magrittetorch.tools.setup

Contains the data structure of the images of a model.

class magrittetorch.tools.setup.LamdaFileReader(fileName)

Reader for LAMDA line data files.

extractCollisionPartner(line, species, elem)

Returns collision partner and whether it is ortho or para (for H2)

readColumn(start, nElem, columnNr, type)

Returns a column of data as a list

magrittetorch.tools.setup.create_rotation_matrix(n: ndarray) → ndarray

Helper function to create rotation matrices. Returns a 3x3 orthonormal matrix around n.

magrittetorch.tools.setup.getSpeciesNumber(species: Species, name: str) → int

Returns number of species given by ‘name’

Parameters:

  • species (Magrittetorch species object) – Contains the information about the chemical species in the model

  • name (str) – name of the chemical species

:raises KeyError : if the species name is not found in the list of chemical species:

magrittetorch.tools.setup.getSpeciesNumberList(species: Species, name: list[str]) → list[int]

Returns number of species given by ‘name’

Parameters:

  • (Species) (species)

  • (list[str]) (name)

:raises KeyError : if the species name is not found in the list of chemical species:

magrittetorch.tools.setup.set_Delaunay_boundary(model: Model) → Model

Setter for the boundary, assuming all points are the cell centers of a Voronoi tesselation. Only supported for 1D.

Parameters:

model (Magrittetorch model object) – Magrittetorch model object to set.

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_Delaunay_neighbor_lists(model: Model) → Model

Setter for the neighbor lists for each point, assuming they are the cell centers of a Voronoi tesselation.

Parameters:

(Model) (model)

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_boundary_condition_1D(model: ~magrittetorch.model.model.Model, T_in: ~astropy.units.quantity.Quantity = <Quantity 2.72548 K>, T_out: ~astropy.units.quantity.Quantity = <Quantity 2.72548 K>)

Setter for incoming black body radiation boundary condition at each boundary point.

Parameters:

  • model (Magrittetorch model object) – Magrittetorch model object to set.

  • T_in (float) – Boundary temperature at the inner boundary.

  • T_out (float) – Boundary temperature at the outer boundary.

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_boundary_condition_CMB(model: Model) → Model

Setter for incoming CMB boundary condition at each boundary point.

Parameters:

model (Magrittetorch model object) – Magrittetorch model object to set.

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_boundary_condition_zero(model: Model) → Model

Setter for incoming zero boundary condition at each boundary point.

Parameters:

model (Magrittetorch model object) – Magrittetorch model object to set.

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_linedata_from_LAMDA_file(model: Model, fileNames: list[str] | str, config: dict[str, list[int]] = {})

Set line data by reading it from a data file in LAMDA format.

Parameters:

  • model (Magrittetorch model object) – Magrittetorch model object to set.

  • fileNames (list of strings) – List of file names for the LAMDA line data files.

  • config (dict) – Optionally specify specific radiative transitions to consider.

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_quadrature(model: Model, nquads: int) → Model

Setter for the quadrature roots and weights for the Gauss-Hermite quadrature, used for integrating over (Gaussian) line profiles.

Parameters:

  • model (Model) – Magrittetorch model object

  • nquads (int) – Number of frequency quadrature points per line

Returns:

Updated Magrittetorch object

Return type:

Model

magrittetorch.tools.setup.set_rays_spherical_symmetry(model: Model, nrays: int, uniform: bool = True, nextra: int = 0, step: int = 1) → Model

Setter for rays in a 1D spherically symmetric model.

Parameters:

  • model (Magrittetorch model object) – Magrittetorch model object to set.

  • nrays (int) – Number of rays to use

  • uniform (bool) – Whether or not to use uniformly distributed rays.

  • nextra (int) – Number of extra rays to add.

  • step (int) – Step size used to step through the points when shooting rays (step=1 uses all points).

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object

magrittetorch.tools.setup.set_uniform_rays(model: Model, nrays: int, randomize: bool = False, first_ray: ndarray = array([1., 0., 0.])) → Model

Setter for rays to uniformly distributed directions.

Parameters:

  • model (Model) – Magrittetorch model object to set.

  • nrays (int) – Number of rays to use

  • randomized (bool) – Whether or not to randomize the directions of the rays.

  • first_ray (np.ndarray) – Direction vector of the first ray in the ray list. Has dimensions [3]

Returns:

out – Updated Magrittetorch object.

Return type:

Magrittetorch model object