Simulating Chandra ACIS-S LETG Spectra with Sherpa
Sherpa Threads (CIAO 4.12 Sherpa v1)
This thread illustrates the use of the Sherpa fake_pha command to simulate a spectrum of a point source as would be observed with a different Chandra instrument configuration than that used to produce the user's existing data and source model. We simulate ACIS-S/LETG +1/-1 LEG spectral orders using a source model expression tailored to the +1/-1 HEG and MEG orders of a real ACIS-S/HETG data set.
If you do not have experience with simulating X-ray spectral data in Sherpa, you may wish to follow the "step-by-step" example in the introductory simulation thread, before attempting the sample analysis in this thread.
Last Update: 11 Dec 2019 - Updated for CIAO 4.12 by replacing print_window calls with the equivalent Matplotlib command plt.savefig.
- Getting started - downloading calibration response files for simulations
- Defining the Instrument Response for the Simulation
- Establishing the Source Model Expression for the Simulation
- Running the Simulation with fake_pha
- Writing the Simulated Data to Output Files
- Fitting the Simulated Data
- Scripting It
Getting started - downloading calibration response files for simulations
In order to simulate a Chandra ACIS-S/LETG spectrum with Sherpa, we must define an instrument response with the appropriate ARF (ancillary response function) and RMF (redistribution matrix function) files. These files may be downloaded from the Chandra Proposal Planning page of the CalDB (Calibration Database) website, where sample RMFs and corresponding ARFs positioned at the aimpoint of the ACIS-S array (and at selected off-axis points) are available.
In this thread, we use the files aciss_leg1_cy21.grmf, aciss_leg-1_cy21.grmf, aciss_leg1_cy21.garf, and aciss_leg-1_cy21.garf, positioned at the default pointing for ACIS-S.
The Sherpa fake_pha command calculates a synthetic 1-D spectral data set based on a defined instrument response and source model expression. For details on the functionality of this command, with examples of its usage, see the threads "Simulating 1-D Data: the Sherpa FAKE_PHA Command" and "Simulating Chandra ACIS-S Spectra with Sherpa"
Sample ObsID used: 459 (HETG/ACIS-S, 3C 273)
The ACIS-S/HETG data files used to establish the appropriate source model expression for the simulated data were created by following several of the CIAO Grating threads:
spectra: 459_heg_m1_bin10.pha 459_heg_p1_bin10.pha 459_meg_m1_bin10.pha 459_meg_p1_bin10.pha gARFs: 459_heg_m1.arf 459_heg_p1.arf 459_meg_m1.arf 459_meg_p1.arf
The spectra used in the fitting session were binned by a factor of 10. The data files are available in sherpa.tar.gz, as explained in the Sherpa Getting Started thread.
Defining the Instrument Response for the Simulation
Armed with a source model expression resulting from a satisfactory fit to the ACIS-S/HETG data, we may begin the simulation process by establishing the instrument response corresponding to the default pointing of the ACIS-S detector, using the ACIS-S/LETG grating ARF and RMF files retrieved from the CalDB website:
sherpa> arf1 = unpack_arf("aciss_leg1_cy21.garf") sherpa> arf2 = unpack_arf("aciss_leg-1_cy21.garf") sherpa> print(arf1) name = aciss_leg1_cy21.garf energ_lo = Float64 energ_hi = Float64 specresp = Float64 bin_lo = Float64 bin_hi = Float64 exposure = 28398.4546994 ethresh = 1e-10 sherpa> print(arf2) name = aciss_leg-1_cy21.garf energ_lo = Float64 energ_hi = Float64 specresp = Float64 bin_lo = Float64 bin_hi = Float64 exposure = 28398.4896985 ethresh = 1e-10 sherpa> rmf1 = unpack_rmf("aciss_leg1_cy21.grmf") sherpa> rmf2 = unpack_rmf("aciss_leg-1_cy21.grmf") sherpa> print(rmf1) name = aciss_leg-1_cy21.grmf detchans = 8192 energ_lo = Float64 energ_hi = Float64 n_grp = UInt64 f_chan = UInt32 n_chan = UInt32 matrix = Float64 offset = 1 e_min = Float64 e_max = Float64 ethresh = 1e-10 sherpa> print(rmf2) name = aciss_leg-1_cy21.grmf detchans = 8192 energ_lo = Float64 energ_hi = Float64 n_grp = UInt64 f_chan = UInt32 n_chan = UInt32 matrix = Float64 offset = 1 e_min = Float64 e_max = Float64 ethresh = 1e-10
Here, the ARF and RMF data are loaded and assigned to a set of variables with the unpack_arf and unpack_rmf commands. These variables will be used to assign the instrument response to the faked data sets we will create in the next section, "Running the Simulation with fake_pha."
Establishing the Source Model Expression for the Simulation
The fake_pha command has four required arguments: data set ID, ARF, RMF, and exposure time. In this thread, we simulate a LETG spectrum with the source model parameter values resulting from a fit to a HETG grating spectrum. The detailed steps taken to establish this model can be found here, and include:
- defining the instrument response for the real data
- filtering the data
- defining the source and background models
- examining method & statistic settings
- examining fit results
This saved Sherpa session, including all defined data sets, models, and instrument responses, may be restored with the Sherpa restore command, as follows:
If restore fails to load the state file, due to version incompatibility, the source model defined in the file can be loaded into Sherpa:
sherpa> set_source(1, atten.abs1 * bpl1d.bpow1) sherpa> abs1.hcol = 1.81e+20 sherpa> abs1.heiRatio = 0.1 sherpa> abs1.heiiRatio = 0.01 sherpa> bpow1.gamma1 = 0.424711 sherpa> bpow1.gamma2 = 0.0496577 sherpa> bpow1.eb = 10.62 sherpa> bpow1.ref = 1 sherpa> bpow1.ampl = 0.00548927 sherpa> freeze(abs1)
Since we want to run the simulation using the source model tailored to the ACIS-S/HETG data, we use the set_source command to assign this source model expression to each of the LEG orders, as well as name the corresponding faked data sets which will be produced in our simulation.
The following steps assume that the ACIS-S/HETG spectral orders correspond to data set IDs 1 through 4 in the saved state file.
sherpa> show_source(1) Model: 1 (atten.abs1 * bpl1d.bpow1) Param Type Value Min Max Units ----- ---- ----- --- --- ----- abs1.hcol frozen 1.81e+20 1e+17 1e+24 abs1.heiRatio frozen 0.1 0 1 abs1.heiiRatio frozen 0.01 0 1 bpow1.gamma1 thawed 0.424711 -10 10 bpow1.gamma2 thawed 0.0496577 -10 10 bpow1.eb thawed 10.62 0 1000 bpow1.ref frozen 1 -3.40282e+38 3.40282e+38 bpow1.ampl thawed 0.00548927 1e-20 3.40282e+38 sherpa> set_source("faked_leg1", get_source(1)) sherpa> set_source("faked_leg-1", get_source(1))
Running the Simulation with fake_pha
Simulating the Chandra ACIS-S/LETG spectra means taking the model expression defined for the ACIS-S/HETG data, folding it through the Chandra ACIS-S/LETG response, and applying Poisson noise to the counts predicted by the model. The simulation is run with fake_pha, which has four required arguments: data set ID, ARF, RMF, and exposure time. In this thread, we will simulate ACIS-S/LETG spectra using the gARF and gRMF files downloaded from the CalDB website, a source model tailored to the ACIS-S/HETG data, and an exposure time of 50 ks.
We are now ready to run the simulations with fake_pha:
sherpa> fake_pha("faked_leg1", arf1, rmf1, exposure=50000) sherpa> fake_pha("faked_leg-1", arf2, rmf2, exposure=50000)
These commands associate the data IDs "faked_leg1" and "faked_leg-1" with simulated source data sets for the +1 and -l ACIS-S/LETG orders, respectively, based on the assumed exposure time, instrument responses, and source model expression; Poisson noise is added to the modeled data.
Note that as of Sherpa in CIAO 4.7 the WARNING message is printed out when the previously saved sherpa session is being used.
Note that we could have said the following instead:
sherpa> fake_pha("faked_leg1", arf="aciss_leg1_cy21.garf", rmf="aciss_leg1_cy21.grmf", exposure=50000) sherpa> fake_pha("faked_leg-1", arf="aciss_leg-1_cy21.garf", rmf="aciss_leg-1_cy21.grmf", exposure=50000)
For detailed information on the available options for setting the 'arf' and 'rmf' arguments of fake_pha, refer to the fake_pha ahelp file.
We may inspect some basic properties of the new data sets with the show_data command; e.g.,:
sherpa> show_data("faked_leg1") Data Set: faked_leg1 Filter: 0.1199-12.3219 Energy (keV) Noticed Channels: 1-8192 name = faked channel = Float64 counts = Float64 staterror = None syserror = None bin_lo = None bin_hi = None grouping = None quality = None exposure = 50000 backscal = None areascal = None grouped = False subtracted = False units = energy rate = True plot_fac = 0 response_ids =  background_ids =  RMF Data Set: faked_leg1:1 name = aciss_leg1_cy21.grmf detchans = 8192 energ_lo = Float64 energ_hi = Float64 n_grp = UInt64 f_chan = UInt32 n_chan = UInt32 matrix = Float64 offset = 1 e_min = Float64 e_max = Float64 ethresh = 1e-10 ARF Data Set: faked_leg1:1 name = aciss_leg1_cy21.garf energ_lo = Float64 energ_hi = Float64 specresp = Float64 bin_lo = Float64 bin_hi = Float64 exposure = 28398.4546994 ethresh = 1e-10
Note that had we not applied a previously defined, properly normalized source model expression to the faked data, we would have had to re-normalize the simulated data to match the flux (or counts) required by the real source data. This process is illustrated in the threads "Simulating Chandra ACIS-S Spectra with Sherpa" and "Simulating 1-D Data: the Sherpa FAKE_PHA Command."
Writing the Simulated Data to Output Files
We may use the save_pha command to write the simulated data as a PHA file, with a header containing the exposure time value and paths to the ARF and RMF files:
There is also an option to save the data to an ASCII file:
Fitting the Simulated Data
The simulated data set may be filtered and fit as any other data set in Sherpa.
sherpa> set_analysis("wave") sherpa> ignore() sherpa> notice(5., 11.) sherpa> show_filter() Data Set Filter: faked_leg-1 4.9937-10.9937 Wavelength (Angstrom) Data Set Filter: faked_leg1 4.9937-10.9937 Wavelength (Angstrom)
Then, we can fit the simulated data with the source model expression we used to create it:
sherpa> set_method("neldermead") sherpa> set_stat("chi2datavar") sherpa> fit("faked_leg1", "faked_leg-1") Datasets = 'faked_leg-1', 'faked_leg1' Method = neldermead Statistic = chi2datavar Initial fit statistic = 13238.5 Final fit statistic = 956.339 at function evaluation 556 Data points = 962 Degrees of freedom = 958 Probability [Q-value] = 0.509069 Reduced statistic = 0.998266 Change in statistic = 12282.2 bpow1.gamma1 1.47627 bpow1.gamma2 1.36488 bpow1.eb 10.0355 bpow1.ampl 0.0212984 sherpa> plot("fit","faked_leg1","fit","faked_leg-1")
The resulting plot is shown in Figure 1.
Figure 1: Plot of fit to simulated ACIS-S/LETG source spectra
sherpa> conf("faked_leg1", "faked_leg-1") bpow1.ampl lower bound: -0.000301301 bpow1.eb lower bound: ----- bpow1.gamma2 lower bound: ----- bpow1.gamma1 lower bound: -0.0253374 bpow1.eb upper bound: ----- bpow1.gamma2 upper bound: ----- bpow1.gamma1 upper bound: 0.0254042 bpow1.ampl upper bound: 0.000304188 Datasets = 'faked_leg1', 'faked_leg-1' Confidence Method = confidence Iterative Fit Method = None Fitting Method = neldermead Statistic = chi2datavar confidence 1-sigma (68.2689%) bounds: Param Best-Fit Lower Bound Upper Bound ----- -------- ----------- ----------- bpow1.gamma1 1.47627 -0.0253374 0.0254042 bpow1.gamma2 1.36488 ----- ----- bpow1.eb 10.0355 ----- ----- bpow1.ampl 0.0212984 -0.000301301 0.000304188 sherpa> show_fit() Optimization Method: NelderMead name = simplex ftol = 1.19209289551e-07 maxfev = None initsimplex = 0 finalsimplex = 9 step = None iquad = 1 verbose = 0 Statistic: Chi2DataVar Chi Squared with data variance. The variance in each bin is estimated from the data value in that bin. If the number of counts in each bin is large, then the shape of the Poisson distribution from which the counts are sampled tends asymptotically towards that of a Gaussian distribution, with variance sigma(i)^2 = N(i,S) + [A(S)/A(B)]^2 N(i,B) where N is the number of on-source (and off-source) bins included in the fit. The background term appears only if an estimate of the background has been subtracted from the data. See Also -------- Chi2Gehrels, Chi2ModVar, Chi2XspecVar Fit:Datasets = 'faked_leg-1', 'faked_leg1' Method = neldermead Statistic = chi2datavar Initial fit statistic = 13238.5 Final fit statistic = 956.339 at function evaluation 556 Data points = 962 Degrees of freedom = 958 Probability [Q-value] = 0.509069 Reduced statistic = 0.998266 Change in statistic = 12282.2 bpow1.gamma1 1.47627 bpow1.gamma2 1.36488 bpow1.eb 10.0355 bpow1.ampl 0.0212984 sherpa> print(get_conf_results()) datasets = ('faked_leg1', 'faked_leg-1') methodname = confidence iterfitname = none fitname = neldermead statname = chi2datavar sigma = 1 percent = 68.2689492137 parnames = ('bpow1.gamma1', 'bpow1.gamma2', 'bpow1.eb', 'bpow1.ampl') parvals = (1.4762746856552618, 1.3648834135674637, 10.035541125876929, 0.021298380827865157) parmins = (-0.025337403224972688, None, None, -0.00030130089500429724) parmaxes = (0.02540421685552019, None, None, 0.00030418830039797423) nfits = 72
We can group the data so that each bin contains a specified minimum number of counts, and then change the fit statistic to something more suitable to calculate the errors. Finally, we can view the results of the new fit with the plot_fit_delchi command:
sherpa> group_counts("faked_leg1", 15) sherpa> group_counts("faked_leg-1", 15) sherpa> plot_fit_delchi("faked_leg1") sherpa> plot_fit_delchi("faked_leg-1")
Figure 2: Plot of fit to simulated ACIS-S/LETG +1 order spectrum, with residuals
Figure 3: Plot of fit to simulated ACIS-S/LETG -1 order spectrum, with residuals
The plots may be saved as PostScript files accordingly:
sherpa> plot_fit_delchi("faked_leg1") sherpa> plt.savefig("sim_fit_p1.ps") sherpa> plot_fit_delchi("faked_leg-1") sherpa> plt.savefig("sim_fit_m1.ps")
The file fit.py is a Python script which performs the primary commands used above; it can be executed by typing %run -i fit.py on the Sherpa command line.
The Sherpa script command may be used to save everything typed on the command line in a Sherpa session:
sherpa> script(filename="sherpa.log", clobber=False)
(Note that restoring a Sherpa session from such a file could be problematic since it may include syntax errors, unwanted fitting trials, et cetera.)
|02 Apr 2009||Created for CIAO/Sherpa 4.1|
|28 Apr 2009||replaced use of atten model with Sherpa user model "atten_wave"; new script command is available with CIAO 4.1.2|
|13 Jan 2010||updated for CIAO 4.2; new calibration response files used in simulation|
|13 Jul 2010||updated for CIAO 4.2 Sherpa v2: removal of S-Lang version of thread.|
|15 Dec 2011||reviewed for CIAO 4.4: a work-around for a save_pha bug was added; response files used in simulations were updated for Chandra proposal cycle 13|
|13 Dec 2012||reviewed for CIAO 4.5: group commands no longer clear the existing data filter|
|12 Dec 2013||reviewed for CIAO 4.6: fixed typos, updated calibration files, show restore warning messages.|
|03 Mar 2014||updated for Chandra proposal cycle 16|
|30 Jan 2015||updated for Chandra proposal cycle 17|
|15 Dec 2015||updated for Chandra proposal cycle 18|
|06 Dec 2016||updated for Chandra proposal cycle 19; include defining source model found in the restored state file, that would fail to load in newer versions of Sherpa.|
|24 Apr 2018||updated for CIAO 4.10, no new content.|
|19 Mar 2019||updated for CIAO 4.11, fits revised.|
|11 Dec 2019||Updated for CIAO 4.12 by replacing print_window calls with the equivalent Matplotlib command plt.savefig.|