INTEGRAL data anlsyis can be performed with ISDC's Off-line Science Analysis (OSA) package, and the data analysis manual is provided by ISDC.
In this page, we explain an alternative and hopefully easier way to analyze INTEGRAL ISGRI and JEMX data. Still we are dependent on OSA, but we run OSA components differently from standard OSA methods (i.e., running og_create, ibis_science_analysis and jemx_science_analysis).
We provide simple c-shell scripts isgr_scw_analysis.csh and jemx_scw_analysis.csh, in which we call ISDC and ftools directly to perform necessary tasks, rather than through "ISDCroot scripts". People who prefer shell scripting to GUI interface might find our scripts useful.
To configure without ROOT, "ac_stuff/configure --without-cern-root". Also, do not forget "unsetenv ROOTSYS", if you had accidentally set up ROOTSYS environmental variable. However, when doing "source $ISDC_ENV/bin/isdc_init_env.csh", ROOTSYS environmental parameter may be required (this shall be fixed soon). Untill this problem is fixed, you can set just a dummy value, such as "setenv ROOTSYS abcdefg" or whatever.
Install the IC (Instrument Characteristic) package and the catalog following the standard procedure. Currently, you need to install *all* the IC and catalogs, even if you would analyze only one or two instruments. SPI and OMC occupy most volumes of the IC and catalog data, while many people will analyze only ISGR and JEMX. Soon, this requirement of the entire IC will be mended, and you will be required to install only ISGRI and JEMX related callibration files to analyze ISGRI and JEMX data.
For example, I would like to download only "scw.fits" (Science Window index file) and jemx and isgri related files for all the Science Windows (ScWs) in Revolution 55.
cd /local/data/subaru4/ebisawa/INTEGRAL/scw/0055 lftp -c "open ftp://isdcarc.unige.ch/arc/rev_2/scw/0055 && mirror -I *0.001/j*fits* -I *0.001/i*fits* -I *0.001/swg.fits* -X *[12].001/"lftp is a very useful tool for this kind of purpose. In this example, I downloaded only files which are necessary to analyze ISGRI and JEMX from pointing Science Windows (i.e., excluding slews). Note, pointing Science Window names always end with *0.001 (001 is the processing version number, which should be 000 for the first processing), so I excluded directories ending with 1.001 or 2.001.
mkdir -p $REP_BASE_PROD/aux/adp/0055.001 cd $REP_BASE_PROD/aux/adp/0055.001 lftp -c "open ftp://isdcarc.unige.ch/arc/rev_2/aux/adp/0055.001 && mirror -I attitude* -I orbit* -I time* -X logs/" mkdir -p $REP_BASE_PROD/aux/adp/ref cd $REP_BASE_PROD/aux/adp/ref lftp -c "open ftp://isdcarc.unige.ch/arc/rev_2/aux/adp/ref && mirror -I *"
setenv REP_BASE_PROD /local/data/subaru4/ebisawa/INTEGRAL setenv ISDC_REF_CAT "/local/data/subaru4/ebisawa/INTEGRAL/cat//hec/gnrl_refr_cat_0017.fits[1]" setenv ISDC_ENV /local/data/subaru4/ebisawa/INTEGRAL/osa_sw-4.2 source $ISDC_ENV/bin/isdc_init_env.csh setenv COMMONLOGFILE +common_log.txtThe last COMMONLOGFILE setting is not required but useful to keep a log with the name "common_log.txt".
Then, modify the initial part of isgr_scw_analysis.csh and jemx_scw_analysis.csh to specify the Science Window data location. After that, in any directory, run these scripts. Several OSA executables are executed, and you will see the following files in the current directory.
GNRL-OBSG-GRP.fits INDEX_j_ima_cor_intensity.fits isgri_mosa_res.fits jmx2_rsti_ima.fits GNRL-SCWG-GRP.fits INDEX_j_ima_shadowgram.fits isgri_pif.fits jmx2_sky_ima.fits INDEX_ii_cat_extract.fits INDEX_j_ima_src_find.fits isgri_sky_ima.fits jmx2_srcl_arf.fits INDEX_ii_shadow_build.fits INDEX_j_src_spectra.fits isgri_sky_res.fits jmx2_srcl_bsp.fits INDEX_ii_shadow_ubc-BIN_I.fits isgri_catalog.fits isgri_spectrum.fits jmx2_srcl_cat.fits INDEX_ii_shadow_ubc-BIN_S.fits isgri_catalog.reg isgri_srcl_res.fits jmx2_srcl_cat.reg INDEX_ii_skyimage.fits isgri_cor_shad.fits isgri_srcl_res.reg jmx2_srcl_res.fits INDEX_ii_spectra_extract.fits isgri_detector_shadowgram.fits isgri_srcl_res_significant.fits jmx2_srcl_res.reg INDEX_j_bin_evts_spectra.fits isgri_efficiency_shadowgram.fits jmx2_evts_shd.fits jmx2_srcl_spe.fits INDEX_j_cat_extract.fits isgri_grou_shd.fits jmx2_find_res.fits INDEX_j_ima_basic_recon.fits isgri_mosa_ima.fits jmx2_full_dsp.fitsThose INDEX*fits files are temporary index files which are needed to run ISDC tasks. Files which have names like i*fits and j*fits are the output files. They are identical to what you get by running the standard ISDC tools ibis_science_analysis and jemx_science_analsys. Note, user GTI selection capability has not implemented in these c-shell scripts. You will have to implemnet "gti_merge" task for this purpose (or, just use standard ISDC programs ibis_science_analysis or jemx_science_analysis).
Standard Scinece Window images are already created by ISDC
pipe-line, and found in the ISDC archives. You may download
these images, and run
To obtain all the JEMX2 Science Window images of Revolution 55:
lftp -c "open ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001 && mirror -I ssj2_00550???0010/scw/005500???010.001/jmx2_sky_ima.fits.gz"Now you have the following files under the current direcotry:
ssj2_005500020010/scw/005500020010.001//jmx2_sky_ima.fits.gz ssj2_005500030010/scw/005500030010.001//jmx2_sky_ima.fits.gz ssj2_005500040010/scw/005500040010.001//jmx2_sky_ima.fits.gz ... ssj2_005500900010/scw/005500900010.001//jmx2_sky_ima.fits.gz ssj2_005500910010/scw/005500910010.001//jmx2_sky_ima.fits.gz ssj2_005500930010/scw/005500930010.001//jmx2_sky_ima.fits.gzYou can check the pointing directions of these images:
foreach file (*/scw/*/*fits.gz)
set RA = `fkeyprint ${file}+2 CRVAL1 | grep Sky | awk '{printf("%10.3f\n",$3)}'`
set DEC = `fkeyprint ${file}+2 CRVAL2 | grep Sky | awk '{printf("%10.3f\n",$3)}'`
set TSTART = `fkeyprint ${file}+2 TSTART | grep Start | awk '{printf("%15.3f\n",$3)}'`
echo $file $TSTART $RA $DEC
end
ssj2_005500020010/scw/005500020010.001/jmx2_sky_ima.fits.gz 245.613 -60.150 ssj2_005500030010/scw/005500030010.001/jmx2_sky_ima.fits.gz 241.603 -60.315 ... ssj2_005500630010/scw/005500630010.001/jmx2_sky_ima.fits.gz 253.820 -31.727 ssj2_005500640010/scw/005500640010.001/jmx2_sky_ima.fits.gz 256.097 -33.165 ssj2_005500650010/scw/005500650010.001/jmx2_sky_ima.fits.gz 147.064 -48.030 ssj2_005500660010/scw/005500660010.001/jmx2_sky_ima.fits.gz 146.925 -47.900 .. ssj2_005500910010/scw/005500910010.001/jmx2_sky_ima.fits.gz 39.422 67.267 ssj2_005500930010/scw/005500930010.001/jmx2_sky_ima.fits.gz 39.422 67.267You might also want to check the scheduling information at http://www.rssd.esa.int/integral_webapps/index.jsp?past?0?2253
OK, we decide to make a mosaic image from the GCDE pointings. We choose the following Scinece Window image files, and put the list in the "listfile"
ssj2_005500480010/scw/005500480010.001/jmx2_sky_ima.fits.gz ssj2_005500490010/scw/005500490010.001/jmx2_sky_ima.fits.gz ssj2_005500500010/scw/005500500010.001/jmx2_sky_ima.fits.gz ssj2_005500510010/scw/005500510010.001/jmx2_sky_ima.fits.gz ssj2_005500520010/scw/005500520010.001/jmx2_sky_ima.fits.gz ssj2_005500530010/scw/005500530010.001/jmx2_sky_ima.fits.gz ssj2_005500540010/scw/005500540010.001/jmx2_sky_ima.fits.gz ssj2_005500550010/scw/005500550010.001/jmx2_sky_ima.fits.gz ssj2_005500560010/scw/005500560010.001/jmx2_sky_ima.fits.gz ssj2_005500570010/scw/005500570010.001/jmx2_sky_ima.fits.gz ssj2_005500580010/scw/005500580010.001/jmx2_sky_ima.fits.gz ssj2_005500590010/scw/005500590010.001/jmx2_sky_ima.fits.gz ssj2_005500600010/scw/005500600010.001/jmx2_sky_ima.fits.gz ssj2_005500610010/scw/005500610010.001/jmx2_sky_ima.fits.gz ssj2_005500620010/scw/005500620010.001/jmx2_sky_ima.fits.gz ssj2_005500630010/scw/005500630010.001/jmx2_sky_ima.fits.gz ssj2_005500640010/scw/005500640010.001/jmx2_sky_ima.fits.gzWe run varmosaic:
varmosaic listfile jemx2_rev55_gc.fitsNow you see a rather smooth jemx mosaic image as shown below. GX349+2 is clearly seen. This is the Primary of the file, which is the Significance map of the first energy band (varmosaic creates mosaics of significance map, intensity, variance, and exposure map).
Note, ftools/cfitsio has a nice capability that they can access remote files directly through Intenet. Consequently, you do not have to donwload invididual Scinece Window images, but specify the remote files at ISDC archives directly in the "listfile".
For example, you may specify the following in the "listfile",
ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500480010/scw//005500480010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500490010/scw//005500490010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500500010/scw//005500500010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500510010/scw//005500510010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500520010/scw//005500520010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500530010/scw//005500530010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500540010/scw//005500540010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500550010/scw//005500550010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500560010/scw//005500560010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500570010/scw//005500570010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500580010/scw//005500580010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500590010/scw//005500590010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500600010/scw//005500600010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500610010/scw//005500610010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500620010/scw//005500620010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500630010/scw//005500630010.001/jmx2_sky_ima.fits.gz ftp://isdcarc.unige.ch/arc/rev_2/obs_jmx/0055.001/ssj2_005500640010/scw//005500640010.001/jmx2_sky_ima.fits.gz
then varmosaic opens and reads these remote files on the fly. You will get exactly the same image above as when local files are input.