Requirements

• Nuskybgd interacts with Xspec via PyXspec; you must install HEASOFT from source to use PyXspec.

  Download HEASOFT

• You need a Python 3 (3.6 or newer) environment.

• We recommend installing nuskybgd in its own virtual environment (i.e., using a "miniconda" installation).

• The build instructions for pyXspec can be found here. Please build and confirm that pyXspec is working first before attempting to install nuskybgd.

Notes and attribution

• Based on the IDL implementation of nuskybgd.

• This has been forked from the original repository from achronal.

• The original paper citation for nuskybgd is Wik et al., 2014. If you use nuskybgd in your work, please cite this paper.

Contributing and Support

If you'd like to say hello, drop onto the NuSTAR Slack channel from the NuSTAR Observer's page.

Please feel free to report issues and/or code pull requests.

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Installation

1. Environment variables

These standard HEASARC environment variables must be set up before anything else. Modify the paths to point to the correct location on your machine.

# bash, zsh example

# HEASARC CALDB
export CALDB=/soft/astro/heasarc/CALDB

2. Create a new environement for nuskybgd, using python 3.7

create create --name nuskybgd-py py=3.7
conda activate nuskybgd-py

2. Install the python dependencies for nuskybgd

cd ~/git/nuskybgd-py
pip install -r requirements.txt

3. Build and install nuskybgd

cd ~/git/nuskbygd-py
pip install -e .

nuskybgd is now callable from the command line in your python shell. While nuskybgd-py is a python repo, we typically recommend calling the various routines from the command line for simplicity.

You are now ready to run nuskybgd!

Below is the original QuickStart guide from achronal. elow consists of achronal's original quickstart guide for setting up the environment. An additional practical example can be found from bwgref here.

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Quickstart Guide

1. Before you begin:

Assuming you have the 'default' layout for files, e.g. cleaned event files are in [target name]/[obs id]/event_cl, the examples below puts background modelling related files in a folder named bgd inside event_cl.

Create the bgd/ folder if this is the first time.

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2. Preparations

2.1 Make an image

Use mkimgs.py to create a counts image for WCS reference.

# (cd into the top level)
./mkimgs.py ./ 50002031004 3 20

This creates the file imA3to20keV.fits and imB3to20keV.fits, which are counts images between 3-20 keV seen by each detector module. These images are used later for their WCS information. All subsequent image products are projections onto the same WCS grid as these.

2.2 Extract spectra from background regions

Note about regions

Region masking is handled by pyregion. If in doubt, test whether your region results in the mask as expected, directly with pyregion.

In general:

The mask is created by rendering each entry in the region file in sequence, changing pixels to 1 for an include region or changing pixels to 0 for an exclude region. Therefore, order matters! The final value in a given pixel depends on the last region that covers it.

Is this behaviour the same in all software? I would not bet on it. It is particularly ambiguous if you are just looking at the regions in DS9, as to whether the include or exclude region takes precedence. To be completely safe, create regions such that all exclude regions come after all include regions.

The same consideration should be given to region type. Stick to circle, box, and ellipse to be safe.

Create some background regions and extract spectra from both A and B modules, e.g. I selected three background regions in DS9 and saved them in ds9 fk5 format, bgd1.reg, bgd2.reg, and bgd3.reg.

# New syntax for getspecnoarf.py
# In event_cl/
getspecnoarf.py nu90201039002A01_cl.evt reg=bgd/bgd1.reg \
    indir=. outdir=bgd outprefix=bgd1A \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd1A.log

getspecnoarf.py nu90201039002A01_cl.evt reg=bgd/bgd2.reg \
    indir=. outdir=bgd outprefix=bgd2A \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd2A.log

getspecnoarf.py nu90201039002A01_cl.evt reg=bgd/bgd3.reg \
    indir=. outdir=bgd outprefix=bgd3A \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd3A.log

getspecnoarf.py nu90201039002B01_cl.evt reg=bgd/bgd1.reg \
    indir=. outdir=bgd outprefix=bgd1B \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd1B.log

getspecnoarf.py nu90201039002B01_cl.evt reg=bgd/bgd2.reg \
    indir=. outdir=bgd outprefix=bgd2B \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd2B.log

getspecnoarf.py nu90201039002B01_cl.evt reg=bgd/bgd3.reg \
    indir=. outdir=bgd outprefix=bgd3B \
    attfile=../auxil/nu90201039002_att.fits.gz >& bgd/bgd3B.log

This creates spectral product files, among which are the ungrouped PI spectra files named like bgd1A_sr.pha, grouped spectra files bgd1A_sr_g30.pha, and the response matrix file bgd1A_sr.rmf. We will use these files for the next step.

Extract the spectrum of an extended source in the aperture defined by src.reg.

# In event_cl/
mkdir spec

getspecnoarf.py nu90201039002A01_cl.evt reg=src1.reg \
    indir=. outdir=spec outprefix=src1A \
    attfile=../auxil/nu90201039002_att.fits.gz >& spec/src1A.log

getspecnoarf.py nu90201039002B01_cl.evt reg=src.reg \
    indir=. outdir=spec outprefix=src1B \
    attfile=../auxil/nu90201039002_att.fits.gz >& spec/src1B.log

Fix the spectral products' RESPFILE keywords (optional)

Spectral products from the old version of getspecnoarf.py wrote relative paths in the RESPFILE keyword of the PHA file, so that the latter must be loaded from the same relative path for XSPEC to find the RMF file. You can fix the RESPFILE keyword in the PHA files to remove the directory name, which lets you load the spectrum when working in the same directory as it.

# In event_cl/ or where the spectral files are
find . -iname "*.pha" -type f -exec phafix.py {} \;

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3. Create and fit the background model

3.1 Instrument maps

Create image masks for the detectors. Do this for each module, nu*A01_cl.evt and nu*B01_cl.evt.

Command line:

# In event_cl/

nuskybgd mkinstrmap nu90201039002A01_cl.evt

nuskybgd mkinstrmap nu90201039002B01_cl.evt

Python:

from nuskybgd.cli import mkinstrmap
mkinstrmap(['mkinstrmap', 'nu90201039002A01_cl.evt'])
mkinstrmap(['mkinstrmap', 'nu90201039002B01_cl.evt'])

This creates the files newinstrmapA.fits and newinstrmapB.fits, which are image masks for the detectors.

3.2 Aspect histogram images

Make images of the 2D histogram of the pointing position, one for each module.

Command line:

# In event_cl/

nuskybgd aspecthist nu90201039002A_det1.fits gtifile=nu90201039002A01_gti.fits \
    out=aspecthistA.fits

nuskybgd aspecthist nu90201039002B_det1.fits gtifile=nu90201039002B01_gti.fits \
    out=aspecthistB.fits

Python:

from nuskybgd.cli import aspecthist
aspecthist(['aspecthist', 'nu90201039002A_det1.fits',
    'gtifile=nu90201039002A01_gti.fits', 'out=aspecthistA.fits'])
aspecthist(['aspecthist', 'nu90201039002B_det1.fits',
    'gtifile=nu90201039002B01_gti.fits', 'out=aspecthistB.fits'])

This creates the files aspecthistA.fits and aspecthistB.fits in the directory event_cl/. They are images representing a 2D histogram in time of the pointing position.

3.3 Background aperture images

Create images of the aperture background model and detector mask convolved with the aspect. For each module, one image is created for the aperture background and four images for the detector masks.

Command line:

# In event_cl/bgd/

nuskybgd projbgd refimg=../imB3to20keV.fits out=bgdapA.fits \
	mod=A det=1234 chipmap=../newinstrmapA.fits aspect=../aspecthistA.fits

nuskybgd projbgd refimg=../imB3to20keV.fits out=bgdapB.fits \
	mod=B det=1234 chipmap=../newinstrmapB.fits aspect=../aspecthistB.fits

Python:

from nuskybgd.cli import projbgd
projbgd(['projbgd', 'refimg=../imB3to20keV.fits', 'out=bgdapA.fits',
    'mod=A', 'det=1234', 'chipmap=../newinstrmapA.fits',
    'aspect=../aspecthistA.fits'])
projbgd(['projbgd', 'refimg=../imB3to20keV.fits', 'out=bgdapB.fits',
    'mod=B', 'det=1234', 'chipmap=../newinstrmapB.fits',
    'aspect=../aspecthistB.fits'])

This creates the files bgdapA.fits and bgdapB.fits, which are the aperture background images rotated and convolved with the aspect histogram images, and det0Aim.fits, det1Aim.fits, det2Aim.fits, det3Aim.fits, det0Bim.fits, det1Bim.fits, det2Bim.fits, and det3Bim.fits, which are the detector masks rotated and convolved with the aspect histogram images. The files are in the directory event_cl/bgd/.

3.4 The background model

Run nuskybgd fit (requires PyXspec) to create an XSPEC save file bgdparams.xcm, which contains the background models with preset normalizations.

First, create a file bgdinfo.json in bgd/ with the following structure (nuskybgd fit --help will print this template). The file names for the images are default values so you may not need to modify them, but the files for the background regions need to be updated for your data. The "regfiles" list must correspond to the files in the "bgfiles" list.

The setting "fcxb_config" "links" are used to tie Xspec model parameters for the FCXB model normalization. These are comprised of a list of two values for the spectrum numbers to tie together. In the example below, all of the spectra for FPMB are tied to the spectra for identical regions from FPMA. Note that the Xspec spectrum number starts at 1. Without this setting, all of the FCXB normalizations are set to free.

{
    "bgfiles": [
        "bgd1A_sr_g30.pha", "bgd1B_sr_g30.pha",
        "bgd2A_sr_g30.pha", "bgd2B_sr_g30.pha",
        "bgd3A_sr_g30.pha", "bgd3B_sr_g30.pha"
    ],

    "regfiles": [
        "bgd1.reg", "bgd1.reg",
        "bgd2.reg", "bgd2.reg",
        "bgd3.reg", "bgd3.reg"
    ],

    "refimgf": "bgdapA.fits",

    "bgdapfiles": {
        "A": "bgdapA.fits",
        "B": "bgdapB.fits"
    },

    "bgddetfiles": {
        "A": [
            "det0Aim.fits",
            "det1Aim.fits",
            "det2Aim.fits",
            "det3Aim.fits"
        ],
        "B": [
            "det0Bim.fits",
            "det1Bim.fits",
            "det2Bim.fits",
            "det3Bim.fits"
        ]
    },

    "fcxb_config": {
        "links": [
            [1, 2],
            [3, 4],
            [5, 6]
        ]
    }
}

Then, run nuskybgd fit, directing stdout to a log file. Check the log to see if the task encountered any problems. Most of the logged output comes from Xspec.

Command line:

# In event_cl/bgd/
nuskybgd fit bgdinfo.json savefile=IC342bgd >& fit.log

Python: (Warning for interactive use: Xspec will flood the terminal with messages)

from nuskybgd.cli import fit
fit(['fit', 'bgdinfo.json', 'savefile=IC342bgd'])

After successfully running nuskybgd fit, the save file (in this case, IC342bgd.xcm) can be loaded in Xspec to recreate the same state. From there, the user can examine and tweak with the model. They can also save a modified version of it, preferably under a different name, to experiment with for the next step.

# Start xspec, then input these commands
@IC342bgd.xcm
ignore **:**-3. 150.-**
cpd /xw
setplot energy
setplot command res y 1e-4 0.04
plot ldata delchi

The generated background model then needs to be fitted to the background spectra.

The first thing the user should check is whether the preset normalizations provide a close fit to the background spectra. If the background regions do not have extended emission, the user may be able to obtain a good background model by simply running fit in Xspec.

The save file contains settings for Xspec fit equivalent to the following: statistic chi; method leven 30000 1e-4; ignore **:**-3. 150.-** The user should change this setting as required.

On the other hand, if the background regions do contain extended emission, simply running fit may not be enough, because the excess emission from the real source cannot be accounted for by the preset model components. In that case, the user must use discretion to account for the additional source(s). Due to the number of free parameters in the nuskybgd model and possible degeneracies with any added source models, it may be necessary to hand-tune the fit and not fit everything simultaneously.

Do not remove any of the nuskybgd generated models or change their names.

When the model is OK, write the current state to a save file under a different name to the nuskybgd generated save file. This save file contains model parameters for the background components. The subsequent tasks will look for these using the model component names.

# Creates a save file mymodel.xcm
save all mymodel

The saved xcm file should not contain any general XSPEC/Tcl scripts because PyXspec will not properly execute it.

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4. Applying the fitted background

4.1 Spectral analysis --- calculate the background model for a source region

To calculate the amount of background in some source region, create a region file and extract the spectrum from it. For this example, the region file is named src1.reg and the grouped spectrum file is src1_g30.pha. Use nuskybgd spec on the best fit model save file.

nuskybgd spec bgdinfo.json mymodel.xcm src1.reg src1_g30.pha

See the help message of nuskybgd spec for what it does. This step creates a new Xspec save file, bgd_src1.xcm (for custom output file name, use the optional argument savefile= to specify it.)

This save file is very similar to the input, with the addition of the source spectrum, and the background model parameter values have been calculated for the source spectrum region. The background model parameters are free, and the user can verify the quality of the background subtraction and tweak the model.

When the background model is satisfactory, create an Xspec save file with the command save all bgd_src1_mymodel and use this for the following step. Otherwise, just use the output from nuskybgd spec (as below).

nuskybgd simplify bgdinfo.json bgd_src1.xcm

This final step removes the spectra from the background regions from the saved Xspec state, leaving only the source spectrum. The background model parameters are frozen, and the user can load this save file in Xspec and proceed to adding their source model. The default output file name for the example command above is bgd_only_src1.xcm, but this can be customized using the savefile= argument.

4.2 Generate background images

Images of the model background sources can be created from the Xspec save file obtained in the previous step. For example, to generate images of the model counts between 3 and 20 keV,

nuskybgd image bgdinfo.json mymodel.xcm 3 20

This results in two files for each background source (A and B), as well as images of the FCXB in each background spectrum region.

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Add detabs to rmf

Creates det0A.rmf, det1A.rmf, etc... in bgd/

cd /Users/qw/astro/nustar/IC342_X1/90201039002/event_cl
absrmf.py nu90201039002A01_cl.evt bgd/det
absrmf.py nu90201039002B01_cl.evt bgd/det

Create fake spectra of apbgd and fcxb components

cd bgd/
imrefspec.py AB 0123