The kmos_sci_red recipe =============================================================== .. data:: kmos_sci_red Synopsis -------- Reconstruct obj/sky-pairs individually and combine them afterwards Description ----------- Two data frames are expected in order to have a sky IFU for the IFU Objects. If an OH spectrum is given in the SOF file the lambda axis will be corrected using the OH lines as reference. Every IFU containing an object will be reconstructed and divided by telluric and illumination correction. By default these intermediate cubes are saved to disk. The reconstructed objects with the same object name are combined. In order to combine a specific object, the parameters --name or --ifus can be used. For exposures taken with the templates KMOS_spec_obs_mapping8 and KMOS_spec_obs_mapping24, all active IFUs are combined. Input files ^^^^^^^^^^^^ :: DO KMOS category Type Explanation Required #Frames -------- ----- ----------- -------- ------- SCIENCE RAW The science frames Y >=1 XCAL F2D x calibration frame Y 1 YCAL F2D y calibration frame Y 1 LCAL F2D Wavelength calib. frame Y 1 WAVE_BAND F2L Table with start-/end-wavelengths Y 1 MASTER_FLAT F2D Master flat Y 0,1 ILLUM_CORR F2I Illumination correction N 0,1 TELLURIC F1I normalised telluric spectrum N 0,1 TELLURIC_GEN F1I normalised telluric spectrum N 0,1 OH_SPEC F1S Vector holding OH lines N 0,1 Output files ^^^^^^^^^^^^ :: DO KMOS category Type Explanation -------- ----- ----------- SCI_COMBINED F3I Combined cubes with noise SCI_RECONSTRUCTED F3I Reconstructed cube with noise EXP_MASK F3I Exposure time mask (not for mapping-templates!) SCI_INTERIM_OBJECT F3I (optional) Intermediate reconstructed object cubes used for sky tweaking, no noise (set --sky_tweak and --save_interims) SCI_INTERIM_SKY F3I (optional) Intermediate reconstructed sky cubes used for sky tweaking, no noise (set --sky_tweak and --save_interims) SCI_COMBINED_COLL (optional) Collapsed combined cube (set --collapse_combined) SCI_RECONSTRUCTED_COLL (optional) Collapsed reconstructed cube (set --collapse_reconstructed) Constructor ----------- .. method:: cpl.Recipe("kmos_sci_red") :noindex: Create an object for the recipe kmos_sci_red. :: import cpl kmos_sci_red = cpl.Recipe("kmos_sci_red") Parameters ---------- .. py:attribute:: kmos_sci_red.param.imethod Method to use for interpolation during reconstruction. ["NN" (nearest neighbour), "lwNN" (linear weighted nearest neighbor), "swNN" (square weighted nearest neighbor), "MS" (Modified Shepard's method)"CS" (Cubic spline)] (str; default: 'CS') [default="CS"]. .. py:attribute:: kmos_sci_red.param.smethod Method to use for interpolation during shifting. ["NN" (nearest neighbour), "CS" (Cubic spline)] (str; default: 'CS') [default="CS"]. .. py:attribute:: kmos_sci_red.param.method The shifting method: 'none': no shifting, combined directly, 'header': shift according to WCS (default), 'center': centering algorithm, 'user': read shifts from file (str; default: 'header') [default="header"]. .. py:attribute:: kmos_sci_red.param.fmethod The fitting method (applies only when method='center'): 'gauss': fit a gauss function to collapsed image (default), 'moffat': fit a moffat function to collapsed image (str; default: 'gauss') [default="gauss"]. .. py:attribute:: kmos_sci_red.param.name Name of the object to combine. (str; default: '') [default=""]. .. py:attribute:: kmos_sci_red.param.ifus The indices of the IFUs to combine. "ifu1;ifu2;..." (str; default: '') [default=""]. .. py:attribute:: kmos_sci_red.param.oscan Apply Overscan Correction (bool; default: True) [default=True]. .. py:attribute:: kmos_sci_red.param.pix_scale Change the pixel scale [arcsec]. Default of 0.2" results into cubes of 14x14pix, a scale of 0.1" results into cubes of 28x28pix, etc. (float; default: 0.2) [default=0.2]. .. py:attribute:: kmos_sci_red.param.suppress_extension Suppress arbitrary filename extension.(TRUE (apply) or FALSE (don't apply) (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.neighborhoodRange Defines the range to search for neighbors in pixels (float; default: 1.001) [default=1.001]. .. py:attribute:: kmos_sci_red.param.filename The path to the file with the shift vectors.(Applies only to method='user') (str; default: '') [default=""]. .. py:attribute:: kmos_sci_red.param.flux TRUE: Apply flux conservation. FALSE: otherwise (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.background TRUE: Apply background removal. FALSE: otherwise (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.fast_mode FALSE: cubes are shifted and combined,TRUE: cubes are collapsed and then shifted and combined (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.extrapolate Applies only to 'smethod=CS' when doing sub-pixel shifts: FALSE: shifted IFU will be filled with NaN's at the borders,TRUE: shifted IFU will be extrapolated at the borders (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.xcal_interpolation TRUE: Interpolate xcal between rotator angles. FALSE: otherwise (bool; default: True) [default=True]. .. py:attribute:: kmos_sci_red.param.edge_nan Set borders of cubes to NaN before combining them.(TRUE (apply) or FALSE (don't apply) (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.no_combine Don't combine cubes after reconstruction.(TRUE (apply) or FALSE (don't apply) (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.no_subtract Don't sky subtract object and references.(TRUE (apply) or FALSE (don't apply) (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.sky_tweak Use modified sky cube for sky subtraction.(TRUE (apply) or FALSE (don't apply) (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.skip_sky_oh_align Skip the OH alignment for the SKY (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.discard_subband Ignore last sub-band in the sky tweaking (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.stretch Stretch sky in the sky tweaking (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.stretch_degree Stretch polynomial degree (int; default: 8) [default=8]. .. py:attribute:: kmos_sci_red.param.stretch_resampling Stretch resampling method (linear/spline) (str; default: 'spline') [default="spline"]. .. py:attribute:: kmos_sci_red.param.tbsub Subtract thermal background from input cube.(TRUE (apply) or FALSE (don't apply) (bool; default: True) [default=True]. .. py:attribute:: kmos_sci_red.param.b_samples The number of samples in wavelength for the reconstructed cube (int; default: 2048) [default=2048]. .. py:attribute:: kmos_sci_red.param.obj_sky_table The path to the file with the modified obj/sky associations. (str; default: '') [default=""]. .. py:attribute:: kmos_sci_red.param.velocity_offset Specify velocity offset correction in km/s for lambda scale (float; default: 0.0) [default=0.0]. .. py:attribute:: kmos_sci_red.param.save_interims Save interim object and sky cubes. Can only be used together with --sky_tweak (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.collapse_reconstructed Flag to collapse the reconstructed images (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.collapse_combined Flag to collapse the combined images (bool; default: False) [default=False]. .. py:attribute:: kmos_sci_red.param.cmethod Apply "average", "median", "sum", "min_max." or "ksigma". (str; default: 'ksigma') [default="ksigma"]. .. py:attribute:: kmos_sci_red.param.cpos_rej The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0) [default=3.0]. .. py:attribute:: kmos_sci_red.param.cneg_rej The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0) [default=3.0]. .. py:attribute:: kmos_sci_red.param.citer The number of iterations for kappa-sigma-clipping. (int; default: 3) [default=3]. .. py:attribute:: kmos_sci_red.param.cmax The number of maximum pixel values to clip with min/max-clipping. (int; default: 1) [default=1]. .. py:attribute:: kmos_sci_red.param.cmin The number of minimum pixel values to clip with min/max-clipping. (int; default: 1) [default=1]. The following code snippet shows the default settings for the available parameters. :: import cpl kmos_sci_red = cpl.Recipe("kmos_sci_red") kmos_sci_red.param.imethod = "CS" kmos_sci_red.param.smethod = "CS" kmos_sci_red.param.method = "header" kmos_sci_red.param.fmethod = "gauss" kmos_sci_red.param.name = "" kmos_sci_red.param.ifus = "" kmos_sci_red.param.oscan = True kmos_sci_red.param.pix_scale = 0.2 kmos_sci_red.param.suppress_extension = False kmos_sci_red.param.neighborhoodRange = 1.001 kmos_sci_red.param.filename = "" kmos_sci_red.param.flux = False kmos_sci_red.param.background = False kmos_sci_red.param.fast_mode = False kmos_sci_red.param.extrapolate = False kmos_sci_red.param.xcal_interpolation = True kmos_sci_red.param.edge_nan = False kmos_sci_red.param.no_combine = False kmos_sci_red.param.no_subtract = False kmos_sci_red.param.sky_tweak = False kmos_sci_red.param.skip_sky_oh_align = False kmos_sci_red.param.discard_subband = False kmos_sci_red.param.stretch = False kmos_sci_red.param.stretch_degree = 8 kmos_sci_red.param.stretch_resampling = "spline" kmos_sci_red.param.tbsub = True kmos_sci_red.param.b_samples = 2048 kmos_sci_red.param.obj_sky_table = "" kmos_sci_red.param.velocity_offset = 0.0 kmos_sci_red.param.save_interims = False kmos_sci_red.param.collapse_reconstructed = False kmos_sci_red.param.collapse_combined = False kmos_sci_red.param.cmethod = "ksigma" kmos_sci_red.param.cpos_rej = 3.0 kmos_sci_red.param.cneg_rej = 3.0 kmos_sci_red.param.citer = 3 kmos_sci_red.param.cmax = 1 kmos_sci_red.param.cmin = 1 You may also set or overwrite some or all parameters by the recipe parameter `param`, as shown in the following example: :: import cpl kmos_sci_red = cpl.Recipe("kmos_sci_red") [...] res = kmos_sci_red( ..., param = {"imethod":"CS", "smethod":"CS"}) .. seealso:: `cpl.Recipe `_ for more information about the recipe object. Bug reports ----------- Please report any problems to `Alex Agudo Berbel, Yves Jung `_. Alternatively, you may send a report to the `ESO User Support Department `_. Copyright --------- This file is part of the CRIRES 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 .. codeauthor:: Alex Agudo Berbel, Yves Jung