hazel package¶

Subpackages¶

hazel.codes package
- Module contents

Submodules¶

hazel.atmosphere module¶

class hazel.atmosphere.General_atmosphere(atm_type, name)¶

Bases: object

Methods

`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle models
`init_reference`([check_borders])	Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode
`reset_reference`()	Reset reference model to the original reference loaded from file
`set_reference`([cycle])	Set reference model to that of the current parameters
`to_physical`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.
`to_transformed`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.

allocate_info_cycles(n_cycles)¶

Set the appropriate variables to store per-cycle models

Parameters:: n_cycles (int) – Number of cycles
Return type:: None

init_reference(check_borders=False)¶

Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode

Parameters:: check_borders (bool) – Check that the input parameters are inside the ranges of parameters
Return type:: None

reset_reference()¶

Reset reference model to the original reference loaded from file

Parameters:: None –
Return type:: None

set_reference(cycle=None)¶

Set reference model to that of the current parameters

Parameters:: None –
Return type:: None

to_physical()¶

Transform the atmospheric parameters from transformed domain to physical domain given the ranges. This only applies in inversion mode

Parameters:: None –
Return type:: None

to_transformed()¶

Transform the atmospheric parameters from transformed domain to physical domain given the ranges. This only applies in inversion mode

Parameters:: None –
Return type:: None

hazel.chromosphere module¶

class hazel.chromosphere.Hazel_atmosphere(working_mode, name='')¶

Bases: General_atmosphere

Methods

`add_active_line`(line, spectrum, wvl_range)	Add an active lines in this atmosphere
`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle models
`init_reference`([check_borders])	Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode
`load_reference_model`(model_file, verbose)	Load a reference model or a model for every pixel for synthesis/inversion
`nodes_to_model`()	Transform from nodes to model
`reset_reference`()	Reset reference model to the original reference loaded from file
`set_parameters`(pars, ff)	Set the parameters of this model chromosphere
`set_reference`([cycle])	Set reference model to that of the current parameters
`synthesize`([stokes, returnRF, nlte])	Carry out the synthesis and returns the Stokes parameters
`to_physical`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.
`to_transformed`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.

print_parameters
select_coordinate_system

add_active_line(line, spectrum, wvl_range)¶

Add an active lines in this atmosphere

Parameters:

lines (str) – Line to activate: [‘10830’,’5876’]
spectrum (Spectrum) – Spectrum object
wvl_range (float) – Vector containing wavelength range over which to synthesize this line

Return type:

None

load_reference_model(model_file, verbose)¶

Load a reference model or a model for every pixel for synthesis/inversion

Parameters:

model_file (str) – String with the name of the file. Extensions can currently be “1d” or “h5”
verbose (bool) – verbosity flag

Return type:

None

nodes_to_model()¶

Transform from nodes to model

Parameters:: None –
Return type:: None

print_parameters(first=False, error=False)¶

select_coordinate_system()¶

set_parameters(pars, ff)¶

Set the parameters of this model chromosphere

Parameters:

pars (list of float) – This list contains the following parameters in order: Bx, By, Bz, tau, v, delta, beta, a
ff (float) – Filling factor

Return type:

None

synthesize(stokes=None, returnRF=False, nlte=None)¶

Carry out the synthesis and returns the Stokes parameters

Parameters:

stokes (float) – An array of size [4 x nLambda] with the input Stokes parameter.

Returns:

stokes –

Stokes parameters, with the first index containing the wavelength displacement and the remaining: containing I, Q, U and V. Size (4,nLambda)

Return type:

float

hazel.configuration module¶

class hazel.configuration.Configuration(filename)¶: Bases: object

hazel.exceptions module¶

exception hazel.exceptions.Error¶

Bases: Exception

Base class for other exceptions

exception hazel.exceptions.NumericalErrorHazel¶

Bases: Error

Raised when there was a problem with Hazel

exception hazel.exceptions.NumericalErrorSIR¶

Bases: Error

Raised when there was a problem with SIR

hazel.forward_nn module¶

class hazel.forward_nn.Dataset(hyperparameters, tau_all, ne_all, vturb_all, T_all, vlos_all)¶

Bases: Dataset

Methods

__call__(index)

Call self as a function.

class hazel.forward_nn.Forward(gpu=0, checkpoint=None, readir=None, verbose=0)¶

Bases: object

Methods

predict

predict(tau_all, ne_all, vturb_all, T_all, vlos_all)¶

hazel.graphnet module¶

class hazel.graphnet.EncodeProcessDecode(node_input_size, edge_input_size, global_input_size, latent_size, mlp_hidden_size, mlp_n_hidden_layers, n_message_passing_steps, output_size)¶

Bases: Module

Methods

`add_module`(name, module)	Add a child module to the current module.
`apply`(fn)	Apply `fn` recursively to every submodule (as returned by `.children()`) as well as self.
`bfloat16`()	Casts all floating point parameters and buffers to `bfloat16` datatype.
`buffers`([recurse])	Return an iterator over module buffers.
`children`()	Return an iterator over immediate children modules.
`compile`(args, *kwargs)	Compile this Module's forward using `torch.compile()`.
`cpu`()	Move all model parameters and buffers to the CPU.
`cuda`([device])	Move all model parameters and buffers to the GPU.
`double`()	Casts all floating point parameters and buffers to `double` datatype.
`eval`()	Set the module in evaluation mode.
`extra_repr`()	Set the extra representation of the module.
`float`()	Casts all floating point parameters and buffers to `float` datatype.
`forward`(node, edge_attr, edge_index, u, batch)	Forward pass of the GraphNet
`get_buffer`(target)	Return the buffer given by `target` if it exists, otherwise throw an error.
`get_extra_state`()	Return any extra state to include in the module's state_dict.
`get_parameter`(target)	Return the parameter given by `target` if it exists, otherwise throw an error.
`get_submodule`(target)	Return the submodule given by `target` if it exists, otherwise throw an error.
`half`()	Casts all floating point parameters and buffers to `half` datatype.
`ipu`([device])	Move all model parameters and buffers to the IPU.
`load_state_dict`(state_dict[, strict, assign])	Copy parameters and buffers from `state_dict` into this module and its descendants.
`modules`()	Return an iterator over all modules in the network.
`named_buffers`([prefix, recurse, ...])	Return an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.
`named_children`()	Return an iterator over immediate children modules, yielding both the name of the module as well as the module itself.
`named_modules`([memo, prefix, remove_duplicate])	Return an iterator over all modules in the network, yielding both the name of the module as well as the module itself.
`named_parameters`([prefix, recurse, ...])	Return an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.
`parameters`([recurse])	Return an iterator over module parameters.
`register_backward_hook`(hook)	Register a backward hook on the module.
`register_buffer`(name, tensor[, persistent])	Add a buffer to the module.
`register_forward_hook`(hook, *[, prepend, ...])	Register a forward hook on the module.
`register_forward_pre_hook`(hook, *[, ...])	Register a forward pre-hook on the module.
`register_full_backward_hook`(hook[, prepend])	Register a backward hook on the module.
`register_full_backward_pre_hook`(hook[, prepend])	Register a backward pre-hook on the module.
`register_load_state_dict_post_hook`(hook)	Register a post hook to be run after module's `load_state_dict` is called.
`register_module`(name, module)	Alias for `add_module()`.
`register_parameter`(name, param)	Add a parameter to the module.
`register_state_dict_pre_hook`(hook)	Register a pre-hook for the `load_state_dict()` method.
`requires_grad_`([requires_grad])	Change if autograd should record operations on parameters in this module.
`set_extra_state`(state)	Set extra state contained in the loaded state_dict.
`share_memory`()	See `torch.Tensor.share_memory_()`.
`state_dict`(*args[, destination, prefix, ...])	Return a dictionary containing references to the whole state of the module.
`to`(args, *kwargs)	Move and/or cast the parameters and buffers.
`to_empty`(*, device[, recurse])	Move the parameters and buffers to the specified device without copying storage.
`train`([mode])	Set the module in training mode.
`type`(dst_type)	Casts all parameters and buffers to `dst_type`.
`xpu`([device])	Move all model parameters and buffers to the XPU.
`zero_grad`([set_to_none])	Reset gradients of all model parameters.

__call__
decode
encode
process
process_step
weights_init

decode(node)¶

encode(node, edge_attr)¶

forward(node, edge_attr, edge_index, u, batch)¶

Forward pass of the GraphNet

Parameters:

node (float) – Information of the nodes, an array of size (n_nodes, node_attr_size). node_attr_size is the number of features encoded in the nodes
edge_attr (float) – Information of the edges, an array of size (n_edges, edge_attr_size). edge_attr_size is the number of features encoded in the edges
edge_index (int) – Indices of the input and output edges, an array of size (2, n_edges).
u (float) – [description]
batch ([type]) – [description]

Returns:

[description]

Return type:

[type]

process(node, edge_attr, edge_index, u, batch)¶

process_step(processor_network, node, edge_attr, edge_index, u, batch)¶

weights_init()¶

hazel.hsra module¶

hazel.hsra.hsra_continuum(x)¶

hazel.io module¶

class hazel.io.Generic_SIR_file(filename)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

class hazel.io.Generic_hazel_file(filename)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

class hazel.io.Generic_mask_file(filename, root)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

class hazel.io.Generic_observed_file(filename, root)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

class hazel.io.Generic_output_file(filename)¶

Bases: object

Methods

close
get_npixel
open
write

close()¶

get_npixel()¶

open(model)¶

write(model, pixel=0, randomization=0)¶

class hazel.io.Generic_parametric_file(filename)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

class hazel.io.Generic_stray_file(filename)¶

Bases: object

Methods

close
get_npixel
open
read

close()¶

get_npixel()¶

open()¶

read(pixel=None)¶

hazel.model module¶

class hazel.model.Model(config=None, working_mode='synthesis', verbose=0, debug=False, rank=0, randomization=None, root='')¶

Bases: object

Methods

`add_chromosphere`(atmosphere)	Programmatically add a chromosphere
`add_parametric`(atmosphere)	Programmatically add a parametric atmosphere
`add_photosphere`(atmosphere)	Programmatically add a photosphere
`add_spectral`(spectral)	Programmatically add a spectral region
`add_straylight`(atmosphere)	Programmatically add a straylight atmosphere
`add_topology`(atmosphere_order)	Add a new topology
`backtracking_parabolic`(dchi2, ddchi2[, ...])	Do the backtracking to get an optimal value of lambda in the LM algorithm
`compute_chi2`([only_chi2, weights])	Compute chi2 for all spectral regions
`compute_uncertainty`()	Compute the uncertainty in the parameters at the minimum with the current Hessian
`find_active_parameters`(cycle)	Find all active parameters in all active atmospheres in the current cycle
`flatten_parameters_to_reference`(cycle)	Flatten all current parameters to the reference atmosphere
`init_sir`()	Initialize SIR for this synthesis.
`init_sir_external`()	Initialize SIR for this synthesis
`invert`([randomize, randomization_ind])	Invert all atmospheres
`invert_external`(algorithm[, use_jacobian])	Invert all atmospheres
`modified_svd_inverse`(H[, tol])	Compute the inverse of the Hessian matrix using a modified SVD, by thresholding each subpsace separately
`normalize_ff`(nodes)	Normalize all filling factors so that they add to one to avoid later problems.
`randomize`()	Randomize all free parameters to lie uniformly in the interval [-2,2] in the transformed domain
`remove_unused_atmosphere`()	Remove unused atmospheres
`set_new_model`(nodes)	Set the nodes of the current model to the values passed on the arguments
`set_nlte`(option)	Set calculation of Ca II 8542 A to NLTE
`setup`()	Setup the model for synthesis/inversion.
`synthesize`([perturbation])	Synthesize all atmospheres
`synthesize_and_compute_rf`([compute_rf, ...])	Compute response functions for all free parameters according to all active_parameters
`synthesize_spectral_region`(spectral_region)	Synthesize all atmospheres for a single spectral region and normalize to the continuum of the quiet Sun at disk center
`use_configuration`(config_dict)	Use a configuration file

backtracking_brent
close_output
exit_hazel
open_output
read_observation
write_output

add_chromosphere(atmosphere)¶

Programmatically add a chromosphere

Parameters:: atmosphere (dict) – Dictionary containing the following data ‘Name’, ‘Spectral region’, ‘Height’, ‘Line’, ‘Wavelength’, ‘Reference atmospheric model’, ‘Ranges’, ‘Nodes’
Return type:: None

add_parametric(atmosphere)¶

Programmatically add a parametric atmosphere

Parameters:: atmosphere (dict) – Dictionary containing the following data ‘Name’, ‘Spectral region’, ‘Wavelength’, ‘Reference atmospheric model’, ‘Type’, ‘Ranges’, ‘Nodes’
Return type:: None

add_photosphere(atmosphere)¶

Programmatically add a photosphere

Parameters:: atmosphere (dict) – Dictionary containing the following data ‘Name’, ‘Spectral region’, ‘Height’, ‘Line’, ‘Wavelength’, ‘Reference atmospheric model’, ‘Ranges’, ‘Nodes’
Return type:: None

add_spectral(spectral)¶

Programmatically add a spectral region

Parameters:: spectral (dict) – Dictionary containing the following data ‘Name’, ‘Wavelength’, ‘Topology’, ‘Weights Stokes’, ‘Wavelength file’, ‘Wavelength weight file’, ‘Observations file’, ‘Mask file’
Return type:: None

add_straylight(atmosphere)¶

Programmatically add a straylight atmosphere

Parameters:: atmosphere (dict) – Dictionary containing the following data ‘Name’, ‘Spectral region’, ‘Reference atmospheric model’, ‘Ranges’, ‘Nodes’
Return type:: None

add_topology(atmosphere_order)¶

Add a new topology

Parameters:: topology (str) – Topology
Return type:: None

backtracking_brent(dchi2, ddchi2, maxiter=10, bounds=[-3.0, 3.0], tol=0.01)¶

backtracking_parabolic(dchi2, ddchi2, direction='down', maxiter=5, lambda_init=0.001, current_chi2=10000000000.0)¶

Do the backtracking to get an optimal value of lambda in the LM algorithm

Parameters:

dchi2 (float) – Gradient of the chi2
ddchi2 (float) – Second order derivatives with which the Hessian is computed
direction (str, optional) – Direction on which do the backtracking (‘down’/’up’ for decreasing/increasing lambda)
maxiter (int) – Maximum number of iterations
lambda_init (float) – Initial value of lambda
current_chi2 (float) – Current best chi2 to compare with those of the backtracking

Returns:

lambda_opt (float) – Optimal value of lambda found. Bracketed value if bracketing has been possible or just the best value otherwise
bracketed (bool) – True if the best value has been bracketed
best_chi2 (float) – Best value of chi2 found

close_output()¶

compute_chi2(only_chi2=False, weights=None)¶

Compute chi2 for all spectral regions

Parameters:

obs (float) – Vector of observations
only_chi2 (bool) – Control whether the gradient and Hessian is returned

Return type:

None

compute_uncertainty()¶

Compute the uncertainty in the parameters at the minimum with the current Hessian

Parameters:: None –
Return type:: None

exit_hazel()¶

find_active_parameters(cycle)¶

Find all active parameters in all active atmospheres in the current cycle

Parameters:: cycle (int) – Cycle to consider
Return type:: None

flatten_parameters_to_reference(cycle)¶

Flatten all current parameters to the reference atmosphere

Parameters:: cycle (int) – Current cycle
Return type:: None

init_sir()¶

Initialize SIR for this synthesis. This version does not make use of any external file, which might be not safe when running in MPI mode.

Parameters:: None –
Return type:: None

init_sir_external()¶

Initialize SIR for this synthesis

Parameters:: None –
Return type:: None

invert(randomize=False, randomization_ind=None)¶

Invert all atmospheres

Parameters:: None –
Return type:: None

invert_external(algorithm, use_jacobian=False, **kwargs)¶

Invert all atmospheres

Parameters:: None –
Return type:: None

modified_svd_inverse(H, tol=1e-08)¶

Compute the inverse of the Hessian matrix using a modified SVD, by thresholding each subpsace separately

Parameters:

H (float) – Hessian matrix
tol (float) – Tolerance for the singular value of each subspace

Return type:

None

normalize_ff(nodes)¶

Normalize all filling factors so that they add to one to avoid later problems. We use a softmax function to make sure they all add to one and can be unconstrained

ff_i = exp(x_i) / sum(exp(x_i))

Parameters:: None –
Return type:: None

open_output()¶

randomize()¶: Randomize all free parameters to lie uniformly in the interval [-2,2] in the transformed domain

read_observation()¶

remove_unused_atmosphere()¶

Remove unused atmospheres

Parameters:: None –
Return type:: None

set_new_model(nodes)¶

Set the nodes of the current model to the values passed on the arguments

Parameters:: nodes (float) – Array with the new set of nodes
Return type:: None

set_nlte(option)¶

Set calculation of Ca II 8542 A to NLTE

Parameters:: option (bool) – Set to True to use NLTE, False to use LTE

setup()¶

Setup the model for synthesis/inversion. This setup includes adding the topologies, removing unused atmospheres, reading the number of cycles for the inversion and some sanity checks

Parameters:: None –
Return type:: None

synthesize(perturbation=False)¶

Synthesize all atmospheres

Parameters:: perturbation (bool) – Set to True if you are synthesizing with a perturbation. In this case, the synthesis is saved in spectrum.stokes_perturbed instead of spectrum.stokes
Return type:: None

synthesize_and_compute_rf(compute_rf=False, include_jacobian=False)¶

Compute response functions for all free parameters according to all active_parameters

Parameters:: compute_rf (bool (optional, default False)) – If True, then compute the response functions. If not, just compute the synthesis.
Return type:: None

synthesize_spectral_region(spectral_region, perturbation=False)¶

Synthesize all atmospheres for a single spectral region and normalize to the continuum of the quiet Sun at disk center

Parameters:

spectral_region (str) – Spectral region to synthesize
perturbation (bool) – Set to True if you are synthesizing with a perturbation. In this case, the synthesis is saved in spectrum.stokes_perturbed instead of spectrum.stokes

Return type:

None

use_configuration(config_dict)¶

Use a configuration file

Parameters:: config_dict (dict) – Dictionary containing all the options from the configuration file previously read
Return type:: None

write_output(randomization=0)¶

hazel.multiprocess module¶

class hazel.multiprocess.Iterator(use_mpi=False)¶

Bases: object

Methods

`mpi_parent_work`([start, end])	MPI parent work
`mpi_workers_work`()	MPI workers work
`nonmpi_work`([start, end])	Do the synthesis/inversion for all pixels in the models
`run_all_pixels`([start, end])	Run synthesis/inversion for all pixels

cleanup
get_rank
use_model

cleanup(*args)¶

get_rank(n_workers=0)¶

mpi_parent_work(start=0, end=None)¶

MPI parent work

Parameters:

start (int) – Initial pixel, by default 0
end (int) – Final pixel, by default the number of pixels in the observations

Return type:

None

mpi_workers_work()¶

MPI workers work

Parameters:: None –
Return type:: None

nonmpi_work(start=0, end=None)¶

Do the synthesis/inversion for all pixels in the models

Parameters:: model (model) – Model to be synthesized
Return type:: None

run_all_pixels(start=0, end=None)¶

Run synthesis/inversion for all pixels

Parameters:

start (int, optional) – Initial pixel, by default 0
end (int) – Final pixel, by default the number of pixels in the observations

use_model(model=None)¶

class hazel.multiprocess.tags(value, names=None, *values, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: IntEnum

Attributes:

denominator: the denominator of a rational number in lowest terms
imag: the imaginary part of a complex number
numerator: the numerator of a rational number in lowest terms
real: the real part of a complex number

Methods

`as_integer_ratio`(/)	Return a pair of integers, whose ratio is equal to the original int.
`bit_count`(/)	Number of ones in the binary representation of the absolute value of self.
`bit_length`(/)	Number of bits necessary to represent self in binary.
`conjugate`	Returns self, the complex conjugate of any int.
`from_bytes`(/, bytes[, byteorder, signed])	Return the integer represented by the given array of bytes.
`is_integer`(/)	Returns True.
`to_bytes`(/[, length, byteorder, signed])	Return an array of bytes representing an integer.

DONE = 1¶

DONOTHING = 4¶

EXIT = 2¶

READY = 0¶

START = 3¶

hazel.parametric module¶

class hazel.parametric.Parametric_atmosphere(working_mode, name='')¶

Bases: General_atmosphere

Methods

`add_active_line`(spectrum, wvl_range)	Add an active lines in this atmosphere
`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle models
`init_reference`([check_borders])	Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode
`load_reference_model`(model_file, verbose)	Load a reference model or a model for every pixel for synthesis/inversion
`nodes_to_model`()	Transform from nodes to model
`reset_reference`()	Reset reference model to the original reference loaded from file
`set_parameters`(pars, ff)	Set parameters of the model
`set_reference`([cycle])	Set reference model to that of the current parameters
`synthesize`([stokes, nlte])	Carry out the synthesis and returns the Stokes parameters
`to_physical`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.
`to_transformed`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.

print_parameters

add_active_line(spectrum, wvl_range)¶

Add an active lines in this atmosphere

Parameters:: None –
Return type:: None

load_reference_model(model_file, verbose)¶

Load a reference model or a model for every pixel for synthesis/inversion

Parameters:

model_file (str) – String with the name of the file. Extensions can currently be “1d” or “h5”
verbose (bool) – verbosity flag

Return type:

None

nodes_to_model()¶

Transform from nodes to model

Parameters:: None –
Return type:: None

print_parameters(first=False, error=False)¶

set_parameters(pars, ff)¶

Set parameters of the model

Parameters:

pars (list of floats) – Values of the parameters: lambda0, sigma, depth, a
ff (float) – Filling factor

Return type:

None

synthesize(stokes=None, nlte=None)¶

Carry out the synthesis and returns the Stokes parameters

Parameters:

stokes (float) – An array of size [4 x nLambda] with the input Stokes parameter.

Returns:

stokes –

Stokes parameters, with the first index containing the wavelength displacement and the remaining: containing I, Q, U and V. Size (4,nLambda)

Return type:

float

hazel.photosphere module¶

class hazel.photosphere.SIR_atmosphere(working_mode, name='', root='', verbose=0)¶

Bases: General_atmosphere

Methods

`add_active_line`(lines, spectrum, wvl_range, ...)	Add an active lines in this atmosphere
`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle models
`get_parameters`()	Get the curent parameters as a model
`init_reference`([check_borders])	Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode
`interpolate_nodes`(log_tau, reference, nodes, ...)	Generate a model atmosphere by interpolating the defined nodes.
`interpolate_nodes_rf`(log_tau, reference, ...)	Generate a model atmosphere by interpolating the defined nodes.
`list_lines`()	List the lines available in SIR for synthesis
`load_reference_model`(model_file, verbose)	Load a reference model or a model for every pixel for synthesis/inversion
`model_to_nodes`()	Transform from model to nodes
`nodes_to_model`()	Transform from nodes to model
`reset_reference`()	Reset reference model to the original reference loaded from file
`set_parameters`(model, ff, vmac)	Set the parameters of the current model to those passed as argument
`set_reference`([cycle])	Set reference model to that of the current parameters
`synthesize`(stokes_in[, returnRF, nlte])	Carry out the synthesis and returns the Stokes parameters and the response functions to all physical variables at all depths
`to_physical`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.
`to_transformed`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.

print_parameters

add_active_line(lines, spectrum, wvl_range, verbose)¶

Add an active lines in this atmosphere

Parameters:

lines (str) – Line to activate
spectrum (Spectrum) – Spectrum object
wvl_range (float) – Vector containing wavelength range over which to synthesize this line

Return type:

None

get_parameters()¶

Get the curent parameters as a model

Parameters:: None –
Returns:: model
Return type:: a 6xN photspheric model

interpolate_nodes(log_tau, reference, nodes, nodes_location)¶

Generate a model atmosphere by interpolating the defined nodes. The interpolation order depends on the number of nodes.

Parameters:

log_tau (float) – Vector of log optical depth at 500 nm
reference (float) – Vector with the reference atmosphere to which the nodes are added
nodes (float) – List with the position of the nodes

Returns:

Vector with the interpolated atmosphere

Return type:

real

interpolate_nodes_rf(log_tau, reference, nodes, lower, upper)¶

Generate a model atmosphere by interpolating the defined nodes. The interpolation order depends on the number of nodes.

Parameters:

log_tau (float) – Vector of log optical depth at 500 nm
reference (float) – Vector with the reference atmosphere to which the nodes are added
nodes (float) – List with the position of the nodes

Returns:

Vector with the interpolated atmosphere

Return type:

real

list_lines()¶: List the lines available in SIR for synthesis

load_reference_model(model_file, verbose)¶

Load a reference model or a model for every pixel for synthesis/inversion

Parameters:

model_file (str) – String with the name of the file. Extensions can currently be “1d” or “h5”
verbose (bool) – Verbosity

Return type:

None

model_to_nodes()¶

Transform from model to nodes

Parameters:: None –
Return type:: None

nodes_to_model()¶

Transform from nodes to model

Parameters:: None –
Return type:: None

print_parameters(first=False, error=False)¶

set_parameters(model, ff, vmac)¶

Set the parameters of the current model to those passed as argument

Parameters:

model_in (float) – Array with the model
ff (float) – Value of the filling factor
vmac (float) – Value of the macroturbulent velocity

Return type:

None

synthesize(stokes_in, returnRF=False, nlte=False)¶

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

Parameters:

stokes_in (float) – An array of size [4 x nLambda] with the input Stokes parameter. It is irrelevant in this case because we assume that all SIR atmospheres have the Planck function as boundary.
returnRF (bool, optional) – Return response functions

Returns:

stokes (float) –

Stokes parameters, with the first index containing the wavelength displacement and the remaining
containing I, Q, U and V. Size (5,nLambda)
rf (float (optional)) –

Response functions to T, Pe, vmic, B, v, theta, phi, all of size (4,nLambda,nDepth), plus the RF to macroturbulence of size (4,nLambda)
It is not returned if returnRF=False

hazel.sir module¶

class hazel.sir.Sir¶

Bases: object

Methods

synth
synthRF

synth(model, macroturbulence, filling_factor, stray)¶

synthRF(model, macroturbulence, filling_factor, stray)¶

hazel.spectrum module¶

class hazel.spectrum.Spectrum(wvl=None, weights=None, observed_file=None, name=None, stokes_weights=None, los=None, boundary=None, mask_file=None, instrumental_profile=None, save_all_cycles=False, root='', wvl_lr=None)¶

Bases: object

Methods

`add_mask_file`(mask_file)	Add a new file with a mask
`add_name`(name)	Add a new name to this spectral region
`add_observed_file`(observed_file)	Add a new file with observations and open it
`add_spectrum`(wvl, wvl_lr)	Add a new spectrum, initializing the Stokes parameters containers
`add_stokes_weights`(weights)	Add Stokes weights
`add_weights`(weights)	Add new weights for the Stokes parameters
`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle spectra
`close_observation`()	Close the file with the observations for this spectrum
`next_pixel`()	Skip to next pixel
`open_observation`()	Open the file with the observations for this spectrum
`read_mask`([pixel])	Read the next pixel with mask
`read_observation`([pixel])	Read the next pixel with observations
`read_straylight`([pixel])	Read the next pixel with straylight
`set_boundary`(boundary)	Set a new value for the boundary condition
`set_los`(los)	Set a new value for the LOS
`set_normalization`(normalization)	Set a new value for the LOS

add_mask_file(mask_file)¶

Add a new file with a mask

Parameters:: mask_file (str) – File with the mask
Return type:: None

add_name(name)¶

Add a new name to this spectral region

Parameters:: name (str) – Name of the region
Return type:: None

add_observed_file(observed_file)¶

Add a new file with observations and open it

Parameters:: observed_file (str) – File with the observations
Return type:: None

add_spectrum(wvl, wvl_lr)¶

Add a new spectrum, initializing the Stokes parameters containers

Parameters:: wvl (float) – Wavelength axis
Return type:: None

add_stokes_weights(weights)¶

Add Stokes weights

Parameters:: weights (float) – Array of size 4 with the weights for all Stokes parameters
Return type:: None

add_weights(weights)¶

Add new weights for the Stokes parameters

Parameters:: weights (float) – Weights
Return type:: None

allocate_info_cycles(n_cycles)¶

Set the appropriate variables to store per-cycle spectra

Parameters:: n_cycles (int) – Number of cycles
Return type:: None

close_observation()¶

Close the file with the observations for this spectrum

Parameters:: None –
Return type:: None

next_pixel()¶

Skip to next pixel

Parameters:: None –
Return type:: None

open_observation()¶

Open the file with the observations for this spectrum

Parameters:: None –
Return type:: None

read_mask(pixel=None)¶

Read the next pixel with mask

Parameters:: pixel (int) – Pixel to read
Return type:: None

read_observation(pixel=None)¶

Read the next pixel with observations

Parameters:: pixel (int) – Pixel to read
Return type:: None

read_straylight(pixel=None)¶

Read the next pixel with straylight

Parameters:: pixel (int) – Pixel to read
Return type:: None

set_boundary(boundary)¶

Set a new value for the boundary condition

Parameters:: los (list or array of size 4) – I0, Q0, U0, V0
Return type:: None

set_los(los)¶

Set a new value for the LOS

Parameters:: los (list or array of size 3) – theta, phi and gamma of the line-of-sight
Return type:: None

set_normalization(normalization)¶

Set a new value for the LOS

Parameters:: los (str) – ‘off-limb’ or ‘on-disk’
Return type:: None

hazel.stray module¶

class hazel.stray.Straylight_atmosphere(working_mode, name='')¶

Bases: General_atmosphere

Methods

`add_active_line`(spectrum, wvl_range)	Add an active lines in this atmosphere
`allocate_info_cycles`(n_cycles)	Set the appropriate variables to store per-cycle models
`init_reference`([check_borders])	Initialize the reference atmosphere to the values of the parameters, doing the inverse transformation if in inversion mode
`load_reference_model`(model_file, verbose)	Load a reference model or a model for every pixel for synthesis/inversion
`nodes_to_model`()	Transform from nodes to model
`reset_reference`()	Reset reference model to the original reference loaded from file
`set_reference`([cycle])	Set reference model to that of the current parameters
`set_straylight`(stokes)	Load a reference model or a model for every pixel for synthesis/inversion
`synthesize`([nlte])	Carry out the synthesis and returns the Stokes parameters
`to_physical`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.
`to_transformed`()	Transform the atmospheric parameters from transformed domain to physical domain given the ranges.

print_parameters
set_parameters

add_active_line(spectrum, wvl_range)¶

Add an active lines in this atmosphere

Parameters:: None –
Return type:: None

load_reference_model(model_file, verbose)¶

Load a reference model or a model for every pixel for synthesis/inversion

Parameters:

model_file (str) – String with the name of the file. Extensions can currently be “1d” or “h5”
verbose (bool) – verbosity flag

Return type:

None

nodes_to_model()¶

Transform from nodes to model

Parameters:: None –
Return type:: None

print_parameters(first=False, error=False)¶

set_parameters(pars, ff)¶

set_straylight(stokes)¶

Load a reference model or a model for every pixel for synthesis/inversion

Parameters:

model_file (str) – String with the name of the file. Extensions can currently be “1d” or “h5”
verbose (bool) – verbosity flag

Return type:

None

synthesize(nlte=None)¶

Carry out the synthesis and returns the Stokes parameters

Parameters:

None –

Returns:

stokes –

Stokes parameters, with the first index containing the wavelength displacement and the remaining: containing I, Q, U and V. Size (4,nLambda)

Return type:

float

hazel.tools module¶

class hazel.tools.File_chromosphere(file=None, mode='single')¶

Bases: object

Class that defines a model atmosphere and can be used to easily save observations

Methods

`save`(file[, default])	Save the curent observation
`set_default`([n_pixel, default])	Set the atmosphere to one of the default ones available in the code
`set_size`([n_pixel])	Set the number of pixels of the current atmosphere

save(file, default=None)¶

Save the curent observation

Parameters:: file (str) – Name of the output files. Extensions will be added to it
Return type:: None

set_default(n_pixel=1, default='disk')¶

Set the atmosphere to one of the default ones available in the code

Parameters:

n_pixel (int (optional, equal to 1 as default)) – Number of pixels of the output
default (str ('disk' -> on-disk observations, 'offlimb' -> off-limb observations)) –

Return type:

None

set_size(n_pixel=1)¶

Set the number of pixels of the current atmosphere

Parameters:: n_pixel (int (optional, equal to 1 as default)) – Number of pixels of the output
Return type:: None

class hazel.tools.File_observation(file=None, mode='single')¶

Bases: object

Class that defines an observation. This can be used to easily save observations in the appropriate format

Methods

`save`(file)	Save the curent observation
`set_size`(n_lambda[, n_pixel])	Set the number of wavelengths and number of pixels of the current observation

save(file)¶

Save the curent observation

Parameters:: file (str) – Name of the output files. Extensions will be added to it
Return type:: None

set_size(n_lambda, n_pixel=1)¶

Set the number of wavelengths and number of pixels of the current observation

Parameters:

n_lambda (int) – Number of wavelength points
n_pixel (int (optional, equal to 1 as default)) – Number of pixels of the output

Return type:

None

class hazel.tools.File_photosphere(file=None, mode='single')¶

Bases: object

Class that defines a model photosphere and can be used to easily save observations

Methods

`save`(file[, default])	Save the curent model
`set_default`([n_pixel, default])	Set the atmosphere to one of the default ones available in the code
`set_size`(nz[, n_pixel])	Set the number of depth points and number of pixels of the current atmosphere

list_models

list_models()¶

save(file, default=None)¶

Save the curent model

Parameters:: file (str) – Name of the output files. Extensions will be added to it
Return type:: None

set_default(n_pixel=1, default='hsra')¶

Set the atmosphere to one of the default ones available in the code

Parameters:

n_pixel (int (optional, equal to 1 as default)) – Number of pixels of the output
default (str ('hsra' -> Harvard-Smithsonian Reference Atmosphere)) –

Return type:

None

set_size(nz, n_pixel=1)¶

Set the number of depth points and number of pixels of the current atmosphere

Parameters:

nz (int) – Number of depth points of the atmosphere
n_pixel (int (optional, equal to 1 as default)) – Number of pixels of the output

Return type:

None

hazel.transforms module¶

hazel.transforms.physical_to_transformed(x, lower, upper)¶

Transform from physical parameters to unconstrained physical parameters

Parameters:

x (float) – Any array
lower (float) – Lower limit of the parameter
upper (float) – Upper limit of the parameter

Returns:

out – Transformed parameters

Return type:

float

hazel.transforms.transformed_to_physical(x, lower, upper)¶

Transform from unconstrained physical parameters to physical parameters

Parameters:

x (float) – Any array
lower (float) – Lower limit of the parameter
upper (float) – Upper limit of the parameter

Returns:

out – Transformed parameters

Return type:

float

hazel.util module¶

hazel.util.fvoigt(damp, v)¶

Fast implementation of the Voigt-Faraday function

Parameters:

damp (float) – damping parameter
v (float) – normalized wavelength (lambda-lambda0) / sigma

Returns:

voigt, faraday – Value of the Voigt and Faraday functions

Return type:

float

Notes

A rational approximation to the complex error function is used after Hui, Armstrong, and Wray(1978, JQSRT 19, 509). H and F are the real and imaginary parts of such function, respectively. The procedure is inspired on that in SIR (Ruiz Cobo & del Toro Iniesta 1992, ApJ 398, 385). On its turn, that routine was taken from modifications by A. Wittmann (1986) to modifications by S.K. Solanki (1985) to an original FORTRAN routine written by J.W. Harvey and A. Nordlund.

hazel.util.i0_allen(wavelength, muAngle)¶: Return the solar intensity at a specific wavelength and heliocentric angle wavelength: wavelength in angstrom muAngle: cosine of the heliocentric angle

hazel.util.isint(str)¶

hazel.util.lower_dict_keys(d)¶

hazel.util.show_tree(hdf5_file)¶

hazel package¶

Subpackages¶

Submodules¶

hazel.atmosphere module¶

hazel.chromosphere module¶

hazel.configuration module¶

hazel.exceptions module¶

hazel.forward_nn module¶

hazel.graphnet module¶

hazel.hsra module¶

hazel.io module¶

hazel.model module¶

hazel.multiprocess module¶

hazel.parametric module¶

hazel.photosphere module¶

hazel.sir module¶

hazel.spectrum module¶

hazel.stray module¶

hazel.tools module¶

hazel.transforms module¶

hazel.util module¶

Module contents¶