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Last modified: 15 June 2010
Where are the PDFs?
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Extract a Spectrum from the ACIS Readout Streak

CIAO 4.2 Science Threads


Overview

Last Update: 15 Jun 2010 - The background spectrum exposure time also needs to be scaled.

Synopsis:

While ACIS reads out a frame, it is still taking data. Photons detected during the readout are clocked out in the wrong row and so have incorrect CHIPY values. For a bright source, you get a streak along the entire column of the source. These streak photons can be used for spectral analysis by adjusting the exposure time in the final spectrum.

An on-axis Response Matrix File (RMF) and Ancillary Response File (ARF) are also created for use in the analysis. The responses are made for the on-axis location because that is where the events hit the detector before being read out at an incorrect position.

Purpose:

To generate source and background PI (PHA) spectra from the streak events of an ACIS source and build the proper RMFs and ARFs.

Read this thread if:

you are working with any ACIS imaging observation which exhibits a readout streak.



Contents


Get Started

Sample ObsID used: 3662 (ACIS-S, HER X-1)

File types needed: evt2; asol1; pbk0

Please ensure that you have set up ardlib to use the bad pixel file for your observation before following this thread.

Using Consistent Calibration: mkrmf vs mkacisrmf

The tool mkacisrmf is used to create RMFs for:

  • all -120 ACIS data taken in (V)FAINT mode that has the time-dependent gain adjustment and CTI correction applied
  • -120 ACIS GRADED mode data on the back-illuminated chips (ACIS-S1 and S3) only
  • -110 ACIS data taken on the back-illuminated chips (ACIS-S1 and S3) only

All new analyses with these types of data should be done with mkacisrmf instead of mkrmf. This thread gives the syntax for both tools in the Calculate the RMFs section; it is up to the user to chose the appropriate method for the analysis.

It is important that the calibration applied to the event file is consistent with the RMF tool chosen, as explained in the "Using Consistent Calibration" section of the why topic. If necessary, reprocess your data with the correct gain file before beginning this thread.


Downloading acis_fef_lookup

This thread uses the acis_fef_lookup script, which is part of the CIAO Scripts distribution. The CIAO scripts package should be the following version or newer: 

unix% cat $ASCDS_CONTRIB/VERSION.CIAO_scripts
14 Dec 2009

Please check that you have at least this version of the scripts package installed before continuing. If you do not have the scripts installed or need to update to a newer version, refer to the Scripts page.


Define the Source and Background Regions

We need to define several regions: one for the readout streak and a streak-free background region. Additionally, an on-axis source region is defined around the object. 

unix% ds9 3662_evt2.fits &

The streak region is defined with a rectangle (see this FAQ on how to rotate shapes in ds9); the acis_streak_map tool is another method that may be used to create the streak region file. The background region is a wider rectangle which excludes the source region. The two regions are shown in separate frames in Figure 1. The on-axis source region is shown in red in both frames

Figure 1: Extraction regions on the event file

[Thumbnail image: The streak region around the jet is a rotated rectangle; the background region is a larger rectangle which excludes the streak region. The on-axis streak region is shown in both frames]

[Version: full-size]

[Print media version: The streak region around the jet is a rotated rectangle; the background region is a larger rectangle which excludes the streak region. The on-axis streak region is shown in both frames]

Figure 1: Extraction regions on the event file

The streak region is shown in the left frame and the background region is in the right frame. The red line through the center of the background region indicates the excluded portion of the region. The on-axis source region is shown in red in both frames

To save the regions, follow these steps:

  1. Region → Save Regions... → Save As "streak.reg" (streak), "streak_bg.reg" (background), and "onaxis.reg" (on-axis source).
  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 region files look like: 

unix% cat streak.reg
# Region file format: CIAO version 1.0
rotbox(3973.3876,3656.4142,13.065366,699.50852,332.558)

unix% cat streak_bg.reg
# Region file format: CIAO version 1.0
rotbox(3971.7453,3657.4308,122.95122,699.99999,332.558)
-rotbox(3973.3876,3656.4142,13.065366,699.50852,332.558)

unix% cat onaxis.reg
# Region file format: CIAO version 1.0
circle(4173.999,4043.9959,25.999999)

Extract Spectrum of Object

The spectra are extracted in pulse invariant (PI) space to create a histogram of number of counts vs. PI channel: 

unix% punlearn dmextract
unix% pset dmextract infile="3662_evt2.fits[sky=region(streak.reg)][bin pi]"
unix% pset dmextract outfile=herx1.pi
unix% dmextract
Input event file  (3662_evt2.fits[sky=region(streak.reg)][bin pi]): 
Enter output file name (herx1.pi):

And for the background spectrum: 

unix% pset dmextract infile="3662_evt2.fits[sky=region(streak_bg.reg)][bin pi]"
unix% pset dmextract outfile=herx1_bg.pi
unix% dmextract
Input event file  (3662_evt2.fits[sky=region(streak_bg.reg)][bin pi]): 
Enter output file name (herx1_bg.pi):

You can check the parameter file that was used with plist dmextract.


Locate Centroids (dmstat)

The responses are made for the on-axis location because that is where the events hit the detector before being read out at an incorrect position.

Since the calibration varies across the chips, we need to locate the centroid (in chip coordinates) of the on-axis source region. This information will be used to create the ARF and to select the FEF (FITS Embedded Function) to use in calculating the RMF with mkrmf. 

unix% dmstat "3662_evt2.fits[sky=region(onaxis.reg)][cols chipx,chipy,ccd_id,x,y]"
chip(chipx, chipy)[pixel]
    min:        ( 80 827 )            @:        ( 19103 16594 )
    max:        ( 164 911 )           @:        ( 103349 14719 )
   mean:        ( 121.6962529 868.3099628 )
  sigma:        ( 15.342811518 15.53880314 )
    sum:        ( 29603222 211220740 )
   good:        ( 243255 243255 )
   null:        ( 0 0 )


ccd_id
    min:        7             @:        1
    max:        7             @:        1
   mean:        7
  sigma:        0
    sum:        1702785
   good:        243255
   null:        0

sky(x, y)[pixel]
    min:        ( 4148.0029297 4018.0319824 )         @:        ( 176095 185976 )
    max:        ( 4199.9956055 4069.9790039 )         @:        ( 182148 152100 )
   mean:        ( 4173.873478 4043.4555486 )
  sigma:        ( 10.076932348 10.178223086 )
    sum:        ( 1015315592.9 983590779.46 )
   good:        ( 243255 243255 )
   null:        ( 0 0 )

The centroid of the distribution is at (chipx,chipy)=(121.70,868.31). The source position in sky coordinates is (x,y)=(4173.87,4043.46) and is on ccd_id=7 (ACIS-S3).

You can check the parameter file that was used with plist dmstat.


Calculate the On-axis RMF

The syntax for both mkacisrmf and mkrmf are given in this section. Users must choose the appropriate tool for the data and calibration.

The observation used in this thread (ObsID 3662) was taken at the -120 C focal plane temperature and has the TGAIN and CTI calibrations applied. Therefore, it is possible to use mkacisrmf to create the RMF file.

Using mkacisrmf (mkacisrmf)

The Creating ACIS RMFs with mkacisrmf thread has details on using the mkacisrmf tool. First determine which gain file was used in the data processing: 

unix% dmkeypar 3662_evt2.fits gainfile echo+
acisD2000-01-29gain_ctiN0005.fits

This event file has been reprocessed with the version 5 gain file. For this gain, use the acisD2000-01-29p2_respN0005.fits file as the infile parameter. The ccd_id value and (chipx,chipy) position from dmstat are also input: 

unix% punlearn mkacisrmf
unix% pset mkacisrmf infile=$CALDB/data/chandra/acis/p2_resp/acisD2000-01-29p2_respN0005.fits 
unix% pset mkacisrmf outfile=herx1_mkacisrmf.rmf
unix% pset mkacisrmf energy=0.1:11.0:0.01
unix% pset mkacisrmf channel=1:1024:1
unix% pset mkacisrmf chantype=PI
unix% pset mkacisrmf wmap=none
unix% pset mkacisrmf ccd_id=7 chipx=121.70 chipy=868.31
unix% pset mkacisrmf gain=$CALDB/data/chandra/acis/det_gain/acisD2000-01-29gain_ctiN0005.fits

unix% mkacisrmf
scatter/rsp matrix file (/soft/ciao/CALDB/data/chandra/acis/p2_resp/acisD2000-01-29p2_respN0005.fits): 
RMF output file (herx1_mkacisrmf.rmf): 
WMAP file (none): 
energy grid in keV (lo:hi:bin) (0.1:11.0:0.01): 
channel grids in pixel (min:max:bin) (1:1024:1): 
channel type (PI|PHA) (PI): 
filter CCD-ID (0:9) (7): 
filter chipx in pixel (121): 
filter chipy in pixel (868): 
gain file (/soft/ciao/CALDB/data/chandra/acis/det_gain/acisD2000-01-29gain_ctiN0005.fits): 

INFO: Effective user energy (keV) grids will be re-arranged in 
     0.25000 - 11.00000    


Single region, #2172 , processed.

The ACIS detector is calibrated over the range 0.224004 - 12 keV. The warning indicates that mkacisrmf has adjusted the energy grid to fall within the calibrated range.

You can check the parameter file that was used with plist mkacisrmf.

If you use mkacisrmf to create the RMFs, you can now continue to the Calculate the ARFs step.

Using mkrmf (acis_fef_lookup, mkrmf)

First acis_fef_lookup is needed to determine the correct FEF. The ccd_id value and (chipx,chipy) position from dmstat are input: 

unix% punlearn acis_fef_lookup
unix% acis_fef_lookup 3662_evt2.fits 7 121.70 868.31 
/soft/ciao/CALDB/data/chandra/acis/fef_pha/acisD2000-01-29fef_pha_ctiN0004.fits[2][ccd_id=7,chipx=97:128,chipy=865:896]

You can check the parameter file that was used with plist acis_fef_lookup.

Now that we have the FEFs, we can compute the RMF with mkrmf. The energy range (keV) for axis1 should cover the detector response range, which is 0.224004 - 12 keV for ACIS. The default for extraction in PI space is axis2=1:1024:1. 

unix% punlearn mkrmf
unix% pset mkrmf infile="/soft/ciao/CALDB/data/chandra/acis/fef_pha/acisD2000-01-29fef_pha_ctiN0004.fits[2][ccd_id=7,chipx=97:128,chipy=865:896]"
unix% pset mkrmf outfile=herx1.rmf
unix% pset mkrmf axis1="energy=0.1:11.0:0.01"
unix% pset mkrmf axis2="pi=1:1024:1"
unix% mkrmf
name of FEF input file (/soft/ciao/CALDB/data/chandra/acis/fef_pha/acisD2000-01-29fef_pha_ctiN0004.fits[2][ccd_id=7,chipx=97:128,chipy=865:896]):
name of RMF output file (herx1.rmf):
axis-1(name=lo:hi:btype) (energy=0.1:11.0:0.01):
axis-2(name=lo:hi:btype) (pi=1:1024:1):

You can check the parameter file that was used with plist mkrmf.


Calculate the On-axis ARF

1. Compute the Aspect Histogram (asphist)

The aspect histogram, a binned representation of aspect motion during the observation, is created. The aspect solution files are supplied as a stack. In this example, there is only one asol1.fits file, but many observations will have multiple files to include: 

unix% cat pcad_asol1.lis
pcadf141954141N002_asol1.fits

unix% punlearn asphist
unix% pset asphist infile="@pcad_asol1.lis"
unix% pset asphist outfile=herx1.asphist
unix% pset asphist evtfile="3662_evt2.fits[ccd_id=7]"
unix% asphist
Aspect Solution List Files (@pcad_asol1.lis): 
Aspect Histogram Output File (herx1.asphist): 
Event List Files (3662_evt2.fits[ccd_id=7]):

You can check the parameter file that was used with plist asphist.

2. Compute the ARF (mkarf)

In addition to the aspect histogram file, the on-axis source position calculated by dmstat is input to mkarf. The RMF file is used to define the energy grid (engrid) to ensure that the ARF is made on the same grid.

To obtain an accurate ARF at the very edge of a CCD, subarray or window, it is necessary to include the mask file (msk1.fits). 

unix% punlearn mkarf
unix% pset mkarf asphistfile="herx1.asphist[ASPHIST]"
unix% pset mkarf outfile=herx1.arf
unix% pset mkarf obsfile="3662_evt2.fits[EVENTS]"
unix% pset mkarf maskfile=acisf03662_000N002_msk1.fits
unix% pset mkarf pbkfile=acisf141955042N002_pbk0.fits
unix% pset mkarf detsubsys=ACIS-S3
unix% pset mkarf engrid="grid(herx1_mkacisrmf.rmf[cols ENERG_LO,ENERG_HI])"
unix% pset mkarf sourcepixelx=4173.87 sourcepixely=4043.46

unix% mkarf 
Aspect Histogram File (herx1.asphist[ASPHIST]):
Output File Name (herx1.arf):
Source X Pixel (4173.87):
Source Y Pixel (4043.46):
Energy grid spec (grid(herx1_mkacisrmf.rmf[cols ENERG_LO,ENERG_HI])):
Name of fits file with obs info (evt file -- include extension) (3662_evt2.fits[EVENTS]):
Verbosity (0:5) (0):
Detector Name (ACIS-S3):
Grating for zeroth order ARF (NONE|LETG|HETG) (NONE):
NONE, or name of ACIS window mask file (acisf03662_000N002_msk1.fits):
NONE, or the name of the parameter block file (acisf141955042N002_pbk0.fits):

You can check the parameter file that was used with plist mkarf.


Correct the Streak Exposure Time

As the spectrum was made from streak data, not on-axis data, it is necessary to correct the exposure time in the spectrum file headers.

It takes 40 μs to transfer the charge from one row to another when reading out ACIS data. For the standard 1024 rows of a chip, the full time is then 

1024 * 0.000040 = 0.04096

The full ACIS frame time is 3.24104 seconds. The ratio of the 1024 readout time to the ACIS frame time is: 

0.04096/3.24104 = 0.0126379

Since there are only have 800 rows in this region, it's further reduced to: 

0.012954 * (800/1024) = 0.00987336

Retrieve the exposure value from the header of the event file and scale it by this factor: 

unix% dmkeypar 3662_evt2.fits EXPOSURE echo+
49579.136114336

49579.136114336 * 0.00987336 = 489.51

Now update the spectrum file headers with the new exposure: 

unix% punlearn dmhedit
unix% dmhedit infile=herx1.pi filelist="" operation=add key=EXPOSURE value=489.51
unix% dmhedit infile=herx1_bg.pi filelist="" operation=add key=EXPOSURE value=489.51

Update File Headers (dmhedit)

Finally, add the background and response filenames to the header of the streak spectrum file. 

unix% dmhedit infile=herx1.pi filelist="" operation=add key=BACKFILE value=herx1_bg.pi
unix% dmhedit infile=herx1.pi filelist="" operation=add key=RESPFILE value=herx1_mkacisrmf.rmf
unix% dmhedit infile=herx1.pi filelist="" operation=add key=ANCRFILE value=herx1.arf

Fitting

To fit the streak spectrum using the RMF and ARF, simply read the source spectrum FITS file into Sherpa, subtract the background, and fit it. See the Introduction to Fitting PHA Spectra thread for details. 



Parameters for /home/username/cxcds_param/dmextract.par


        infile = 3662_evt2.fits[sky=region(streak_bg.reg)][bin pi] Input event file
       outfile = herx1_bg.pi      Enter output file name
          (bkg = )                Background region file or fixed background (counts/pixel/s) subtraction
        (error = gaussian)        Method for error determination(gaussian|gehrels|<variance file>)
     (bkgerror = gaussian)        Method for background error determination(gaussian|gehrels|<variance file>)
      (bkgnorm = 1.0)             Background normalization
          (exp = )                Exposure map image file
       (bkgexp = )                Background exposure map image file
      (sys_err = 0)               Fixed systematic error value for SYS_ERR keyword
          (opt = pha1)            Output file type
     (defaults = ${ASCDS_CALIB}/cxo.mdb -> /soft/ciao/data/cxo.mdb) Instrument defaults file
         (wmap = )                WMAP filter/binning (e.g. det=8 or default)
      (clobber = no)              OK to overwrite existing output file(s)?
      (verbose = 0)               Verbosity level
         (mode = ql)
    

Parameters for /home/username/cxcds_param/dmstat.par


        infile = 3662_evt2.fits[sky=region(onaxis.reg)][cols chipx,chipy,ccd_id,x,y] Input file specification
   out_columns = chipx,chipy,ccd_id,x,y Output Column Label
       out_min = 80,827,7,4148.0029297,4018.0319824 Output Minimum Value
   out_min_loc = 19103,16594,1,176095,185976 Output Minimum Location Value
       out_max = 164,911,7,4199.9956055,4069.9790039 Output Maximum Value
   out_max_loc = 103349,14719,1,182148,152100 Output Maxiumum Location Value
      out_mean = 121.6962529,868.3099628,7,4173.873478,4043.4555486 Output Mean Value
    out_median =                  Output Median Value
     out_sigma = 15.342811518,15.53880314,0,10.076932348,10.178223086 Output Sigma Value
       out_sum = 29603222,211220740,1702785,1015315592.9,983590779.46 Output Sum of Values
      out_good = 243255,243255,243255,243255,243255 Output Number Good Values
      out_null = 0,0,0,0,0        Output Number Null Values
    out_cnvrgd =                  Converged?
 out_cntrd_log =                  Output Centroid Log Value
out_cntrd_phys =                  Output Centriod Phys Value
out_sigma_cntrd =                  Output Sigma Centriod Value
     (centroid = yes)             Calculate centroid if image?
       (median = no)              Calculate median value?
        (sigma = yes)             Calculate the population standard deviation?
         (clip = no)              Calculate stats using sigma clipping?
       (nsigma = 3)               Number of sigma to clip
      (maxiter = 20)              Maximum number of iterations
      (verbose = 1)               Verbosity level
         (mode = ql)              
    

Parameters for /home/username/cxcds_param/mkacisrmf.par


        infile = /soft/ciao/CALDB/data/chandra/acis/p2_resp/acisD2000-01-29p2_respN0006.fits scatter/rsp matrix file
       outfile = herx1_mkacisrmf.rmf RMF output file
          wmap = none             WMAP file
        energy = 0.1:11.0:0.01    energy grid in keV (lo:hi:bin)
       channel = 1:1024:1         channel grids in pixel (min:max:bin)
      chantype = PI               channel type
        ccd_id = 7                filter CCD-ID
         chipx = 121              filter chipx in pixel
         chipy = 868              filter chipy in pixel
          gain = /soft/ciao/CALDB/data/chandra/acis/det_gain/acisD2000-01-29gain_ctiN0006.fits gain file
     (asolfile = )                aspect solution file or a stack of asol files
      (obsfile = )wmap -> none)   obs file
      (logfile = )                log file
      (contlvl = 100)             # contour level
      (geompar = geom)            pixlib geometry parameter file
       (thresh = 1e-06)           low threshold of energy cut-off probability
      (clobber = no)              overwrite existing output file (yes|no)?
      (verbose = 0)               verbosity level (0 = no display)
         (mode = ql)
    

Parameters for /home/username/cxcds_param/acis_fef_lookup.par


        infile = 3662_evt2.fits   Source file (event or spectrum)
        chipid = 7                ACIS chip number
         chipx = 121              ACIS chip x coordinate
         chipy = 868              ACIS chip y coordinate
       outfile = /soft/ciao/CALDB/data/chandra/acis/fef_pha/acisD2000-01-29fef_pha_ctiN0004.fits[2][ccd_id=7,chipx=97:128,chipy=865:896] FEF file to use
      (quality = no)              Should you use the FEF file (if no use mkacisrmf)?
      (verbose = 0)               Verbose level
         (mode = ql)
    

Parameters for /home/username/cxcds_param/mkrmf.par


        infile = /soft/ciao/CALDB/data/chandra/acis/fef_pha/acisD2000-01-29fef_pha_ctiN0004.fits[2][ccd_id=7,chipx=97:128,chipy=865:896] name of FEF input file
       outfile = herx1.rmf        name of RMF output file
         axis1 = energy=0.1:11.0:0.01 axis-1(name=lo:hi:btype)
         axis2 = pi=1:1024:1      axis-2(name=lo:hi:btype)
      (logfile = STDOUT)          name of log file
      (weights = )                name of weight file
       (thresh = 1e-5)            low threshold of energy cut-off probability
       (outfmt = legacy)          RMF output format (legacy|cxc)
      (clobber = no)              overwrite existing output file (yes|no)?
      (verbose = 0)               verbosity level (0 = no display)
        (axis3 = none)            axis-3(name=lo:hi:btype)
        (axis4 = none)            axis-4(name=lo:hi:btype)
        (axis5 = none)            axis-5(name=lo:hi:btype)
         (mode = ql)
    

Parameters for /home/username/cxcds_param/asphist.par


        infile = @pcad_asol1.lis  Aspect Solution List Files
       outfile = herx1.asphist    Aspect Histogram Output File
       evtfile = 3662_evt2.fits[ccd_id=7] Event List Files
       dtffile =                  Live Time Correction List Files for HRC
      (geompar = geom)            Parameter file for Pixlib Geometry files
       (res_xy = 0.5)             Aspect Resolution x and y in arcsec
     (res_roll = 600.)            Aspect Resolution roll in arcsec
      (max_bin = 10000.)          Maximal number of bins
      (clobber = no)              Clobber output
      (verbose = 0)               Verbose
         (mode = ql)
    

Parameters for /home/username/cxcds_param/mkarf.par


   asphistfile = herx1.asphist[ASPHIST] Aspect Histogram File
       outfile = herx1.arf        Output File Name
  sourcepixelx = 4173.87          Source X Pixel
  sourcepixely = 4043.46          Source Y Pixel
        engrid = grid(herx1_mkacisrmf.rmf[cols ENERG_LO,ENERG_HI]) Energy grid spec
       obsfile = 3662_evt2.fits[EVENTS] Name of fits file with obs info (evt file -- include extension)
       pbkfile = acisf141955042N002_pbk0.fits NONE, or the name of the parameter block file
     detsubsys = ACIS-S3          Detector Name
       grating = NONE             Grating for zeroth order ARF
      maskfile = acisf03662_000N002_msk1.fits NONE, or name of ACIS window mask file
       verbose = 0                Verbosity
       (dafile = CALDB)           NONE, CALDB, or name of ACIS dead-area calibration file
       (mirror = HRMA)            Mirror Name
(ardlibparfile = ardlib.par)      name of ardlib parameter file
      (geompar = geom)            Parameter file for Pixlib Geometry files
      (clobber = no)              Overwrite existing files?
         (mode = ql)              Enter mode for parameter file.

History

17 Jul 2009 new for CIAO 4.1
15 Sep 2009 corrected a typo in dmhedit command (was "key=key=EXPOSURE")
22 Jan 2010 reviewed for CIAO 4.2: updated results to match archived data; ds9 region file format menu has changed
09 Mar 2010 The ACIS detector is calibrated over the range 0.224004 - 12 keV; choosing values outside this range results in a warning from mkacisrmf.
15 Jun 2010 The background spectrum exposure time also needs to be scaled.
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Last modified: 15 June 2010