MIR Tutorial (Charlie Qi 01/31/2014)
		 

1. MIR setup

2. General procedures
a. data inspection
b. tsys correction
c. bandpass cal
d. gain cal
e. data output: MIRIAD or FITS

Details:

a. data inspection
   MIR programs: readdata, plot_continuum, plot_spectra, plot_var

   - Data structure: headers (in, bl, sp) and their corresponding pointers.
     * help,/str to get the variable names
     * filtering: use wrappers vs function dat_filter; stackable
                  before reset
       blcd vs baseline; sb vs sideband; rec vs rx; band vs band;  
       tssb: tsys; integ: scan seconds
       wt: weighting; nch: channel numbers; prbl: projected baseline (m)
       ampave: averaged amplitude; phaave: averaged phase
     * mir_save,/new: to create new subset.

   - example 1. find out on source observing time. 
             2. where is pointing data ?
	     3. how many channels in a specific chunk ?

   - plot_continuum 
     * c1 pseudo continuum band. can be generated by uti_avgband
     * uti_avgband uses the center 82 MHz of each 104 MHz chunk. 
   - plot_spectra
     * plot_spectra
     * select,/p,/re,source='IMLUP',sideband='u'
       plot_spectra,x='fsky',frame_v='sb',color='band', preavg=2
   - plot_var (take note on the IF1 and IF2 tsys)
     * plot_var,x='prbl',y='ampave',frame_var='sb',color='blcd'
     * plot_var,y='ampave',x='el',frame_var='blcd,sb',color='source'
     * plot_var,x='prbl',y='ampave',frame_v='sb',color_v='source'

b. tsys correction:
   - tsys replacement

c. bandpass cal. 
   - check atmospheric absorption ( e.g. at 358 ghz)
   - calibrator selection (compiled by Mark Gurwell)
      3C111=0418+380, BLLac=2202+422 have very deep, narrow CO, other 
      lines, other sources of concern would be 0359+509, 0530+135, 
      NRAO530=1733-130, and even 3C454.3 (though that is not as deep).

      For solar system sources, Neptune has broad CO absorption plus 
      an ~80 MHz wide emission peak (so bad there) as well as HCN 
      emission over about 100 MHz.

      Titan has lines all over the place so avoid.

      Mars, Venus have ~200 MHz CO absorption lines that can be up to 
      40% of the continuum in depth.  Isotopes can exhibit ~5%
      absorption as well.

      Uranus has no known spectral lines.  Callisto and Ganymede are 
      also very good (solid bodies, no appreciable atmosphere).  
      Same with Mercury if out of sun avoidance zone.

      Jupiter and Saturn may be ok, but when they are highly resolved 
      may not be sufficient because nulls can happen within the 4 GHz 
      IF and that will screw things up. Saturn 279 GHz PH3 line ?

   - recommend baseline-based amplitude bandpass cal, see log 15345
   - separate phase and amplitude bandpass cal. 
     the usual procedures:
         antenna-based phase bandpass cal
	 regenerate continuum with uti_avgband
	 baseline-based amplitude bandpass cal
   - keywords: preavg, ntrim, smoothing

d  gain cal
   - get flux information first.
   - keyword preavg

e  output
   - idl2miriad, libfile='filelocation' ...

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3. Tips

a. take notes

b. save and restore datasets

c. check the data filter

d. type 'retall' if anything crashes


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Extras

1. baseline correction.
 a. see reference page in SMA Observer Center.
 b. check antennas file.

2  flux calibration and measurement

 a. source selection (compiled by Mark again)
    Best - Titan
    Good - Callisto, Uranus*, Neptune* (if 12+GHz away from CO lines)
    Almost as good - Mars*, Ganymede
    Not Good - Saturn, Venus, Jupiter, Pluto
    Here, * means beware of overresolving the source!

 b. IDL> select,/p,/re, band='c1'
    IDL> gain_cal,cal_type='pha',/connect,/non_point,tel_bsl='telescope',
                    refant=?
          - type "all yes" when it asks for calibrator names and fluxes
          - then type "yes" to apply the solution
    IDL> select,/p,/re, band='c1'
    IDL> gain_cal,x='hours',poly=0,cal_type='amp',/preavg,/non_point,
                   tel_bsl='telescope',refant=?
          - type "all no" and then type "callisto yes"
          - then type "yes" to apply the solution.
    IDL> select,/p,/re, band='c1'
    IDL> flux_measure
          - type 'V' for vector average

 c. compare with Mark's table.  
    - plot_var,x='prbl',y='ampave',frame_v='sb',color_v='source'

3. multiple sources dopplerTracking
   - uti_doppler_fix
 
4. data fix (see MIR cookbook webpage) 

5. DBA track, if1/if2 phase offsets. 
   - uti_difif to check the difference of if1/if2
     plot_continuum,y='difif',/preavg


mir_restore,'difif.save'

select,source='16',/p,/re
uti_difif
plot_continuum,y='difif',/preavg

select,source='16',/p,/re
gain_cal,/difif,tel_bsl='telescope',cal_type='pha',refant=6,/connect,/preavg,x='hours'

select,source='16',/p,/re
uti_avgband

select,source='16',/p,/re
uti_difif

plot_continuum,y='difif',/preavg