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2 changes: 2 additions & 0 deletions CHANGES/0.9.12-0.9.13.txt
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Added DataPlot.plotAllA to plot all available A for a given ion in a triangular matrix of subplots.
Added the ICFs from Delgado-Inglada, Morisset & Stasinska 2014
240 changes: 240 additions & 0 deletions CHANGES/0.9.13-1.0.1.txt
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r613 -

Atomic data: The levels are now taken from a dedicated file (one for each ion) where NIST data are stored. The energies, statistic weigths are for example not anymore in the "atom" data files. The format of the ascii data files have been changed, see the manual for a description of the new format. Better not to use anymore fits data files, they are obsoletes.
The NIST raw data are available through e.g. o3.NIST. The number of level is limited to the levels for which atomic data are available. See documentation for more.

Chianti data are available, only if the user installed the Chianti database somewhere and has set the environment variable XUVTOP to the location of the data. PyNeb does NOT provide Chianti data and is not responsible for the errors that may be found in these data.

The directory where the pypics files of the emissivities is now only created when needed, not at every start of pyneb as it was before.

We have received a lot of data from Nick Sterling, thanks a lot to him.

MonteCarlo generation of fake observations is available.

Grotrian diagram has a better look, with colors!

New default data set is PYNEB_14_03
'PYNEB_14_03': {'H1': {'rec': 'h_i_rec_SH95.fits'},
'He1': {'rec': 'he_i_rec_P12corr13.fits'},
'He2': {'rec': 'he_ii_rec_SH95.fits'},
'Al2': {'atom': 'al_ii_atom_JSP86-HK87-VVF96-KS86.dat', 'coll': 'al_ii_coll_KHAF92-TBK85-TBK84.dat'},
'Ar2': {'atom': 'ar_ii_atom_Bal06.dat', 'coll': 'ar_ii_coll_PB95.dat'},
'Ar3': {'atom': 'ar_iii_atom_MB09.dat', 'coll': 'ar_iii_coll_MB09.dat'},
'Ar4': {'atom': 'ar_iv_atom_MZ82.dat', 'coll': 'ar_iv_coll_RB97.dat'},
'Ar5': {'atom': 'ar_v_atom_LL93-MZ82-KS86.dat', 'coll': 'ar_v_coll_GMZ95.dat'},
'Ba2': {'atom': 'ba_ii_atom_C04.dat', 'coll': 'ba_ii_coll_SB98.dat'},
'Ba4': {'atom': 'ba_iv_atom_BHQZ95.dat', 'coll': 'ba_iv_coll_SB98.dat'},
'C1': {'atom': 'c_i_atom_FFS85.dat', 'coll': 'c_i_coll_JBK87-PA76.dat'},
'C2': {'atom': 'c_ii_atom_GMZ98.dat', 'coll': 'c_ii_coll_BP92.dat'},
'C3': {'atom': 'c_iii_atom_G83-NS78-WFD96.dat', 'coll': 'c_iii_coll_Bal85.dat'},
'C4': {'atom': 'c_iv_atom_WFD96.dat', 'coll': 'c_iv_coll_AK04.dat'},
'Ca5': {'atom': 'ca_v_atom_M83-KS86.dat', 'coll': 'ca_v_coll_GMZ95.dat'},
'Cl2': {'atom': 'cl_ii_atom_MZ83.dat', 'coll': 'cl_ii_coll_T04.dat'},
'Cl3': {'atom': 'cl_iii_atom_M83-KS86.dat', 'coll': 'cl_iii_coll_BZ89.dat'},
'Cl4': {'atom': 'cl_iv_atom_KS86-MZ82-EM84.dat', 'coll': 'cl_iv_coll_GMZ95.dat'},
'Fe3': {'atom': 'fe_iii_atom_Q96_J00.dat', 'coll': 'fe_iii_coll_Z96.dat'},
'K4': {'atom': 'k_iv_atom_M83-KS86.dat', 'coll': 'k_iv_coll_GMZ95.dat'},
'K5': {'atom': 'k_v_atom_M83-KS86.dat', 'coll': 'k_v_coll_BZL88.dat'},
'Mg5': {'atom': 'mg_v_atom_GMZ97.dat', 'coll': 'mg_v_coll_BZ94.dat'},
'Mg7': {'atom': 'mg_vii_atom_GMZ97.dat', 'coll': 'mg_vii_coll_LB94-U.dat'},
'N1': {'atom': 'n_i_atom_KS86-WFD96.dat', 'coll': 'n_i_coll_PA76-DMR76.dat'},
'N2': {'atom': 'n_ii_atom_GMZ97-WFD96.dat', 'coll': 'n_ii_coll_T11.dat'},
'N3': {'atom': 'n_iii_atom_GMZ98.dat', 'coll': 'n_iii_coll_BP92.dat'},
'N4': {'atom': 'n_iv_atom_WFD96.dat', 'coll': 'n_iv_coll_RBHB94.dat'},
'Na4': {'atom': 'na_iv_atom_GMZ97.dat', 'coll': 'na_iv_coll_BZ94.dat'},
'Na6': {'atom': 'na_vi_atom_GMZ97.dat', 'coll': 'na_vi_coll_LB94.dat'},
'Ne2': {'atom': 'ne_ii_atom_Bal06.dat', 'coll': 'ne_ii_coll_GMB01.dat'},
'Ne3': {'atom': 'ne_iii_atom_GMZ97.dat', 'coll': 'ne_iii_coll_McLB00.dat'},
'Ne4': {'atom': 'ne_iv_atom_BBZ89-BK88.dat', 'coll': 'ne_iv_coll_G81.dat'},
'Ne5': {'atom': 'ne_v_atom_GMZ97-U-BD93.dat', 'coll': 'ne_v_coll_LB94.dat'},
'Ne6': {'atom': 'ne_vi_atom_GMZ98.dat', 'coll': 'ne_vi_coll_ZGP94.dat'},
'Ni3': {'atom': 'ni_iii_atom_B01.dat', 'coll': 'ni_iii_coll_B01.dat'},
'O1': {'atom': 'o_i_atom_WFD96.dat', 'coll': 'o_i_coll_BK95.dat'},
'O2': {'atom': 'o_ii_atom_Z82-WFD96.dat', 'coll': 'o_ii_coll_Kal09.dat'},
'O3': {'atom': 'o_iii_atom_SZ00-WFD96.dat', 'coll': 'o_iii_coll_SSB14.dat'},
'O4': {'atom': 'o_iv_atom_GMZ98.dat', 'coll': 'o_iv_coll_BP92.dat'},
'O5': {'atom': 'o_v_atom_H80-NS79.dat', 'coll': 'o_v_coll_BBDK85.dat'},
'S2': {'atom': 's_ii_atom_PKW09.dat', 'coll': 's_ii_coll_TZ10.dat'},
'S3': {'atom': 's_iii_atom_PKW09.dat', 'coll': 's_iii_coll_TG99.dat'},
'S4': {'atom': 's_iv_atom_JKD86-DHKD82.dat', 'coll': 's_iv_coll_DHKD82.dat'},
'Si2': {'atom': 'si_ii_atom_BL93-CSB93-N77.dat', 'coll': 'si_ii_coll_DK91.dat'},
'Si3': {'atom': 'si_iii_atom_M83-OKH88-FW90-KS86.dat', 'coll': 'si_iii_coll_DK94.dat'},
'Xe3': {'atom': 'xe_iii_atom_BHQZ95.dat', 'coll': 'xe_iii_coll_SB98.dat'},
'Xe4': {'atom': 'xe_iv_atom_BHQZ95.dat', 'coll': 'xe_iv_coll_SB98.dat'},
'Xe6': {'atom': 'xe_vi_atom_BHQZ95.dat', 'coll': 'xe_vi_coll_SB98.dat'},
'Kr3': {'atom': 'kr_iii_atom_BH86.dat', 'coll':'kr_iii_coll_S97.dat'},
'Kr4': {'atom': 'kr_iv_atom_BH86.dat', 'coll': 'kr_iv_coll_S97.dat'},
'Kr5': {'atom': 'kr_v_atom_BH86.dat', 'coll': 'kr_v_coll_S97.dat'},
'Se3': {'atom': 'se_iii_atom_BH86.dat', 'coll': 'se_iii_coll_S97.dat'},
'Se4': {'atom': 'se_iv_atom_B05.dat', 'coll': 'se_iv_coll_B05.dat'},
'Br3': {'atom': 'br_iii_atom_BH86.dat', 'coll': 'br_iii_coll_S97.dat'},
'Br4': {'atom': 'br_iv_atom_BH86.dat', 'coll': 'br_iv_coll_S97.dat'},
'Rb4': {'atom': 'rb_iv_atom_BH86.dat', 'coll': 'rb_iv_coll_S97.dat'},
'Rb5': {'atom': 'rb_v_atom_BH86.dat', 'coll': 'rb_v_coll_S97.dat'},
'Rb6': {'atom': 'rb_vi_atom_BH86.dat', 'coll': 'rb_vi_coll_S97.dat'}

Important changes have been made to the LINE_LABEL_LIST, breaking backward compatibility with 0.9.x versions, leading to 1.0.x versions.
There is still an access to the old dictionary, available from pyneb.utils.init.OLD_LINE_LABEL_LIST. But we strongly recommend to use the uptodate values as defined by default.

Al2 NEW 4451A 4463A 4488A 164.2m 54.1m
Al2 OLD 4453A 4465A 4490A 162.3m 53.9m
===================
Ar3 NEW 3154A 6.37m
Ar3 OLD 3157A 6.4m
===================
Ar4 NEW 7332A 56.2m
Ar4 OLD 7331A 56.4m
===================
Ar5 NEW 1218A 1229A 1249A 1520A 2262A 4.93m
Ar5 OLD 4.9m
===================
Ba2 NEW 6497A 6854A 5854A 6142A 4524A 4900A 2.05m 1.76m
Ba2 OLD 6499A 6856A 5855A 6143A 4526A 4901A 2.1m 1.8m
===================
Ba4 NEW 5697A
Ba4 OLD 5698A
===================
Br3 NEW 7.94m
Br3 OLD 7.9m
===================
C1 NEW 9808A 9824A 9850A 2963A 2965A 2967A 4246A 8271A 609.6m 230.3m 370.3m
C1 OLD 9807A 9823A 9849A 609.7m 230.0m 369.3m
===================
C2 NEW 2322A 3131A 3133A 1869A 4636A 4637A 157.6m 454.4m 198.8m 353.3m 3967.2m
C2 OLD 2324A 2326A 3132A 3134A 1324A 1326A 3078A 3080A 3081A 4638A 4763A 157.8m 540.2m 270.1m 540.0m 17.6m
===================
C3 NEW 2000A 2003A 422.0m 124.9m 177.4m
C3 OLD 2002A 2004A 416.7m 125.0m 178.6m
===================
C4 NEW 92.8m
C4 OLD
===================
Ca5 NEW 5309A 2413A 3998A 4.16m 3.05m
Ca5 OLD 5311A 2414A 3999A 4.2m 3.0m
===================
Cl2 NEW 9381A 3586A 3719A 6162A 10.0m 33.3m
Cl2 OLD 9356A 3588A 3717A 6165A 10.4m 37.2m
===================
Cl3 NEW 151.5m 108.0m
Cl3 OLD 153.2m 107.5m
===================
Cl4 NEW 1463A 1474A 1493A 1833A 2793A 20.3m 7.45m
Cl4 OLD 20.4m 7.5m
===================
Fe3 NEW 4701A 4734A 4755A 5011A 5085A 5270A 4881A 4925A 4931A 5412A 8729A 8838A 3240A 3286A 3319A 3323A 3335A 3355A 3357A 3366A 3371A 3406A 4046A 4080A 4097A 4607A 4770A 4778A 9701A 9960A 5440A 6096A
Fe3 OLD 4703A 4735A 4756A 5013A 5086A 5272A 4882A 4926A 4932A 5413A 4989A 8731A 8840A
===================
H1r NEW ATOM
['1216A', '1026A', '973A', '6563A', '4861A', '4341A', '4102A', '3970A', '3889A', '3835A', '3798A', '1.87m', '1.28m', '1.09m', '9546A', '9229A']
===================
He1r NEW ATOM
['5876A', '2945A', '3188A', '3614A', '3889A', '3965A', '4026A', '4121A', '4388A', '4438A', '4472A', '4713A', '4922A', '5016A', '5048A', '5876A', '6678A', '7065A', '7281A', '9464A', '10830A', '11013A', '11969A', '12527A', '12756A', '12785A', '12790A', '12846A', '12968A', '12985A', '13412A', '15084A', '17003A', '18556A', '18685A', '18697A', '19089A', '19543A', '20425A', '20581A', '20602A', '21120A', '21132A', '21608A', '21617A']
===================
He2r NEW ATOM
['1640A', '1215A', '1084A', '4686A', '3203A', '6560A', '5411A', '4859A']
===================
He3NEW ATOM
['4686A', '5876A']
===================
K4 NEW 7109A
K4 OLD 7110A
===================
K5 NEW 6222A 31.0m
K5 OLD 6223A 31.4m
===================
Kr3 NEW 1.88m 1.07m
Kr3 OLD 1.9m 1.1m
===================
Kr4 NEW 4.26m
Kr4 OLD 4.3m
===================
Kr5 NEW 2.67m 1.32m
Kr5 OLD 2.7m 1.3m
===================
Mg5 NEW 2992A 3.96m
Mg5 OLD 2994A 4.0m
===================
Mg7 NEW 943A 953A 970A 1537A 4790A 3.42m
Mg7 OLD 847A 855A 868A 1296A 3034A 3.4m
===================
N1 NEW
N1 OLD 1094.1m 1.0m 27777.8m
===================
N2 NEW 2137A 2139A 2143A 3177A 7092A 205.3m 76.4m 121.8m
N2 OLD 2142A 2144A 2148A 3188A 7147A 205.4m 76.3m 121.5m
===================
N3 NEW 2280A 2288A 2280A 763A 3334A 3335A 71.0m 123.3m 1492.1m
N3 OLD 2291A 2291A 765A 1359A 3338A 3340A 71.2m 123.8m 909.1m
===================
N4 NEW 1575A 158.4m
N4 OLD 1574A 158.7m
===================
Na4 NEW 2804A 6.34m
Na4 OLD 2805A 6.3m
===================
Na6 NEW 2816A 2872A 2972A 1378A 14.39m
Na6 OLD 2815A 2871A 2970A 1377A 14.3m
===================
Ne4 NEW 224.9m 1579.3m
Ne4 OLD 221.2m 1587.3m
===================
Ne5 NEW 2973A 1721A 4083A 24.3m
Ne5 OLD 2975A 1722A 4090A 24.2m
===================
Ne6 NEW 997A 1010A 986A 559A 563A 1271A 1278A 1289A 559A 563A 1270A 1277A 1288A 433A 436A 766A 769A 772A 1928A 1929A 7.65m 22.7m 15.5m 334.4m
Ne6 OLD 1005A 1017A 1011A 567A 572A 1309A 1316A 1324A 567A 572A 1305A 1313A 1324A 7.6m 22.4m 15.6m 909.1m
===================
Ni3NEW ATOM
['7890A', '8500A', '6000A', '6401A', '6534A', '6682A', '6797A', '7125A', '6946A']
===================
O1 NEW 5577A
O1 OLD 5579A
===================
O2 NEW 499.3m 5023.7m 40.7m 121.3m
O2 OLD 505.3m 5076.1m 40.8m 121.8m
===================
O3 NEW 5833A 88.3m 32.6m
O3 OLD 5839A 87.6m 32.5m
===================
O4 NEW 1801A 1806A 1812A 608A 1076A 1078A 1080A 2671A 2672A 76.7m 53.9m 719.2m
O4 OLD 791A 1804A 1808A 1814A 790A 1803A 1808A 1814A 609A 1077A 1079A 1081A 2673A 2674A 76.0m 54.3m 588.2m
===================
O5 NEW 73.5m 32.6m
O5 OLD 71.6m 33.0m
===================
Rb4 NEW 1.44m
Rb4 OLD 1.4m
===================
Rb5 NEW 2.84m
Rb5 OLD 2.8m
===================
Rb6 NEW 1.95m 1.01m
Rb6 OLD 1.9m 1.0m
===================
S2 NEW 1.03m
S2 OLD 1.0m
===================
S3 NEW 33.5m
S3 OLD 33.6m
===================
S4 NEW 29.0m
S4 OLD 29.2m
===================
Se3 NEW 5.74m 2.54m 4.55m
Se3 OLD 5.7m 2.5m 4.6m
===================
Se4 NEW 2.28m
Se4 OLD 2.3m
===================
Si2 NEW 8007A 8077A 8193A 7997A 8067A 8183A 92.3m 631.5m
Si2 OLD 8009A 8080A 8196A 7999A 8070A 8185A 91.7m 646.8m
===================
Si3 NEW 3315A 3329A 77.7m 38.2m
Si3 OLD 3316A 3330A 78.0m 38.3m
===================
Xe3 NEW 1.23m 1.02m 1.11m 1.37m
Xe3 OLD 1.2m 1.0m 1.1m 1.4m
===================
Xe4 NEW 2.36m 1.31m
Xe4 OLD 2.4m 1.3m
===================
35 changes: 35 additions & 0 deletions CHANGES/0.9.3-0.9.4.txt
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User level

* The line label S3_33.5m is changed to S3_33.6m

* pn.Atom.getEnergy and Atom.plotGrotrian changes in unit parameter:
from '1/Angstrom' to '1/Ang'
from 'Rydberg' to 'Ryd'
* pn.Atom.plotGrotrian changes in look.
* pn.isValid: a new method to check if a line label is valid.
* pn.Observation.readData: a bug when 'lines_in_rows' and not errIsRelative is corrected.
* pn.Observation.getError: new method to obtain errors from an Observation object.
* pn.ICF: 'K94_A30.n' ICFs were O/O+, while it should be 1/(1-N+/N)). Correct now.
* pn.ICF: adding new ICFs: 'Gral04_10b', 'G07_1.d2' and 'G07_1.P92'
* pn.ICF.getAvailableICFs and pn.UCF.printAllICFs now take type_ as argument, which may be 'HII', 'PNe', 'All' or a list of them
* pn.ICF.delICF: new method to remove an ICF from the list
* pn.ICF.getElemAbundanceFromStrategy: new method
* pn.Diagnostics.delDiag: now accepts label='All'
* pn.Diagnostics.addDiagsFromObs: a new method to add diagnostics from a given Observation object
* pn.emisGrid.plotImage: now accepts cblabel as parameter to give the colorbar label
* pn.RedCorr: a new extinction law from Blagrave 2007
* pn.RedCorr: better determination of EBV from cHbeta (and reverse).
* pn.atomicData.getAllPredefinedDict(): new method

===========================================================================
Devel level

* pn.Atom.getTemDen does not issue anymore division by zero errors.
* pn.ICF: new _max_pass parameter to control the loops in getElemAbundance.
* pn.utils.misc.revert_seterr: new function to revert the options of np.seterr to a value saved in oldsettings.
* pn.utils.physics contains a dictionary of the configurations of the ground state levels.

===========================================================================
To see the diferences: click on the file : Show history, go to history panel, click on a version : Compare

ToDo: resolver el probelma de las energias... y de los lambdas/niveles de blends
7 changes: 7 additions & 0 deletions CHANGES/0.9.4-0.9.5.txt
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The main change is that Atom is not anymore in charge of reading the atomic data files. It only calls AtomDataFits and CollDataFits (in the present case, but later will be able to call ascii parser, or Chianti, or other).
This change if transparent for the user, as all the useful methods of Atom are preserved by pointing to the corresponding methods in one of the two classes.

* The scan_orders keyword in plotData is deprecated.
* a new format "lines_in_cols2" in Observation is added, to be tested and further replace the "lines_in_cols". It uses the np.genfromtxt function.
* Extrapolation of CollData when using Chebichev method is now copying the last element, and not using anymore te Chebichev extrapolation. Interpolation is kept the same.
* Fixing a bug that occurred when the number of levels in the transition probabilities table is greater than the number of levels in the collision strengths table.
12 changes: 12 additions & 0 deletions CHANGES/0.9.5-0.9.6.txt
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A new format for the data, where the errors are in columns, following the corresponding intensity. It is read with fileFormat='lines_in_rows_err_cols'

Example:

LINE TT err TT2 err TT3 err
cHbeta 1.2 0.0 1.5 0.2 1.1 0.2
O3_5007A 1.5 0.15 1.3 .2 1.1 0.1
H1_6563A 2.89 0.05 1.6 0.3 1.3 0.1
N2_6584A 1. 0.20 0.3 0.5 1.5 0.1

obs = pn.Observation('tt.dat',fileFormat='lines_in_rows_err_cols', corrected = False)

36 changes: 36 additions & 0 deletions CHANGES/0.9.6-0.9.7.txt
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The ICFs of NeIII from PHC07 were incorrectly attributed to NeII. Bug corrected.
Two ICFs changed:
RR04 changed for the more updated RR05
GRal04_10a, b are in fact special cases of a PTPR92 icf. GRal0410a, b have been changed for PTPR92_21
Two ICF added for Fe by RR05, based on observational data

The headers of a few atomic data files were updated (e.g., 'gs' added to 'Fe3', recombination files now have references)

A new function pn.atomicData.printAllSources has been added to display the atomic data
references of all ions at once (or a specified subset of them)

A new function printSources added to recombination lines

A new function plotLineRatio has been added to EmisGrid

A warning is issued in plotGrotrian when a level inversion is found

Ascii data can be read directly from Atom, the filename extension must be ".dat". Two new Objects AtomDataAscii and CollDataAscii are called when .dat files are used. They are similar to AtomDataFits and CollDataFits and should issue the same methods.

Some reorganisation of the methods from AtomDataFits, etc to Atom.

Multiprocessing can be used to compute Atom.getTemDen on massive data. The number of processors Config.Nprocs is set by default by Config to mp.cpu_count(), can be changed at any time. Multiprocs use is set/unset by Config.use_multiprocs() and Config.unuse_multiprocs()

RecAtom is more similar to Atom, with getIonAbund accepting to_eval keyword.

Some new lines and blends:
LINE_LABEL_LIST['C4'] = ['1548A', '1551A']
BLEND_LIST['C4_1550A+'] = 'I(2,1)+I(3,1)'
BLEND_LIST['O3_1664A+'] = 'L(1660)+L(1666)'
BLEND_LIST['O4_1400A+'] = 'I(3,1)+I(3,2)+I(4,1)+I(4,2)+I(5,1)+I(5,2)'
BLEND_LIST['N3_1751A+'] = 'I(3,1)+I(3,2)+I(4,1)+I(4,2)+I(5,1)+I(5,2)'
BLEND_LIST['Ne4_2423A+'] = 'I(2,1)+I(3,1)'

By default, the pypics files are now stored in a .pypics directory in the CURRENT directory, and not anymore in the $HOME directory. This allows to easily have different pypics files for different projects, without recomputing them each time one change the working project.

Atom.atomFitsFile and Atom.collFitsFile are deprecated, prefer Atom.atomFile and Atom.collFile
8 changes: 8 additions & 0 deletions CHANGES/0.9.7-0.9.8.txt
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Added module stellar.py in utils. It contains a Zanstra class to compute Zanstra stellar T and a couple of methods to deal with stellar luminosities.

Corrected a bug in the He I and He II atomic files that coased the code to crash

The input to Atom and RecAtom is no longer case-sensitive (i.e. pn.Atom('Ne', 2), pn.Atom('ne', 2), pn.Atom('NE', 2) and pn.Atom('nE', 2) are all valid calls)

Added small function getAllPossibleIons to return the list of all the atoms for which data existe (as opposed to those that are included in the current atomic data dictionary, which may be less).

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