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--- data_reduction [2013/09/05 07:49]
mjc [Image Pre-Processing]
+++ data_reduction [2025/07/03 00:31] (current)
onken Update for v2
@@ Line 1: / Line 1: @@
 ==== PyWiFeS Data Reduction ====
+**The processes in version 2 of PyWiFeS largely build upon the excellent work of the previous PyWiFeS developers. Thus, we retain the original documentation here, but note that several aspects have undergone significant revision in the current version, described in Onken et al. (in prep). Documentation for the new processes may also be found in [[https://pywifes-pipeline.readthedocs.io/en/latest/index.html| our ReadTheDocs site]] or in the README and CHANGELOG files in [[https://github.com/PyWiFeS/pywifes| the GitHub repository]] **
 This page details the algorithms and techniques employed in PyWiFeS data reduction procedures.  For details on how to actually run the reduction script, see the [[documentation| main documentation]] page. For the ordered list of reduction steps in the default reduction script, see the [[default_reduction| default reduction steps]] page.
@@ Line 60: / Line 62: @@
 ==== Flat-fielding ====
-flat-cleanup, response function calc
+Flat-fielding for WiFeS is slightly complicated for two reasons: (1) the smooth spectrum quartz lamp in the WiFeS internal calibration unit does not provide uniform spatial illumination that mimics the illumination from the telescope; and (2) reflections internal to the WiFeS instrument create a diffuse glow and "horseshoe" reflection (see Figure below) which strongly affect the flatfield solution, especially at very blue wavelengths on the blue detector.
+The internal reflections for WiFeS flat-field data are corrected using the novel 'interslice_cleanup' routine developed by Fred Vogt.  This routine uses the space between slitlets to fit for the shape of the WiFeS internal reflections (see Figure below) and subtracts this reflection model from the flat-field data.  This routine has provided excellent flat-fielding, and is especially important in yielding an accurate spatial flat-field (illumination) correction.
 {{:wiki:flat_sub_b.png?260|}}{{:wiki:deflat_slice.png?350|}}
+Ideally a flat-field solution should correct for three effects:
+  - Differences in quantum efficiency for individual pixels on the detector (i.e., "hot" or "cold" pixels).
+  - Rapid variations in the dichroic throughput with wavelength (dichroic "wiggles") and its variation across the instrument field of view.
+  - Variation in the overall instrument throughput across the instrument field of view (i.e., spatial throughput, or "illumination", variations).
+For WiFeS, the first two are achieved with the smooth spectrum (quartz) lamp in the WiFeS calibration unit, while the final effect is corrected by use of twilight sky observations.  A schematic representation of the PyWiFeS response function calculation is show below, and is described in greater detail in the PyWiFeS paper.
 {{ :wiki:flatfield_wifes.png?600 |}}
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 ----
 ==== Data Cube Generation ====
-wire, ADR
+Final WiFeS data cubes are generated by resampling the flux values at the observed (x,y,λ) positions onto a rectilinear grid grid of (α,δ,λ).  The true y value for each pixel in the WiFeS field of view is derived using a wire frame observation (see Figure below).
 {{ :wiki:wire_wifes.png?600 |}}
+Light from the same origin on the sky is dispersed to different positions due to the effect of Atmospheric Differential Refraction (ADR; [[http://adsabs.harvard.edu/abs/1982PASP...94..715F|Filippenko 1992]]), which is sometimes referred to as Differential Atmospheric Refraction (DAR).  For WiFeS the ADR deflections in x and y are calculated (see Figure below) using observation details in the FITS header.
 {{ :wiki:adr_wifes.png?600 |}}
-----
+The true (α,δ) coordinates derived from the wire frame and ADR calculation, and the observed λ values from the wavelength solution, are used as input to the WiFeS cube generation routine.  The output of this routine is still in MEF format (to facilitate visual inspection of individual slitlets).
+----
 ==== Flux Calibration ====
-links to stdstar catalogs...
+After WiFeS data have undergone standard image processing steps (e.g., bias subtraction, cosmic ray rejection, flat-fielding), the absolute flux scale of the data must still be assessed.  This is done by observing spectrophotometric standard stars and comparing their observed fluxes to reference spectra.  In PyWiFeS this is done with the procedure outlined schematically in the Figure below, using routines defined in the 'wifes_calib' sub-module.
 {{ :wiki:flux_cal_wifes.png?600 |}}
+The flux calibration step corrects for the smooth instrument throughput curve, as well as atmospheric extinction.  However sharp absorption features caused by molecules in the atmosphere (primarily O<sub>2</sub> and H<sub>2</sub>O) remain, and must be corrected in object spectra (bottom panel below) by measuring their structure in the spectra of flux-calibrated smooth spectrum stars (top panel below).
 {{ :wiki:telluric_wifes.png?400 |}}
+== Spectrophotometric Standard Star Catalogs ==
+Flux calibration requires a set of reference spectra of spectrophotometric standard stars.  Included in PyWiFeS are two spectra catalogs:
+  * [[http://adsabs.harvard.edu/abs/1999PASP..111.1426B|Bessell et al., 1999]]
+  * [[http://adsabs.harvard.edu/abs/1990AJ.....99.1621O|Oke et al., 1990]]
+Another excellent specphot standard star catalog we recommend downloading is:
+  * [[http://adsabs.harvard.edu/abs/2005PASP..117..810S|Stritzinger et al., 2005]], Carnegie specphot standards, availaible [[http://www.das.uchile.cl/~mhamuy/SPECSTDS/|here]]
+Planned future catalogs of spectrophotometric standard stars which will soon be available are:
+  * All-Sky HST spectrophotometric standards (Bessell et al., in prep.)
+  * Gaia spectrophotometric standard star catalog ([[http://adsabs.harvard.edu/abs/2012MNRAS.426.1767P|Pancino et al., 2012]])

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