Marcosertoli/satakihino #263
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marcosertoli
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Jul 31, 2023
* 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]>
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Fixed Bayes workflow