Remove the ACIS Readout Streak

Get Started

Download the sample data: 1712 (ACIS-S, 3C273)

unix% download_chandra_obsid 1712 evt2,asol

Figure 1 shows the prominent readout streak on the S3 chip, which will be removed by running this thread. There may also be streaks on the S4 chip, which are due to a flaw in the serial readout of the chips; use the tool destreak to remove those streaks.

Figure 1: ACIS readout streak

[Version: full-size]

Figure 1: ACIS readout streak

The streak photons are clocked out in the wrong row and so have incorrect CHIPY values.

Get Source Location

acisreadcorr uses the source position to determine which events may have a misplaced CHIPY value. There are several ways to estimate the source position:

1. With ds9:

   unix% ds9 acisf01712N005_evt2.fits &
   

   From the ds9 display (Figure 2), we can estimate that the center of the source is at (4082.25,4076.25).

   Figure 2: Getting the source location from ds9

   

   [Version: full-size]

   

   Figure 2: Getting the source location from ds9

   The circle is used to estimate the source location as (4082.25,4076.25).

2. With dmstat:
   

   The value obtained from visual inspection with ds9 can be improved by computing the centroid with dmstat. Here we filter the event file and bin it into an image around the location of the source. Even though the source is completely cratered, the centroid can often be a robust estimate for the source location.

   unix% punlearn dmstat
   dmstat "acisf01712N005_evt2.fits[sky=circle(4082.25,4076.25,20)][bin sky=1]" centroid+ sig- med-
   EVENTS_IMAGE(x, y)
       min:	0 	      @:	( 4083.75 4056.75 )
       max:	162 	      @:	( 4085.75 4078.75 )
   cntrd[log] :	( 20.365025631 20.422719799 )
   cntrd[phys]:	( 4082.1150256 4076.1727198 )
      good:	1264 
      null:	336
   

   A radius of 20 was chosen to enclose most of the wings of the PSF but to avoid the jet. The source location is given as (4082.1,4076.2).

3. From a catalog:
   use the known source position from SIMBAD, NED, or another reputable source.

   From SIMBAD, the known position for 3C 273 is (RA,DEC) = (12:29:06.700, +02:03:08.60).

   dmcoords is used to to convert (RA,Dec) to sky(x,y) coordinates.

   unix% punlearn dmcoords
   unix% dmcoords acisf01712N005_evt2.fits op=cel celfmt=hms ra=12:29:06.700 dec=+02:03:08.60
   unix% pget dmcoords x y
   4082.181976564152
   4076.110245719566
   

   The celfmt=hms is used to indicate that the coordinates are provided in sexagesimal format.

   The source position in sky pixels is (4082.2, 4076.1). This value will be used in the rest of the thread.

Create a Background Spectrum

Removing all the photons from the affected area would leave a black streak instead of a bright one. We wish instead to leave the background photons where they are. For this reason, it is possible to input a background PI spectrum. The tool then attempts to leave background photons - consistent with the given PI spectrum and distributed evenly in time - where the streak once was.

First, we need to select a background region. This can be from any area of the chip that doesn't contain any bright regions; Figure 3 shows the region used. For help on rotating regions in ds9, see this FAQ.

Figure 3: Region for background spectrum

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Figure 3: Region for background spectrum

The background region is selected from a source-free region on the same chip away from the readout streak.

To save the regions, follow these steps:

1. Region → Save Regions... → Save As "bkg.reg".
2. After choosing "OK" in the region filename dialog, a format dialog is opened. Set the format to "CIAO" and the coordinate system to "Physical".

The resulting file will look something like this:

unix%  more bkg.reg 
# Region file format: CIAO version 1.0
rotbox(4410.92,4353.0555,389.55054,66.92414,24.719781)

The tool dmextract is now used to create the spectrum of this region:

unix% punlearn dmextract
unix% pset dmextract infile="acisf01712N005_evt2.fits[sky=region(bkg.reg)][bin pi=1:1024:1]"
unix% pset dmextract outfile=bkg_pi.fits
unix% dmextract
Input event file  (acisf01712N005_evt2.fits[sky=region(bkg.reg)][bin pi=1:1024:1]): 
Enter output file name (bkg_pi.fits): 

The contents of the parameter file may be checked using plist dmextract.

NOTE: if your observation was taken with a subarray defined, read the Observations Using Subarrays caveat before proceeding.

The background spectrum should be binned to be the same size as your event file. If you were to bin this example to 1:1023:1, for instance, it may cause photons with PI=1024 to be attributed to the source erroneously. Changing the binning is only a concern if you have filtered your event file such that there are no longer 1024 channels of PI.

Run acisreadcorr

The dx and dy parameters may need to be adjusted before running the tool. The default value for dx (2 pixels), or a number close to it, should be fine for on-axis point sources. dy can be estimated by drawing a circle in ds9 and finding the diameter (Figure 4). These values determine the width of the region to be cleaned and how close to get to the source, respectively.

Figure 4: Choosing dy for the observation

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Figure 4: Choosing dy for the observation

dy, the number of rows to be avoided around a source, can be estimated from the diameter of a circle drawn in ds9 (50 px).

Now we have all the necessary information to run acisreadcorr. The same aspect solution list file, @pcad_asol1.lis, is used:

unix% cat pcad_asol1.lis
pcadf01712_001N001_asol1.fits

unix% punlearn acisreadcorr
unix% pset acisreadcorr infile=acisf01712N005_evt2.fits
unix% pset acisreadcorr outfile=acis_1712_corr_evt2.fits
unix% pset acisreadcorr aspect=@pcad_asol1.lis
unix% pset acisreadcorr x=4082.2 y=4076.1
unix% pset acisreadcorr dx=5 dy=50
unix% pset acisreadcorr bkg=bkg_pi.fits
unix% acisreadcorr 
Input dataset/block specification (acisf01712N005_evt2.fits): 
Output dataset/block specification (acis_1712_corr_evt2.fits): 
Aspect file (@pcad_asol1.lis): 
Sky X position (pixels) (4082.2): 
Sky Y position (pixels) (4076.1):

The contents of the parameter file may be checked using plist acisreadcorr.

Examine the Results

The newly created file can be viewed in ds9:

unix% ds9 acis_1712_corr_evt2.fits &

as seen in Figure 5.

Figure 5: Event file with streak removed (used background spectrum)

[Version: full-size]

Figure 5: Event file with streak removed (used background spectrum)

Only events consistent, spectrally, with the background are left in the readout streak area. All the other events have been moved to the source location positon.

The new event file is compared to the original event file in Figure 6.

Figure 6: Comparison of original and filled event files

[Version: full-size]

Figure 6: Comparison of original and filled event files

The original event file is in the left frame and the file with readout streak removed is in the right frame.

Figure 7 shows an image of a nearly identical acisreadcorr run. The only difference is that a background spectrum was not supplied to the tool (i.e. bkg=""). The streak has been removed and a stripe of zero counts replaces it.

Figure 7: Event file with streak removed (without background spectrum)

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Figure 7: Event file with streak removed (without background spectrum)

If a background spectrum is not provided, the streak is removed and a stripe of zero counts replaces it.

dmcopy may be used to see which photons were flagged by the tool. Status bit 22 marks photons identified as background and bit 21 marks out-of-time source events. In the following filters, the bits are numbered from the right, starting at zero:

unix% dmcopy "acis_1712_corr_evt2.fits[status=xxxxxxxxxx10xxxxxxxxxxxxxxxxxxxxx]" \
      flag_bkg.fits

unix% dmcopy "acis_1712_corr_evt2.fits[status=xxxxxxxxxx01xxxxxxxxxxxxxxxxxxxxx]" \
      flag_source.fits

Displaying these event files side-by-side produces Figure 8.

Figure 8: Photons flagged by acisreadcorr

[Version: full-size]

Figure 8: Photons flagged by acisreadcorr

The background photons are in the left frame and the out-of-time source photons are in the right frame. The right frame is set at zoom=4.

Caveats

unix% dmkeypar acis_repro_evt2.fits NROWS echo+
128

1024 / (subarray delta y)

1024 / 128 = 8

unix% dmkeypar bkg_pi.fits BACKSCAL echo+
0.00038847826236539

calculate new value:	0.00038847826236539 * 8 = 0.00310782609892312

unix% dmhedit infile=bkg_pi.fits filelist="" operation=add \
      key=BACKSCAL value=0.00310782609892312 unit="[pixel]" comment="Fractional area"

unix% dmkeypar bkg_pi.fits BACKSCAL echo+
0.0031078260989231