Extraction and calibration for S14 data:

1.  Set up the directory structure for Campaign NN (01, etc)

chmod /home/ioc/campaign_NN  (edit NN)

mkdir IRS_070_14
chmod 775 IRS_070_14
cd IRS_070_14
cp /home/ioc/campaign_01/IRS_070_14/setup.bat .
setup.bat
cp ../IRS_070_13/target.lst .

If an old target.lst is not available, then create a new one in step 2 below.

2.  Create target.lst file, in this example Camp. 1, S14.0 pipeline version
The output must be edited to have the form
delumi    calsfx_1A_delUmi      8244224 8245760 8246016 8246272 8246528 
i.e. all AORkeys for a given target on one line.

qdb "select object,'  ',aorname,'  ',aorkey from onlinedata where expid=0 and dcenum=0 and subdir~'01-14.0' and aorname~'calsfx-1'" | sort | uniq > target.lst

(This step is currently done for IRS_070_14 directories using the last command
in the sequence for Step 1 above.)

3.a.  Generate the file list:  file.lst 

qdb "select subdir,localfile,' ',fovid from onlinedata where subdir~'01-14.0' and aorname~'calsfx-1' order by aorkey,expid,dcenum" > file.lst

3.b.  Generate the module file lists in IDL.

mk_bat_lst,'file.lst','target.lst'

4.  Generate the batch files to process spectra in the module subdirectories

In IDL in SL:

mk_bat_cp,'file.lst','sl.lst','runcp.bat'
mk_bat_file,'sl.lst','imdiff.idl',option=31
mk_bat_file,'sl.lst','imfor.idl',option=71
mk_bat_file,'sl.lst','imclean.idl',option=27
mk_bat_file,'sl.lst','extract/runex.bat',option=44
mk_bat_file,'sl.lst','convert.idl',option=5
mk_bat_file,'sl.lst','offset.idl',option=6
mk_bat_cc,'sl.lst','cc.a1.lst'
mk_bat_join,'sl.lst','join.a1.idl',option=1,/plot

In IDL in LL:

mk_bat_cp,'file.lst','ll.lst','runcp.bat'
mk_bat_file,'ll.lst','imdiff.idl',option=30
mk_bat_file,'ll.lst','imfor.idl',option=70
mk_bat_file,'ll.lst','imdiffx.idl',option=33
mk_bat_file,'ll.lst','imclean.idl',option=27
mk_bat_file,'ll.lst','extract/runex.bat',option=44
mk_bat_file,'ll.lst','convert.idl',option=5
mk_bat_file,'ll.lst','offset.idl',option=6
mk_bat_cc,'ll.lst','cc.a1.lst'
mk_bat_join,'ll.lst','join.a1.idl',option=1,/plot

In IDL in SH:

through Camp. 16:

mk_bat_cp,'file.lst','sh.lst','runcp.bat'
mk_bat_file,'sh.lst','imclean.idl',option=22
mk_bat_file,'sh.lst','extract/runex.bat',option=41
mk_bat_file,'sh.lst','convert.idl',option=5
mk_bat_file,'sh.lst','offset.idl',option=6
mk_bat_cc,'sh.lst','cc.a1.lst'
mk_bat_join,'sh.lst','join.idl',option=5,/plot
mk_bat_join,'sh.lst','trim.idl',option=61

Camp. 17 on:

mk_bat_cp,'file.lst','sh.lst','runcp.bat'
mk_bat_file,'sh.lst','imdiff.idl',option=38
mk_bat_file,'sh.lst','imfor.idl',option=78
mk_bat_file,'sh.lst','imclean.idl',option=27
mk_bat_file,'sh.lst','extract/runex.bat',option=41
mk_bat_file,'sh.lst','convert.idl',option=5
mk_bat_file,'sh.lst','offset.idl',option=6
mk_bat_cc,'sh.lst','cc.a1.lst'
mk_bat_join,'sh.lst','join.idl',option=5,/plot
mk_bat_join,'sh.lst','trim.idl',option=61

In IDL in LH:

through Camp. 16:

mk_bat_cp,'file.lst','lh.lst','runcp.bat'
mk_bat_file,'lh.lst','imclean.idl',option=22
mk_bat_file,'lh.lst','extract/runex.bat',option=41
mk_bat_file,'lh.lst','convert.idl',option=5
mk_bat_file,'lh.lst','offset.idl',option=6
mk_bat_cc,'lh.lst','cc.a1.lst'
mk_bat_join,'lh.lst','join.idl',option=5,/plot
mk_bat_join,'lh.lst','trim.idl',option=61

Camp 17 on:

mk_bat_cp,'file.lst','lh.lst','runcp.bat'
mk_bat_file,'lh.lst','imdiff.idl',option=38
mk_bat_file,'lh.lst','imfor.idl',option=78
mk_bat_file,'lh.lst','imclean.idl',option=27
mk_bat_file,'lh.lst','extract/runex.bat',option=41
mk_bat_file,'lh.lst','convert.idl',option=5
mk_bat_file,'lh.lst','offset.idl',option=6
mk_bat_cc,'lh.lst','cc.a1.lst'
mk_bat_join,'lh.lst','join.idl',option=5,/plot
mk_bat_join,'lh.lst','trim.idl',option=61
--------------------------------------------------------------------------
In lores (out of IDL):

cp ../SL/sl.lst .

In IDL in lores:

mk_bat_join,'sl.lst','join.idl',option=2,/plot
mk_bat_join,'sl.lst','clean.idl',option=3
mk_bat_join,'sl.lst','spplot.idl',option=4

5.  Check and run the batch files to prepare images for extraction

For campaigns 25 on, the imclean.idl file must be edited to change 
the version of the superrogue_M.fits file to superrogue_M_33.fits.

> chmod 764 runcp.bat
> runcp.bat
IDL> @imdiff.idl          (SL and LL, and for Camp 17 on, SH and LH)
IDL> @imfor.idl           (SL and LL, and for Camp 17 on, SH and LH)
IDL> @imdiffx.idl         (LL only)
IDL> @imclean.idl

In lores:

> cp ../SL/sl.lst .

In IDL in lores:

mk_bat_join,'sl.lst','join.idl',option=2,/plot
mk_bat_join,'sl.lst','clean.idl',option=35
mk_bat_join,'sl.lst','spplot.idl',option=4

Go into the extract subdirectory and ensure that the necessary
calibration and namelist files are in place.  The subdirectory "qa" 
should be present and empty.  The subdirectory "cal" should contain 
the wavesamp file and psf_fov file.  The latter is not needed in the 
hi-res directories.  Make sure that the version numbers match those 
called in the namelist files: profile.nl, ridge.nl, extract.nl.  If 
any of these files are not present, copy them from a previous
campaign.

6.  Run the extractions.

Log onto one of the Solaris computers supporting the offline pipeline 
(for the moment, these are isc1-6).  Source the pipeline code:

> source /usr/local/pipeline/S13/env.csh

Go into the extract subdirectory of each module directory and run the
extractions:

> chmod 764 runex.bat
> runex.bat > run01.dat
  (or run02.dat etc. if run01.dat already exists)

7.  Complete the calibration process.

Move up to the module directory and put the data in the appropriate 
locations.

IDL> convert.idl
mv *.sp.fits spectra
mv *.sp.tbl tables
mv *.pro.tbl profiles

(There's more, but we'll stop here for the moment)