XMM-Newton Science Analysis System: User Guide

4.4.3 How to get pixels flagged "ON_BADPIX" back into the eventlist

Using the recommended selection expressions #XMMEA_EP and #XMMEA_EM, or even the more restrictive FLAG==0, pixels flagged as bad are not taken into account in the analysis. For specific circumstances it might be desired to revise a bad pixel flag and to make the pixel available again to the analysis using the task ebadpixupdate.

An important point regarding the bad pixels is that there are essentially three separate (though not exclusive) sets of bad pixels that must be dealt with. These are (1) bad pixels up-linked to the satellite and eliminated on-board, (2) bad pixels identified in the CCF but not up-linked, and (3) additional bad pixels associated with the particular observation in question. A corresponding list of bad pixels, individually for each CCD, is provided by the BADPIX**-extension tables inside the eventlist FITS-file.

• Create eventlist files still containing bad pixels. Per default, all EPIC pipeline processing tasks (e[m/p]proc or e[m/p]chain) perform the search for bad pixels both in CCFs and in the individual observation and flag the corresponding events from these bad pixels in the temporary eventlists. However the treatment of bad pixels at the time of the creation of the final eventlist file is different for the pn and the MOS pipeline tasks. The pn tasks take over the events from bad pixels into the final event list and assign to them the FLAG==ON_BADPIX, whereas the MOS tasks filter out these bad pixel events such that they do not appear any more in the final eventlist file. To get the MOS bad pixels back into the eventlist, it is necessary to re-run the MOS pipeline tasks using a special parameter to switch off the final filtering:

  emproc flagfilteredevents=yes
  

  or

   
  emchain rejectionflag=764ba000
  

  The use of the emchain parameter rejectionflag=764ba000 is recommended (instead of rejectbadevents=no) because emchain keeps the events flagged as being ON_BADPIX while it still removes all other types of bad events.

• Extract bad pixel table from the eventlist file. The eventlist FITS files contain individual bad pixel tables of all CCDs. These tables can be extracted with the Ftool fv. After opening the eventfile with fv <eventlist_name>, two windows appear: a general fv menu window and a window listing FITS headers and tables of all extensions inside the eventlist file. The extensions of the bad pixel tables are named BADPIX** with ** being the CCD number. The bad pixel table of a specific CCD is presented in a separate window if the All button under the Table column is pressed. The table contains for each entry the pixel position in RAWX/RAWY coordinates, an extension size within the column (YEXTENT), the TYPE (1=hot, 2=flickering, 3=dead) and the BADFLAG indicating to which of the sets the bad pixel belongs: (1) for onboard bad pixel table, (2) for CCF bad pixel table and (3) for detections via the ebadpixupdate task.

  To extract one or more bad pixels tables, mark the corresponding extensions in the Index column and chose Export HDUs... from the File menu. Of course fextract (and fappend, if several bad pixel tables are required) does the job as well.

• Edit the bad pixel table. After saving the extracted bad pixel tables in a new file, open this new file using fv and open the table you want to edit. To delete a bad pixel entry, mark the corresponding row by clicking on the row number and chose Edit $\rightarrow$ Delete $\rightarrow$ Selected rows from the Edit menu. Because bad pixels with BADFLAG=1 are eliminated onboard, these pixels cannot be recovered and their entries must not be changed. You have to pay attention on the YEXTENT column for the corresponding pixel entry. A single bad pixel has YEXTENT=1. If just one bad pixel within an extended region within a column should be recovered, the YEXTENT value can be edited directly. It might be necessary to add an additional row (Edit $\rightarrow$ Insert $\rightarrow$ Row) to define the remaining bad pixels in the column correctly. Save the changed bad pixel table (File $\rightarrow$ Save).

• Update the bad pixel tables in the eventlist file. The last step is to update the FLAG column inside the eventlist. This can be done by the task ebadpixupdate. The task needs as input the changed bad pixel tables and the eventlist file. The following example shows the update of an EPIC eventlist EPICEVENTLIST.FIT. The original bad pixel tables of all 12 CCDs have been exported to a file BADPIXTABLE.FIT. The bad pixel tables of CCD1 and CCD3 have been changed. The FLAG keywords inside the eventlist file are updated by the command:

  ebadpixupdate eventset=EPICEVENTLIST.FIT fromccf=N overwrite=yes \ 
                badpixtables='BADPIXTABLE.FIT:BADPIX01 \
                BADPIXTABLE.FIT:BADPIX03'