* New reader from spectroscopy pre-analysis (currently reading only emissivity and named "spectra")

* Added gaunt factor approximation from Carson 1988

* first commit

* first commit

* second commit, updated background_fit

* added **kwargs to call function

* test

* he_like

* added pi diagnostic

* new changes

* commit

* error with dimensions

* now it works, but the data is not what is wanted to be

* changed impurity from ar to c
changed saving path

* dict

* updated dict, question about model_data in bayes

* now bayes works

* Temporarily stop caching (issues to be solved)

* Copied Bremss bayes opt to new file

* Marcosertoli/satakihino (#263)

* Temporarily stop caching (issues to be solved)

* Copied Bremss bayes opt to new file

---------

Co-authored-by: Marco Sertoli <[email protected]>

* CHanged .sel to .interp for plasma attributes as in other models.

* Ran pre-commit

* Fixed pre-commit errors

* Fixed pre-commit errors

* Reconverted interp to sel.
Made transmission filter a DataArray.
Started moving Aleksandra's spectra filtering to Diode model

* Fixed pre-commit

* Temporarily commented out t-interp case for diode filter (sel instead of interp...)

* st40reader.py passing pre-commit

* Moved background_fit to a method inside the diode filter model and generalised for spectral integration.

* Fixed plotting axes ranges

* Added generalised example that can use phantom data/equilibrium as well as experimental data from SXR cameras and diode filter models/data.

* Added emissivity attribute = local Brems emission integrated over wavelength.
Changed example geometry adding LOS to make inversion possible.

* First stab at file with workflows to calculate Zeff using tomo_1d or Bayesian inference

* Adapted tomo1d examples to run on "pi" bremsstrahlung. Working on phantom and real data.

* Temporary fix to slash channels in spectrometer that are not acquired

* Corrected factor multiplication for zeff calculation from bremsstrahlung

* Initialize variables now easily callable after having instatiated the class

* New example geometry and in standalone method so to be usable also from outside

* Refactored methods to estimate Zeff from bremsstrahlung using inversion or bayesian inference.

* Update bayesmodels.py

adding zeff to saved quantites

* Update bayes_workflow.py

zeff added to plots

* Update example_bayes_opt_brems.py

zeff added to phantom profiles

* Update bayesmodels.py

Zeff -> zeff

* Modified spectrometer reader to select good channels only

* Zeff blob summed over elements

* Zeff blob summed over elements

* Set uncertainty to zero until correctly calculated

* Changed filter limits to nested dictionary to be applicable to diagnostics with multiple quantities

* Corrected minor typo

* Formatting mod to pass pre-commit

* Temporary fix to get abstract reader test to pass.

* Modified workflows to accept both phantoms and experimental data, including fitting of TS.

Four example methods to run at the end of the file.

* Cleaned up so inference works better. Still some inconsistencies between Zeff and Impurity density...

* Refactored to pass pre-commit

* Marcosertoli/reorganize bremss calculation (#267)

* Temporarily stop caching (issues to be solved)

* Copied Bremss bayes opt to new file

* CHanged .sel to .interp for plasma attributes as in other models.

* Ran pre-commit

* Fixed pre-commit errors

* Fixed pre-commit errors

* Reconverted interp to sel.
Made transmission filter a DataArray.
Started moving Aleksandra's spectra filtering to Diode model

* Fixed pre-commit

* Temporarily commented out t-interp case for diode filter (sel instead of interp...)

* st40reader.py passing pre-commit

* Moved background_fit to a method inside the diode filter model and generalised for spectral integration.

* Fixed plotting axes ranges

* Added generalised example that can use phantom data/equilibrium as well as experimental data from SXR cameras and diode filter models/data.

* Added emissivity attribute = local Brems emission integrated over wavelength.
Changed example geometry adding LOS to make inversion possible.

* First stab at file with workflows to calculate Zeff using tomo_1d or Bayesian inference

* Adapted tomo1d examples to run on "pi" bremsstrahlung. Working on phantom and real data.

* Temporary fix to slash channels in spectrometer that are not acquired

* Corrected factor multiplication for zeff calculation from bremsstrahlung

* Initialize variables now easily callable after having instatiated the class

* New example geometry and in standalone method so to be usable also from outside

* Refactored methods to estimate Zeff from bremsstrahlung using inversion or bayesian inference.

* Update bayesmodels.py

adding zeff to saved quantites

* Update bayes_workflow.py

zeff added to plots

* Update example_bayes_opt_brems.py

zeff added to phantom profiles

* Update bayesmodels.py

Zeff -> zeff

* Modified spectrometer reader to select good channels only

* Zeff blob summed over elements

* Zeff blob summed over elements

* Set uncertainty to zero until correctly calculated

* Changed filter limits to nested dictionary to be applicable to diagnostics with multiple quantities

* Corrected minor typo

* Formatting mod to pass pre-commit

* Temporary fix to get abstract reader test to pass.

* Modified workflows to accept both phantoms and experimental data, including fitting of TS.

Four example methods to run at the end of the file.

* Cleaned up so inference works better. Still some inconsistencies between Zeff and Impurity density...

* Refactored to pass pre-commit

---------

Co-authored-by: Marco Sertoli <[email protected]>
Co-authored-by: michael-gemmell <[email protected]>

* Fixed linting issues

* Modified Bayesian phantoms and priors & changed plotting to include a rough uncertainty in Zeff

* Limited Zeff plotting to (0, 10)

* Moved start and end times to call kwargs

* Refactored workflow to get all the steps in the right order.
Both Bayes and Inv now working on phantoms. Inv also on data --> need to find other experimental cases with better EFIT.

* Deleted unused example.

* Fixed pre-commit error

* Fixed issues tied to "c" vs "ar"

* Profile assignment now element dependent

* Deleted print statement in interferometry model

* Deleted example_bayes_opt_brems.py as all zeff profile workflows are now contained in zeff_profile.py

* Deleted background_fit.py that is now included in filter model

* Reverted to previous figheader

---------

Co-authored-by: Marco Sertoli <[email protected]>
Co-authored-by: Aleksandra Alieva <[email protected]>
Co-authored-by: satakihino <[email protected]>
Co-authored-by: michael-gemmell <[email protected]>