Source the GeRT setup file (see §1.3 to setup the GeRT on your system).
unix% source gert_setup.csh
Make an input list of RAW data files.
unix% ls *raw.fits > IN70.lis
The list of input files should match the order in which the data are taken. An example raw data file from the SSC archive has a name like the following:
SPITZER_M2_12345678_0001_0004_2_raw.fits
where
M2 = 70 micron (and M3 = 160 micron)
12345678 = AORKEY
0001 = EXPID exposure sequence number
0004 = DCENUM within the EXPID exposure
2 = archived processing number
Since names are given with leading zeros, "ls" will list the files in the order in which the data were taken. Users should take special care and only include the data they want to reduce in the list, e.g., only PRIMEARR data. For photometry mode observations, one can get EXPIDs associated with 24 micron, 70 micron, and/or 160 micron data for each AOR. If taking photometry data in all three bands, the first set of EXPIDs will be 24 micron, followed by 70 micron, and then followed by 160 micron observations. Read the fits headers to figure out which EXPIDs are associated with which array (keyword FOVNAME). e.g.:
CALER Processing done, BCDs in out/bcd processed in 3 seconds.
Total processing of 8 dce's processed in 25 seconds
IN70.lis is an input list of RAW fits files and OUTdir is output directory of the GeRT products. SLOPER and CALER are the two main steps of processing described in Section 4.2. The symbols "*" indicate stimflash frames while ":" is shown for non-stimflash data.
For default processing, the GeRT reads the header of the first file to determine the data type and picks the appropriate pipeline. The important keywords that control the processing are CHNLNUM, EXPTYPE, and FOVID:
CHNLNUM = 2 for 70 micron
CHNLNUM = 3 for 160 micron
EXPTYPE = scn ==> Scan data, normal science pipeline is run.
EXPTYPE = pht ==> Photometry data, normal science pipeline is run.
If EXPTYPE=pht and FOVID>117, then the data are 70 micron. FINE-scale observations and the appropriate calibration files are chosen.
EXPTYPE = sed ==> 70 micron SED data, SED pipeline is run.
EXPTYPE = tpm ==> Total power mode data, TPM pipeline is run.
EXPTYPE = d2a ==> DARK data, DARK pipeline is run.
EXPTYPE = sfl ==> Illumination Correction (IC) data from scanning, IC pipeline is run.
EXPTYPE = pfl ==> IC data from photometry, IC pipeline is run.
EXPTYPE = ffl ==> IC data from FINE-scale photometry, IC pipeline is run.
EXPTYPE = dfl ==> SED IC data, IC pipeline is run.
EXPTYPE = tfl ==> Total power IC data, IC pipeline is run.
The above listing provides the standard MIPS-Ge data types. See the MIPS Instrument Handbook for a full list of file definitions and for information about the Illumination Correction.
Users can force the GeRT to run a specific pipeline by providing the EXPTYPE on the command line (3rd input argument). For example, if you would like to make your own Illumination Correction (IC) calibration file from your science data you could try the following, e.g.:
unix% $WRAPDIR/gert.pl IN70.lis OUTdir sfl
where "sfl" causes the GeRT to run the IC pipeline.
1.6 My edited namelist files don't seem to work
When editing namelist files, you should include a space before and after the "=" for numerical parameters, and you must end all lines in the namelist with a "," (even comment lines need to be followed by ",". The parameter lines must be within the namelist block (e.g., between &BLOCKNAME and &END).
example of GOOD input:
StimHi = 4,
example of BAD input (don't do):
StimHi = 4
StimHi =4,
StimHi= 4,
StimHi=4
The GeRT namelist files are stripped down versions of the online namelists. Blocks only used online are not included in the offline GeRT namelists. The online input/output (I/O) names of the modules is controlled via namelists, but offline, the GeRT perl script defines the I/O names, which takes precedent over what is listed in the namelist.
