Reducing ACSIS data with CLASS

To run the GILDAS software (class, greg, etc) first type (or enter this in your .login file):

setenv GAG_ROOT_DIR /jcmt_sw/CLASS/GILDAS
setenv GAG_EXEC_SYSTEM x86_64-redhat-g95
source $GAG_ROOT_DIR/etc/login

The latest installed version (December 2010c) can be reached at all 64-bit machines.

If you prefer to use CLASS and other Gildas software to reduce your spectra these are the steps to take:
(at this moment one is working in Grenoble on methods to do the conversion in CLASS itself)
First make cubes of the ACSIS data with makecube or ORACDR. Then extract subcubes of dimension 1,1,nspec from the cubes in NDF format and convert these to FITS format. Read the FITS files into CLASS.

This can be done with the kappa command ndfcopy and the convert command ndf2fits.

The following assumes that you are using the most recent (Deneb) release of the Starlink software.

to FITS

If you have multisubsystem observations made with RxA3, where the first subband is in LSB (USB) and another is in USB (LSB), you have to change the sideband in the header of the USB (LSB) cube:

kappa
wcsattrib file.sdf set sideband USB (LSB)

The simplest ways to convert .sdf files to FITS format is for:
RxA3 and RxW (single spectra):

convert
ndf2fits file.sdf file.fits encoding="fits-class"

kappa
ndfcopy in='file(1,1,)' out=file.sdf exten
./cubecopy file.sdf file_cc.sdf
convert
ndf2fits file_cc.sdf file.fits encoding="fits-class"

To convert maps one needs to do this for all positions in the map.
This is an example of a csh script that finds the dimensions of a cube and extract all spectra

#!/bin/csh -f 
#
# Use: scriptname [ndf_file_name]
#
source /star/etc/login  >& /dev/null 
source /star/etc/cshrc  >& /dev/null 
kappa >& /dev/null 
convert >& /dev/null 

if (`alias kappa` == "") then 
  echo "" 
  echo "Fatal: Initialization error of kappa environment" 
  echo "" 
  exit 
endif 

#  Get the input NDF and strip .sdf extension
if ($# == 0) then
  set def = `parget data_array GLOBAL`
  echo -n "Input MAKECUBE cube /$def/ > "
  set file = $<
  if ("$file" == "") then
     set file = $def
  else if ("$file" == "\!" || "$file" == "\!\!") then
     echo ""
     exit
  endif
else
  set file = "$argv[1]"
  shift
endif
set file = `echo $file | cut -d\. -f1`

# Find dimensions of the NDF file
ndftrace ${file} >& /dev/null
set dims  = `parget dims ndftrace | head -1`
set lbnds = `parget lbound ndftrace | head -1`
set ubnds = `parget ubound ndftrace | head -1`

set xsize = $dims[1]
set ysize = $dims[2]
set xmin =  $lbnds[1]
set xmax =  $ubnds[1]
set ymin =  $lbnds[2]
set ymax =  $ubnds[2]

echo "Map size read in : $xsize x $ysize " 
echo "Xrange read in : $xmin to $xmax "
echo "yrange read in : $ymin to $ymax "

# Extract individual spectra from the NDF and convert to FITS
@ nr = 0
@ i = $xmin 
while ($i <= $xmax) 
  @ j = $ymin 
  while ($j <= $ymax) 
    ndfcopy in="${file}(${i},${j},)" out=${file}_${i}_${j} exten
    ./cubecopy ${file}_${i}_${j} ${file}_cc_${i}_${j}
    ndf2fits ${file}_cc_${i}_${j} ${file}_${i}_${j}.fits encoding="fits-class" 
    echo "Finished  ${file}_${i}_${j}.fits" 
    @ nr ++
    @ j ++ 
  end 
  @ i ++ 
end

stats "${file}(,,~1)" >& /dev/null
set nrpix = `parget numpix stats | head -1`

echo "-----------------------------------------"
echo "$file has $nrpix spectra."
echo "Routine created $nr fits files."
echo "-----------------------------------------"

to CLASS

These files can be converted into class format

%class
LAS90>file out jcmtdata mul (or sin)
LAS90>fits read file.fits
(or alternatively)
LAS90>fits read "/dir/subdir/file.fits"
LAS90>write n

(note: if the scannumber is missing in the fits header one needs to give a number when writing to the output file, or it will be put to 1)

%ls *.fits > files.class

file.fits

fits read file.fits
write 1
etc

%class

LAS90>@files.class

Problems

LAS90> sic\symbol OBSNUM SCAN-NUM
LAS90> sic\symbol NSUBSCAN SUBSCAN
LAS90> sic\symbol MEDTSYS TSYS
LAS90> sic\symbol EXP_TIME OBSTIME
LAS90> sic\symbol LINE NOTAKEY
LAS90> sic\symbol MOLECULE LINE

tau (not calculated for ACSIS data)
weather parameters
beameff
forweff

For help within class, greg, etc type help, or look at the GILDAS homepage.

In the newest version of Greg/Graphic the Explain command is not working. Here is a list of available tasks (run task).

Jan Wouterloot