Compute Single Chip ACIS Exposure Map and Fluxed Image Step-by-Step
[CIAO 3.4 Science Threads]
OverviewLast Update: 6 Mar 2007 - added ACIS dead area correction section and example of setting the pbkfile and dafile parameters Synopsis: mkexpmap generates an exposure map which may be used to convert a counts image of a source to an image in flux units. The computed exposure map is essentially an image of the effective area at each sky position, accounting for the effects of dither motion which are especially important near the edges of the detector. Purpose: To build an exposure map for a single ACIS chip (ccd_id = 7), create a fluxed image, and find an approximation for the source flux. Read this thread if: you are working with an ACIS observation and would like to create an exposure map for one of the chips. If more than one chip is being used, follow the Compute an ACIS Exposure Map (Multiple Chips) and Build Fluxed Image thread instead.
Related Links:
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Contents
- Get Started
- Create An Image
- Compute Exposure Map
- Normalize the Image by the Exposure Map
- Calculate the Source Flux
- Analysis Caveats
- Parameter files:
- History
- Images
Get Started
Sample ObsID used: 1838 (ACIS-S, G21.5-09)
File types needed: evt2; asol1; msk1
In this thread, we assume that all relevant files are in the same working directory.
To create an exposure map, we will use an aspect histogram file - which contains information on the aspect motion during the observation - and an instrument map - which is essentially the product of the detector quantum efficiency and the mirror effective area projected onto the detector surface.
Please ensure that you have set up ardlib to use the bad pixel file for your observation before following this thread.
In this example, the energy range was restricted from 0.3 keV to 10 keV:
unix% dmcopy "acisf01838N001_evt2.fits[energy=300:10000]" acis_1838_evt2.fits
The ACIS dead area correction
There is a fractional area loss per unit time due to cosmic ray flux incident on the ACIS detector. Calibration to account for this ACIS "dead area" was included in CALDB 3.3.0 on 15 December 2006. The correction is non-zero for the 8 front-illuminated ACIS chips; the effect is not detectable for the BI chips, so the nominal calibration value is 0.0. The resulting chipy-dependent reduction in the EA will be approximately 2.2% at the readout, and 4.0% at the top of the chip. Refer to the ACIS Dead Area Correction why topic for technical details.
In CIAO 3.4, the application of the dead area correction is turned off by default. However, users may opt to include it in the analysis by setting the pbkfile and dafile parameters in the mkinstmap step. Refer to the mkinstmap help file for details on these parameters.
Create An Image
First, we need to create the image which will ultimately be normalized by the exposure map.
1. Check Which Chips Are On
The list of chips used in the observation is stored in the DETNAM keyword of the event file:
unix% dmkeypar acis_1838_evt2.fits DETNAM echo+ ACIS-012367
In this case, six chips were on for the observation. Using ds9 to display acis_1838_evt2.fits, we know that the source we are interested in is at sky coordinates (called "physical coordinates" in ds9) close to x = 4072, y = 4249. We can use dmcoords to find out which chip the source is on:
unix% pset dmcoords asolfile="pcadf084244404N001_asol1.fits" unix% dmcoords acis_1838_evt2.fits # dmcoords (CIAO 3.4): Warning: position interpreted as degrees dmcoords>: sky 4072 4249 (RA,Dec): 18:33:33.468 -10:34:08.65 (RA,Dec): 278.38945 -10.56907 deg THETA,PHI 1.267' 5.93 deg (Logical): 4072.00 4249.00 SKY(X,Y): 4072.00 4249.00 DETX,DETY 4250.13 4112.47 CHIP ACIS-S3 370.94 383.55 TDET 4287.94 2085.55 dmcoords>: q
This tells us that the chip we want is ACIS-S3, i.e. ccd_id = 7. A description of the layout of the ACIS focal plane can be found in The Chandra Proposers' Observatory Guide.
2. Bin the Event File
Here we decided to make a full resolution image (blocking by a factor of 1):
unix% more chip_s3.reg # Region file format: CIAO version 1.0 rotbox(4182.860000,4393.150000,1024,1024,93.192576) unix% dmcopy "acis_1838_evt2.fits[sky=region(chip_s3.reg)][bin sky=1]" 1838_img_s3.fits
This FAQ explains several ways of finding the chip boundaries. This creates a full resolution ACIS image (8192 x 8192); this information is used again in the Calculate the Exposure Map step. You may choose to use different binning, but make sure that you change the xygrid appropriately in that step.
Compute Exposure Map
1. Find Peak Energy Of Source
We selected a region around the central source, using ds9, and saved it as obj.reg:
unix% more obj.reg # Region file format: CIAO version 1.0 circle(4072,4249,35)
We can use this file to extract a spectrum of the object in energy space and find the peak energy.
First, we use the CIAO tool dmextract to create a histogram of count-rate as a function of energy. Since we are not binning on pi or pha, we set opt=generic, and we use a bin size of 20 eV to improve the signal to noise:
unix% punlearn dmextract unix% pset dmextract infile="acis_1838_evt2.fits[sky=region(obj.reg)][bin energy=300:10000:20]" unix% pset dmextract outfile=obj_1838_histogram_energy.fits unix% pset dmextract opt=generic unix% dmextract Input event file (acis_1838_evt2.fits[sky=region(obj.reg)][bin energy=300:10000:20]): Enter output file name (obj_1838_histogram_energy.fits):
You can check the dmextract parameter file that was used with plist dmextract.
The resulting histogram can be plotted using
Prism or ChIPS. Choosing
the energy and count_rate columns produces a plot
like this ![[Link to Image 1: Energy versus count rate for the source]](../../imgs/imageicon.gif){kind=small}
.
If you used ChIPS to plot the histogram, then the
PICKPOINTS command can be
used to find the energy corresponding to the peak in the spectrum.
An alternative method involves the use of
dmstat
(to find the maximum count rate),
followed by dmlist
(to locate the corresponding energy):
unix% dmstat "obj_1838_histogram_energy.fits[cols count_rate]"
COUNT_RATE[count/s]
min: 0 @: 6
max: 0.017951569397 @: 71
mean: 0.0037646188012
sigma: 0.0040689885567
sum: 1.8258401186
good: 485
null: 0
unix% dmlist "obj_1838_histogram_energy.fits[count_rate > 0.015][cols energy,count_rate]" data,clean
# ENERGY COUNT_RATE
1710.0 0.0179515693970
1750.0 0.01642377625683
1770.0 0.01616914406680
1830.0 0.01667840844686
1950.0 0.01591451187677
For this dataset, the peak of the measured spectrum is ~1.7 keV.
2. Compute The Aspect Histogram
With the aspect solution file we can create a binned histogram for the chip that was on, detailing the aspect history of the observation:
unix% punlearn asphist unix% pset asphist infile="pcadf084244404N001_asol1.fits" unix% pset asphist outfile=asphist_7.fits unix% pset asphist evtfile="acis_1838_evt2.fits[ccd_id=7]" unix% asphist Aspect Solution List Files (pcadf084244404N001_asol1.fits): Aspect Histogram Output File (asphist_7.fits[ccd_id=7]): Event List Files (acis_1838_evt2.fits): Live Time Correction List Files for HRC ():
There are several things to notice here:
-
In some cases there will be more than one asol1.fits file for an observation. All the files must be input to the infile parameter, either as a list or as a stack (see ahelp stack for more information).
-
The dtffile parameter is left blank (i.e. ``none'') since the dead-time correction is read from the input event file for ACIS data.
-
The ccd_id value may be different for your dataset.
You can check the parameter file that was used with plist asphist.
Plotting
the 2-dimensional POS_OFFSET
vector - composed
of the X_OFFSET and Y_OFFSET columns - in
asphist_7.fits shows the
dither pattern used during the observation .
3. Calculate the Instrument Map
Since the mirror effective area is used to create the instrument map, and that area is energy dependent, it is necessary to decide at what energy to perform the calculation (or whether to use a spectrum as weights). See An Introduction to Exposure Maps (PS, 12pp) and the Calculating Spectral Weights thread for details on weighting a map by a spectrum. In this example we are going to assume a monoenergetic distribution of source photons of 1.7 keV (monoenergy parameter).
Note that it is not necessary for the instrument map to be congruent with the exposure map; the instrument map should describe the chip with full resolution. We will use the default values for the detector region (pixelgrid parameter), creating a 1024 x 1024 pixel image that covers the whole chip.
unix% punlearn mkinstmap unix% pset mkinstmap obsfile="asphist_7.fits[asphist]" unix% pset mkinstmap outfile=instmap_1.7kev_7.fits unix% pset mkinstmap maskfile=acisf01838_000N001_msk1.fits unix% pset mkinstmap detsubsys=ACIS-7 unix% pset mkinstmap pixelgrid="1:1024:#1024,1:1024:#1024" unix% pset mkinstmap spectrumfile=NONE unix% pset mkinstmap monoenergy=1.7
If you wish to include the ACIS dead area correction (not applied in this thread), set the pbkfile and dafile parameters in mkinstmap:
unix% pset mkinstmap pbkfile=acisf084245776N001_pbk0.fits dafile=CALDB
Now run the tool:
unix% mkinstmap Output File Name (instmap_1.7kev_7.fits): Energy Spectrum File (see docs) (NONE): Energy for mono-chromatic map [keV] (0.1:10) (1.7): Pixel grid specification x0:x1:#nx,y0:y1:#ny (1:1024:#1024,1:1024:#1024): Name of fits file + extension with obs info (asphist_7.fits[asphist]): Detector Name (ACIS-7): Grating for zeroth order ARF (NONE|LETG|HETG) (NONE): NONE, or name of ACIS window mask file (acisf01838_000N001_msk1.fits):
Including the maskfile parameter is particularly important if you are interested in having an accurate exposure map at the very edge of a CCD, subarray or window. For more information, see the dictionary entry on mask files.
You can check the parameter file that was used with plist mkinstmap.
4. Calculate the Exposure Map
Now we use mkexpmap and the aspect information stored in the histogram to project the instrument map onto the sky. We need to set the xygrid parameter to produce an exposure map that is the same size as the image created from the event list. The get_sky_limits script (part of the CIAO Scripts distribution) can be used to easily calculate this information from the existing image:
unix% get_sky_limits 1838_img_s3.fits verbose="1"
Checking binning of image: 1838_img_s3.fits
Image has 1080 x 1080 pixels
Lower left (0.5,0.5) corner is x,y= 3643.1, 3853.4
Upper right (1080.5,1080.5) corner is x,y= 4723.1, 4933.4
DM filter is:
x=3643.1:4723.1:#1080,y=3853.4:4933.4:#1080
mkexpmap xygrid value is:
3643.1:4723.1:#1080,3853.4:4933.4:#1080
You can then set the xygrid parameter using the information provided by the script, either manually or via
unix% pset mkexpmap xygrid=")get_sky_limits.xygrid"
(if the latter, do not run get_sky_limits again until after running mkexmap).
Note: If you are computing a low-resolution exposure map and speed is more important than accuracy, set useavgaspect=yes. In doing so, only the average aspect pointing will be used to derive the exposure map; otherwise all points in the aspect histogram will be used. The time required to compute the exposure map is proportional to the number of bins in the aspect histogram; if the aspect histogram contains 100 bins, then the use of this option reduces the run time by a factor of 100, approximately (you may also want to set verbose to 2, since this causes mkexpmap to output percentage-completed information). Using the full aspect solution will help accurately account for chip edges, bad pixels, etc.
unix% punlearn mkexpmap unix% pset mkexpmap instmapfile=instmap_1.7kev_7.fits unix% pset mkexpmap outfile=expmap_1.7kev_7.fits unix% pset mkexpmap xygrid="3643.1:4723.1:#1080,3853.4:4933.4:#1080" unix% pset mkexpmap asphistfile=asphist_7.fits unix% pset mkexpmap useavgaspect=no unix% pset mkexpmap normalize=no unix% mkexpmap Aspect Histogram File (asphist_7.fits): Output File Name (expmap_1.7kev_7.fits): Name of Instrument Map (instmap_1.7kev_7.fits): grid specification syntax x0:x1:#nx,x0:x1:ny (3643.1:4723.1:#1080,3853.4:4933.4:#1080): Use Average Aspect Pointing (no): Exposure map limits: 0.000000e+00, 5.363356e+06 Writing exposure map to expmap_1.7kev_7.fits
The exposure map may be displayed in ds9 .
You can check the mkexpmap parameter file that was used with plist mkexpmap.
Since we set the normalize parameter = no, the exposure map has units of [cm2*s*counts/photon]. This allows us to simply divide the image by the exposure map to derive an image in units of flux [photons/cm2/s/pixel]. If the setting had been left as yes (the default), the units of the exposure map would be [cm2*counts/photon]. Please see the help file for mkexpmap for more details on this.
Normalize the Image by the Exposure Map
The exposure map is in units of [cm2*s*counts/photon] since it was created by projecting the instrument map (in [cm2*counts/photon]) onto the tangent plane of the observation. To create an image in units of [photon/cm2/s/pixel], we simply need to divide by the exposure map. This can be performed in one step with dmimgcalc:
unix% punlearn dmimgcalc unix% pset dmimgcalc infile=1838_img_s3.fits unix% pset dmimgcalc infile2=expmap_1.7kev_7.fits unix% pset dmimgcalc outfile=1838_img_s3_norm.fits unix% pset dmimgcalc operation=div unix% dmimgcalc Input file #1 (1838_img_s3.fits): Input file #2 (expmap_1.7kev_7.fits): output file (1838_img_s3_norm.fits): arithmetic operation (div): warning: CONTENT has 1 different values. warning: DETNAM has different value...Merged...
The messages are related to how the tool merges the header information in the input files. The merging_rules ahelp file explains the rules and how they affect the output file header.
The units of 1838_img_s3_norm.fits are
[photon/cm2/s/pixel].
You can check the parameter file that was used with plist dmimgcalc.
Alternatively, one may use dmimgthresh for a cleaner final product. The strongly variable exposure near the edge of a dithered field may produce "hot" pixels when divided into an image. While technically proper, these hot pixels can be an eyesore, drawing attention to a noisy, uninteresting portion of the image. The dmimgthresh tool may be used to make a "threshold cut" before dividing the image by the exposure map, thus removing the hot pixels:
unix% punlearn dmimgthresh unix% pset dmimgthresh infile=1838_img_s3.fits unix% pset dmimgthresh outfile=1838_img_s3_clean.fits unix% pset dmimgthresh expfile=expmap_1.7kev_7.fits unix% pset dmimgthresh cut=1.5% unix% pset dmimgthresh value=0.0 unix% dmimgthresh Input dataset/block specification (1838_img_s3.fits): Output dataset/block specification (1838_img_s3_clean.fits):
Here we set our threshold at 1.5% of the maximum value of the exposure map. All image pixels with values of exposure less than this value will be set to 0.0 in the output file. The next step would be to divide 1838_img_s3_clean.fits by the exposure map for a final, fluxed image. You may want to adjust these values for your own observation.
You can check the parameter file that was used with plist dmimgthresh.
Calculate the Source Flux
Since the units of the fluxed image are [photon/cm2/s/pixel], adding up the pixel values around a source results in the source flux in [photon/cm2/s]. Note that this flux is an approximation - as discussed in An Introduction to Exposure Maps (PS, 12pp) - since a spectral shape was assumed when using mkinstmap (in this example, a monochromatic source).
Using the source region "flux.reg":
unix% more flux.reg # Region file format: CIAO version 1.0 circle(4070.5,4250.5,112)
the flux can be calculated with either dmstat:
unix% punlearn dmstat unix% dmstat infile="1838_img_s3_norm.fits[sky=region(flux.reg)]" centroid=no 1838_img_s3_norm.fits min: 0 @: ( 4061.6402575 4138.9302575 ) max: 1.4617749002e-05 @: ( 4069.6402575 4250.9302575 ) mean: 1.1458850513e-07 sigma: 3.8186885525e-07 sum: 0.0045160475758 good: 39411 null: 11214
or dmextract:
unix% dmextract infile="1838_img_s3_norm.fits[bin sky=@flux.reg]" outfile="source_flux.fits"
unix% dmlist source_flux.fits"[cols COUNTS,ERR_COUNTS]" data
--------------------------------------------------------------------------------
Data for Table Block HISTOGRAM
--------------------------------------------------------------------------------
ROW COUNTS ERR_COUNTS
1 0.00451604757582 0.06720154444519
Since the input to dmextract was a fluxed image, not an event list, the COUNTS column actually reports the total flux (in [photon/cm2/s]) for the source region. While slightly more involved, the dmextract method can be used on multiple sources in a single command, and the results are conveniently stored in a table.
Analysis Caveats
Users should be cautious about analyzing the data for sources near the edges of the ACIS CCDs.
-
For X-rays passing through the mirrors, the very bottom of each CCD is obscured by the frame store. As a result, some of the events in rows with CHIPY <= 8 are not detected. (The set of rows affected varies from CCD to CCD.) Since the CIAO tools do not compensate for this effect, the ARFs and exposure maps for sources in these regions may be inaccurate.
-
For sources within about thirty-two pixels of any edge of a CCD, the source may be dithered off the CCD during part of an observation. The aspect histogram, which is used to create ARFs and exposure maps, is designed to compensate for this effect.
-
A contaminant has accumulated on the optical-blocking filters of the ACIS detectors, as described in the ACIS QE Degradation why topic. Since there is a gradient in the temperature across the filters (the edges are colder), there is a gradient in the amount of material on the filters. (The contaminant is thicker at the edges.) Within about 100 pixels of the outer edges of the ACIS-I and ACIS-S arrays, the gradient is relatively steep. Therefore, the effective low-energy (' 1 keV) detection efficiency may vary within the dither pattern in this region. The ARF and instrument map tools are designed to read a calibration file which describes this spatial dependence.
Parameters for /home/username/cxcds_param/dmextract.par
#--------------------------------------------------------------------
#
# DMEXTRACT -- extract columns or counts from an event list
#
#--------------------------------------------------------------------
infile = acis_1838_evt2.fits[sky=region(obj.reg)][bin energy=300:10000:20] Input event file
outfile = obj_1838_histogram_energy.fits Enter output file name
(bkg = ) Background region file or fixed background (counts/pixel/s) subtraction
(error = gaussian) Method for error determination(poisson|gaussian|<variance file>)
(bkgerror = gaussian) Method for background error determination(poisson|gaussian|<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 = generic) Output file type: pha1
(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)
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Parameters for /home/username/cxcds_param/asphist.par
#--------------------------------------------------------------------------
#
# Parameter file for the ASPECT HISTOGRAM Tool
#
#--------------------------------------------------------------------------
infile = pcadf084244404N001_asol1.fits Aspect Solution List Files
outfile = asphist_7.fits Aspect Histogram Output File
evtfile = acis_1838_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)
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Parameters for /home/username/cxcds_param/mkinstmap.par
outfile = instmap_1.7kev_7.fits Output File Name
#---------------------------------------------------------------------------
# Energy Band Info
#---------------------------------------------------------------------------
# Currently, this file is a simple ascii file with two columns
spectrumfile = NONE Energy Spectrum File (see docs)
monoenergy = 1.7 Energy for mono-chromatic map [keV]
#
pixelgrid = 1:1024:#1024,1:1024:#1024 Pixel grid specification x0:x1:#nx,y0:y1:#ny
obsfile = asphist_7.fits[asphist] Name of fits file + extension with obs info
detsubsys = ACIS-7 Detector Name
grating = NONE Grating for zeroth order ARF
maskfile = acisf01838_000N001_msk1.fits NONE, or name of ACIS window mask file
(mirror = HRMA) Mirror Name
#
(pbkfile = NONE) NONE, or the name of the parameter block file
(dafile = NONE) NONE, CALDB, or name of ACIS dead-area calibration file
#
(ardlibparfile = ardlib.par) name of ardlib parameter file
(geompar = geom) Parameter file for Pixlib Geometry files
#
(verbose = 0) Verbosity
(clobber = no) Overwrite existing files?
(mode = ql) Enter mode for parameter file.
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Parameters for /home/username/cxcds_param/mkexpmap.par
asphistfile = asphist_7.fits Aspect Histogram File
outfile = expmap_1.7kev_7.fits Output File Name
instmapfile = instmap_1.7kev_7.fits Name of Instrument Map
#
xygrid = 3643.1:4723.1:#1080,3853.4:4933.4:#1080 grid specification syntax x0:x1:#nx,x0:x1:ny
useavgaspect = no Use Average Aspect Pointing
#---------------------------------------------------------------------------
# Aspect Histogram Parameters
# If UseAvgAspect is set to yes, then only the average pointing derived from
# the many pointings in the aspect histogram will be used.
#---------------------------------------------------------------------------
#asphistfile,f,a,"../data/aciss_asphist.fits",,,"Aspect Histogram File"
(normalize = no) Normalize exposure map by exposure time
#
(geompar = geom) Parameter file for Pixlib Geometry files
(verbose = 0) Verbosity
(clobber = no) Overwrite existing files?
(mode = ql) Enter mode for parameter file.
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Parameters for /home/username/cxcds_param/dmimgcalc.par
# parameter file for dmimgcalc
infile = 1838_img_s3.fits Input file #1
infile2 = expmap_1.7kev_7.fits Input file #2
outfile = 1838_img_s3_norm.fits output file
operation = div arithmetic operation
(weight = 1) weight for first image
(weight2 = 1) weight for second image
(lookupTab = ${ASCDS_CALIB}/dmmerge_header_lookup.txt -> /soft/ciao/data/dmmerge_header_lookup.txt) lookup table
(clobber = no) delete old output
(verbose = 0) output verbosity
(mode = ql)
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Parameters for /home/username/cxcds_param/dmimgthresh.par
infile = 1838_img_s3.fits Input dataset/block specification
outfile = 1838_img_s3_clean.fits Output dataset/block specification
(expfile = expmap_1.7kev_7.fits) Exposure map file
(cut = 1.5%) Threshold value
(value = 0) Replacement value
(verbose = 0) Debug Level(0-5)
(clobber = no) Clobber existing file
(mode = ql)
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History
| 23 Dec 2004 | updated for CIAO 3.2: minor changes to parameter files, added Caveats section; include dmcoords asolfile parameter |
| 23 Jun 2005 | CIAO 3.2.2 patch: change to asphist parameter file |
| 19 Dec 2005 | updated for CIAO 3.3: default value of dmextract error and bkgerror parameters is "gaussian"; updated syntax for asphist (GTI filter is associated with the event file rather than the aspect solution); corresponding changes to screen output |
| 24 May 2006 | changed "det" abbreviation to full parameter name ("detsubsys") in mkinstmap call |
| 01 Dec 2006 | updated for CIAO 3.4: CIAO version in warning; parameter file update for mkinstmap |
| 06 Mar 2007 | added ACIS dead area correction section and example of setting the pbkfile and dafile parameters |
