Rerunning the Pipeline

First, create the directory for processed data, PROC, by right-clicking on the ObsID directory and choosing the option ``Create new directory''. Highlight PROC by single-clicking on it. Please note that both the Hera GUI and Command Window rely on this to know where to place the output files. Calling any of the chains will initiate processing on all OM data of that particular mode; currently, only omichain will accept parameters to limit processing to a specific filter or exposure.

To rerun the pipeline on all exposures and filters from the GUI:

1)

In the Available Tools panel, under ``XMM-SAS'', call omichain.

2)

In the task pop-up window, click ``Run''.

To rerun the pipeline on all exposures and filters from the Command Window, type:

omichain

This produces numerous files, including images and regions for each exposure and each filter. If we are interested in the sources detected in the mosaicked, V band image we could run omichain with the appropriate flags.

To rerun the pipeline on the mosaicked, V-band image from the GUI:

1)

In the Available Tools panel, under ``XMM-SAS'', call omichain, Next to ``List of OM filters to be processed'', enter V; next to ``Source detection on stacked images'', click ``yes''. Next to ``Number of sigma for a detection'', enter 2.0; next ``Minimum allowed source significance'', enter 3.0.

2)

In the task pop-up window, click ``Run''.

To rerun the pipeline on the mosaicked, V-band image from the Command Window, type:

omichain filters=V processmosaicedimages=yes omdetectnsigma=2.0
$$ omdetectminsignificance=3.0

where

filters - list of filters to be processed
processmosaicedimages - process the mosaicked sky images?
omdetectnsigma - number of $\sigma$ above background required for a pixel to be considered part of a source
omdetectminsignificance - minimum significance of a source to be included in the source list file

The output files can be used immediately for analysis, though users are strongly urged to examine the output for consistancy first (see §9.3.2). The chains apply all necessary corrections, so no further processing or filtering needs to be done. Please note that the chains do not produce output files with exactly the same names as those in the PPS directory (they also produce some files which are not included in the PPS directory at all.) Table 9.2 lists the file ID equivalences between repipelined and PPS files.

Table 9.2: File ID equivalences between repipelined and PPS OM files.

Repipelined	PPS Name	Description
Name
EVLIST	none	FAST mode events list
FIMAG_	FIMAG_	combined full-frame image
FLAFLD	none	flatfield
FSIMAG	FSIMAG	combined full-frame sky image
HSIMAG	HSIMAG	full-frame HIRES sky image mosaic
IMAGE_	IMAGE_	image from any filter or GRISM
IMAGE_	IMAGEF	FAST mode image
LSIMAG	LSIMAG	full-frame LORES sky image mosaic
OBSMLI	OBSMLI	combined observation source list
REGION	SWSREG	sources region file
REGION	SFSREG	FAST mode sources region file
REGION	SGSREG	GRISM ds9 regions
RIMAGE	GIMAGE	GRISM rotated image
RSIMAG	RSIMAG	default mode sky mosaic
SIMAGE	SIMAGE	sky aligned image
SIMAGE	SIMAGF	FAST mode sky aligned image
SIMAGE	none	GRISM sky aligned image
SPCREG	SPCREG	GRISM ds9 spectrum regions
SPECLI	SPECLI	GRISM specra list
SPECTR	SPECTR	source extracted spectra
SUMMAR	SUMMAR	observation summary
SWSRLI	SWSRLI	sources list
SWSRLI	SFSRLI	FAST mode sources list
SWSRLI	SGSRLI	GRISM sources list
TIMESR	TIMESR	FAST mode source timeseries
TSHPLT	TSHPLT	tracking history plot
TSTRTS	TSTRTS	tracking star timeseries