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Last modified: 28 Jul 2016

URL: http://cxc.harvard.edu/ciao/threads/marx/

Using MARX to Create an Event File from ChaRT Rays

CIAO 4.9 Science Threads


Overview

Synopsis:

The output of ChaRT is a set of rays (a PSFRAYS table) that cannot be used directly in your analysis; it must be converted into a suitable format, i.e. a pseudo-events file. This thread describes how to use the MARX software to do this conversion by projecting the rays onto the detector-plane, and then accounting for the detector (ACIS or HRC).

Using MARX allows the user to take into account all changes to the photon distribution emerging from the HRMA due to the detector response. In particular, the detector QE & QEU and the roll are accounted for. In addition to simulating the detector response, MARX uses the ray weights to account for the mirror effects, i.e. different efficiency of different shells at different angles/energies.

This thread is not a definitive guide to using MARX. There are many more options and parameters discussed in the MARX manual.

Related Links:

Last Update: 28 Jul 2016 - Added information about suggested ACIS-S AspectBlur.


Contents


Get Started

This example uses HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits, which was created in the Introduction to ChaRT Data Files thread. In addition to the ray files, the actual observation data are also retrieved

Download the sample data: 942 (ACIS-S, NGC 4244)

The rest of this thread assumes the data have been reprocessed with chandra_repro.


Setting up MARX

This thread requires the MARX software. If you do not have MARX installed you can install it using the install_marx script or manually by following these instructions (may be necessary for some OSX users).

[WARNING]
Installing MARX on OSX

The default C compiler in OSX is clang, which is aliased to gcc. While MARX compiles successfully with clang, several problematic issues have been seen in the resulting MARX build. The MARX developers suggest using a true gcc compiler, obtainable at http://hpc.sourceforge.net/ for Max OS X, as noted in Known Bugs and Limitations—Max OS X. The real gcc needs to be manually installed and put early in the PATH environment variable, otherwise the broken Mac OS X version will be picked up. Prior to installing MARX, it may also be worthwhile to set the CC environment variable to the gcc

For example, if the new gcc is installed in /usr/local/bin/, then set the C compiler variable CC:

(t)csh% setenv CC /usr/local/bin/gcc

or

bash% export CC=/usr/local/bin/gcc

Set up your environment to access all the files and directories which MARX needs:

unix% setenv MARX_DIR <local_marx_directory>
unix% set path = ($path $MARX_DIR/bin)
unix% setenv MARX_DATA_DIR $MARX_DIR/share/marx/data

Alternatively, the MARX DataDirectory parameter can be defined to point to the data files. By default, this parameter is set to the contents of the $MARX_DATA_DIR environment variable. At this point, your system is ready to run simulations


Get Source Coordinates

Before running the simulation, it is necessary to determine the nominal position of the detector during the observation. These values are stored in the header of the level=2 events file:

unix% dmlist acisf00942_repro_evt2.fits header | grep _NOM
0055 RA_NOM                     184.3430399825           Real8        Nominal RA
0056 DEC_NOM                     37.7808853898           Real8        Nominal Dec
0057 ROLL_NOM                   230.8753656982           Real8        Nominal Roll

Additionally, the source coordinates for the PSF are required. These were determined in the Determine the Off-axis Angle section of the Preparing to Run ChaRT thread. The values are stored in the ChaRT header

unix% dmlist HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits header | egrep "SRC_(RA|DEC)" 
0010 SRC_RA               184.237458333 [deg]            String       Input source Right Ascension
0011 SRC_DEC              37.7265805556 [deg]            String       Input source Declination

Lastly we check if the ChaRT simulation used an aspect solution by inspecting the value of the ASOLFILE keyword. If present, this keyword must match the one used with MARX.

unix% dmkeypar HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits ASOLFILE echo+
pcadf075214790N004_asol1.fits.gz

The gzip, .gz, extension can be omitted.


Using simulate_psf script

The simulate_psf script automates the steps needed to run the ChaRT generated ray files, run them through marx, and produce an image of the PSF.

unix% pset simulate_psf infile=acisf00942_repro_evt2.fits 
unix% pset simulate_psf outroot=chart
unix% pset simulate_psf ra=184.237458333 
unix% pset simulate_psf dec=37.7265805556
unix% pset simulate_psf simulator=file
unix% pset simulate_psf rayfile=HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits
unix% pset simulate_psf projector=marx
unix% simulate_psf mode=h
simulate_psf
          infile = acisf00942_repro_evt2.fits
         outroot = chart
              ra = 184.237458333
             dec = 37.7265805556
    spectrumfile = 
      monoenergy = INDEF
            flux = INDEF
       simulator = file
         rayfile = HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits
       projector = marx
     random_seed = -1
            blur = 0.07000000000000001
  readout_streak = no
          pileup = no
           ideal = yes
        extended = yes
         binsize = 1
          numsig = 7
         minsize = INDEF
         numiter = 1
        keepiter = no
        asolfile = 
       marx_root = /soft/marx-5.3.0
         verbose = 1
            mode = h

Started check_setup
Finished check_setup
Performing iteration 1 of 1
Started run_marx
Finished run_marx
Started create_psf_image
Finished create_psf_image
Started create_average_image
Finished create_average_image

Final output PSF image is : chart.psf

Users may need to adjust the blur parameter as is discussed below.

This completes this thread. Users may wish the review the information about some common mistakes. Otherwise they may use the PSF image created in this step for their analysis.

The next alternative section is the step-by-step instructions showing how to setup and run marx.


Step by Step

Setting up Ray Projection

In order to analyze the spatial distribution of the PSF, we need to project the PSF rays in HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits onto the detector plane. MARX enables us to do so.

Multiple Iterations

The steps in this thread need to be repeated for each ChaRT ray file individually. The individual images are combined in the Creating an Image of the PSF thread.

Since all the simulation parameters are the same, users only need to change the name of the rays file and the output directory for each run.

Copy over the parameter file locally:

unix% cp $MARX_DIR/share/marx/pfiles/marx.par ./marx.par
unix% chmod +w ./marx.par

and set the necessary parameters:

unix% pset ./marx SAOSACFile=HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits
unix% pset ./marx OutputDir=marx_output_i0000.dir
unix% pset ./marx SourceType=SAOSAC

unix% pset ./marx RA_Nom=184.34304
unix% pset ./marx Dec_Nom=37.78089
unix% pset ./marx Roll_Nom=230.87537
unix% pset ./marx SourceRA=184.237458333
unix% pset ./marx SourceDEC=37.7265805556

unix% pset ./marx DitherModel=FILE
unix% pset ./marx DitherFile=pcadf075214790N004_asol1.fits

unix% pset ./marx DetectorType=ACIS-S 
unix% pset ./marx GratingType=NONE
unix% pset ./marx ExposureTime=0.0

There are a few things to note in the pset commands:

  • Make sure to use the correct detector for the DetectorType parameter; valid options are HRC-S, ACIS-S, HRC-I, or ACIS-I.
  • The Exposuretime is set to 0.0 to ensure that the simulated output has the desired exposure length. The "Simulation Control: Exposure Time" section of the MARX manual [PDF] has more information on setting this parameter.

[TIP]
Setting ACIS DetectorType Value

MARX defines the ACIS DetectorType values to be specific sets of CCDs:

  • ACIS-I = ACIS-0123
  • ACIS-S = ACIS-456789

If you have data that is taken at the imaging aimpoint, but on the spectroscopic array (e.g. aimpoint on ACIS-I3/3, but data on ACIS-S3/7) or vice-versa (aimpoint on ACIS-7, but data on ACIS-3), the DetectorType selected must match which CCD the data falls on, i.e. not the aimpoint array. Subsequently, a large DetOffsetZ value is to be expected.

Correcting for SIM Offset

Observations are often made with the science instrument module (SIM) is often offset from its nominal position. If these offsets are not included in the MARX run, the simulated PSF will not be placed at the correct location on the detector. The nominal MARX SIM positions are at:

Detector SIM_X [mm] SIM_Y [mm] SIM_Z [mm]
ACIS-I -0.78234819833843 0 -233.5924630914
ACIS-S -0.68426746699586 0 -190.1325231040
HRC-I -1.0402925884 0 126.9854943053
HRC-S (spec) -1.4295857921 0 250.4559758190
HRC-S (image) -1.5333365632 0 250.4559758190

and can be also looked up in the $MARX_DATA_DIR/caldb/telD1999-07-23aimptsN0002.fits file or by running the MARX ray projection with the default offset values of zero.

To determine the offset, first, compare the SIM values in the original Chandra events file to the ACIS-S values in the table.

unix% dmlist acisf00942_repro_evt2.fits header | grep SIM_
0039 SIM_X                   -0.68282252473119           Real8        SIM focus pos (mm)
0040 SIM_Y                                   0           Real8        SIM orthogonal axis pos (mm)
0041 SIM_Z                     -190.1400660499           Real8        SIM translation stage pos (mm)

MARX SIM_X: -0.68426746699586
MARX SIM_Y: 0
MARX SIM_Z: -190.1325231040

Some observations are done with an offset of several millimeters. The difference, calculated as event_file_value - marx_value, is small in this case:

SIM_X: -0.68282252473119 - (-0.68426746699586) =  0.00144494

SIM_Z: -190.1400660499   - (-190.1325231040)   = -0.00754295

The SIM offset generally has a negligible effect on the off-axis angle, but often manifests itself by placing the source at a different position angle relative to the detector aimpoint. The determined SIM offsets can then be set:

unix% pset ./marx DetOffsetX=0.00144494
unix% pset ./marx DetOffsetY=0
unix% pset ./marx DetOffsetZ=-0.00754295

At the start of the mission, the SIM was located on-axis, but has since drifted due to changes in telescope geometry, with effects that can no longer be neglected. Fortunately, if an aspect solution is used for the observation's dither model, MARX will account for this drift using the available positional information at all points in time from the aspect solution file.


Blurring Effects

When simulating real Chandra data, to avoid pixelization effects in the pseudo-events file, there is an AspectBlur parameter which should be set. Users may experiment with the appropriate values of AspectBlur; we suggest values of 0.2 arcsec for ACIS-I, 0.25 arcsec for ACIS-S, and 0.07 arcsec for HRC as suitable for typical data, based on a limited set of simulations.

For ACIS-I:
unix% pset ./marx AspectBlur=0.20

For ACIS-S:
unix% pset ./marx AspectBlur=0.25

For HRC:
unix% pset ./marx AspectBlur=0.07
[NOTE]
Blurring in MARX v4

MARX v4 has a similar parameter—with a physically different underpinning—called DitherBlur, which has since been supplanted by AspectBlur in MARX v5. In MARX v4, the aspect reconstruction process introduces small positional errors in the derived sky positions for events, roughly 0.35 arcsec for ACIS and 0.18 arcsec for HRC.

For ACIS:
unix% pset ./marx DitherBlur=0.35

For HRC:
unix% pset ./marx DitherBlur=0.18

Projecting the Rays

Now run the tool. Note the syntax (@@) required to use the local parameter file; see Example 9 of ahelp parameter for details.

unix% marx @@./marx.par
MARX version 5.0.0, Copyright (C) 2002-2012 Massachusetts Institute of Technology

... screen output omitted ...

Opening ASPSOL fits file pcadf075214790N004_asol1.fits
[Using ASPSOL dither model]
Initializing source type SAOSAC...
Opening SAOSAC fits file HRMA_ra184.23746_dec37.72658_source_flux_chart.dat_dithered_i0000_rays.fits
System initialized.

Starting simulation.  NumRays to collect = 1000000, dNumRays = 100000
Collecting 100000 photons...
	8387 collected.
Reflecting from HRMA
Detecting with ACIS-S

Writing output to directory 'marx_output.dir' ...
Total photons: 8387, Total Photons detected: 2193, (efficiency: 0.261476)
  (efficiency this iteration  0.261476)  Total time: 50307.129827

It should not be expected that the SIM_* header keywords of the observed events file and projected pseudo-events file be identical.


Create an Events File

MARX creates a number of ASCII files in the specified directory (marx_output_i0000.dir):

unix% ls marx_output_i0000.dir
b_energy.dat  det_theta.dat  obs.par      sky_roll.dat  xpos.dat    zcos.dat
det_dy.dat    energy.dat     pha.dat      time.dat      ycos.dat    zpos.dat
det_dz.dat    marx.par       sky_dec.dat  xcos.dat      ypixel.dat
detector.dat  mirror.dat     sky_ra.dat   xpixel.dat    ypos.dat

These .dat files need to be converted to a FITS events file before they can be used in CIAO. The MARX tool marx2fits does this, given the directory name and the output filename.

unix% marx2fits --pixadj=EDSER marx_output_i0000.dir marx_output_i0000.fits 
Examining marx_output_i0000.dir/time.dat
Examining marx_output_i0000.dir/detector.dat
Examining marx_output_i0000.dir/energy.dat
Examining marx_output_i0000.dir/b_energy.dat
Examining marx_output_i0000.dir/xpos.dat
Examining marx_output_i0000.dir/ypos.dat
Examining marx_output_i0000.dir/zpos.dat
Examining marx_output_i0000.dir/xcos.dat
Examining marx_output_i0000.dir/ycos.dat
Examining marx_output_i0000.dir/zcos.dat
Examining marx_output_i0000.dir/xpixel.dat
Examining marx_output_i0000.dir/ypixel.dat
Examining marx_output_i0000.dir/pha.dat
Examining marx_output_i0000.dir/mirror.dat
Examining marx_output_i0000.dir/sky_ra.dat
Examining marx_output_i0000.dir/sky_dec.dat
Examining marx_output_i0000.dir/sky_roll.dat
Examining marx_output_i0000.dir/det_dy.dat
Examining marx_output_i0000.dir/det_dz.dat
Examining marx_output_i0000.dir/det_theta.dat
[IMPORTANT]
--pixadj=EDSER

Users should only use --pixadj=EDSER option when they supply ChaRT an aspect solution -- either via specifying OBS_ID or by uploading a file.

Using EDSER without the aspect solution will lead to rectangular artifacts that will no match the data. For simulation done without an aspect solution users should use --pixadj=EXACT.

[TIP]
Including Pileup?

If the objective of running ChaRT and MARX is to simulate an observation, as opposed to generate a model PSF, then you may want to include pileup effects. First you need to be sure that your simulation parameters exactly matched the observation (for example the spectrum flux was not artifically increased to increase sampling of the PSF). If these are not correct, the observed pileup cannot be matched to the simulation.

To include pileup, you must run the marxpileup tool:

unix% cp $MARX_DIR/share/marx/pfiles/marxpileup.par . 
unix% marxpileup MarxOutputDir=marx_output_i0000.dir

and to apply the pileup effects on the pseudo-events file, include the --pileup flag to process the pileup simulation with marx2fits.

unix% marx2fits --pixadj=EDSER --pileup marx_output_i0000.dir/pileup marx_output_i0000.fits 

Note: With pileup enabled, it is unclear how to apply an ad-hoc normalization to get the simulation to match the data. One can try to use a region away from the core of the PSF; however, if the observed data does have any extended emission (dust halo, PWN, etc) then the result will be incorrect.

*In MARX 5.0.0, marxpileup introduces an offset on the source position, placing the source between 0.2-0.4 arcsec at 40 degrees from the readout streak, in the direction of the streak. A future MARX release will fix this issue.


The file may be viewed in ds9:

unix% ds9 acisf00942_repro_evt2.fits marx_output_i0000.fits &
[Thumbnail image: The events file created by MARX includes the ACIS readput streak.]

[Version: full-size]

[Print media version: The events file created by MARX includes the ACIS readput streak.]

Figure 1: The events file created by MARX

The level 2 event file (left) with the ChaRT+MARX simulation, MARX , (right).


Common Mistakes

This section will provide some examples of mistakes users will commonly make when attempting to use ChaRT and MARX

Failure to Provide MARX the aspect solution file

If ChaRT was run using an aspect asolution -- either by specifying the OBS_ID or by uploading a file, and the user fails to use that file when running MARX, the result will be a dithered PSF as shown in Figure 2.

[Thumbnail image: Using MARX with dither ray file, but omitting the aspect solution]

[Version: full-size]

[Print media version: Using MARX with dither ray file, but omitting the aspect solution]

Figure 2: Using MARX with dither ray file, but omitting the aspect solution

If an aspect solution file is used with ChaRT then the same file must be used with MARX. Failure to do so will result in the MARX output appearing dithered. This can be seen with the data in this thread as shown here.

unix% marx @@./marx OutputDir=bad_aspect DitherModel=NONE
unix% marx2fits --pixadj=EDSER bad_aspect bad_aspect.fits
unix% ds9 bad_aspect.fits

Increasing flux to generate more rays

In ChaRT 2, the exposure time of the simulation is limited by the length of the aspect solution. Users may therefore be tempted to increase the photon flux in the spectrum in order to generate more rays. This strategy can backfire especially if trying to model pileup.

The increased photon flux over the same time interval will be seen by MARX as an increase in the number of piled up events. Spatially this has the effect of depressing the core of the PSF as shown in Figure 3.

[Thumbnail image: Comparison of radial profile for bright PSF]

[Version: full-size]

[Print media version: Comparison of radial profile for bright PSF]

Figure 3: Comparison of radial profile for bright PSF

A comparison of the radial profile of the observed counts (black curve) to the ChaRT+MARX simulation where the flux in the spectrum was increased multiplied by 100.
unix% dmtcalc source_flux_chart.dat 100x_source_flux_chart.dat expression="source=100.0*source"

Using marxpileup and the marx2fits --pileup flag, this generated a PSF with 130189 counts, compared to 2161 counts when using the best fit, unweighted, spectral model.

The radial profiles were extracted with dmextract and the counts in the PSF have been normalized to the counts in the observed dataset by taking the ratio of the counts in an annulus with inner radius=5 and outer radius=30 pixels.

While the tails of the radial profiles agree well, the core of the PSF is significantly depressed relative to the observed counts.

Users who require a large number of events in their PSF should generate multiple realizations and combine the image as discussed in the Creating an Image of the PSF thread.


Using EDSER without aspect solution

Another common mistake is to attempt to simulate the PSF using the EDSER subpixel algorithm, marx2fits --pixadj=EDSER, without having supplied ChaRT an aspect solution.

[Thumbnail image: Subpixel PSFs generated with different pixadj values without aspect.]

[Version: full-size]

[Print media version: Subpixel PSFs generated with different pixadj values without aspect.]

Figure 4: Subpixel PSFs generated with different pixadj values without aspect.

The PSF at the same location as in Figure 1, binned at subpixel resolution (0.2 pixels), with rays generated without an aspect solution.

(Upper Left) is the subpixel image created using marx2fits --pixadj=EDSER; the stippling effect is due to the quantization of the event locations within a pixel that EDSER imposes. (Lower Left) is the same with --pixadj=NONE which shows a similar quantization effect. (Lower Right) uses --pixadj=RANDOMIZE; careful inspection shows a box-like structure which is not seen in the observed dataset. (Upper Right) is the output when using --pixadj=EXACT.

It the ChaRT simulation did not include an aspect solution,

unix% dmkeypar HRMA_ra0.09479_dec-0.03055_en2.3_flux0.001_pointed_i0000_rays.fits ASOLFILE echo+
none

then users should use --pixadj=EXACT.


Summary

The output file (marx_output_i0000.fits) is a pseudo-events file that can be used, for example, to create an image of the PSF.


History

27 Jun 2003 original version, updated for CIAO 3.0: layout
02 Dec 2004 added note about setting ExposureTime parameter
16 Feb 2005 reviewed for CIAO 3.3: no changes
31 Jul 2007 updates for ciao3.4
18 Aug 2008 updated for CIAO 4.0: MARX v4.2.0; minor changes to screen output; image converted to inline
09 Oct 2008 updated to MARX v4.3.0
18 Feb 2009 updated to MARX v4.4.0
19 Mar 2009 updated MARX v4.4.0 syntax to find modified parameter file first
18 Feb 2010 updated to MARX v4.5.0; added Correcting for an Offset section; added mention of the MARX DataDirectory parameter
15 Dec 2010 reviewed for CIAO 4.3: no changes
22 Feb 2012 reviewed for CIAO 4.4: point to MARX 4.5 page
01 Oct 2012 reviewed for PSF site overhaul. Updates for some MARX 5.0 syntax needed for ChaRT v1 compatibility
29 Mar 2013 Updated file version from N003 to N004.
01 May 2013 Added a note about pileup and normalization.
10 Jul 2014 Added information about using the DY_AVG and DZ_AVG header values.
20 Aug 2014 Updated to use MARX v5.
11 May 2015 Updated for ChaRT v2. New information about aspect. New section about combining images from multiple iterations.
29 Feb 2016 Added a note about using install_marx script.
06 Apr 2016 Revised AspectBlur values.
11 Apr 2016 Added warning about installing MARX on OSX with default C compiler.
10 Jun 2016 Revised information about handling the SIM offset and added information about the MARX AspectBlur parameter.
16 Jun 2016 simulate_psf can now be used to project rays using marx.
28 Jul 2016 Added information about suggested ACIS-S AspectBlur.


Last modified: 28 Jul 2016
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