Spectral Extraction at SPE level

The ``standard'' spectral extraction procedure is carried out at the SPE level of the jemx_science_analysis script by re-formatting the source fluxes found at the IMA step. The file jmx2_srcl_res.fits serves as input for the spectral extraction in each ScW. It is important to note, however, that j_ima_iros will always find a little bit different source positions in different ScWs. The deviation of the found source position from the true one may lead to an error in determination of the source spectrum. To avoid this difficulty it is recommended to create a ``user catalog'' with the names and positions of the sources for which you want to extract the spectra.

For example, in the considered case, the source of interest is the Crab and one can just copy the corresponding line from the general reference catalog:

fcopy "${ISDC_REF_CAT}[NAME=='Crab']" user_cat.fits

In the new user_cat.fits file you have to change the FLAG column to 1: in this case jemx_science_analysis would directly copy the source position information to the jmx2_srcl_res.fits after IMA step (see Sections 6.7.6 and 8.6.1 for an explanation on the possible FLAG values).