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6. Preparing the Data for Processing

Throughout this Primer, it will be assumed that the user wants to perform all tasks through the Command Window. For instructions on reducing data with the GUI, see the ABC Guide to Data Reduction with the Hera GUI.

In the sections that follow, data from the HEASARC archive are used to illustrate how to run tasks for each instrument on XMM-Newton; new users are encouraged to use these sample data, though in should be noted that any data from the relevant instrument will do. Information about the example datasets are in Table 6.1.

Table 6.1: Example datasets used in this Guide.
Instrument Chapter ObsID Object
EPIC 7 0123700101 Lockman Hole
EPIC (Timing mode) 7.3 0122700101 G21.5-09
RGS 8 0153950701 Mkn 421
OM (Image mode) 9.2 0123700101 Lockman Hole
OM (Fast mode) 9.3 0411081601 Mkn 421
OM (Grism mode) 9.4 0125320801 BPM 16274

Regardless of which instrument you are interested in, one task is necessary to prepare the data for processing, odfingest. To demonstrate odfingest, and a host of other tasks in §7, we will use the Lockman Hole data with ObsID 0123700101, though any dataset will work equally well.

To begin, either run anonymous Hera by clicking on the ``H'' next to the dataset in the archive (see §4), or download the dataset from the HEASARC archive and initialize standard Hera (see §4.1 and § 4.2, respectively).

Select all the zipped files in the ODF directory and unzip them; multiple files can be selected at once by holding the shift or control key, and right-clicking on the selected files will bring up a menu with the option to unzip them. (This takes a long time.)

The task odfingest extends the Observation Data File (ODF) summary file with data extracted from the instrument housekeeping data files and the calibration database. It is required for reprocessing the ODF data with the pipeline tasks, as well as for many other tasks, and it is only necessary to run it once on any dataset. If for some reason odfingest must be rerun, you must first delete the earlier file it produced. This file largely follows the naming convention described in §5.3.3, but has SUM.SAS appended to it. Hera will automatically set the environment parameter SAS_ODF to the SUM.SAS file in the active dataset's ODF directory, if one exists. If there is no SUM.SAS file, the SAS_ODF variable maintains its default value (the dataset's ODF directory).

To run odfingest, first make sure that the ODF directory is highlighted in the GUI, then click `Cmd Window'. Due to network security issues, you cannot use the standard linux commands to navigate between directories, move files, etc. The only way to be certain that your Command Window is in the correct directory is to highlight the directory it in the GUI, then call up a new Command Window.

In the Command Window, enter


The command and parameters will be echoed and dialog from the task will be shown as in a normal terminal. The warnings can be ignored. The prompt will return when it is complete.

At this point, the data is ready to be repipelined and analyzed. Data from the EPIC camera is discussed in §7, the RGS is in §8, and the OM is in §9. It is strongly recommended that all reprocessed data be kept in its own directory, and all the following chapters will assume that tasks are being called from the PROC directory.

To make PROC, select and right-click on the ObsID directory; the option to create a new directory will be in the menu. Select PROC and call up a new Command Window. (The old one can be closed.) Please note that new directories will always be placed in the directory that was highlighted when the command was given, and similarly, all processing and analysis tasks that are called will be run from (and place output in) whichever directory is highlighted. So if you flip between directories often, it is a good idea to verify you are where you want to be before calling a task.

next up previous contents
Next: 7. An EPIC Data Up: XMM ABC Guide with Previous: 5. Data   Contents
Lynne Valencic 2013-12-13