pySIR

Python wrapper for the Stokes Inversion based on Response functions code by Ruiz Cobo & del Toro Iniesta (1992)

Compilation

Local compilation

python setup.py build_ext --inplace

Systemwide installation

python setup.py install

Example

import pysir
lines = [['200,201',-500.,10.,1500.]]
SIR = pysir.SIR(lines)

psf = np.loadtxt('PSF.dat', dtype=np.float32)
SIR.setPSF(psf[:,0].flatten(), psf[:,1].flatten())
out = np.loadtxt('model.mod', dtype=np.float32, skiprows=1)[:,0:8]
stokes, rf = SIR.synthesize(out)

Methods of the class

Instantiation

Initialize the SIR synthesis code for a set of spectral lines using

SIR = pysir.SIR(lines)

The number of wavelength points to be synthesized and the number of total spectral lines in all blends can be obtained from the variables SIR.nLambda and SIR.nLines, respectively.

It only contains an input parameter lines, which is a list of lists containing the information for the lines to be synthesized Each region is defined is defined by a list containing the following elements:

- A string defining which lines are synthesized in the region. E.g. '1,2,3'
- Initial wavelength displacement in mA
- Step in mA
- Final wavelength displacement in mA

For example

lines = [['200,201', -500.0, 10.0, 1500.0], ['2', -750.0, 10.0, 1300.0]]

`SIR.listLines`

Lists the lines available in SIR for synthesis

`SIR.setPSF(lambda, transmission)`

Define the spectral PSF to be convolved with the profiles. lambda is the displacement with respect to the maximum in mA and transmission is the transmission of the PSF (it is normalized to unit area in the code).

`SIR.synthesize(model, departure=None, macroturbulence=0.0, fillingFactor=1.0, stray=0.0, returnRF=True, cartesian=False)`

Carry out the synthesis and returns the Stokes parameters and the response functions to all physical variables at all depths.

Input parameters

model

The model is defined as the following array, which can be of size [nDepth,7] if the electron pressure is not known and computed in hydrostatic equilibrium, or [nDepth,8] if it is known.

In case the electron pressure is to be computed in hydrostatic equilibrium, the model has the following structure:

model (float array): an array of size [nDepth, 7], where the columns contain the depth stratification of:

- log tau
- Temperature [K]    
- Microturbulent velocity [cm/s]
- Magnetic field strength or Bx (in cartesian) [G]
- Line-of-sight velocity [cm/s]
- Magnetic field inclination [deg] or By [deg] (in cartesian)
- Magnetic field azimuth [deg] or Bz [deg] (in cartesian)

If the electron pressure is known, the model has the following structure:

model (float array): an array of size [nDepth, 8], where the columns contain the depth stratification of:

- log tau
- Temperature [K]
- Electron pressure [dyn cm^-2]
- Microturbulent velocity [cm/s]
- Magnetic field strength or Bx (in cartesian) [G]
- Line-of-sight velocity [cm/s]
- Magnetic field inclination [deg] or By [deg] (in cartesian) 
- Magnetic field azimuth [deg] or Bz [deg] (in cartesian)

departure

An array of size [2, nLines, nDepth] that contains the departure coefficient (the ratio between the populations in non-LTE and in LTE) of the lower and upper levels of each transition at all heights. LTE populations are used by default if departure is not passed to the method.

macroturbulence

Macroturbulence velocity in cm/s. This velocity defines a Gaussian kernel that will convolve the final spectrum.

fillingFactor

Not used. Keep it at its default value.

stray

Not used. Keep it at its default value.

returnRF

If True, the output will contain the response functions (i.e., derivatives of the Stokes parameters with respect to the input parameters). If False, it only returns the synthetic spectra.

cartesian

If True, then the magnetic field is defined with the (Bx,By,Bz) components. Check the definition of the model to see which columns contain this information. If False, the magnetic field vector is given in spherical components (B,inclination,azimuth).

Return values

stokes: (float array) Stokes parameters, with the first index containing the wavelength displacement and the remaining
                            containing I, Q, U and V. Size (5,nLambda)
rf: (float array) Response functions to T, Pe, vmic, B, v, theta, phi. Size (4,nLambda,nDepth)

Files

The following files are needed:

- LINEAS: defines the available lines
- THEVENIN: defines the abundances

Dependencies

- cython
- gfortran_linux-64

cdiazbas / pySIR