Xmm - Revision history

Nekrasov: /* Data */

2025-08-12T10:06:15Z

Data

Nekrasov: /* Data */

2025-08-12T10:05:33Z

Data

Nekrasov: /* Data */

2025-08-12T10:02:28Z

Data

Nekrasov: /* Data */

2025-08-12T09:56:17Z

Data

Nekrasov: /* Data */

2025-08-11T13:11:08Z

Data

Wilms: /* Workaround for the xmmscripts */

2024-01-04T15:30:39Z

Workaround for the xmmscripts

Wilms: /* XMM EPIC Data Extraction */

2024-01-04T15:28:49Z

XMM EPIC Data Extraction

Knies at 13:21, 1 August 2018

2018-08-01T13:21:18Z

Ballhausen at 13:14, 11 April 2018

2018-04-11T13:14:43Z

Ballhausen: Created page with " ====== XMM Data Extraction ====== After the system got updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain". This functio..."

2018-04-11T13:04:18Z

Created page with " ====== XMM Data Extraction ====== After the system got updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain". This functio..."

New page

====== XMM Data Extraction ======

After the system got updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain".
This function can set/add an attribute to the HDU (Header/Data Unit).
The solution is to call
**'source $SOFTDIR/sas_init.csh'**
at the beginning of each script in order to initialize SAS inside your script.

A little example script:

#!/bin/csh
source $SOFTDIR/sas_init.csh # initialize the SAS software
set xmmscripts = ${XMMTOOLS} # make sure the proper xmmscripts are loaded

set obsid = '0147190101'
set datadir = /eu/X-ray/XMM/data/????/$obsid/odf

${xmmscripts}/xmmprepare --datadir=$datadir --prepdir=$obsid --pn # prepare the data
${xmmscripts}/xmmextract --prepdir=$obsid --pn --full # full extraction of the chip
${xmmscripts}/xmmextract --prepdir=$obsid --pn --srcreg=src.fits --bkgreg=bkg.fits # source and background extraction of the chip

note that it is usually better to have the data preparation and the extraction in separate scripts (since one usually prepares once and then tries several extractions with different settings).
The xmmscripts need the region files to be fits files. You can convert them via
ds9tocxc outset=outfilename.fits < infilename.reg

==== Workaround for the xmmscripts ====
There were some problems occuring with the XMM-data extraction. Joern has implemented a workaround in the xmmscripts that has to be called as shown in the example below.
Here the issues:
- If your observation includes sub-observations, choose one of them. Do this with "onlyexp=1" not "onlyexp=PNU001" for example.
- Since our Calibration database gets updated frequently, we ran into the problem that new calibration files only like the latest SAS. As it is very problematic to just install the new SAS, there is a workaround. You have to address the calibration files that are working with our SAS version until the new SAS is installed (we must be patient as this is not trivial). The following, however, works perfectly:

example:

#!/bin/csh
setenv XMMTOOLS /home/wilms/xmmscripts
source ~wilms/progmapper15/progmapper.csh
${XMMTOOLS}/xmmprepare --datadir=/eu/X-ray/XMM/data/2290/0679780201/odf/
--prepdir=./test --pn --analysisdate=2014-01-11T01:05:00.000

====== XMM OM Data Extraction ======

For extracting the data of the Optical Monitor (OM) onboard XMM, there exist three tools which do this automatically: ''omichain'', ''omfchain'' and ''omgchain''.
"i" stands for image mode, "f" for fast mode and "g" for grism mode. Which mode you have can be found on the XMM log browse site: [[http://xmm2.esac.esa.int/external/xmm_obs_info/obs_view_frame.shtml]].
If you want to extract your images you first have to set some paths:

$source $SOFTDIR/sas_init.csh
$setenv SAS_ODF path_to_your_data #normally /eu/X-ray/XMM/data/rev/ObsID/odf/
$cifbuild
$setenv SAS_CCF ccf.cif
$odfingest
$setenv SAS_ODF `ls -1 *SUM.SAS`

After this you can run

$omichain #or omfchain, omgchain

You can also do the extraction step-by-step. For a description see [[http://xmm.esac.esa.int/sas/current/documentation/threads/omi_stepbystep.shtml]].
At the end you should have several images (''*IMAGE*''), region files (''*REGION*'') and source lists (''*SWSRLI*'') for the OM exposures and filters. The nomenclatur for the files are:

* IOOOOOOOOOODDUEEETTTTTTSXXX.FFF or POOOOOOOOOODDUEEETTTTTTSXXX.FFF (for PPS product files)
* OOOOOOOOOO = XMM-ObsID (10 characters)
* DD = Data source idetifier (here OM)
* U = exposure flag (S = sched, U = unsched, X = not aplicable)
* EEE = exposure number within the instrument observation (3 characters)
* TTTTTT = product type (6 characters)
* S = 0 or data subset number/character
* XXX = source number or slew step number (3 characters)
* FFF = file format (3 characters)

From all exposures for one filter a mosaiced sky image is produced which contains ''*SIMAG?.FIT''. The ? stands for the filter: L = UVW1, M = UVM2, S = UVW2, B = B, U = U, V = V.
Open the image with ds9 and have a look if your source is seen and where it is. You can check this by loading a region file, produced e.g. by simbad2ds9, into the image.

Then check the detector images (''P*IMAGE_*000.FIT'') for your source (it can be, that some detector images don't contain your source because the window was off). Load the region file which belongs to the detector image (''*REGION*000.ASC'', e.g. ''P0090050801OMS006IMAGE_0000.FIT'' -> ''I0090050801OMS006REGION0000.ASC'') and identify the number of your source.

{{:satext:image_region.jpeg?200|}}

Look into the source list for your exposure (''P*SWSRLI*.FIT'') and note the SRC_ID in the last column. Open the combined source list (''*COMBO*'') and search for your SRC_ID. Here you can find all the magnitudes and fluxes of your source for the different filters.

====== Choosing correct XMM-EPIC filter ======

Choosing the correct EPIC filter for your observation depends on the
visual magnitudes of the other objects (usually stars) in the EPIC
field of view.

The XMM user's handbook (sect. 3.3.6;
http://xmm.esac.esa.int/external/xmm_user_support/documentation/uhb/epicfilters.html) recommends:

Thick filter: suppress up to magnitudes of -2 to -1 (pn), or +1 to +4 (mos)

Medium filter: if there is nothing above magnitude ~ 6 to 9

Thin filter: for point sources that are 12 mag fainter than thick filter limitations

The UHB notes that these magnitudes apply when you use the full frame mode; if you use a partial window mode, then sources up to 2-3 magnitudes brighter than these values should be okay.

Use the United States Naval Observatory catalog at
http://www.nofs.navy.mil/data/fchpix/ to find the stars within a 9'
radius.

At that website, enter your R.A. and Decl., and for the output file
options in the left column, unclick everything except RA,DEC,
magnitude, and offset from center. Then click 'retrieve data' in the
right column.

Next window: Click on "USNO B1.0 Star List" to download a gzipped
ASCII file with typically hundreds of rows/stars for lines of sight
away from the Galactic Plane (or many thousands of rows/stars for
lines of sight in the Galactic Plane).

Example file: See /home/markowitz/proposals/xmm2014/GS1826USNO for a
Galactic XRB, GS1826, located in the Galactic Bulge (optically-crowded
fields).

The star list is ordered by R.A., and but you can then re-order the ASCII list
by magnitude, e.g.,

cat GS1826USNO | grep -v '#' | awk '{print $7 " " $12}' | sort -g > starlist_sortB

cat GS1826USNO | grep -v '#' | awk '{print $8 " " $12}' | sort -g > starlist_sortR

since the B and R magnitudes are columns 7 and 8, and distance from the center
of f.o.v. (in arcsec) is column 12

Ignore the rows with zero magnitudes; a zero means unmeasured flux.

For these example files, e.g., /home/markowitz/proposals/xmm2014/starlist_sortB
we see that the brightest B- and R-band magnitudes are 10.0-10.3, including some
objects that are only 3-5' from the center, and at least one that's only 1.2'
from the center, so one cannot use the thin epic filter; one must use
the MEDIUM filter for all three EPIC cameras.

[[Category:Data Extraction]]

@@ Line 2: / Line 2: @@
 Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
-If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: [[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])Jonathan Knies[[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]]), [[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])Amy Joyce[[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])) ??Esin Gulbahar?? and the observation will be downloaded for you.
+If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: ~~Jonathan Knies~~, ~~Amy Joyce~~ ??Esin Gulbahar?? and the observation will be downloaded for you.
 Note (as of 12.08.2025): since xmmsas version 22 we cannot run it natively on the cluster. Instead, we have a docker image for this. Otherwise, downgrade xmmsas to version 21 "module load xmmsas/21" if you want to use the algorithm below.

@@ Line 2: / Line 2: @@
 Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
-If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: {{strikethrough|Jonathan Knies}}, {{strikethrough|Amy Joyce}}) ??Esin Gulbahar?? and the observation will be downloaded for you.
+If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: [[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])Jonathan Knies[[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]]), [[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])Amy Joyce[[User:Nekrasov|Nekrasov]] ([[User talk:Nekrasov|talk]])) ??Esin Gulbahar?? and the observation will be downloaded for you.
 Note (as of 12.08.2025): since xmmsas version 22 we cannot run it natively on the cluster. Instead, we have a docker image for this. Otherwise, downgrade xmmsas to version 21 "module load xmmsas/21" if you want to use the algorithm below.

@@ Line 2: / Line 2: @@
 Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
-If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: ~~Jonathan Knies~~, ~~Amy Joyce~~) ??Esin Gulbahar?? and the observation will be downloaded for you.
+If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: {{strikethrough|Jonathan Knies}}, {{strikethrough|Amy Joyce}}) ??Esin Gulbahar?? and the observation will be downloaded for you.
 Note (as of 12.08.2025): since xmmsas version 22 we cannot run it natively on the cluster. Instead, we have a docker image for this. Otherwise, downgrade xmmsas to version 21 "module load xmmsas/21" if you want to use the algorithm below.

@@ Line 2: / Line 2: @@
 Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
-If the observation you want to analyze is not in the archives: contact the XMM admin (Jonathan Knies - !outdated person!) and the observation will be downloaded for you.
+If the observation you want to analyze is not in the archives: contact the XMM admin (Outdated: ~~Jonathan Knies~~, ~~Amy Joyce~~) ??Esin Gulbahar?? and the observation will be downloaded for you.
 == XMM EPIC Data Extraction ==

@@ Line 2: / Line 2: @@
 Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
-If the observation you want to analyze is not in the archives: contact the XMM admin (Jonathan Knies) and the observation will be downloaded for you.
+If the observation you want to analyze is not in the archives: contact the XMM admin (Jonathan Knies - !outdated person!) and the observation will be downloaded for you.
 == XMM EPIC Data Extraction ==

@@ Line 35: / Line 35: @@
 "xmmextract" is a very powerful script, use its "--help" argument to get a list of all arguments.
-==== Workaround for the xmmscripts ====
+Further important points:
-There were some problems occuring with the XMM-data extraction. Joern has implemented a workaround in the xmmscripts that has to be called as shown in the example below.
 # If your observation includes sub-observations, choose one of them. Do this with "onlyexp=1" not "onlyexp=PNU001" for example.
 # Since our Calibration database gets updated frequently, we ran into the problem that new calibration files only like the latest SAS. As it is very problematic to just install the new SAS, there is a workaround. You have to address the calibration files that are working with our SAS version until the new SAS is installed (we must be patient as this is not trivial). The following, however, works perfectly:

@@ Line 6: / Line 6: @@
 == XMM EPIC Data Extraction ==
-After the system got updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain".
+After the system was updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain".
 This function can set/add an attribute to the HDU (Header/Data Unit).
 The solution is to call
@@ Line 13: / Line 13: @@
 A little example script:
       #!/bin/csh
@@ Line 26: / Line 25: @@
       ${xmmscripts}/xmmextract --prepdir=$obsid --pn --srcreg=src.fits --bkgreg=bkg.fits    # source and background extraction of the chip
-note that it is usually better to have the data preparation and the extraction in separate scripts (since one usually prepares once and then tries several extractions with different settings).
+Note that it is usually better to have the data preparation and the extraction in separate scripts (since one usually prepares once and then tries several extractions with different settings).
 The xmmscripts need the region files to be fits files. You can convert them via
       ds9tocxc outset=outfilename.fits < infilename.reg
 ==== Workaround for the xmmscripts ====
@@ Line 39: / Line 44: @@
       #!/bin/csh
       ${XMMTOOLS}/xmmprepare --datadir=/eu/X-ray/XMM/data/2290/0679780201/odf/
       --prepdir=./test --pn --analysisdate=2014-01-11T01:05:00.000
 == XMM OM Data Extraction ==

@@ Line 1: / Line 1: @@
-====== XMM Data Extraction ======
+Always use the remeis archives at /eu/X-ray/XMM/data/ instead of downloading observation files yourself. You can search for the data of an observation by typing something like '''find /eu/X-ray/xmm/data/????/obsID/odf -type d''' - replacing obsID with your observation ID.
 After the system got updated from Ubuntu 11 to Ubuntu 12 a problem occured with the function "dssetattr" inside the "epchain".
@@ Line 41: / Line 45: @@
-====== XMM OM Data Extraction ======
+== XMM OM Data Extraction ==
 For extracting the data of the Optical Monitor (OM) onboard XMM, there exist three tools which do this automatically: ''omichain'', ''omfchain'' and ''omgchain''.
@@ Line 81: / Line 85: @@
-====== Choosing correct XMM-EPIC filter ======
+== Choosing correct XMM-EPIC filter ==
 Choosing the correct EPIC filter for your observation depends on the
@@ Line 132: / Line 136: @@
 from the center, so one cannot use the thin epic filter; one must use
 the MEDIUM filter for all three EPIC cameras.
 [[Category:Data Extraction]]

@@ Line 5: / Line 5: @@
 This function can set/add an attribute to the HDU (Header/Data Unit).
 The solution is to call
-**'source $SOFTDIR/sas_init.csh'**
+''''source $SOFTDIR/sas_init.csh''''
 at the beginning of each script in order to initialize SAS inside your script.
@@ Line 29: / Line 29: @@
 There were some problems occuring with the XMM-data extraction. Joern has implemented a workaround in the xmmscripts that has to be called as shown in the example below.
 Here the issues:
-  - If your observation includes sub-observations, choose one of them. Do this with "onlyexp=1" not "onlyexp=PNU001" for example.
+# If your observation includes sub-observations, choose one of them. Do this with "onlyexp=1" not "onlyexp=PNU001" for example.
-  - Since our Calibration database gets updated frequently, we ran into the problem that new calibration files only like the latest SAS. As it is very problematic to just install the new SAS, there is a workaround. You have to address the calibration files that are working with our SAS version until the new SAS is installed (we must be patient as this is not trivial). The following, however, works perfectly:
+# Since our Calibration database gets updated frequently, we ran into the problem that new calibration files only like the latest SAS. As it is very problematic to just install the new SAS, there is a workaround. You have to address the calibration files that are working with our SAS version until the new SAS is installed (we must be patient as this is not trivial). The following, however, works perfectly:
 example:
@@ Line 44: / Line 44: @@
 For extracting the data of the Optical Monitor (OM) onboard XMM, there exist three tools which do this automatically: ''omichain'', ''omfchain'' and ''omgchain''.
-"i" stands for image mode, "f" for fast mode and "g" for grism mode. Which mode you have can be found on the XMM log browse site: [[http://xmm2.esac.esa.int/external/xmm_obs_info/obs_view_frame.shtml]].
+"i" stands for image mode, "f" for fast mode and "g" for grism mode. Which mode you have can be found on the XMM log browse site: http://xmm2.esac.esa.int/external/xmm_obs_info/obs_view_frame.shtml.
 If you want to extract your images you first have to set some paths:
@@ Line 58: / Line 58: @@
       $omichain   #or omfchain, omgchain
-You can also do the extraction step-by-step. For a description see [[http://xmm.esac.esa.int/sas/current/documentation/threads/omi_stepbystep.shtml]].
+You can also do the extraction step-by-step. For a description see http://xmm.esac.esa.int/sas/current/documentation/threads/omi_stepbystep.shtml.
-At the end you should have several images (''*IMAGE*''), region files (''*REGION*'') and source lists (''*SWSRLI*'') for the OM exposures and filters. The nomenclatur for the files are:
+At the end you should have several images (<code>*IMAGE*</code>), region files (<code>*REGION*</code>) and source lists (<code>*SWSRLI*</code>) for the OM exposures and filters. The nomenclatur for the files are:
-   * IOOOOOOOOOODDUEEETTTTTTSXXX.FFF or POOOOOOOOOODDUEEETTTTTTSXXX.FFF (for PPS product files)
+* IOOOOOOOOOODDUEEETTTTTTSXXX.FFF or POOOOOOOOOODDUEEETTTTTTSXXX.FFF (for PPS product files)
-   * OOOOOOOOOO = XMM-ObsID (10 characters)
+* OOOOOOOOOO = XMM-ObsID (10 characters)
-   * DD = Data source idetifier (here OM)
+* DD = Data source idetifier (here OM)
-   * U = exposure flag (S = sched, U = unsched, X = not aplicable)
+* U = exposure flag (S = sched, U = unsched, X = not aplicable)
-   * EEE = exposure number within the instrument observation (3 characters)
+* EEE = exposure number within the instrument observation (3 characters)
-   * TTTTTT = product type (6 characters)
+* TTTTTT = product type (6 characters)
-   * S = 0 or data subset number/character
+* S = 0 or data subset number/character
-   * XXX = source number or slew step number (3 characters)
+* XXX = source number or slew step number (3 characters)
-   * FFF = file format (3 characters)
+* FFF = file format (3 characters)
-From all exposures for one filter a mosaiced sky image is produced which contains ''*SIMAG?.FIT''. The ? stands for the filter: L = UVW1, M = UVM2, S = UVW2, B = B, U = U, V = V.
+From all exposures for one filter a mosaiced sky image is produced which contains *SIMAG?.FIT. The ? stands for the filter: L = UVW1, M = UVM2, S = UVW2, B = B, U = U, V = V.
 Open the image with ds9 and have a look if your source is seen and where it is. You can check this by loading a region file, produced e.g. by simbad2ds9, into the image.
-Then check the detector images (''P*IMAGE_*000.FIT'') for your source (it can be, that some detector images don't contain your source because the window was off). Load the region file which belongs to the detector image (''*REGION*000.ASC'', e.g. ''P0090050801OMS006IMAGE_0000.FIT'' -> ''I0090050801OMS006REGION0000.ASC'') and identify the number of your source.
+Then check the detector images (<code>P*IMAGE_*000.FIT</code>) for your source (it can be, that some detector images don't contain your source because the window was off). Load the region file which belongs to the detector image (<code>*REGION*000.ASC</code>, e.g. <code>P0090050801OMS006IMAGE_0000.FIT</code> -> ''I0090050801OMS006REGION0000.ASC</code>) and identify the number of your source.
-{{:satext:image_region.jpeg?200|}}
+[[File:image_region.jpeg|thumb]]
-Look into the source list for your exposure (''P*SWSRLI*.FIT'') and note the SRC_ID in the last column. Open the combined source list (''*COMBO*'') and search for your SRC_ID. Here you can find all the magnitudes and fluxes of your source for the different filters.
+Look into the source list for your exposure (<code>P*SWSRLI*.FIT</code>) and note the SRC_ID in the last column. Open the combined source list (<code>*COMBO*</code>) and search for your SRC_ID. Here you can find all the magnitudes and fluxes of your source for the different filters.
@@ Line 119: / Line 119: @@
 by magnitude, e.g.,
-cat GS1826USNO | grep -v '#' | awk '{print $7 "  " $12}' | sort -g >   starlist_sortB
+ cat GS1826USNO | grep -v '#' | awk '{print $7 "  " $12}' | sort -g >   starlist_sortB
+ cat GS1826USNO | grep -v '#' | awk '{print $8 "  " $12}' | sort -g >   starlist_sortR
 since the B and R magnitudes are columns 7 and 8, and distance from the center