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Adds SRM model with unit handling #227

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7a2eec3
SRM model handles units
jajmitchell Aug 4, 2025
947b14f
Adds changelog
jajmitchell Aug 4, 2025
cda6f81
Fixes test_models
jajmitchell Aug 4, 2025
5c9eb2f
Import requires modules in test_models
jajmitchell Aug 4, 2025
ea38918
Fixes examples
jajmitchell Aug 4, 2025
0c3357c
Tidy comments
jajmitchell Jan 27, 2026
75a4223
Merge branch 'main' into srm-model
jajmitchell Jan 27, 2026
f38afa1
Removes astropy fitting simulated data example
jajmitchell Jan 28, 2026
a3005b8
Pre-commit
jajmitchell Jan 28, 2026
bcca308
Renames input and output units as user facing
jajmitchell Jan 28, 2026
fa249b2
Fixes Tests
jajmitchell Jan 28, 2026
f5e75b9
Fix examples for updates to sphin and docutils
samaloney Jan 29, 2026
f65c176
Pin sphinx<9 so doc build works.
samaloney Jan 30, 2026
8afdd79
Disable parallel doc build
samaloney Jan 30, 2026
b016d88
Update examples/fitting_NuSTAR_spectra-glesener2020.py
jajmitchell Jan 30, 2026
8c42844
Update examples/fitting_RHESSI_spectra.py
jajmitchell Jan 30, 2026
d336fed
updates to matrix model
settwi Jan 30, 2026
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1 change: 1 addition & 0 deletions changelog/227.feature.rst
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Adds unit handling to :class:`sunkit_spex.models.instrument_response.MatrixModel`.
30 changes: 18 additions & 12 deletions examples/fitting_NuSTAR_spectra-duncan2021.py
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Fitting NuSTAR Spectra: Duncan *et al.* 2021 comparison
=========================================================

This spectrum corresponds to the may1618 microflare in [Duncan2021]_.
This spectrum corresponds to the may1618 microflare in `Duncan2021`_.

An example of fitting multiple spectra simultaneously with 2 models where each model is allowed to vary at different times

We also allow the gain slope response parameter to vary.

.. _Duncan2021: https://iopscience.iop.org/article/10.3847/1538-4357/abca3d
"""

import warnings
Expand Down Expand Up @@ -81,6 +83,7 @@
#####################################################
#
# freeze the ones we don't want to vary

spec.params["C_spectrum1"] = {"Status": "frozen"}

#####################################################
Expand All @@ -95,6 +98,7 @@
#####################################################
#
# Fit lower energy range with the first thermal model first

spec.params["T2_spectrum1"] = "frozen"
spec.params["EM2_spectrum1"] = "frozen"
spec.energy_fitting_range = [2.5, 4]
Expand All @@ -116,6 +120,7 @@
#####################################################
#
# Need the gain slope to vary too for this microflare but only needed for the 6.7 keV line

print(spec.rParams)
spec.rParams["gain_slope_spectrum1"] = "free"
spec.rParams["gain_slope_spectrum2"] = spec.rParams["gain_slope_spectrum1"]
Expand Down Expand Up @@ -156,21 +161,17 @@
# For the 2 thermal model fitting
#
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
# | Model Parameter | XSPEC (Duncan et al. 2021) [*]_ | This Work |
# | Model Parameter | XSPEC (Duncan et al. 2021) | This Work |
# +========================================+===============================================+==========================================+
# | Temperature 1 [MK] | :math:`4.1^{+0.1}_{-0.1}` | 4.8\ |pm|\ 0.3 |
# | Temperature 1 [MK] | :math:`4.1^{+0.1}_{-0.1}` | :math:`4.8 \pm 0.3` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
# | Emission Measure 1 [cm\ :sup:`-3`] | :math:`1.4^{+0.6}_{-0.4}\times10^{47}` | 7.6 |pm| 2.4\ |x|\ 10 :sup:`46` |
# | Emission Measure 1 [cm\ :sup:`-3`] | :math:`1.4^{+0.6}_{-0.4} \times 10^{47}` | :math:`7.6 \pm 2.4 \times 10^46` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
# | Temperature 2 [MK] | :math:`10.00^{+0.03}_{-0.03}` | 10.4\ |pm|\ 0.1 |
# | Temperature 2 [MK] | :math:`10.00^{+0.03}_{-0.03}` | :math:`10.4 \pm 0.1` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
# | Emission Measure 2 [cm\ :sup:`-3`] | :math:`4.6^{+0.1}_{-0.2}\times10^{45}` | 4.3 |pm| 0.3\ |x|\ 10 :sup:`45` |
# | Emission Measure 2 [cm\ :sup:`-3`] | :math:`4.6^{+0.1}_{-0.2} \times 10^{45}` | :math:`4.3 \pm 0.3 \times 10^45` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
#
# .. |pm| replace:: :math:`\pm`
# .. |x| replace:: :math:`\times`
# .. [*] Duncan *et al.* 2021's may1618 microflare
# .. [Duncan2021] https://iopscience.iop.org/article/10.3847/1538-4357/abca3d

#####################################################
#
Expand All @@ -179,8 +180,13 @@
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
# | Model Parameter | XSPEC (Duncan et al. 2021) | This Work |
# +========================================+===============================================+==========================================+
# | Gain Slope | 0.977\ |pm|\ 0.002 | 0.978\ |pm|\ 0.001 |
# | Gain Slope | :math:`0.977 \pm 0.002` | :math:`0.978 \pm 0.001` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+
#
# .. _[Duncan2021]: https://iopscience.iop.org/article/10.3847/1538-4357/abca3d

#####################################################
# Although these values are slightly different, it is important to note that XSPEC and sunkit-spex work from different atomic databases. We also note that for a similar isothermal fit the temperature can drop/rise if the emission measure rises/drops and so fitting not just one but two of these models allows for these to vary more. We do see that this work (for this microflare) produces higher temperatures but correspondingly lower emission measures.
# Although these values are slightly different, it is important to note that XSPEC and sunkit-spex work from different
# atomic databases. We also note that for a similar isothermal fit the temperature can drop/rise if the emission measure
# rises/drops and so fitting not just one but two of these models allows for these to vary more. We do see that this
# work (for this microflare) produces higher temperatures but correspondingly lower emission measures.
31 changes: 15 additions & 16 deletions examples/fitting_NuSTAR_spectra-glesener2020.py
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Fitting NuSTAR Spectra: Glesener *et al.* 2020 comparison
=========================================================

A real example from [Glesener2020]_ of fitting two NuSTAR spectra simultaneously with gain correction.
A real example from `Glesener2020`_ of fitting two NuSTAR spectra simultaneously with gain correction.

.. _Glesener2020: https://iopscience.iop.org/article/10.3847/2041-8213/ab7341
"""

import warnings
Expand Down Expand Up @@ -198,23 +200,20 @@
# For the thermal and cold thick target total model we compare
#
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Model Parameter | OSPEX (Glesener et al. 2020) [*]_ | This Work (just FPMB) | This Work (FPMA&B) |
# | Model Parameter | OSPEX (Glesener et al. 2020) | This Work (just FPMB) | This Work (FPMA&B) |
# +========================================+===============================================+==========================================+==========================================+
# | Temperature [MK] | 10.3\ |pm|\ 0.7 | 11.3\ |pm|\ 0.7 | 11.2\ |pm|\ 0.4 |
# | Temperature [MK] | :math:`10.3 \pm 0.7` | :math:`11.3 \pm 0.7` | :math:`11.2 \pm 0.4` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Emission Measure [cm\ :sup:`-3`] | 5.0 |pm| 1.3\ |x|\ 10 :sup:`45` | 3.7 |pm| 0.9\ |x|\ 10 :sup:`45` | 3.7 |pm| 0.5\ |x|\ 10 :sup:`45` |
# | Emission Measure [cm\ :sup:`-3`] | :math:`5.0 \pm 1.3 \times 10^45` | :math:`3.7 \pm 0.9 \times 10^45` | :math:`3.7 \pm 0.5 \times 10^45` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Electron Flux [e$^{-}$ s$^{-1}$] | 2.1\ |pm|\ 1.1\ |x|\ 10 :sup:`35` | 2.2\ |pm|\ 1.1\ |x|\ 10 :sup:`35` | 1.6\ |pm|\ 0.5\ |x|\ 10 :sup:`35` |
# | Electron Flux [e$^{-}$ s$^{-1}$] | :math:`2.1 \pm 1.1 \times 10^35` | :math:`2.2 \pm 1.1 \times 10^35` | :math:`1.6 \pm 0.5 \times 10^35` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Index | 6.2\ |pm|\ 0.6 | 6.5\ |pm|\ 0.8 | 6.5\ |pm|\ 0.6 |
# | Index | :math:`6.2 \pm 0.6` | :math:`6.5 \pm 0.8` | :math:`6.5 \pm 0.6` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Low Energy Cut-off [keV] | 6.2\ |pm|\ 0.9 | 6.5\ |pm|\ 1.0 | 6.7\ |pm|\ 0.7 |
# | Low Energy Cut-off [keV] | :math:`6.2 \pm 0.9` | :math:`6.5 \pm 1.0` | :math:`6.7 \pm 0.7` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
#
# .. |pm| replace:: :math:`\pm`
# .. |x| replace:: :math:`\times`
# .. [*] Glesener *et al.* 2020
# .. [Glesener2020] https://iopscience.iop.org/article/10.3847/2041-8213/ab7341
# .. _Glesener2020: https://iopscience.iop.org/article/10.3847/2041-8213/ab7341


#####################################################
Expand Down Expand Up @@ -344,15 +343,15 @@
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Model Parameter | OSPEX (Glesener et al. 2020) | This Work (just FPMB) | This Work (FPMA&B) |
# +========================================+===============================================+==========================================+==========================================+
# | Temperature [MK] | 10.2\ |pm|\ 0.7 | 11.2\ |pm|\ 0.6 | 11.2\ |pm|\ 0.4 |
# | Temperature [MK] | :math:`10.2 \pm 0.7` | :math:`11.2 \pm 0.6` | :math:`11.2 \pm 0.4` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Plasma Density [cm\ :sup:`-3`] | 6.0 |pm| 2.0\ |x|\ 10 :sup:`9` | 5.0 |pm| 1.3\ |x|\ 10 :sup:`9` | 5.7 |pm| 1.1\ |x|\ 10 :sup:`9` |
# | Plasma Density [cm\ :sup:`-3`] | :math:`6.0 \pm 2.0 \times 10^9` | :math:`5.0 \pm 1.3 \times 10^9` | :math:`5.7 \pm 1.1 \times 10^9` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Electron Flux [e$^{-}$ s$^{-1}$] | 1.8\ |pm|\ 0.8\ |x|\ 10 :sup:`35` | 2.0\ |pm|\ 0.8\ |x|\ 10 :sup:`35` | 1.6\ |pm|\ 0.5\ |x|\ 10 :sup:`35` |
# | Electron Flux [e$^{-}$ s$^{-1}$] | :math:`1.8 \pm 0.8\times 10^35` | :math:`2.0 \pm 0.8 \times 10^35` | :math:`1.6 \pm 0.5 \times 10^35` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Index | 6.3\ |pm|\ 0.7 | 6.6\ |pm|\ 0.8 | 6.5\ |pm|\ 0.6 |
# | Index | :math:`6.3 \pm 0.7` | :math:`6.6 \pm 0.8` | :math:`6.5 \pm 0.6` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+
# | Low Energy Cut-off [keV] | 6.5\ |pm|\ 0.9 | 6.7\ |pm|\ 0.9 | 6.7\ |pm|\ 0.7 |
# | Low Energy Cut-off [keV] | :math:`6.5 \pm 0.9` | :math:`6.7 \pm 0.9` | :math:`6.7 \pm 0.7` |
# +----------------------------------------+-----------------------------------------------+------------------------------------------+------------------------------------------+

#####################################################
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19 changes: 9 additions & 10 deletions examples/fitting_NuSTAR_spectra-simultaneously.py
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Fitting NuSTAR Spectra: Simultaneous Fitting
============================================

A real example from [Cooper2021]_ of fitting two NuSTAR spectra simultaneously.
A real example from `Cooper2021`_ of fitting two NuSTAR spectra simultaneously.

.. _Cooper2021: https://academic.oup.com/mnras/article/507/3/3936/6354806
"""

import warnings
Expand Down Expand Up @@ -120,21 +122,18 @@
# Comparison
#
# +------------------------------------------+-----------------------------------------------+------------------------------------------+
# | Model Parameter | XSPEC (Cooper et al. 2021) [*]_ | This Work |
# | Model Parameter | XSPEC (Cooper et al. 2021) | This Work |
# +==========================================+===============================================+==========================================+
# | Temperature 1 [MK] | :math:`3.05^{+0.04}_{-0.35}` | 3.19\ |pm|\ 0.23 |
# | Temperature 1 [MK] | :math:`3.05^{+0.04}_{-0.35}` | :math:`3.19 \pm 0.23` |
# +------------------------------------------+-----------------------------------------------+------------------------------------------+
# | Emission Measure 1 [cm\ :sup:`-3`] | :math:`1.70^{+1.99}_{-0.08}\times10^{47}` | 1.45 |pm| 0.72\ |x|\ 10 :sup:`46` |
# | Emission Measure 1 [cm\ :sup:`-3`] | :math:`1.70^{+1.99}_{-0.08}\times10^{47}` | :math:`1.45 \pm 0.72 \times 10^46` |
# +------------------------------------------+-----------------------------------------------+------------------------------------------+
# | Temperature 2 [MK] | :math:`6.60^{+0.20}_{-0.61}` | 7.13\ |pm|\ 0.97 |
# | Temperature 2 [MK] | :math:`6.60^{+0.20}_{-0.61}` | :math:`7.13 \pm 0.97` |
# +------------------------------------------+-----------------------------------------------+------------------------------------------+
# | Emission Measure 2 [cm\ :sup:`-3`] | :math:`3.8^{+4.0}_{-0.7}\times10^{43}` | 2.80 |pm| 2.80\ |x|\ 10 :sup:`43` |
# | Emission Measure 2 [cm\ :sup:`-3`] | :math:`3.8^{+4.0}_{-0.7}\times10^{43}` | :math:`2.80 \pm 2.80 \times 10^43` |
# +------------------------------------------+-----------------------------------------------+------------------------------------------+
#
# .. |pm| replace:: :math:`\pm`
# .. |x| replace:: :math:`\times`
# .. [*] Cooper *et al.* 2021's microflare 10, pre-flare.
# .. [Cooper2021] https://academic.oup.com/mnras/article/507/3/3936/6354806
# .. _Cooper2021: https://academic.oup.com/mnras/article/507/3/3936/6354806

#####################################################
# Although these values are slightly different (almost or are within error margins), it is important to note that XSPEC and sunkit-spex work from different atomic databases. We also note that for a similar isothermal fit the temperature can drop/rise if the emission measure rises/drops and so fitting not just one but two of these models allows for these to vary more. We do see that this work (for this microflare time) produces slightly higher temperatures but correspondingly lower emission measures.
Expand Down
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