Calculating K-corrections using Sherpa
Sherpa Threads (CIAO 4.6 Sherpa v1)
Overview
Synopsis:
In this thread we demonstrate the use of the Sherpa calc_kcorr function to calculate K-corrections for any of the spectral models available from Sherpa. As an example, we calculate the corrections necessary for the flux measured in the 0.5-2.0 keV energy range from a thermal plasma (as described by the Mewe-Kaastra-Liedahl - aka MEKAL - model) for a range of redshifts and gas temperatures. The aim is to emulate the figure presented in Appendix B of Jones et al. 1998, ApJ, 495, 100-114.
Purpose:
Related Links:
- Appendix B of Jones et al. 1998, ApJ, 495, 100-114 compares the K-corrections for different temperatures of an optically thin thermal MEKAL model.
- The K correction by Hogg et al. is a short pedagogical paper which discusses the K correction (it discusses optical magnitudes rather than X-ray fluxes but the principles are the same).
- A large number of other papers discuss the topic of K-corrections; for instance Section IIa of Yoshii & Takahara, ApJ, 1988, 326, 1, Poggianti, A&AS, 1997, 122, 399, Sandage's "The Deep Universe" Lecture Notes and references therein.
Last Update: 5 Dec 2013 - updated for CIAO 4.6: plots and calculated results updated, updated Python syntax.
Contents
- Getting started: setting up the spectral model
- Evaluating the model
- Calculating the K-correction
- Changing the model parameters
- Caveats
- Scripting It
- History
- Images
Getting started: setting up the spectral model
In order to calculate the K-correction of a model in Sherpa, we simply define the model using the set_source command, assign it to a Sherpa dataset ID (even if we are not interested in fitting the model to a data spectrum), and then specify, with the calc_kcorr function, our desired redshift and energy range for this model.
In the following example, we use the Mewe-Kaastra-Liedahl thermal plasma model from the XSPEC library (xsmekal), setting the plasma temperature to 7 keV and the metal abundance to 0.3 times the cosmic abundance.
sherpa> set_source(xsmekal.plasma) sherpa> plasma.kt = 7 sherpa> plasma.abundanc = 0.3
Since we are interested only in the ratio of the fluxes within two passbands, the value of the model normalization is not important; however, it is important that the redshift be left at the default (frozen) value of 0, and not changed to the value of the source of interest. Note that the Sherpa command show_source may be used to examine the model parameter settings, but not until the model has been assigned to a Sherpa data set ID, as shown in the next section.
Evaluating the model
To calculate the K-correction, we need to access the model spectrum — i.e., the flux in units of ergs cm^{-2}s^{-1} for each energy bin.
Since we are interested in the unconvolved model spectrum, we do not need to establish an instrument response model (i.e., supply an ARF or RMF). While it is possible to use the calc_kcorr() command with a convolved model, it will only work if the associated responses covers the required energy range — the observed range multiplied by (1.0+z_{max}), which may not be the case if using broad energy bands, such as 2-10 keV.
1. Defining the energy grid of the model
Since we are not fitting the model to a source data spectrum, Sherpa does not know what energy grid over which to calculate the model. We therefore make use of the dataspace1d command to create a blank data set with the desired grid. It is important to ensure that the energy grid covers both the observed and rest-frame energy bands.
For the rest-frame energy range (0.5-2.0 keV) and redshift range (0-2) considered in this example, we need to ensure that the model is evaluated over at least 0.5 to 4.0 keV. It does not matter if the energy range is larger than that, so we choose 0.1 to 10 keV, with a grid spacing of 0.01 keV:
sherpa> dataspace1d(0.1, 10, 0.01) sherpa> show_data() Data Set: 1 Filter: 0.1050-9.9950 x name = dataspace1d xlo = Float64[990] xhi = Float64[990] y = Float64[990] staterror = None syserror = None
2. Displaying the model
Now that our model (with default model ID "1") is associated with a data set (data set ID "1") - the blank data set created with the dataspace1d command - we may use the show_source command to examine the model parameter settings:
sherpa> show_source() Model: 1 xsmekal.plasma Param Type Value Min Max Units ----- ---- ----- --- --- ----- plasma.kT thawed 7 0.0808 79.9 keV plasma.nH frozen 1 1e-05 1e+19 cm-3 plasma.Abundanc frozen 0.3 0 1000 plasma.redshift frozen 0 0 10 plasma.switch frozen 1 0 1 plasma.norm thawed 1 0 1e+24
The Sherpa plot_source command may be used to display the unconvolved model amplitudes in photons/cm^{2}/s, and the appropriate ChIPS commands for setting the axis scale, axis limits, axis labels, and title of the resulting plot, as shown below:
sherpa> plot_source() sherpa> log_scale() sherpa> limits(X_AXIS, 0.08, AUTO) sherpa> set_plot_xlabel("Energy (keV)") sherpa> set_plot_ylabel("Spectrum (photon/cm^2/s)") sherpa> set_plot_title("XSMEKAL model: kT = 7 keV, Abundance = 0.3")
Figure 1 shows the resulting plot.
Here we have used the log_scale command to set both the x- and y-axes to a logarithmic scale, and the limits command to set the minimum energy value on the x-axis to 0.08 keV.
Calculating the K-correction
Sherpa includes the calc_kcorr() function for calculating the K-correction for a given spectral model, redshift, and pair of energy passbands. Below we show how to use this function, and then discuss how the function works.
Using calc_kcorr()
Now that we have defined the source model spectrum, we can use the calc_kcorr() function to calculate the K-correction. To calculate the K-correction for an object at redshift 0.4, using the model assigned to (blank) data set 1, we would do:
sherpa> calc_kcorr(0.4, 0.5, 2.0, id=1) 0.84275326187162003
This command returns the K-correction for a flux measured in the observed 0.5-2.0 keV energy band, in order to get the flux in the rest-frame 0.5-2.0 keV band for an object at a redshift of 0.4. If you want to convert to a different rest-frame energy band, simply supply the band as extra parameters, as shown below for the rest-frame 0.1-2.4 keV energy range.
sherpa> calc_kcorr(0.4, 0.5, 2.0, 0.1, 2.4, id=1) 1.3534834855510445
Instead of a single (i.e. scalar) value for the redshift, a one-dimensional array can be supplied, containing a range of redshifts. Here we calculate the correction values for the redshift range 0-2 with a step size of 0.1 (using the Numpy 'arange' function), and then plot redshift versus K-correction:
sherpa> z = np.arange(0.0, 2.1, 0.1) sherpa> kc = calc_kcorr(z, 0.5, 2.0, id=1) sherpa> clear() sherpa> add_histogram(z, kc) sherpa> limits(X_AXIS, 0, 2) sherpa> set_plot_xlabel("Redshift") sherpa> set_plot_ylabel("K-correction") sherpa> set_plot_title("XSMEKAL model: kT = 7 keV, Abundance = 0.3")
Figure 2 shows the resulting plot.
How calc_kcorr() works
The K-correction is calculated as the ratio of the flux in the rest-frame energy band to that in the observed band (for instance, see Appendix B of Jones et al. 1998, ApJ, 495, 100-114). If we denote the low and high energies of the rest-frame band as elo and ehi, then for a source at redshift z, the flux within the observed band would be as follows:
- observed band: elo*(1+z) to ehi*(1_z)
- rest-frame band: elo to ehi
The Sherpa calc_energy_flux command is used to compute the unconvolved model energy flux within the desired energy range, in units of ergs/cm^{2}/sec:
sherpa> z = 0.4 sherpa> rest_flux = calc_energy_flux(0.5, 2., id=1) sherpa> obs_flux = calc_energy_flux(0.5*(1+z), 2.*(1+z), id=1) sherpa> rest_flux 5.6190415962230666e-10 sherpa> obs_flux 6.6674812788550647e-10 sherpa> kcorr = rest_flux / obs_flux sherpa> kcorr 0.84275326187162003
The calc_energy_flux() function returns the source flux within the rest-frame 0.5-2.0 keV range and the observed 0.7-2.8 (0.5*1.4 - 2.0*1.4) keV range; dividing the two values gives the K-correction for this spectral model, redshift, and energy range.
Displaying the models being evaluated
Here we demonstrate how to use the Sherpa get_model_plot function to read the model amplitudes into Python variables and then display them with ChIPS plotting commands (type "get*?" at the Sherpa prompt for the full list of Sherpa get commands). We evaluate the model over both the observed and rest-frame 0.5-2.0 keV energy ranges by defining the appropriate energy grids with the dataspace1d command, and then plot the resulting models together in one frame.
sherpa> # Define energy grids over which to evaluate the model: sherpa> # rest-frame energy range sherpa> dataspace1d(0.5, 2.0, 0.01, id=2) sherpa> # observed energy range sherpa> dataspace1d(0.7, 2.8, 0.01, id=3) sherpa> Evaluate the model over the defined energy grids sherpa> by assigning it to the blank data sets 2 and 3 sherpa> set_source(2, plasma) sherpa> set_source(3, plasma) sherpa> # Retrieve the model amplitudes: sherpa> rest_dep = get_model_plot(2).y sherpa> obs_dep = get_model_plot(3).y sherpa> print(rest) sherpa> print(obs) sherpa> # Retrieve the energy axis information sherpa> rest_indep = get_model_plot(2).x sherpa> obs_indep = get_model_plot(3).x sherpa> print(rest_indep) sherpa> print(obs_indep) sherpa> # Display the two energy ranges (with a slight offset in y): sherpa> clear() sherpa> add_histogram(rest_indep, rest_dep*0.8) sherpa> set_histogram(["line.color", "red"]) sherpa> add_histogram(obs_indep, obs_dep*1.2) sherpa> set_histogram(["line.color", "green"]) sherpa> #Customize the plot: sherpa> limits(X_AXIS, 0.4, 3.0) sherpa> limits(Y_AXIS, AUTO, 0.006) sherpa> log_scale(Y_AXIS) sherpa> set_plot_xlabel("Energy (keV)") sherpa> set_plot_ylabel("Flux") sherpa> set_plot_title("XSMEKAL model: kT = 7 keV, Abundance = 0.3")
Figure 3 shows the resulting plot, with the models offset for display purposes.
Changing the model parameters
In this section we show how calc_kcorr() can be used to generate K-corrections for a range of values of a given model parameter (here the plasma temperature). The aim is to emulate Figure 7 of Jones et al. 1998, ApJ, 495, 100-114. We therefore calculate the corrections for plasma temperatures of 1, 2, 4, and 10 keV using the following commands, which are available as a Sherpa Python script (plot_kcorrs.py):
#Clear existing data and model definitions in the current Sherpa session: clean() #Define the range of redshifts in which we are interested (here using the Numpy 'arange' function): z = np.arange(0.0, 2.01, 0.01) #Define an energy grid which covers at least 0.5-2.0 keV for the redshift range z = 0 to 2: elo = 0.5 ehi = 2.0 dataspace1d(0.1, 7.0, 0.01, id=1) #Define the model: set_source(xsmekal.plasma) plasma.abundanc = 0.3 #Calculate the K-correction for a 1 keV plasma model: plasma.kt = 1 k1 = calc_kcorr(z, elo, ehi, id=1) #Calculate the K-correction for a 2 keV plasma model: plasma.kt = 2 k2 = calc_kcorr(z, elo, ehi, id=1) #Calculate the K-correction for a 4 keV plasma model: plasma.kt = 4 k4 = calc_kcorr(z, elo, ehi, id=1) #Calculate the K-correction for a 10 keV plasma model: plasma.kt = 10 k10 = calc_kcorr(z, elo, ehi, id=1) #Calculate the analytic solution using a power law #(using the numpy Python package for mathematical operations on arrays): z = np.array(z) kpl = 1./np.sqrt(1+z) #Plot the model curves: clear() add_curve(z, k1) add_curve(z, k2) add_curve(z, k4) add_curve(z, k10) current_curve("all") set_curve(["symbol.style", "none"]) add_curve(z, kpl) set_curve(["symbol.style", "none"]) set_curve(["line.style", "shortdash"]) set_curve(["line.color","red"]) set_plot_xlabel("Redshift") set_plot_ylabel("K_{0.5-2.0 keV}") set_plot_title("xsmekal model, abundance = 0.3 solar") limits(X_AXIS, 0, 2) limits(Y_AXIS, 0, 3) add_label(1.2, 2.0, "kT = 1 keV") add_label(1.2, 1.3, "kT = 2 keV") add_label(1.5, 0.9, "kT = 4 keV") add_label(1.0, 0.5, "kT = 10 keV") print_window("plasmakT_kcorr.png") save("sherpa_plot_session.save") #finished quit()
Figure 4 shows the resulting plot, which can be compared to Figure 7 of Jones et al. (1998).
Caveats
1. Accuracy
The accuracy of the K-correction is determined by the width of the energy bins. We shall illustrate this by using the xspowerlaw model, for which an analytic solution for the K-correction exists: for a photon index of Γ, the K-correction is given by k(z) = (1+z)^{Γ-2}. Below we calculate the corrections for two bin widths — 0.1 and 0.01 keV — and compare them to the analytic solution.
#Clear existing data and model definitions in the current Sherpa session: sherpa> clean() # Define a power law model: sherpa> set_source(xspowerlaw.p1) sherpa> p1.phoindex = 3 #Define the redshift range and the analytic solutions: sherpa> z = [0, 0.2, 0.4, 0.6, 0.8, 1] sherpa> z = np.array(z) sherpa> kz = np.power((1+z),(3-2)) #Calculate the K-correction for the model evaluated over two different energy grids: sherpa> dataspace1d(0.1, 10, 0.1, id=1) sherpa> kz1 = calc_kcorr(z, 0.5, 2.0, id=1) sherpa> set_source(2, p1) sherpa> dataspace1d(0.1, 10, 0.01, id=2) sherpa> kz2 = calc_kcorr(z, 0.5, 2.0, id=2) #Write the results to file with the write_arrays routine available in the crates_contrib module of the CIAO contributed scripts package. (Note that the Sherpa command save_arrays may also be used, however it does not allow the user to specify the Python string format in which the data values should be written to file, as write_arrays does). sherpa> from crates_contrib.utils import * sherpa> write_arrays("out.dat", [z, kz, kz1, kz2], format='{:.5g}') sherpa> !more out.dat 0 1 1 1 0.2 1.2 1.2046 1.2003 0.4 1.4 1.409 1.4007 0.6 1.6 1.6133 1.601 0.8 1.8 1.8176 1.8014 1 2 2.0218 2.0017
The output columns list the redshift, analytic solution, then the values calculated by calc_kcorr() for the two bin widths (0.1 and then 0.01 keV). As can be seen, the smaller grid spacing produces results closer to the true value. The choice of grid spacing depends on the model(s) used and the desired accuracy: for instance, in this example the error introduced by using a bin width of 0.1 keV is likely to be much smaller than the error on the measured flux of the source or uncertainties in the model parameters used to calculate the K-correction.
Scripting It
The file fit.py is a Python script which performs the primary commands used above; it can be executed by typing execfile("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, etcetera.)
The CXC is committed to helping Sherpa users transition to new syntax as smoothly as possible. If you have existing Sherpa scripts or save files, submit them to us via the CXC Helpdesk and we will provide the CIAO/Sherpa 4.6 syntax to you.
History
14 Dec 2004 | updated for CIAO 3.2: script version and path |
21 Dec 2005 | reviewed for CIAO 3.3: no changes |
01 Dec 2006 | reviewed for CIAO 3.4: no changes |
16 Aug 2010 | Sherpa commands and ChIPS plots updated for CIAO 4.2 |
05 Dec 2013 | updated for CIAO 4.6: plots and calculated results updated, updated Python syntax. |