exojax.utils package¶

Submodules¶

exojax.utils.astrofunc module¶

Astronomical messy functions.

Astronomy is the oldest science in the world.
That’s why we need this module.

exojax.utils.astrofunc.getjov_gravity(Rp, Mp)¶

gravity in cgs from radius and mass in the Jovian unit.

Parameters

Rp – radius in the unit of Jovian radius
Mp – radius in the unit of Jovian mass

Returns

gravity (cm/s2)

Note

Mpcgs=Mp*const.MJ, Rpcgs=Rp*const.RJ then gravity is given by (const.G*Mpcgs/Rpcgs**2)

exojax.utils.astrofunc.getjov_logg(Rp, Mp)¶

logg from radius and mass in the Jovian unit.

Parameters

Rp – radius in the unit of Jovian radius
Mp – radius in the unit of Jovian mass

Returns

logg

Note

Mpcgs=Mp*const.MJ, Rpcgs=Rp*const.RJ, then logg is given by log10(const.G*Mpcgs/Rpcgs**2)

exojax.utils.chopstacks module¶

exojax.utils.chopstacks.buildwall(x, edge='half')¶

building conventional walls.

Parameters

x – input bins
edge – how to define the edge. half=cutting a half bin at the edges. full=extending a half bin at the edge

Returns

walls

exojax.utils.constants module¶

constants.

constants in cgs or km/s
logm_ucgs=np.log10(m_u*1.e3) where m_u = scipy.constants.m_u.
Tref: reference temperature used in exojax.spec

exojax.utils.gpkernel module¶

Kernels used in Gaussian process.

exojax.utils.gpkernel.gpkernel_RBF(t, tau, a, err)¶

RBF kernel with diagnoal error.

Parameters

t – variable vector (N)
tau – scale parameter (scalar)
a – amplitude (scalar)
err – diagnonal error vector (N)

Returns

kernel

exojax.utils.grids module¶

generate various grids

exojax.utils.grids.check_eslog_wavenumber_grid(nus, crit1=1e-05, crit2=1e-14, gridmode='ESLOG')¶

checking if wavenumber_grid is evenly spaced in a logarithm scale (ESLOG) or a liner scale (ESLIN)

Parameters

nus – wavenumber grid
crit1 – criterion for the maximum deviation of log10(nu)/median(log10(nu)) from ESLOG
crit2 – criterion for the maximum deviation of log10(nu) from ESLOG
gridmode – ESLOG or ESLIN

Returns

True (wavenumber grid is ESLOG) or False (not)

exojax.utils.grids.check_scale_xsmode(xsmode)¶

checking if the scale of xsmode assumes ESLOG(log) or ESLIN(linear)

Parameters: xsmode – xsmode
Returns: ESLOG/ESLIN/UNKNOWN

exojax.utils.grids.delta_velocity_from_resolution(resolution)¶

delta velocity from spectral resolution R

Parameters: resolution – spectral resolution

Note

See also [#294](https://github.com/HajimeKawahara/exojax/issues/294) and exojax/tests/figures/functions/delta_velocity_comp.py

Returns: delta velocity

exojax.utils.grids.velocity_grid(resolution, vmax)¶

generate velocity grid for a rigid rotation

Parameters

resolution – spectral resolution
vmax – maximum velocity (or Vsini) allowed (km/s)

Returns

delta velocity grid

Return type

1D array

exojax.utils.grids.warn_resolution(resolution, crit=700000.0)¶

warning poor resolution.

Parameters

resolution – spectral resolution
crit – critical resolution

exojax.utils.grids.wavenumber_grid(x0, x1, N, unit='cm-1', xsmode='lpf')¶

generating the recommended wavenumber grid based on the cross section computation mode.

Parameters

x0 – start wavenumber (cm-1) or wavelength (nm) or (AA)
x1 – end wavenumber (cm-1) or wavelength (nm) or (AA)
N – the number of the wavenumber grid (even number)
unit – unit of the input grid
xsmode – cross section computation mode (lpf, dit, modit, premodit)

Note

The wavenumber (nus) and wavelength (wav) grids are in ascending orders. Therefore, wav[-1] corresponds to the wavelength of nus[0]. ESLIN sets evenly-spaced linear grid in wavenumber space while ESLOG sets evenly-spaced log grid both in wavenumber and wavelength spaces.

Returns: wavenumber grid evenly spaced in log space in ascending order (nus) corresponding wavelength grid (AA) in ascending order (wav). wav[-1] corresponds to nus[0] spectral resolution

exojax.utils.indexing module¶

exojax.utils.indexing.find_or_add_index(new_index, index_array)¶

find a position of a new index in index_array, if not exisited add the new index in index_array

Parameters

new_index – new index investigated
index_array – index array

Returns

position, index_array updated

exojax.utils.indexing.uniqidx(input_array)¶

compute indices based on uniq values of the input M-dimensional array.

Parameters: input_array – input array (N,M), will use unique M-dim vectors
Returns: unique index, unique value

Examples

>>> a=np.array([[4,1],[7,1],[7,2],[7,1],[8,0],[4,1]])
>>> uidx, uval=uniqidx(a) #->[0,1,2,1,3,0], [[4,1],[7,1],[7,2],[8,0]]

exojax.utils.indexing.uniqidx_neibouring(index_array)¶

compute indices based on uniq values of the input index array and input index + one vector

Parameters: index_array – input index array (N,M), will use unique M-dim vectors
Returns: unique index (udix) neibouring index (nidx) for udix [N_uidx, 3] multi index as a function of nidx

exojax.utils.indexing.unique_rows(x)¶

memory saved version of np.unique(,axis=0)

Notes

Originally from a snippet/Answer #4 (https://discuss.dizzycoding.com/find-unique-rows-in-numpy-array/?amp=1)

Parameters: x (2D array) – 2D array (N x M), need to be C-contiguous
Returns: unique 2D array (N’ x M), where N’ <= N, removed duplicated M vector.
Return type: 2D array

exojax.utils.instfunc module¶

Utility Functions about Instruments.

exojax.utils.instfunc.R2STD(resolution)¶

exojax.utils.instfunc.resolution_eslin(nu)¶

min max spectral resolution for ESLIN.

Parameters: nu – wavenumber bin
Returns: min, approximate, max of the resolution

exojax.utils.instfunc.resolution_eslog(nu)¶

spectral resolution for ESLOG.

Parameters: nu – wavenumber bin
Returns: resolution

exojax.utils.instfunc.resolution_to_gaussian_std(resolution)¶

compute Standard deveiation of Gaussian velocity distribution from spectral resolution.

Parameters: resolution – spectral resolution R
Returns: standard deviation of Gaussian velocity distribution (km/s)

exojax.utils.isodata module¶

Mass number and abundance list.

exojax.utils.isodata.read_mnlist()¶

loading mass number list.

Note

this code reads data/atom/iso_mn.txt, taken from https://www.chem.ualberta.ca/~massspec/atomic_mass_abund.pdf The isotopic mass data is from G. Audi, A. H. Wapstra Nucl. Phys A. 1993, 565, 1-65 and G. Audi, A. H. Wapstra Nucl. Phys A. 1995, 595, 409-480. The percent natural abundance data is from the 1997 report of the IUPAC Subcommittee for Isotopic Abundance Measurements by K.J.R. Rosman, P.D.P. Taylor Pure Appl. Chem. 1999, 71, 1593-1607.

Returns: dictionary of mass number, keys=”isotope”,”mass_number”,”abundance”

exojax.utils.isotopes module¶

exojax.utils.isotopes.exact_isotope_name_from_isotope(simple_molecule_name, isotope)¶

exact isotope name from isotope (number)

Parameters

simple_molecular_name (str) – simple molecular name such as CO
isotope (int) – isotope number starting from 1

Returns

exact isotope name such as (12C)(16O)

Return type

str

exojax.utils.isotopes.get_isotope(atom, isolist)¶

get isotope info.

Parameters

atom – simple atomic symbol, such as “H”, “Fe”
isolist – isotope list

Returns

isotope list, such as “1H”, “2H” mass_number: mass_number list abundance: abundance list

Return type

iso

exojax.utils.isotopes.get_stable_isotope(atom, isolist)¶

get isotope info.

Parameters

atom – simple atomic symbol, such as “H”, “Fe”
isolist – isotope list

Returns

stabel isotope such as “1H”, “2H” mass_number: mass_number abundance: abundance

Return type

iso

exojax.utils.molname module¶

exojax.utils.molname.e2s(molname_exact)¶

convert the exact molname (used in ExoMol) to the simple molname.

Parameters: molname_exact – the exact molname
Returns: simple molname

Examples

>>> print(e2s("12C-1H4"))
>>> CH4
>>> print(e2s("23Na-16O-1H"))
>>> NaOH
>>> print(e2s("HeH_p"))
>>> HeH_p
>>> print(e2s("trans-31P2-1H-2H")) #not working
>>> Warning: Exact molname  trans-31P2-1H-2H cannot be converted to simple molname
>>> trans-31P2-1H-2H

exojax.utils.molname.s2e_stable(molname_simple)¶

convert the simple molname to the exact molname (used in ExoMol) using stable isotopes.

Parameters: molname_simple – simple molname
Returns: exact molname

exojax.utils.molname.split_simple(molname_simple)¶

split simple molname.

Parameters: molname_simple – simple molname
Returns: atom list number list

Example

>>> split_simple("Fe2O3")
>>> (['Fe', 'O'], ['2', '3'])

exojax.utils.recexomol module¶

Get Recommendation from ExoMol.

exojax.utils.recexomol.get_exomol_database_list(molecule, isotope_full_name)¶

Parse ExoMol website and return list of available databases, and recommended database.

Parameters

molecule – str
isotope_full_name – str, isotope full name (ex. 12C-1H4 for CH4,1). Get it from

Returns

database list database recomendation

Example

databases, recommended = get_exomol_database_list(“CH4”, “12C-1H4”) >>> [‘xsec-YT10to10’, ‘YT10to10’, ‘YT34to10’], ‘YT34to10’

Note

This function is borrowed from radis (https://github.com/radis/radis by @erwanp). See https://github.com/radis/radis/issues/319 in detail.

exojax.utils.url module¶

url.

This module contains various url for downloading. Because url can be changed by the orner of the site, you might need to change it. Or, if you notice the change, it would be great if you send a pull-request.

exojax.utils.url.url_ExoMol()¶

return URL for ExoMol.

Returns: URL for ExoMol db

exojax.utils.url.url_Exomol_iso(molecule, isotope_full_name)¶

return URL for ExoMol for isotope.

Returns: URL for ExoMol for isotope

exojax.utils.url.url_HITEMP()¶

return URL for HITEMP bz2 parfile.

Returns: URL for HITEMP bz2 file

exojax.utils.url.url_HITEMP10()¶

return URL for HITEMP2010.

Returns: URL for HITEMP2010 db

exojax.utils.url.url_HITRAN12()¶

return URL for HITRAN 12 parfile.

Returns: URL for HITRAN 12 parfile

exojax.utils.url.url_HITRANCIA()¶

return URL for HITRAN CIA ciafile.

Returns: URL for HITRAN CIA file

exojax.utils.url.url_developer_data()¶

return URL for data in exojax.

Returns: URL for ExoJAX

exojax.utils.zsol module¶

solar abundance.

Solar abundance data
AAG21 = Asplund, M., Amarsi, A. M., & Grevesse, N. 2021, arXiv:2105.01661

exojax.utils.zsol.nsol(database='AAG21')¶

provide solar abundance dictionary.

Parameters: database – name of database.
Returns: number ratio of solar abundance

Example

>>>  nsun=nsol()
>>>  print(nsun["Fe"])
>>>  2.6602622265852853e-05

exojax.utils package¶

Submodules¶

exojax.utils.astrofunc module¶

exojax.utils.chopstacks module¶

exojax.utils.constants module¶

exojax.utils.gpkernel module¶

exojax.utils.grids module¶

exojax.utils.indexing module¶

exojax.utils.instfunc module¶

exojax.utils.isodata module¶

exojax.utils.isotopes module¶

exojax.utils.molname module¶

exojax.utils.recexomol module¶

exojax.utils.url module¶

exojax.utils.zsol module¶

Module contents¶