HIRedux Extraction

• The following routines all apply to a single object, i.e. multiple exposures of that object will be reduced together.
• Most of the following routines take the hires structure, and the setup, chip and obj_id tags.

All Obj
hires_allobj :: Run all extraction routines described below. At present, I tend to run the extraction steps separately to check the progress of the code. Currently, it is preferable to run hires_allobj with these options:
IDL> hires_allobj , hires, 1, /procall

Process the Image

1. hires_proc :: Bias subtract and flat field the Raw image. This routine takes the index number of the hires structure as input or keywords setup and obj. The index number is the integer in the first column of the file 'hires.list'. The resulting image is output in 'Final/' and is a flattened flux and inverse variance fits file (one gzipped fits image with two extensions per file). Output is 'Final/f_name.fits'
       Example: IDL> hires_proc, hires, SETUP=setup, OBJ=obj_id
       Example: IDL> rslt = hires_proc_sngl('rawfil', [chip])
       Time : 1min per image
       Check : xatv, 'Final/f_name.fits'
   • You know the code is working right when you check the image and it looks reasonable.
   • At this step, I strongly recommend that you check that the order traces match your object. I have found at least a couple of cases where the flat is not aligned with the object. Am investigating the physical origin. Anyhow, checking will be tough unless there is a decent amount of sky in your data. But try this
     • xatv, 'Final/f_name.fits'
     • hires_chktrcflat, hires, setup, chip, /nostop, /fit
   • If there is a serious offset (i.e. more than one pixel), contact me. You are likely to have troubles with sky subtraction and extraction.
   • If things look fine with one frame, I suspect they are all fine.

2. hires_objcr (Optional, recommended with caution) :: Compares two or more images to identify cosmic rays. For two images, it uses the difference of the two images scaled to the exposure times and is quite conservative. One should NOT use this on multiple exposures of the same object if the object has moved along the slit.
       Example: IDL> hires_objcr, hires, setup, obj_id, chip, [exp], /CHK
       Time : 3min per pair
   • You know the code is working right when you run with the /CHK keyword and the code is not identifiying excessive CR's along the object profile. This will happen (in particular) if the object has moved significantly along the slit in between exposures.

Identify and Trace the Object

• hires_fntobj :: This code automatically identifies the object in each order (rectify+collapse) and then traces using trace_crude. A PCA analysis is then performed on the coefficients of each trace to determine a smoothed (quasi-2D) solution that is useful for interpolation and extrapolation. The code then creates and Object structure hiresobstrct that contains the trace and will contain the 1D extractions. Output: 'Extract/Obj_name.fits'
      Example: IDL> hires_fntobj, hires, setup, obj_id, chip, /CHK
      Time : fast
• This code creates an object structure in the Extract/ directory (e.g. 'Extract/Obj_mb0033.fits.gz') which holds information relating to the trace and extraction of the spectra. Here is a link to the code which lists the tags used.
• BRIGHT OBJECTS or the B DECKERS :: If you are extracting a very bright object and/or using the B deckers, you may wish to extend the boxcar beyond the default value (it is 75%). In this case, set OBJAPER=[value,value], e.g. [0.9,0.9]. If you designate /STD, it uses [0.85, 0.85]. Note you can even choose values in excess of 1 but (1) you should skip sky subtraction and (2) will need to use /EXTENBOX in the Extract step.
• You know the code is working right when you run with the /CHK keyword and the fit to the position in the slit fraction is nearly constant and well fit as a function of trace number. Also, the image with the trace overplotted should look sensible. Alternatively (or in addition), check the QA output (e.g. 'QA/Obj01/qa_fntobj_0022B.ps.gz'). The X0 and PCA0 coefficients should be well fit and the remaining PCA coefficients should show small variation. Finally, the reduced_chi2 should be < 0.1 (blue) or <0.01 (red).
• QA: HERE is an example of the QA. It is quite similar to the Edgeflat QA.
  • The first page plots the position of the object in the slit as a function of order number (non-physical). The position is relative, i.e. 0.5 is the center of the slit. The trend is primarily atmospheric although funny things appear when the orders begin to overlap.
  • The second page shows output from the PCA analysis. The x0 and PCA0 components should be well fit (there may be red, rejected outliers).
    1. PCA1 should be confined to a small range of values (the magnitude is not particularly relevant) but may not. It is a modest but not major concern so long as the values are well fit.
    2. PCA2-4 should each be confined to a small range of values (the magnitude is not particularly relevant).
  • The third page shows the row-by-row centroid and the fits. This is not the final trace, but it should look good by eye.

Sky Subtraction

• hires_skysub :: Performs sky subtraction on an order by order basis using a bspline fitting algorithm to all sky pixels in a given order (the object is masked). The sky spectrum is also cross-correlated with the UVES sky line list to investigate a shift. At the moment, while it calculates the shift, it does nothing with the value. The sky subtracted image is only used to derive the object profile in the next step. That is, don't fret if the image isn't so great, we are just after the zero level here.
• Output: Sky subtracted 2D image appended to the unsubtracted flux and the variance 2D images (e.g. 'Final/f_name.fits'). Also the bspline coefficients are written to 'Sky/sky_name.fits'
      Example: IDL> hires_skysub, hires, setup, obj_id, chip, [/CHK, /FCHK]
      Time : 10min per exposure
• Examine the final product (and get wavelength info) by:
      IDL> xatv, 'Final/f_name.fits', getsky=2, WVIMG='Arcs/Arc_nameI.fits'
• You know the code is working right when you run with /FCHK and the final image shows 'random' noise in places where sky lines used to be. You can also run with /CHK to examine the order by order fits. Finally, the QA file (e.g. 'QA/Obj01/qa_skysub_0022B.ps.gz') shows a zoom in on key sky lines in the red or several small patches in the blue.
• BRIGHT OBJECTS and/or the B DECKERS :: If you are observing bright objects and/or using the B deckers, you may wish to ignore sky subtraction. In fact, unless you had exquisite seeing, I claim you CANNOT do sky subtraction with the B deckers. Therefore you should skip this step.

Extraction

• hires_extract :: This procedure is quite involved. It is generally based on mike_box (written primarily by S. Burles) which fits an optimal profile and the sky to the data and then extracts. The main modification is that I take the optimal profile and sky fit and then extract in a different manner than mike_box.
• Output: The tags .box_fx, .box_var, .box_wv, .fx, .var, .wave and .fin_trc are usually all filled
      Example: IDL> hires_extract, hires, setup, obj_id, chip, [/RESCHK, /SKIPSKYSUB]
      Time : 15min per exposure (longer for high SNR data)
• Examine the final product:
      IDL> hires_specplt, [/BOX]
• You know the code is working right when the reduced chi^2 values are 1.2 or lower (a bit higher for very bright objects).
• BRIGHT OBJECTS or the B DECKERS :: If you are observing bright objects and/or using the B deckers, you may have skipped sky subtraction as noted above. In this case, you will need to turn /SKIPSKYSUB on. For BRIGHT targets, I recommend you use the /BBOX switch which turns on /SKIPSKYSUB, /NOMEDSCATT (scattered light will be fit on all chips), /EXTENBOX (in case you demand a boxcar larger than the nominal slit length) and /NOPROF (no optimal profile fitting).