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Update and tidy #6

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merged 67 commits into from
May 6, 2023
Merged

Update and tidy #6

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29a8701
autoaddition of priors in BaysarPosterior instanciation as been moved…
dgahle Sep 28, 2020
84cbbdb
get_priors in BaysarPosterior now checks what priors have been added …
dgahle Sep 28, 2020
1693fc3
updated .gitignore to not track things in .idea folders (pycharm)
dgahle Sep 28, 2020
00033fe
updated .gitignore to not track things in .idea/ folders (pycharm)
dgahle Sep 28, 2020
63e804e
.gitignore changes unsuccessful
dgahle Sep 28, 2020
0d98728
.gitignore changes unsuccessful
dgahle Sep 28, 2020
903ccda
Changes to .gitignore to ignore pycharm files
dgahle Sep 28, 2020
197183c
updated to ignore pycharm stuff. To update .gitignore 'git rm -r --ca…
dgahle Sep 28, 2020
6881905
Updated ChargeStateOrderPrior to be based on a gaussian high pass cos…
dgahle Sep 29, 2020
c4f6bd3
Updated TauPrior so that the threshold (mean) of the gaussian high pa…
dgahle Sep 29, 2020
07d7abc
New baysar module calibration added. Development made outside of bays…
dgahle Sep 29, 2020
0259a4e
New baysar module calibration renamed to calibrate
dgahle Sep 29, 2020
296c5bf
Debug: Update of a variable name from "wave" to "wavelengths". This w…
dgahle Sep 29, 2020
7cab3d8
rtol in isclose for area conservation check in spectral convolusion h…
dgahle Sep 29, 2020
8da980e
Debug (syntax error): missing bracket in isclose
dgahle Sep 29, 2020
6837554
Input to calibration function is in A so the instrument function is n…
dgahle Sep 30, 2020
8a4a5ff
Update to get_adf11 function to check if the file exists and raises a…
dgahle Oct 2, 2020
a4898d2
added some comments showinf the flow of units
dgahle Oct 3, 2020
7f9411f
In BalmerHydrogenLine the excitation, recombination and total fitted …
dgahle Oct 3, 2020
7bc3330
Addition of isclose check (with raise ValueError) that area is conser…
dgahle Oct 3, 2020
9ba4f7d
Typo correction in ADAS406Lines in saving tec406_rhs and _lhs.
dgahle Oct 3, 2020
ea84b53
fixed linear interpolation of taus in ADAS406Lines __call__ function
dgahle Oct 3, 2020
851d31e
Increase resolution of (te, ne, tau) grid for atomic rates interpolat…
dgahle Oct 4, 2020
68a2f2b
ChargeStateOrderPrior update: Addition of element history and ion sor…
dgahle Oct 4, 2020
f35bdab
ChargeStateOrderPrior update: Generalisation to n number of Spectrome…
dgahle Oct 4, 2020
669e16d
Convolution area conservation is enforces by scaling the spectra by t…
dgahle Oct 7, 2020
fc58e3c
Update of legend().draggable() to fig.set_draggable() to keep up with…
dgahle Oct 8, 2020
053ae96
Bug fix: error in reading input dictionary in PlasmaLine for 'no_samp…
dgahle Oct 9, 2020
4e830d5
recombination neutral source and been made before ionisation neutral …
dgahle Oct 10, 2020
1afdb8b
Addition of StarkToPeakPrior, NeutralPowerPrior, and CiiiPrior prior …
dgahle Oct 25, 2020
3802a82
Instrument function can now be passed and implimented into wavelength…
dgahle Oct 25, 2020
a0456c4
Debug: Fixed f_rec typo in BalmerHydrogenLine.
dgahle Oct 25, 2020
f7a53e0
StarkToPeakPrior added as a default prior to BaysarPosterior.
dgahle Oct 25, 2020
c001f37
StarkToPeakPrior updated that cost components are scaled by f_rec (an…
dgahle Oct 27, 2020
2f1d6f1
In auto prior section line 109 self.posterior_components -> self.post…
dgahle Dec 22, 2020
06b3e80
Error in used of within to check that noise regions where within wave…
dgahle Dec 22, 2020
2e24fa8
Cold neutrals/ions now removes Ti as a few parameter.
dgahle Dec 28, 2020
481c750
XLine ems estimation didn't work. Has been replaces with an external/…
dgahle Dec 28, 2020
d1e79d5
set_sensible_bounds updated to include sensible bounds for XLines
dgahle Dec 28, 2020
4e6ba83
Update of estimate_XLine: Integration range defaults to 2*pixel width…
dgahle Dec 29, 2020
94158df
Update doppler_wavelengths in HydrogenLineShape as it was asymmetrical
dgahle Dec 29, 2020
2b37885
Update to data saved in BalmerHydrogenLine __call__ excitation emissi…
dgahle Jan 5, 2021
07a6367
ne_tau feature added to ADAS406Lines. Cannot be used in forward model…
dgahle Jan 7, 2021
3c2956d
Update to evolutionary_gradient_ascent. Prints initial population mod…
dgahle Jan 9, 2021
e33a015
Addition of NIVTauPrior to improve inference from N III/IV ratios.
dgahle Feb 2, 2021
807e675
Updated estimate_XLine. Doubled estimation of XLine and make bounds 1…
dgahle Feb 11, 2021
f374ba5
Update to _random_start. Corrected error message for bounds check.
dgahle Feb 11, 2021
ded5177
EsymmtricCauchyPlasma updata with dr input. If not None then there is…
dgahle Feb 18, 2021
a5ad5d8
Addition of SlabPlasma for slab analysis of emission features.
dgahle Feb 18, 2021
eecc97f
DoubleSlabPlasma added for 2 slab analysis of 2 emission features (or…
dgahle Feb 19, 2021
2ded0df
Full integration of concstar model into use of ionisation balances fr…
dgahle Feb 23, 2021
eca6f7f
Error in linear interpolation of power rates.
dgahle Feb 23, 2021
b7de8bc
Addition of BolometryPrior. This takes the charge states being modell…
dgahle Feb 23, 2021
07462ea
Debugging BolometryPrior and increasing cached data.
dgahle Feb 24, 2021
67e9c9d
Addition of B II data and ADF11 SCDs, ACDs, PLTs, and PRBs.
dgahle Mar 6, 2021
bf58081
adf11 dict is built for each element and then used to evaluate the io…
dgahle Mar 6, 2021
41b39b5
H prb file referrence was incorrect (now corrected).
dgahle Apr 2, 2021
9ec514c
New scripts to make synthetic spectra from SOLPs. Loads data from MDS…
dgahle Apr 2, 2021
94234f6
Addition of TeMinPrior to prevent degeneracy between peak Te and back…
dgahle Apr 19, 2021
365a075
Addition of TeTauPrior to correlate tau and Te max
dgahle Apr 19, 2021
8db4568
Addition of plot_fit_pres for cleaner presentation style fit plots (s…
dgahle Apr 19, 2021
7b7e2e3
Pre move to github commit
dgahle Feb 11, 2022
3e44139
shouldn't be in repo
dgahle Feb 11, 2022
f515617
TauFromTeEms (from Inter-BaySAR) used to get SOLPS taus in EmissionPr…
dgahle Sep 26, 2022
7f26915
Added Inter-BaySAR to BaySAR proper.
dgahle Sep 26, 2022
874e3a8
Debug: weighted concentrations was actually weighted densities. Now c…
dgahle Sep 26, 2022
2717a2f
Merge branch 'main' into dev
dgahle May 6, 2023
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,9 @@ __pycache__/
*$py.class

# files to be removed from repro
.idea/
*iml
*xml
*.pyc
./unit_test/
./demo/
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11 changes: 0 additions & 11 deletions baysar/.idea/BaySAR.iml
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7 changes: 0 additions & 7 deletions baysar/.idea/misc.xml
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8 changes: 0 additions & 8 deletions baysar/.idea/modules.xml
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7 changes: 0 additions & 7 deletions baysar/.idea/vcs.xml
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237 changes: 0 additions & 237 deletions baysar/.idea/workspace.xml
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