean (float; default: 10.0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.mean_factor [default = 10.0].
qc_fpn_xmin1 (int; default: 512). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_xmin1 [default = 512].
qc_fpn_xmax1 (int; default: 1536). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_xmax1 [default = 1536].
qc_fpn_ymin1 (int; default: 512). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_ymin1 [default = 512].
qc_fpn_ymax1 (int; default: 1536). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_ymax1 [default = 1536].
qc_fpn_xmin2 (int; default: 1350). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_xmin2 [default = 1350].
qc_fpn_xmax2 (int; default: 1390). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_xmax2 [default = 1390].
qc_fpn_ymin2 (int; default: 1000). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_ymin2 [default = 1000].
qc_fpn_ymax2 (int; default: 1200). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_fpn_ymax2 [default = 1200].
qc_thresh_min (int; default: 0). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_thresh_min [default = 0].
qc_thresh_max (int; default: 49000). The full name of this option for the EsoRex configuration file is sinfoni.lamp_flats.qc_thresh_max [default = 49000].
Data reduction method: (str; default: ´Normal´). The full name of this option for the EsoRex configuration file is sinfoni.bp.method [default = Normal].
Threshold Sigma Factor: to remove the column intensity tilt only pixels which lie within a defined noiselimit are used to fit a straight line (float; default: 2.0). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.sigma_factor [default = 2.0].
Bad pixel Method Index1: median of nearest neighbors,2: absolute distances check, 3: mean of nearest spectral neighbors (int; default: 1). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.method_index [default = 1].
Factor: if |pixel - sinfo_median| > factor * standard deviation -> then the pixel value is replaced by the median of the 8 nearest neighbors (float; default: 999.0). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.factor [default = 999.0].
Iterations: number of iterations to of median filtering to find bad pixel clusters (int; default: 8). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.iterations [default = 8].
low_rejection: percentage of rejected low intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.low_rejection [default = 0.1].
high_rejection: percentage of rejected high intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.high_rejection [default = 0.1].
llx: to compute image statistics on a rectangularzone of the image the coordinates of the rectangle are needed:lower left x coordinate (int; default: 1350). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.llx [default = 1350].
lly: to compute image statistics on a rectangularzone of the image the coordinates of the rectangle are needed:lower left y coordinate (int; default: 1000). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.lly [default = 1000].
urx: to compute image statistics on a rectangularzone of the image the coordinates of the rectangle are needed:upper right x coordinate (int; default: 1390). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.urx [default = 1390].
ury: to compute image statistics on a rectangularzone of the image the coordinates of the rectangle are needed:upper right y coordinate (int; default: 1200). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.ury [default = 1200].
Threshold Index: indicator that indicates if the values beyond a threshold deviation from the mean are flagged as bad pixels (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.threshold_index [default = True].
Mean Factor: factor to the clean standard deviation to define the threshold deviation from the clean mean (float; default: 999.0). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.mean_factor [default = 999.0].
the minimum value of real data. For J band data taken after 31/01/2018 the default is 0.05. (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.min_cut [default = 0.1].
the maximum value of real data (float; default: 50000.0). The full name of this option for the EsoRex configuration file is sinfoni.bp_dist.max_cut [default = 50000.0].
lower rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.stacked.low_rejection [default = 0.1].
higher rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.stacked.high_rejection [default = 0.1].
Flat Index: (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.stacked.flat_index [default = True].
Normalize master flat to its smoothed value (to remove lamp response curve). 0 (no smooth). 1 (apply fft filter along y).2 (apply running median filter along y). (int; default: 0). The full name of this option for the EsoRex configuration file is sinfoni.stacked.mflat_norm_smooth [default = 0].
Normalization smoothing radii (int; default: 16). The full name of this option for the EsoRex configuration file is sinfoni.stacked.mflat_smooth_rad [default = 16].
BP Mask Interpolation Switch: indicates if the bad pixel mask should be applied (1) or not (0) (int; default: 1). The full name of this option for the EsoRex configuration file is sinfoni.stacked.mask_index [default = 1].
indicates if the bad pixels should be indicated (yes) or interpolated (no) (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.stacked.ind_index [default = False].
Max distance bad-good pix: (int; default: 4). The full name of this option for the EsoRex configuration file is sinfoni.stacked.mask_rad [default = 4].
Gaussian Convolution Switch: (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.stacked.gauss_index [default = False].
Kernel Half Width (int; default: 2). The full name of this option for the EsoRex configuration file is sinfoni.stacked.kernel_half_width [default = 2].
Warp Fix Index: (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.stacked.warpfix_ind [default = True].
Warpfix kernel: (str; default: ´tanh´). The full name of this option for the EsoRex configuration file is sinfoni.stacked.warpfix_kernel [default = tanh].
qc_thresh_min (int; default: 0). The full name of this option for the EsoRex configuration file is sinfoni.stacked.qc_thresh_min [default = 0].
qc_thresh_max (int; default: 49000). The full name of this option for the EsoRex configuration file is sinfoni.stacked.qc_thresh_max [default = 49000].
indicates if the raw sky frame should be subtracted (TRUE) or (FALSE) (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.stacked.sub_raw_sky [default = True].
Calib Indicator: FALSE: if the dispersion relation is already known, the routine can jump to the waveMap section TRUE: if the dispersion relation must first be determined (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.distortion.calib_indicator [default = True].
Minimum Of Difference: minimum difference of mean and median column intensity to carry out the cross correlation (float; default: 10.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.min_diff_mean_med_col_int [default = 10.0].
Half Width: half width of a box within which the line must be placed (int; default: 7). The full name of this option for the EsoRex configuration file is sinfoni.distortion.half_width [default = 7].
Sigma: sigma of Gaussian which is convolved with the artificial spectrum generated using the line list (float; default: 2.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.sigma [default = 2.0].
FWHM: initial guess value for the fwhm of the Gaussian used for the line fit (float; default: 2.83). The full name of this option for the EsoRex configuration file is sinfoni.distortion.fwhm [default = 2.83].
Minimum Of Amplitude: of the Gaussian to do the fit (float; default: 5.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.min_amplitude [default = 5.0].
Maximum Residuals value: beyond this value the fit is rejected (float; default: 0.5). The full name of this option for the EsoRex configuration file is sinfoni.distortion.max_residual [default = 0.5].
Number of A coefficients: number of polynomial coefficients for the dispersion relation (int; default: 4). The full name of this option for the EsoRex configuration file is sinfoni.distortion.n_a_coefficients [default = 4].
Number of B coefficients: number of polynomial coefficients for the polynomial fit of the dispersion coefficients (int; default: 2). The full name of this option for the EsoRex configuration file is sinfoni.distortion.n_b_coefficients [default = 2].
Sigma Factor: Factor of the standard deviation of the polynomial coefficients of the dispersion relation beyond which the coefficients are not used for the fit (float; default: 1.5). The full name of this option for the EsoRex configuration file is sinfoni.distortion.sigma_factor [default = 1.5].
Write Coefficients Index: indicates if the coefficients should be written into a file or not (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.distortion.write_coeffs_ind [default = True].
Write Parameter Index: indicates if the fit parameters should be written into a file or not (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.distortion.write_par_ind [default = True].
Minimal Slitlets´s Distance in spectral direction (int; default: 15). The full name of this option for the EsoRex configuration file is sinfoni.distortion.pixel_dist [default = 15].
Pixel Tolerance: allowed pixel position tolerance between estimated and fitted line position (float; default: 5.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.pixel_tol [default = 5.0].
Wavelength Map Indicator: indicates if the wavelength calibration map should be generated (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.distortion.wave_map_ind [default = False].
Magnificator Factor: magnifying factor for the number of pixels in the columns needed for FFT (int; default: 8). The full name of this option for the EsoRex configuration file is sinfoni.distortion.mag_factor [default = 8].
Slit Position Indicator: indicates if the fits of the slitlet edge positions should be carried through or not (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.distortion.slit_pos_indicator [default = True].
Fit Boltzmann Indicator: indicates if the fits of the slitlet edge positions is carried trough by using a Boltzmann function as model function (bool; default: True). The full name of this option for the EsoRex configuration file is sinfoni.distortion.fit_boltz_indicator [default = True].
Fit Edge Indicator: indicates if the fits of the slitlet edge positions is carried through by using a simple edge function as model function (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.distortion.fit_edge_indicator [default = False].
Estimate Indicator: indicates if the fits of the slitlet edge positions is carried through by using a list of estimated guess positions in a file (TRUE)or if the initial positions are calculated automatically (FALSE). The estimation case is more stable (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.distortion.estimate_indicator [default = False].
Box Length: pixel length of the row box within which the fit is carried out (int; default: 32). The full name of this option for the EsoRex configuration file is sinfoni.distortion.box_length [default = 32].
Y Box: half width of a small box in spectral direction within which the maximal intensity pixel is searched (float; default: 5.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.y_box [default = 5.0].
Difference Tolearance: maximal tolerable difference of the resulting fit positions of the slitlet edges with respect to the expected positions (float; default: 2.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.diff_tol [default = 2.0].
qc_thresh_min (int; default: 0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.qc_thresh_min [default = 0].
qc_thresh_max (int; default: 49000). The full name of this option for the EsoRex configuration file is sinfoni.distortion.qc_thresh_max [default = 49000].
lower rejection: percentage of rejected low intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.distortion.lower_rejection [default = 0.1].
higher rejection: percentage of rejected high intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.distortion.higher_rejection [default = 0.1].
Mask Index: indicator if a bad pixel mask is applied or not (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.distortion.mask_ind [default = False].
Gauss Index: (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.distortion.gauss_ind [default = False].
Kernel Half Width kernel half width of the Gaussian response function (int; default: 2). The full name of this option for the EsoRex configuration file is sinfoni.distortion.kernel_half_width [default = 2].
Half Width (int; default: 4). The full name of this option for the EsoRex configuration file is sinfoni.distortion.ns_half_width [default = 4].
FWHM (float; default: 2.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.ns_fwhm [default = 2.0].
Minimum of Difference (float; default: 1.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.min_diff [default = 1.0].
Dev Tol (float; default: 20.0). The full name of this option for the EsoRex configuration file is sinfoni.distortion.dev_tol [default = 20.0].
arcs threshold factor. median_value(image)+ kappa*sigma is the minimum intensity threshold of accepted imagepixels (float; default: 0.33333). The full name of this option for the EsoRex configuration file is sinfoni.distortion.arcs_thresh_factor [default = 0.33333].
factor which sets minimum arc length (1.0-2) (float; default: 1.19). The full name of this option for the EsoRex configuration file is sinfoni.distortion.arcs_min_arclen_factor [default = 1.19].
Size of window for low pass fileter used inan horizzontal low pass filter to remove unwanted arcs (5-64) (int; default: 14). The full name of this option for the EsoRex configuration file is sinfoni.distortion.arcs_window_size [default = 14].
Size of smoothing factor (1-11) used to prevent for possible intensity drops from detector electronics on fibre illuminated slitlets (1-11) (int; default: 3). The full name of this option for the EsoRex configuration file is sinfoni.distortion.smooth_rad [default = 3].
lower rejection: percentage of rejected low intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.low_rejection [default = 0.1].
higher rejection: percentage of rejected high intensity pixels before averaging (float; default: 0.1). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.high_rejection [default = 0.1].
Mask Index: indicator if a bad pixel mask is applied or not (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.mask_ind [default = False].
Gauss Index: (bool; default: False). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.gauss_ind [default = False].
Kernel Half Width kernel half width of the Gaussian response function (int; default: 2). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.kernel_half_width [default = 2].
Half Width (int; default: 4). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.half_width [default = 4].
FWHM (float; default: 2.0). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.fwhm [default = 2.0].
Minimum of Difference (float; default: 1.0). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.min_diff [default = 1.0].
Dev Tol (float; default: 20.0). The full name of this option for the EsoRex configuration file is sinfoni.north_south_test.dev_tol [default = 20.0].

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.

SEE ALSO

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

ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo-pipeline-manual-19.0.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 sinfo pipeline are sinfo_rec_detlin(7), sinfo_rec_jitter(7), sinfo_rec_mdark(7), sinfo_rec_mflat(7), sinfo_rec_pupil(7), sinfo_rec_wavecal(7), sinfo_utl_bp_mask_add(7), sinfo_utl_cube2ima(7), sinfo_utl_cube2spectrum(7), sinfo_utl_cube_arith(7), sinfo_utl_cube_combine(7), sinfo_utl_cube_create(7), sinfo_utl_ima_arith(7), sinfo_utl_ima_line_corr(7), sinfo_utl_line_oh_select(7), sinfo_utl_skycor(7), sinfo_utl_skymap(7), sinfo_utl_spectrum_divide_by_blackbody(7), sinfo_utl_spectrum_wavelength_shift(7)

VERSION

sinfo_rec_distortion 3.1.0

AUTHOR

Andrea Modigliani <Andrea.Modigliani@eso.org>

BUG REPORTS

Please report any problems to Andrea.Modigliani@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 SINFONI Instrument Pipeline Copyright (C) 2002,2003 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

3.1.0 sinfo_rec_distortion