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README.md

mikerun

Tools for MIKE observing runs

Alex's preparation checklist

  • If you have not, read the MIKE user manual
    • Note this has not really been updated for at least 5+ years, so some info is out of date.
  • make human target catalog
  • make iobs and/or jskycalc catalog
  • make telescope target catalog
  • clear space on laptop for data download/reduction
  • prep scripts for on-the-fly data reduction
  • prep SMHR linelists
  • prep SMHR quick analysis scripts
  • prep google doc for exptime estimate

Slits and binning

The default setting is 0.7x5.00, 2x2 binning, and slow readout. If you go to smaller slits, you will want to decrease the binning.

  • 1.0 x 5.00 -> 2x2 binning
  • 0.7 x 5.00 -> 2x2 binning
  • 0.5 x 5.00 -> 2x1 binning or 1x1 binning
  • 0.35x 5.00 -> 1x1 binning (I have done 2x2 and 2x1 but this underresolves the image..)

The CCD scale is 8.2 pix/arcsec on the blue (0.12 arcsec/pix), 7.5 pix/arcsec on the red (0.13 arcsec/pix). You need >2 pixels per resolution element to be Nyquist sampled.

The focus is checked in the afternoon by the instrument scientist by taking arcs with two 0.35 boxes and measuriing the PSFs. It is not recommended to do any focusing yourself. On my last run, the FWHM was about 2.5 pixels, or ~0.3 arcseconds.

Readout mode

I almost always do slow readout because I do faint objects.

However if you are doing bright objects, doing fast readout should be okay because you won't be read-noise dominated. This is probably always the case for data you want to take with 0.50 or 0.35 slits. (The actual per-pixel read noise is about the same, 3-4 electrons per pixel, but I believe in 2x2 binning the effective read noise goes down by 4x because you only do one read per 4 real pixels.)

IMPORTANT, note that the blue side gain changes by a factor of 2, so your counts will change by 2x! The gain is about 0.5 e-/count for slow readout, but 1 e-/count for fast readout. (Carpy accounts for this during reductions as part of the pixel flat.) The red side gain is about the same, 1 e-/count for both readout modes. The nonlinear limit is also a bit lower for fast readout, so you want to stay below 40k counts instead of 50k counts (see the plots next to the computer in the control room). And of course, make sure that your calibrations match your observations.

Calibrations

  • Quartz flats (for slit distortion tracing)
  • Milky flats (for flat fielding)
  • ThAr arcs (for wavelength calibration)
  • Fringe flats (dome screen flats for removing fringing at the red end. Use -fringekey )
    • This requires a relatively recent carpy version to work
  • Recommended to take at least one RV standard

I usually take 20 quartz, 20 milkys the first afternoon, then 5-10 each afternoon after that. UPDATE: I now usually take 5 quartz each night, given some reduction problems when the temperature changed a lot over a multi-night run. Would be a good idea to take some milky's each night too.

It is recommended in the manual to take milky flats with hot blue stars in twilight, but I do not do this. Instead I just take a ton of afternoon milky flats. However for the very bluest orders (if you're pushing down to 3300-3500A), you will want these because you'll need like 100+ milky flats. You can estimate the flat S/N by sqrt(total counts) and see if it is "infinite" for your needs.

Typical exposure times (TODO). Nonlinearity sets in around 50k counts, so the goal is to have a peak of ~40k. (TODO more detail/checks) for 0.35" slit, a 10s arc seems needed to get enough counts for a good wavelength calibration (sometimes the reduction pipeline fails). However, I think only the first afternoon one needs to be taken like this to get an initial identification, and subsequent arcs could be shorter (5s). I have just started taking 5s arcs for everything, except maybe 3s for 1.0 slit.

Calibration exposure time estimates

Aim for 40k counts at peak in both blue and red. Make sure to check the exposure counts.

Slit Bin Read Quartz B/R Milky B/R Fringe
0.7 2x2 Slow 3.5/1.5 12/10 40
1.0 2x2 Slow 8/7 12/10 40
0.5 2x1 Slow 10/5 38/35 100
0.5 1x1 Fast 30/5 90/60 120?
0.35 2x1 Slow 14/8 50/45 150

3-5sec ThArs are good.

The fringe frames are taken without the diffuser. Put in the screen, turn on both the Qh and Ql lamps, and turn the internal dome lamp to 2.7V.

NOTE: keep the dome lights off (or at least constant) when you take the milky flats. Alex screwed this up once showing people the mirror and got milkys with too much intrinsic noise.

Numbering

I usually number each night starting 1000 for the first night, 2000 for the second night, etc. (For initial calibrations, e.g. milky's, I usually start numbering at 0000)

Alex's setup for quick reductions

  • make calibration frames ahead of time
  • scp raw data to my laptop (r,b)
  • mikedb -d raw_data (Carpy)
  • python splitdb.py (Anaconda), go into different
  • mikesetup -db redMIKE.db -red -all; make (targ_); same with blue. (Carpy)
    • Optional: for red side, take dome flats and do -fringekey fringe
  • run summary plot (code) on reduced data (Anaconda)

Set up (at least) four terminal windows. (1) Copying, mikedb (carpy) (2) Anaconda for split_db (3) blue folder reduction (carpy) (4) red folder reduction (carpy)

Procedure during the night:

  • Copy data to raw_data (e.g. rsync --progress --azvhr user@computer:/path/to/your/data/directory/ .)
  • Run mikedb -d raw_data (terminal 1)
  • Run python split_db.py (terminal 2)
  • If redoing target, remove targ_obj<red/blue> and obj<red/blue>/ directory (terminal 3/4)
  • make regenerate (and/or mikesetup -db <blue/red>MIKE.db -<red/blue> -all) (terminal 3/4)
  • make all (or make targ_obj<red/blue>)

Guanaco computer/MIKE GUI instructions

  • In the MIKE GUI, set the observer and check the DataPath
  • "mike" opens MIKE GUI, if it's not open, also opens overview for MIKE-blue and red
  • "goiraf" opens IRAF (with xgterm; the big red button does it too)
  • dmike xxxx: display image xxxx
  • imexam (gives "l" and "c" for line and column cuts)
  • Editing fields in the MIKE GUI requires you to put the mouse in the edit field, type in the changes, and press enter

Observing

  • Experience shows that for abundances, you only need to take arcs at the beginning, middle, and end of night (good to about 1-2 km/s). For more precise RVs you will want an adjacent arc.
  • You can edit the exposure time on the fly. The best way to stop and read out an exposure is to change the exposure time
  • I would not change readout settings during an exposure, just set it correctly before you begin exposing. But if you make a mistake, you can change it as long as it's not in the 10-30 seconds before the exposure finishes and reads out. I have been burned by changing it too late.
  • I usually take an arc whenever I see the temperature changing a lot (by ~0.5 deg), since this tends to be when it shifts.
  • Arcs can be taken while slewing (unless you want super precise RVs).
  • It's a good idea to take an arc whenever you change the slit, as in principle the slit position could change slightly. But in practice, I haven't noticed a difference (at the 1-2 km/s level).
  • MIKE does not have a rotator. Good for stability, bad for atmospheric dispersion. Because guiding is only done in R band, at airmass > 1.5 if you care about blue light you will want to move the star a bit in the slit. Ian Thompson says he "guides low", i.e. move the star down in the slit viewer. You can and should check this (can do in twilight with a bright star; you can see where the slit is from the sky background), but moving an object down on the slit viewer makes the object trace move right on the blue CCD (as viewed on the MIKE GUI). Note also that the blue and red object locations are flipped on the CCDs (right on blue = left on red). Do this only by about 10-20% of the slit length, or reductions can get painful.

To-do list

  • Add RV standards catalogs/scripts
  • Add hot blue stars catalog?
  • Add code to turn lists of objects/coordinates into a MIKE observing catalog
  • Add something for finding charts
  • Add something for observation planning
  • Add autosummary script
  • Add exposure time calculator

Instrument Notes

  • 3-7-2019: since my last run in Nov 2018, they moved the quartz lamp to be a bit further away. I find calibration times need about 3-4x more exposure to achieve similar counts. The ThAr should not be affected.
  • 6-13-2019: the lamp apparently has been moved back, since we needed much shorter exposure times this run.

Reduction Notes

Make sure to inspect the wavelength calibration output. For instance, look at lampblue/lampblue_lampXXXXfbspecshisto.ps. If the residuals have obvious trends, this means the wavelength calibration is off. It is reasonably common for the blue side calibration to be off by a few tenths of angstroms at order edges. You can also look order-by-order in lampblue/lampblue_lampXXXXfbspecsmatch.ps, which shows which lines are being iteratively rejected in the wavelength solution.

To fix the wavelength calibration, go to lampblue/Makefile and look for these things:

stage-wdist: stage-xdist-copy
...
mikeMatchOrders lampblue_lamp1002fb.fits
mikeFindLines lampblue_lampXXXXfbspecs.fits -fwhm 2.500000 -th 10.000000
mikeMatchLamps lampblue_lampXXXXfbspecs.fits -x 5 -o 4 -maxsh 300

If the error message says that you are not finding enough lines, you can adjust -fwhm (minimum line FWHM) or -th (detection threshold) in mikeFindLines. If the solution is a bad fit, you can change -x or -o for mikeMatchLamps to change the degree of the polynomial fit in the X direction (-x) or in the Y direction (-o for order, I think). I think that Carpy uses all lines in all orders to determine an overall distortion, which helps give pretty good wavelength solutions even in orders without that many arc lines. However, this can also lead to bad fits.

It is fairly common for Carpy to die during wavelength calibration. A common failure mode is when the wavelength solution is bad, so bad that it becomes non-monotonic. There will be an unhelpful error message related to splrep when that happens, because fitting splines requires the input wavelengths to be monotonic. If this happens, it means your wavelength calibration is bad. We have also found in practice that the exact failures can change depending on what version of Carpy you are using (I use an old version on my laptop that I installed in 2015 and don't want to touch because it just works, but right now I do all my final reductions on the Carnegie computers to take advantage of Dan Kelson's latest but non-version-controlled improvements).

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