TRES Reduction Tasks Doug Mink, 2008-Sep-19

[Definitions] [Preparation] [Observation] [Reduction (Pipeline) (Software)] [Distribution] [Archiving]

Checking Data

• tres.trsdate yyyy.mmdd or now
  This task is run before any other TRES tasks because it sets the working directory based on the date. If the day of the month ends in "0", the date should be specified as "yyyy.mmdd". First it transfers to quickdiryyyy.dddd, the processing directory. Then it sets that processing directory and the directory from which to read raw data for all of the top and second level processing taslks (trsproc, trslist, trsfiles, trsgroup, qtres, ctres, ttres, and ftres), so they all can be used with sequence numbers instead of full file names. If the first argument is "now", today's observing date (local date at noon of the observing day) is used.

• tres.trslist 1-300 fibkey=xxx fibsize=x.x apfib=x object=xxxx
  This task lists all of the TRES files meeting specific characteristics. By default it looks in the current working directory, but if trsdate has been run, it looks for files in the raw directory, datedir in a specified instdir, such as /tres on Mt. Hopkins. If outlist is specified, names of files meeting the selection criteria are written to the specified file, one per line, which can be used for many of the tasks below. If verbose=yes, that file contains a tab-separated table of observation parameters for each file.

Quick Look

• tres.qtres reduces a raw spectrum image to one or several multi-order echelle spectra. It uses tres.tproc to all of the process, then splot to plot the resulting date
• tres.ctres reduces a list of raw spectrum images taken of the same object with the same fiber size and binning to dispersion-corrected multi-order echelle spectra with cosmic rays removed by a comparison method. Dispersion shifts are computed using the shift from the closest ThAr spectra or interpolating between the closest ThAr spectra before and after each exposure.
• tres.ttres reduces a list of raw ThAr spectrum images taken with the same fiber size and binning to dispersion-corrected multi-order echelle spectra with cosmic rays removed by a comparison method. The dispersion function is computed by cross-correlating to a reference spectrum in pixel space and adding the resulting shift to the dispersion function of the reference spectrum. tres.tharplot
• tres.ftres reduces a list of raw flat, bias, or dark spectrum images taken with the same fiber size and binning by running CCDPROC, merging amplifiers, and removing cosmic rays with a comparison method.

Pipeline

• tres.trsgroup sorts the data files for the night specified by trsdate into files named by object, configuration, and exposure time: [obj][s m l][b if binned][fiber(s)]_[exposure in seconds]. The string [s m l][b if binned][fiber(s)] is used in many places and referred to as apfib.
• tres.trsproc calls trsgroup, reads the list files of list files it produces, and processes them using the appropriate "quick look" task from the list above. trsgroup is only called to create lists of flat, bias, dark, ThAr, or object files if a list for that type of file does not already exist. The type or types of spectra to reduce is selected by a command line argument which is by default a null string:

  b	Bias images (BIAS is object name)	d	Dark images (DARK is object name)	f	Flat field spectra (FLAT is object name)
  c	Thorium Argon spectra (COMP is object name)	o	Object spectra (all of the rest)

Bias and Dark Files

1. tres.trsproc
   runs tres.ftres to process files through cosmic ray removal:
   mscred.ccdproc trim+ overscan+ fixpix+ to bias-subtract, trim, and remove bad pixels from both amplifiers of all files.
   tres.gaincorr corrects for gain variation between amplifiers. The raw files are moved to the Raw/ subdirectory, and the output files have the same names as the originals.
   tres.tampmerge is run to combine the two amps to single image FITS files.
   tres.tcosmic is run to remove cosmic rays.

2. Check bias files by running tres.txstat on them.
   mscred.combine all of the bias files except those for which any amplifier stands out to an output Zero.fits file. implot it to check for missed bad columns. We are not subtracting bias images, and are relying instead on overscan removal to take care of any bias signal without adding noise from individual pixels.

3. tres.txstat on dark files to check for light leaks.
   mscred.combine them to an output Dark.fits file.
   Check values using plot.implot.
   mscred.ccdproc dark+ on all data files if there is significant dark flux.

Flat Field Files

1. Run tres.trsproc on trsgroup.flatlist which contains a list of lists of FLAT files grouped by fibsize, binning, fibkey, and exposure time.
   tres.ftres flatten=no is run on each list of similarly exposed flat field exposures
   mscred.ccdproc trim+ overscan+ fixpix+ to bias-subtract, trim, and remove bad pixels from all amplifiers of all files.
   tres.gaincorr corrects for gain variation between amplifiers. The raw files are moved to the Raw/ subdirectory, and the output files have the same names as the originals.
   tres.tampmerge flat.*.fits combines the two amps to single image FITS files.

   
   tres.tcosmic @flatxx.fits compares images with the same characteristics and removes cosmic rays from each exposure. Temporary median and limit files are created and my be deleted. Nelson Caldwell developed the algorithm which compares two files at a time, using statistics from the median file to figure out when to reject high pixels.

1. To produce a new flattening file, tres.trssum @flatxx.list flatxx.fits combines multiple flat field exposures of the same type into a single image file.

2. tres.tmakeflat flatxx12.fits
   tres.tmakeflat flatxx3.fits runs apfind, apedit, aptrace, and apflatten on summed dome flats to create pixel to pixel normalization files which are used in the next step to remove IR fringing, more or less.

3. imarith flatxx12.flat.fits * flatxx3.flat.fits flatxx123.flat.fits
   Makes a flattening file for spectra with simultaneous calibration

4. tres.tflat @flatxx.list removes fringing and pixel-to-pixel variations from flat files.

5. Symbolically link (ln -s) flatxx12.fits to flatxx1.fits and flatxx2.fits.

6. Copy apflatxx1.fits and apflatxx2.fits from tresdata$database/ to database/
   If the files are not there, run apfind and apedit on apflatxx1.fits and apflatxx2.fits.

7. Run apedit and aptrace on flatxx1.fits, flatxx2.fits, and flatxx3.fits for each group to set up database files database/apflatxx1, database/apflatxx2, and database/apflatxx3 to be used for extraction.

8. tres.textract flatxx.fits to make an aperture template and to make a pixel to pixel normalization file.

Calibration Lamp (ThAr) Files

1. Use tres.trsgroup to group all of the COMP files by apfib and exposure, so cosmic rays can be removed.
2. tres.ttres @compxx.list flatten+ cosmic+ extract+ disperse+ to trim, remove overscan, merge, and flatten all COMP image files.
   mscred.ccdproc trim+ overscan+ fixpix+ to bias-subtract, trim, and remove bad pixels from all amplifiers of all files.
   tres.gaincorr corrects for gain variation between amplifiers.
   tres.tampmerge is run to merge the two amplifiers of each comparison file to single image FITS files.
   The raw files are optionally moved to the Raw/ subdirectory, and the output files have the same names as the originals.
   tres.tflat @compxx.list removes fringing and pixel-to-pixel variations from comparison lamp files. The original merged, unnormalized file is saved in the Unflat/ directory.
   tres.tcosmic @compxx.fits compares images with the same characteristics and removes cosmic rays from each exposure. Temporary median and limit files are created and my be deleted. Nelson Caldwell developed the algorithm which compares two files at a time, using statistics from the median file to figure out when to reject high pixels.
   tres.textract @compxx.list extracts the calibration spectra, using flatxx.ec.fits as apref. Turn off *all* processing except extraction to produce comp.ec.fits.

3. tres.tcal comp files
   runs rvsao.pxcsao against an appropriate reference comparison lamp file to get a single dispersion-direction pixel shift which is applied to the wavelength solution with which the file is then dispersed. If interactive=yes, the dispersion function can be refined using ecidentify. The cursor "x" command cross-correlates to get a better match between features. "f" fits to the new matches and brings up a display of residuals in which outliers can be deleted with "d" and the dispersion refit with "f" until the graph looks satisfactory, with residuals within 0.015 or so. "q" exits the residuals and another "q" followed by a "y" response exits and writes the revised id file to the database directory. It is then retrieved to add the dispersion function to the spectrum header.

Object Files

1. tres.ctres objects.fits
   or tres.trsproc o to process all objects.
   First mscred.ccdproc trim+ overscan+ fixpix+ bias-subtracts, trims, and removes bad pixels from all amplifiers of all files.
   tres.gaincorr corrects for gain variation between amplifiers.
   tres.tampmerge is run to merge the two amplifiers of each object file to single image FITS files.
   The raw files are moved to the Raw/ subdirectory, and the output files have the same names as the originals.

   tres.tflat divides by the normalization image made by tmakeflat, removing pixel to pixel variation and fringing. The original merged, unnormalized file is saved in the Unflat/ directory.

   tres.tcosmic @objectxx.list compares images from the same object, FIBSIZE, binning, and FIBKEY and removes cosmic rays from each exposure. Temporary median and limit files are created and may be deleted. Nelson Caldwell developed the algorith which compares two files at a time, using statistics from the median file to figure out when to reject high pixels.

   If ctres.sumspec=yes, tres.trssum sums all exposures of a single pointing into a single set of spectra, assigning the sum a new observation sequence number and name. This file is processed just like its components through the following steps.

   tres.textract objects.fits extracts the object spectra, using the appropriate dome flat, flat[size][binning][fiber].flat.fits as the aperture reference.

   tres.tdisp objects.ms.fits adds dispersion functions for each order to each spectrum
   refspec file.ms.fits references="comp.ms",
   dispcor file.ms.fits filed.ms.fits linearize- The original .ec file is moved to Nodisp/.

2. rvsao.xcsao *.fits can be used to find the radial velocities of all of the object spectra, but there are not any good templates yet.