spectrum module

This module contains codes for creating spectra from the AtomDB emissivity files

The modules is separated by the type of spectrum you wish to model. For now, the CIE, NEI and PShock models are implemented.

Roughly speaking, you load a [Modelname]Session, and you can then obtain:

linelist :

list of lines in a certain wavelength interval)

line_emissivity :

the emissivity of a specific line as a function of temperature, line intensity and more.

spectrum :

the emissivity in photons cm^3 bin^-1 s^-1. This requires a response be set first

class pyatomdb.spectrum.CIESession(linefile='$ATOMDB/apec_line.fits', cocofile='$ATOMDB/apec_coco.fits', elements=False, abundset='AG89')

Bases: object

Load and generate a collisional ionization equilibrium spectrum

Parameters:

linefilestring or HDUList, optional

The line emissivity data file (either name or already open)

cocofilestring or HDUList, optional

The continuum emissivity data file (either name or already open)

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

abundsetstring

The abundance set to use. Default AG89.

Examples

Create a session instance:

>>> s=CIESession()

Set up the responses, in this case a dummy response from 0.1 to 10 keV, with area 1cm^2 in each bin

>>> ebins = numpy.linspace(0.1,10,1000)
>>> s.set_response(ebins, raw=True)

(Alternatively, for a real response file, s.set_response(rmffile, arf=arffile)

Turn on thermal broadening

>>> s.set_broadening(True)
Will thermally broaden lines with emissivity > 1.000000e-18 ph cm3 s-1

Return spectrum at 1.0keV

>>> spec = s.return_spectrum(1.0)

spec is in photons cm^5 s^-1 bin^-1; ebins are the bin edges (so spec is 1 element shorter than ebins)

Attributes:

datacachedict

Any Atomdb FITS files which have to be opened are stored here

spectraCIESpectra

Object storing the actual spectral data

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

default_abundsetstring

The abundance set used for the original emissivity file calculation

abundsetstring

The abundance set to be used for the returned spectrum

abundsetvectorarray_like(float)

The relative abundance between default_abundset and abundset for each element

response_setbool

Have we loaded a response (or set a dummy response)

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

broaden_limitfloat

Apply broadening to lines with epsilon > this value (ph cm3 s-1)

thermal_broadeningbool

Apply thermal broadening to lines (default = False)

velocity_broadeningfloat

Apply velocity broadening with this velocity (km/s). If <=0, do not apply.

format_linelist(linelist)

Print out the line list in a nice format, with all the transitions described in more detail

Parameters:

linelistnumpy.array(dtype=linelist)

The linelist returned from “return_linelist”

Returns

——-

strthe formatted linelist

return_line_emissivity(Te, Z, z1, up, lo, specunit='A', teunit='keV', apply_aeff=False, apply_abund=True, log_interp=True)

Get line emissivity as function of Te.

Parameters:

Tefloat or array(float)

Temperature(s) in keV or K

Zint

nuclear charge of element

z1int

ion charge +1 of ion

upint

upper level for transition

loint

lower level for transition

specunit{‘Angstrom’,’keV’}

Units for wavelength or energy (a returned value)

teunit{‘keV’ , ‘K’}

Units of Te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the line emissivity in the linelist to modify their intensities.

apply_abundbool

If true, apply the abundance set in the session to the result.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear. Otherwise linear

Returns:

retdict

Dictionary containing:

Te, tau, teunit : as input

wavelength : line wavelength (A)

energy : line energy (keV)

epsilon : emissivity in ph cm^3 s-1 (or ph cm^5 s^-1 if apply_aeff=True). First index is temperature, second is tau.

return_linelist(Te, specrange, specunit='A', teunit='keV', apply_aeff=False, nearest=False, apply_binwidth=False)

Get the list of line emissivities vs wavelengths

Parameters:

Tefloat

Temperature in keV or K

specrange[float, float]

Minimum and maximum values for interval in which to search

specunit{‘Angstrom’,’keV’}

Units for specrange

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the lines in the linelist to modify their intensities.

nearestbool

Return spectrum at nearest tabulated temperature, without interpolation

apply_binwidthbool

Divide the line emissivity by the width of the bin they occupy to give emissivity per angstrom or per keV.

Returns:

linelistarray(dtype)

The list of lines with lambda (A), energy (keV), epsilon (ph cm3 s-1), epsilon_aeff (ph cm5 s-1) ion (string) and upper & lower levels.

return_spectrum(te, teunit='keV', nearest=False, get_nearest_t=False, log_interp=True, dolines=True, docont=True, dopseudo=True)

Get the spectrum at an exact temperature. Interpolates between 2 neighbouring spectra

Finds HDU with kT closest to desired kT in given line or coco file.

Opens the line or coco file, and looks for the header unit with temperature closest to te. Use result as index input to make_spectrum

Parameters:

tefloat

Temperature in keV or K

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

nearestbool

If set, return the spectrum from the nearest tabulated temperature in the file, without interpolation

get_nearest_tbool

If set, and nearest set, return the nearest tabulated temperature as well as the spectrum.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid, instead of linear.

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

Returns:

spectrumarray(float)

The spectrum in photons cm^5 s^-1 bin^-1, with the response, or photons cm^3 s^-1 bin^-1 if raw is set.

nearest_Tfloat, optional

If get_nearest_t is set, return the actual temperature this corresponds to. Units are same as teunit

set_abund(elements, abund)

Set the elemental abundance, relative to the abundset. Defaults to 1.0 for everything

Parameters:

elementsint or array_like(int)

The elements to change the abundance of

abundfloat or array_like(float)

The new abundances. If only 1 value, set all elements to this abundance Otherwise, should be of same length as elements.

Returns:

None

Examples

Set the abundance of iron to 0.5

>>> myspec.set_abund(26, 0.5)

Set the abundance of iron and nickel to 0.1 and 0.2 respectively

>>> myspec.set_abund([26, 28], [0.1,0.2])

Set the abundance of oxygen, neon, magnesium and iron to 0.1

>>> myspec.set_abund([8,10,12,26],0.1)

set_abundset(abundstring=None)

Set the abundance set.

Parameters:

abundstringstring

The abundance string (e.g. “AG89”, “uniform”. Case insensitive. See atomdb.get_abundance for list of possible abundances

Returns:

none

updates self.abundset and self.abundsetvector.

set_broadening(thermal_broadening, broaden_limit=False, velocity_broadening=0.0, velocity_broadening_units='km/s', thermal_broaden_temperature=None, teunit='keV')

Turn on or off thermal broadening, and the emissivity limit for thost lines

Parameters:

thermal_broadeningbool

If true, turn on broadening. If False, turn it off.

broaden_limitfloat

The emissivity limit for lines to be broadened. If False, this value will not be updated.

velocity_broadeningfloat

velocity broadening to apply. If <=0, not applied

velocity_broadening_unitsstring

Units of velocity_broadening. ‘km/s’ is default and only value so far.

thermal_broaden_temperaturefloat

If not None, use this temperature for all line broadening instead of plasma temperature (keV)

Notes

—–

Updates attributes thermal_broadening, broaden_limit, velocity_broadening,

velocity_broadening_units

set_eebrems(do_eebrems)

Set whether to do the electron-electron bremsstrahlung in the spectrum

Parameters:

do_eebremsbool

If True, include the electron-electron bremsstrahlung calculation If False, don’t (this is default, and matches XSPEC behaviour)

set_response(rmf, arf=False, raw=False, sparse=False)

Set the response. rmf, arf can either be the filenames or the opened files (latter is faster if called repeatedly)

Amends the following items:

self.rmffilestring

The rmf file name

self.rmfstring

The response matrix

self.arffilestring

The arf file name

self.arfstring

The arf data

self.specbinsarray(float)

The spectral bins on which to calculate the spectrum (keV or A)

self.specbin_unitsstring [‘A’,’keV’]

Units of specbins

self.ebinsarray(float)

The spectral bins on which to calculate the spectrum (keV).

self.ebins_outarray(float)

The spectral bins on which to return the spectrum (keV). Can be different from specbins depending on the spectrum

self.response_setbool

A response has been loaded

self.response_typestring

‘raw’, ‘standard’ or ‘sparse’ depending on the type implemented

self.specbins_setbool

The spectral bins are set

self.ebins_checksumstring

The md5checksum of the specbins

Parameters:

rmf: string or HDUlist or array

The response matrix file or energy bins (see raw k/w)

arf: string or HDUlist

The ancillary response file

rawbool

If true, the rmf variable contains the energy bin edges (keV) for all the bins, and each bin has a perfect response. This is effectively a dummy response

sparsebool

If true, the rmf is stored as a sparse matrix and solved using sparse matrix algebra. Useful for large RMFs (e.g. XRISM). Tests show accuracy to 1 part in 10^{15}. Ignored if raw==True

Returns:

none

class pyatomdb.spectrum.CIESession_RS(oscfile='$ATOMDB/apec_osc.fits', cocofile='$ATOMDB/apec_coco.fits', elements=False, abundset='AG89')

Bases: CIESession

Load and generate a collisional ionization equilibrium spectrum

Parameters:

linefilestring or HDUList, optional

The line emissivity data file (either name or already open)

cocofilestring or HDUList, optional

The continuum emissivity data file (either name or already open)

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

abundsetstring

The abundance set to use. Default AG89.

Examples

>> import pyatomdb,atomdb

Create a session instance:

>>> cie_rs = pyatomdb.spectrum.CIESession_RS()

Set up the responses, in this case a dummy response from 0.1 to 10 keV, with area 1cm^2 in each bin

>>> ebins = numpy.linspace(0.1,10,1000)
>>> cie_rs.set_response(ebins, raw=True)

(Alternatively, for a real response file, s.set_response(rmffile, arf=arffile)

Turn on thermal broadening

>>> cie_rs.set_broadening(True)
Will thermally broaden lines with emissivity > 1.000000e-18 ph cm3 s-1

Specify abundance

>>>Abund= atomdb.get_abundance(abundfile=False, abundset=’AG89’, element=[-1], datacache=False, settings=False, show=False)

Return spectrum at 1.0keV and density = 1cm^-3

>>> spec = cie_rs.return_spectrum(1.0, 1.0, Ab=Abund)

spec is in photons cm^5 s^-1 bin^-1; ebins are the bin edges (so spec is 1 element shorter than ebins)

Attributes:

datacachedict

Any Atomdb FITS files which have to be opened are stored here

spectraCIESpectra

Object storing the actual spectral data

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

default_abundsetstring

The abundance set used for the original emissivity file calculation

abundsetstring

The abundance set to be used for the returned spectrum

abundsetvectorarray_like(float)

The relative abundance between default_abundset and abundset for each element

response_setbool

Have we loaded a response (or set a dummy response)

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

broaden_limitfloat

Apply broadening to lines with epsilon > this value (ph cm3 s-1)

thermal_broadeningbool

Apply thermal broadening to lines (default = False)

velocity_broadeningfloat

Apply velocity broadening with this velocity (km/s). If <=0, do not apply.

format_linelist(linelist)

Print out the line list in a nice format, with all the transitions described in more detail

Parameters:

linelistnumpy.array(dtype=linelist)

The linelist returned from “return_linelist”

Returns

——-

strthe formatted linelist

return_line_emissivity(Te, Z, z1, up, lo, specunit='A', teunit='keV', apply_aeff=False, apply_abund=True, log_interp=True)

Get line emissivity as function of Te.

Parameters:

Tefloat or array(float)

Temperature(s) in keV or K

Zint

nuclear charge of element

z1int

ion charge +1 of ion

upint

upper level for transition

loint

lower level for transition

specunit{‘Angstrom’,’keV’}

Units for wavelength or energy (a returned value)

teunit{‘keV’ , ‘K’}

Units of Te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the line emissivity in the linelist to modify their intensities.

apply_abundbool

If true, apply the abundance set in the session to the result.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear. Otherwise linear

Returns:

retdict

Dictionary containing:

Te, tau, teunit : as input

wavelength : line wavelength (A)

energy : line energy (keV)

epsilon : emissivity in ph cm^3 s-1 (or ph cm^5 s^-1 if apply_aeff=True). First index is temperature, second is tau.

return_linelist(Te, specrange, specunit='A', teunit='keV', apply_aeff=False, nearest=False, apply_binwidth=False)

Get the list of line emissivities vs wavelengths

Parameters:

Tefloat

Temperature in keV or K

specrange[float, float]

Minimum and maximum values for interval in which to search

specunit{‘Angstrom’,’keV’}

Units for specrange

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the lines in the linelist to modify their intensities.

nearestbool

Return spectrum at nearest tabulated temperature, without interpolation

apply_binwidthbool

Divide the line emissivity by the width of the bin they occupy to give emissivity per angstrom or per keV.

Returns:

linelistarray(dtype)

The list of lines with lambda (A), energy (keV), epsilon (ph cm3 s-1), epsilon_aeff (ph cm5 s-1) ion (string) and upper & lower levels.

return_spectrum(te, N_e, Ab, teunit='keV', nearest=False, get_nearest_t=False, log_interp=True, dolines=True, docont=True, dopseudo=True)

Get the spectrum at an exact temperature. Interpolates between 2 neighbouring spectra

Finds HDU with kT closest to desired kT in given line or coco file.

Opens the line or coco file, and looks for the header unit with temperature closest to te. Use result as index input to make_spectrum

Parameters:

tefloat

Temperature in keV or K

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

nearestbool

If set, return the spectrum from the nearest tabulated temperature in the file, without interpolation

get_nearest_tbool

If set, and nearest set, return the nearest tabulated temperature as well as the spectrum.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid, instead of linear.

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

Returns:

spectrumarray(float)

The spectrum in photons cm^5 s^-1 bin^-1, with the response, or photons cm^3 s^-1 bin^-1 if raw is set.

nearest_Tfloat, optional

If get_nearest_t is set, return the actual temperature this corresponds to. Units are same as teunit

set_abund(elements, abund)

Set the elemental abundance, relative to the abundset. Defaults to 1.0 for everything

Parameters:

elementsint or array_like(int)

The elements to change the abundance of

abundfloat or array_like(float)

The new abundances. If only 1 value, set all elements to this abundance Otherwise, should be of same length as elements.

Returns:

None

Examples

Set the abundance of iron to 0.5

>>> myspec.set_abund(26, 0.5)

Set the abundance of iron and nickel to 0.1 and 0.2 respectively

>>> myspec.set_abund([26, 28], [0.1,0.2])

Set the abundance of oxygen, neon, magnesium and iron to 0.1

>>> myspec.set_abund([8,10,12,26],0.1)

set_abundset(abundstring=None)

Set the abundance set.

Parameters:

abundstringstring

The abundance string (e.g. “AG89”, “uniform”. Case insensitive. See atomdb.get_abundance for list of possible abundances

Returns:

none

updates self.abundset and self.abundsetvector.

set_broadening(thermal_broadening, broaden_limit=False, velocity_broadening=0.0, velocity_broadening_units='km/s', thermal_broaden_temperature=None, teunit='keV')

Turn on or off thermal broadening, and the emissivity limit for thost lines

Parameters:

thermal_broadeningbool

If true, turn on broadening. If False, turn it off.

broaden_limitfloat

The emissivity limit for lines to be broadened. If False, this value will not be updated.

velocity_broadeningfloat

velocity broadening to apply. If <=0, not applied

velocity_broadening_unitsstring

Units of velocity_broadening. ‘km/s’ is default and only value so far.

thermal_broaden_temperaturefloat

If not None, use this temperature for all line broadening instead of plasma temperature (keV)

Notes

—–

Updates attributes thermal_broadening, broaden_limit, velocity_broadening,

velocity_broadening_units

set_eebrems(do_eebrems)

Set whether to do the electron-electron bremsstrahlung in the spectrum

Parameters:

do_eebremsbool

If True, include the electron-electron bremsstrahlung calculation If False, don’t (this is default, and matches XSPEC behaviour)

set_response(rmf, arf=False, raw=False, sparse=False)

Set the response. rmf, arf can either be the filenames or the opened files (latter is faster if called repeatedly)

Amends the following items:

self.rmffilestring

The rmf file name

self.rmfstring

The response matrix

self.arffilestring

The arf file name

self.arfstring

The arf data

self.specbinsarray(float)

The spectral bins on which to calculate the spectrum (keV or A)

self.specbin_unitsstring [‘A’,’keV’]

Units of specbins

self.ebinsarray(float)

The spectral bins on which to calculate the spectrum (keV).

self.ebins_outarray(float)

The spectral bins on which to return the spectrum (keV). Can be different from specbins depending on the spectrum

self.response_setbool

A response has been loaded

self.response_typestring

‘raw’, ‘standard’ or ‘sparse’ depending on the type implemented

self.specbins_setbool

The spectral bins are set

self.ebins_checksumstring

The md5checksum of the specbins

Parameters:

rmf: string or HDUlist or array

The response matrix file or energy bins (see raw k/w)

arf: string or HDUlist

The ancillary response file

rawbool

If true, the rmf variable contains the energy bin edges (keV) for all the bins, and each bin has a perfect response. This is effectively a dummy response

sparsebool

If true, the rmf is stored as a sparse matrix and solved using sparse matrix algebra. Useful for large RMFs (e.g. XRISM). Tests show accuracy to 1 part in 10^{15}. Ignored if raw==True

Returns:

none

class pyatomdb.spectrum.NEISession(linefile='$ATOMDB/apec_nei_line.fits', cocofile='$ATOMDB/apec_nei_comp.fits', elements=False, abundset='AG89')

Bases: CIESession

Load and generate a Non-equilibrium ionization (NEI) spectrum

Parameters:

linefilestring or HDUList, optional

The line emissivity data file (either name or already open)

cocofilestring or HDUList, optional

The continuum emissivity data file (either name or already open)

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

abundsetstring

The abundance set to use. Default AG89.

Examples

Create a session instance:

>>> s = NEISession()

Set up the responses, in this case a dummy response from 0.1 to 10 keV

>>> ebins = numpy.linspace(0.1,10,1000)
>>> s.set_response(ebins, raw=True)

Turn on thermal broadening

>>> s.set_broadening(True)
Will thermally broaden lines with emissivity > 1.000000e-18 ph cm3 s-1

Return spectrum at 1.0keV, Ne *t = 1e11 cm^-3 s

>>> spec = s.return_spectrum(1.0, 1e11)

spec is in photons cm^3 s^-1 bin^-1; ebins are the bin edges (so spec is 1 element shorter than ebins)

Attributes:

datacachedict

Any Atomdb FITS files which have to be opened are stored here

spectraNEISpectra

Object storing the actual spectral data

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

default_abundsetstring

The abundance set used for the original emissivity file calculation

abundsetstring

The abundance set to be used for the returned spectrum

abundsetvectorarray_like(float)

The relative abundance between default_abundset and abundset for each element

response_setbool

Have we loaded a response (or set a dummy response)

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

broaden_limitfloat

Apply broadening to lines with epsilon > this value (ph cm3 s-1)

thermal_broadeningbool

Apply thermal broadening to lines (default = False)

velocity_broadeningfloat

Apply velocity broadening with this velocity (km/s). If <=0, do not apply.

format_linelist(linelist)

Print out the line list in a nice format, with all the transitions described in more detail

Parameters:

linelistnumpy.array(dtype=linelist)

The linelist returned from “return_linelist”

Returns

——-

strthe formatted linelist

return_line_emissivity(Telist, taulist, Z, z1, up, lo, specunit='A', teunit='keV', apply_aeff=False, apply_abund=True, log_interp=True, init_pop='ionizing', freeze_ion_pop=False)

Get line emissivity as function of Te, tau. Assumes ionization from neutral.

Parameters:

Telistfloat or array(float)

Temperature(s) in keV or K

taulistfloat or array(float)

ionization timescale(s), ne * t (cm^-3 s).

Zint

nuclear charge of element

z1int

ion charge +1 of ion

upint

upper level for transition

loint

lower level for transition

specunit{‘Angstrom’,’keV’}

Units for wavelength or energy (a returned value)

teunit{‘keV’ , ‘K’}

Units of Telist (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the line emissivity in the linelist to modify their intensities.

apply_abundbool

If true, apply the abundance set in the session to the result.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear.

init_popstring or float

if ‘ionizing’ : all ionizing from neutral (so [1,0,0,0…]) if ‘recombining’: all recombining from ionized (so[…0,0,1]) if dict of arrays : the acutal fractional populations (so init_pop[6] is the array for carbon) if single float : the temperature (same units as Te)

freeze_ion_popbool

If True, skip the ion population calculation, use init_pop as the final pop instead.

Returns:

retdict

Dictionary containing:

Te, tau, teunit: as input

wavelength : line wavelength (A)

energy : line energy (keV)

epsilonemissivity in ph cm^3 s-1 (or ph cm^5 s^-1 if apply_aeff=True)

first index is temperature, second is tau. If Te or Tau was supplied as a scalar, then that index is removed

return_linelist(Te, tau, specrange, init_pop='ionizing', specunit='A', teunit='keV', apply_aeff=False, by_ion_drv=False, nearest=False, apply_binwidth=False, log_interp=True, freeze_ion_pop=False)

Get the list of line emissivities vs wavelengths

Parameters:

Tefloat

Temperature in keV or K

taufloat

ionization timescale, ne * t (cm^-3 s).

specrange[float, float]

Minimum and maximum values for interval in which to search

specunit{‘Angstrom’,’keV’}

Units for specrange

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the lines in the linelist to modify their intensities.

by_ion_drvbool

If true, keep lines which are the same but have different ion_drv separate. Otherwise, merge them.

nearestbool

calculate spectrum at nearest temperature in linelist, no interpolation. Ionization fraction calculation still exact.

apply_binwidth

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear.

freeze_ion_popbool

If True, skip the ion population calculation, use init_pop as the final pop instead.

Returns:

linelistarray(linelist)

The list of lines with lambda (A), energy (keV), epsilon (ph cm3 s-1), epsilon_aeff (ph cm5 s-1) ion (string) and upper & lower levels.

return_spectrum(Te, tau, init_pop='ionizing', teunit='keV', nearest=False, log_interp=True, freeze_ion_pop=False)

Get the spectrum at an exact temperature. Interpolates between 2 neighbouring spectra

Finds HDU with kT closest to desired kT in given line or coco file.

Opens the line or coco file, and looks for the header unit with temperature closest to te. Use result as index input to make_spectrum

Parameters:

Tefloat

Temperature in keV or K

taufloat

ionization timescale, ne * t (cm^-3 s).

init_popstring or float

if ‘ionizing’ : all ionizing from neutral (so [1,0,0,0…]) if ‘recombining’: all recombining from ionized (so[…0,0,1]) if dict of arrays : the acutal fractional populations (so init_pop[6] is the array for carbon) if single float : the temperature (same units as Te)

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

nearestbool

If set, return the spectrum from the nearest tabulated temperature in the file, without interpolation

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear.

freeze_ion_popbool

If True, skip the ion population calculation, use init_pop as the final pop instead.

Returns:

spectrumarray(float)

The spectrum in photons cm^5 s^-1 bin^-1, with the response, or photons cm^3 s^-1 bin^-1 if raw is set.

nearest_Tfloat, optional

If nearest is set, return the actual temperature this corresponds to. Units are same as teunit

set_abund(elements, abund)

Set the elemental abundance, relative to the abundset. Defaults to 1.0 for everything

Parameters:

elementsint or array_like(int)

The elements to change the abundance of

abundfloat or array_like(float)

The new abundances. If only 1 value, set all elements to this abundance Otherwise, should be of same length as elements.

Returns:

None

Examples

Set the abundance of iron to 0.5

>>> myspec.set_abund(26, 0.5)

Set the abundance of iron and nickel to 0.1 and 0.2 respectively

>>> myspec.set_abund([26, 28], [0.1,0.2])

Set the abundance of oxygen, neon, magnesium and iron to 0.1

>>> myspec.set_abund([8,10,12,26],0.1)

set_abundset(abundstring=None)

Set the abundance set.

Parameters:

abundstringstring

The abundance string (e.g. “AG89”, “uniform”. Case insensitive. See atomdb.get_abundance for list of possible abundances

Returns:

none

updates self.abundset and self.abundsetvector.

set_broadening(thermal_broadening, broaden_limit=False, velocity_broadening=0.0, velocity_broadening_units='km/s', thermal_broaden_temperature=None, teunit='keV')

Turn on or off thermal broadening, and the emissivity limit for thost lines

Parameters:

thermal_broadeningbool

If true, turn on broadening. If False, turn it off.

broaden_limitfloat

The emissivity limit for lines to be broadened. If False, this value will not be updated.

velocity_broadeningfloat

velocity broadening to apply. If <=0, not applied

velocity_broadening_unitsstring

Units of velocity_broadening. ‘km/s’ is default and only value so far.

thermal_broaden_temperaturefloat

If not None, use this temperature for all line broadening instead of plasma temperature (keV)

Notes

—–

Updates attributes thermal_broadening, broaden_limit, velocity_broadening,

velocity_broadening_units

set_eebrems(do_eebrems)

Set whether to do the electron-electron bremsstrahlung in the spectrum

Parameters:

do_eebremsbool

If True, include the electron-electron bremsstrahlung calculation If False, don’t (this is default, and matches XSPEC behaviour)

set_response(rmf, arf=False, raw=False, sparse=False)

Set the response. rmf, arf can either be the filenames or the opened files (latter is faster if called repeatedly)

Amends the following items:

self.rmffilestring

The rmf file name

self.rmfstring

The response matrix

self.arffilestring

The arf file name

self.arfstring

The arf data

self.specbinsarray(float)

The spectral bins on which to calculate the spectrum (keV or A)

self.specbin_unitsstring [‘A’,’keV’]

Units of specbins

self.ebinsarray(float)

The spectral bins on which to calculate the spectrum (keV).

self.ebins_outarray(float)

The spectral bins on which to return the spectrum (keV). Can be different from specbins depending on the spectrum

self.response_setbool

A response has been loaded

self.response_typestring

‘raw’, ‘standard’ or ‘sparse’ depending on the type implemented

self.specbins_setbool

The spectral bins are set

self.ebins_checksumstring

The md5checksum of the specbins

Parameters:

rmf: string or HDUlist or array

The response matrix file or energy bins (see raw k/w)

arf: string or HDUlist

The ancillary response file

rawbool

If true, the rmf variable contains the energy bin edges (keV) for all the bins, and each bin has a perfect response. This is effectively a dummy response

sparsebool

If true, the rmf is stored as a sparse matrix and solved using sparse matrix algebra. Useful for large RMFs (e.g. XRISM). Tests show accuracy to 1 part in 10^{15}. Ignored if raw==True

Returns:

none

class pyatomdb.spectrum.PShockSession(linefile='$ATOMDB/apec_nei_line.fits', cocofile='$ATOMDB/apec_nei_comp.fits', elements=False, abundset='AG89')

Bases: NEISession

Load and generate a Parallel Shock (PShock) spectrum

Parameters:

linefilestring or HDUList, optional

The line emissivity data file (either name or already open)

cocofilestring or HDUList, optional

The continuum emissivity data file (either name or already open)

elementsiterable of int

Elements to include, listed by atomic number. if not set, include all.

abundsetstring

The abundance set to use. Default AG89.

Examples

Create a session instance:

>>> s=PShockSession()

Set up the responses, in this case a dummy response from 0.1 to 10 keV

>>> ebins = numpy.linspace(0.1,10,1000)
>>> s.set_response(ebins, raw=True)

Turn on thermal broadening

>>> s.set_broadening(True)
Will thermally broaden lines with emissivity > 1.000000e-18 ph cm3 s-1

Return spectrum at 1.0keV, Tau_u = 1e11, Tau_l = 0.0 (default)

>>> spec = s.return_spectrum(1.0, 1e11)

Same with Tau_l = 1e9

>>> spec = s.return_spectrum(1.0, 1e11, tau_l = 1e9)

spec is in photons cm^3 s^-1 bin^-1; ebins are the bin edges (so spec is 1 element shorter than ebins)

Attributes:

datacachedict

Any Atomdb FITS files which have to be opened are stored here

spectraPShockSpectra

Object storing the actual spectral data

elementslist(int)

Nuclear charge of elements to include.

default_abundsetstring

The abundance set used for the original emissivity file calculation

abundsetstring

The abundance set to be used for the returned spectrum

abundsetvectorarray_like(float)

The relative abundance between default_abundset and abundset for each element

response_setbool

Have we loaded a response (or set a dummy response)

dolinesbool

Calculate line emission (default True)

docontbool

Calculate Continuum emission (default True)

dopseudobool

Calculate PseudoContinuum (weak line) emission (default True)

broaden_limitfloat

Apply broadening to lines with epsilon > this value (ph cm3 s-1)

thermal_broadeningbool

Apply thermal broadening to lines (default = False)

velocity_broadeningfloat

Apply velocity broadening with this velocity (km/s). If <=0, do not apply.

format_linelist(linelist)

Print out the line list in a nice format, with all the transitions described in more detail

Parameters:

linelistnumpy.array(dtype=linelist)

The linelist returned from “return_linelist”

Returns

——-

strthe formatted linelist

return_line_emissivity(Telist, tau_ulist, Z, z1, up, lo, tau_llist=0.0, specunit='A', teunit='keV', apply_aeff=False, apply_abund=True, log_interp=True, init_pop='ionizing')

Get line emissivity as function of Te, tau. Assumes ionization from neutral.

Parameters:

Telistfloat or array(float)

Temperature(s) in keV or K

tau_ulistfloat

ionization timescale(s), ne * t (cm^-3 s).

Zint

nuclear charge of element

z1int

ion charge +1 of ion

upint

upper level for transition

loint

lower level for transition

tau_llistfloat

lower limit of ionization timescale(s), ne * t (cm^-3 s).

specunit{‘Angstrom’,’keV’}

Units for wavelength or energy (a returned value)

teunit{‘keV’ , ‘K’}

Units of Telist (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the line emissivity in the linelist to modify their intensities.

apply_abundbool

If true, apply the abundance set in the session to the result.

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear.

Returns:

retdict

Dictionary containing:

Te, tau, teunit: as input

wavelength : line wavelength (A)

energy : line energy (keV)

epsilonemissivity in ph cm^3 s-1 (or ph cm^5 s^-1 if apply_aeff=True)

first index is temperature, second is tau.

return_linelist(Te, tau_u, specrange, tau_l=0.0, init_pop='ionizing', specunit='A', teunit='keV', apply_aeff=False, by_ion_drv=False, nearest=False, apply_binwidth=False)

Get the list of line emissivities vs wavelengths

Parameters:

Tefloat

Temperature in keV or K

tau_ufloat

Upper limit of ionization timescale, ne * t (cm^-3 s).

specrange[float, float]

Minimum and maximum values for interval in which to search

tau_l

lower limit of ionization timescale, ne * t (cm^-3 s) (defaults to 0)

init_popstring or float

if ‘ionizing’ : all ionizing from neutral (so [1,0,0,0…]) if ‘recombining’: all recombining from ionized (so[…0,0,1]) if dict of arrays : the acutal fractional populations (so init_pop[6] is the array for carbon) if single float : the temperature (same units as Te)

specunit{‘Angstrom’,’keV’}

Units for specrange

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

apply_aeffbool

If true, apply the effective area to the lines in the linelist to modify their intensities.

by_ion_drvbool

If true, keep lines which are the same but have different ion_drv separate. Otherwise, merge them.

nearest

apply_binwidth

Returns:

linelistarray(dtype)

The list of lines with lambda (A), energy (keV), epsilon (ph cm3 s-1), epsilon_aeff (ph cm5 s-1) ion (string) and upper & lower levels.

return_spectrum(Te, tau_u, tau_l=0.0, init_pop='ionizing', teunit='keV', nearest=False, log_interp=True)

Get the spectrum at an exact temperature. Interpolates between 2 neighbouring spectra

Finds HDU with kT closest to desired kT in given line or coco file.

Opens the line or coco file, and looks for the header unit with temperature closest to te. Use result as index input to make_spectrum

Parameters:

Tefloat

Temperature in keV or K

tau_ufloat

Upper limit of ionization timescale, ne * t (cm^-3 s).

tau_l

lower limit of ionization timescale, ne * t (cm^-3 s) (defaults to 0)

init_popstring or float

if ‘ionizing’ : all ionizing from neutral (so [1,0,0,0…]) if ‘recombining’: all recombining from ionized (so[…0,0,1]) if dict of arrays : the acutal fractional populations (so init_pop[6] is the array for carbon) if single float : the temperature (same units as Te)

teunit{‘keV’ , ‘K’}

Units of te (kev or K, default keV)

nearestbool

If set, return the spectrum from the nearest tabulated temperature in the file, without interpolation

log_interpbool

Perform linear interpolation on a logT/logEpsilon grid (default), or linear.

Returns:

spectrumarray(float)

The spectrum in photons cm^5 s^-1 bin^-1, with the response, or photons cm^3 s^-1 bin^-1 if raw is set.

set_abund(elements, abund)

Set the elemental abundance, relative to the abundset. Defaults to 1.0 for everything

Parameters:

elementsint or array_like(int)

The elements to change the abundance of

abundfloat or array_like(float)

The new abundances. If only 1 value, set all elements to this abundance Otherwise, should be of same length as elements.

Returns:

None

Examples

Set the abundance of iron to 0.5

>>> myspec.set_abund(26, 0.5)

Set the abundance of iron and nickel to 0.1 and 0.2 respectively

>>> myspec.set_abund([26, 28], [0.1,0.2])

Set the abundance of oxygen, neon, magnesium and iron to 0.1

>>> myspec.set_abund([8,10,12,26],0.1)

set_abundset(abundstring=None)

Set the abundance set.

Parameters:

abundstringstring

The abundance string (e.g. “AG89”, “uniform”. Case insensitive. See atomdb.get_abundance for list of possible abundances

Returns:

none

updates self.abundset and self.abundsetvector.

set_broadening(thermal_broadening, broaden_limit=False, velocity_broadening=0.0, velocity_broadening_units='km/s', thermal_broaden_temperature=None, teunit='keV')

Turn on or off thermal broadening, and the emissivity limit for thost lines

Parameters:

thermal_broadeningbool

If true, turn on broadening. If False, turn it off.

broaden_limitfloat

The emissivity limit for lines to be broadened. If False, this value will not be updated.

velocity_broadeningfloat

velocity broadening to apply. If <=0, not applied

velocity_broadening_unitsstring

Units of velocity_broadening. ‘km/s’ is default and only value so far.

thermal_broaden_temperaturefloat

If not None, use this temperature for all line broadening instead of plasma temperature (keV)

Notes

—–

Updates attributes thermal_broadening, broaden_limit, velocity_broadening,

velocity_broadening_units

set_eebrems(do_eebrems)

Set whether to do the electron-electron bremsstrahlung in the spectrum

Parameters:

do_eebremsbool

If True, include the electron-electron bremsstrahlung calculation If False, don’t (this is default, and matches XSPEC behaviour)

set_response(rmf, arf=False, raw=False, sparse=False)

Set the response. rmf, arf can either be the filenames or the opened files (latter is faster if called repeatedly)

Amends the following items:

self.rmffilestring

The rmf file name

self.rmfstring

The response matrix

self.arffilestring

The arf file name

self.arfstring

The arf data

self.specbinsarray(float)

The spectral bins on which to calculate the spectrum (keV or A)

self.specbin_unitsstring [‘A’,’keV’]

Units of specbins

self.ebinsarray(float)

The spectral bins on which to calculate the spectrum (keV).

self.ebins_outarray(float)

The spectral bins on which to return the spectrum (keV). Can be different from specbins depending on the spectrum

self.response_setbool

A response has been loaded

self.response_typestring

‘raw’, ‘standard’ or ‘sparse’ depending on the type implemented

self.specbins_setbool

The spectral bins are set

self.ebins_checksumstring

The md5checksum of the specbins

Parameters:

rmf: string or HDUlist or array

The response matrix file or energy bins (see raw k/w)

arf: string or HDUlist

The ancillary response file

rawbool

If true, the rmf variable contains the energy bin edges (keV) for all the bins, and each bin has a perfect response. This is effectively a dummy response

sparsebool

If true, the rmf is stored as a sparse matrix and solved using sparse matrix algebra. Useful for large RMFs (e.g. XRISM). Tests show accuracy to 1 part in 10^{15}. Ignored if raw==True

Returns:

none

pyatomdb.spectrum.calc_ee_brems_spec(ebins, Te, dens, teunit='keV')

Calculate the electron-electron bremstrahlung per-bin emissivity

Parameters:

ebinsarray(float)

The spectral bin edges in energy order (keV)

Tefloat

Electron temperature (default, keV)

densfloat

The electron density (cm^-3)

teunitstring

Units of Te (keV by default, K also allowed)

Returns:

eebremsarray(float)

electron-electron bremsstrahlung in ph cm^3 s^-1 bin^-1