Add: SpecDatabase Example in Gallery

[anandxkumar]

Description

This pull request adds example of SpecDatabase in Gallery.

[erwanp]

Hello !! Nice to see SpecDatabase being advertised.

A few things to make it great :

• for the example to work on ReadTheDocs, they'll need to be generated online. For this you cannot use a local database. fetch_hitemp("CO") may work; but it's a slightly big database (no good for 🌳 , remember it's run on every merge to develop!); what about using "OH" for your example ?
• for the image, can you try to use plot_cond which plots a 2D map of the database conditions ?
• could you add a 4th method where you make use of the init_database class of SpectrumFactory ?
• can you add some clickable links to the main classes and methods in the description, i.e. :py:class:`~radis.tools.database.SpecDatabase` ; same with plot_cond and init_database ?
• last but not least, the example gallery can appear in the docstrings of the functions and methods used. For that, you'll need to add .. minigallery:: radis.PATH/TO/FUNCTION in their docstrings. See Add (more) mini galleries of examples in Documentation #136 to know which path to use

[erwanp]

@gugzy and @CorentinGrimaldi , adding you for Review as you use the SpecDatabases ; if you think of features / use cases that should appear on the example gallery !

[codecov-commenter]

Codecov Report

Merging #315 (787bb1c) into develop (3dabb6e) will increase coverage by 0.05%.
The diff coverage is 33.33%.

@@             Coverage Diff             @@
##           develop     #315      +/-   ##
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+ Coverage    74.30%   74.36%   +0.05%     
===========================================
  Files          122      122              
  Lines        14830    14837       +7     
===========================================
+ Hits         11020    11034      +14     
+ Misses        3810     3803       -7     

[anandxkumar]

@erwanp I believe the above line assert (len(z_value)) == len(self.df) needs to be changed into assert (len(self.df[z_value])) == len(self.df) because z_value is just the column name.

Also the above below gives error:

  z = np.array(z_value) ** 0.5  # because the lower the better

TypeError: ufunc 'power' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe

[erwanp]

I looks like that z_value could be used as an external array. What about :

• if z_value is a str ; and a column name, then use z_value = self.df[z_value]
• else let it as it is (so the user can still use an external array of any kind)

np.array(z_value) ** 0.5
looks like something added for specific (old) purposes, it could be removed.

[anandxkumar]

Plotted: db_new.plot_cond('Tgas', 'wstep', 'wstep') where wstep value was decreasing, got the below plot-

I believe the color of the point should be different instead of the whole area or was this intended as we are using ax.contourf which colors the axis instead of point?

[erwanp]

I think I use it to plot the residuals in Fitroom, if you had a look at it. So the area is what we want. Let's use it : maybe compute small matrix of Tgas and wstep (15-20 spectra max, but larger ranges, like up to 3000 K to show some differences) , and plot the calculation time as the Z_label?

It's just to inspire people, no need to spend much time here :)

[anandxkumar]

Added a better example where I'm halving the wstep at every iteration. Now the difference is clearer and we can infer that Violent -> Minimum calc time, yellow -> Maximum Calc Time. Also, the max time taken is 0.17s and overall takes around 0. 40 seconds to fully execute it so it's not expensive.

[anandxkumar]

Plotting 2 graphs, one simple plot of radiance_noslit of different spectrums in SpecDatabase and other Tgas vs wstep using plot_cond(). Any change in the example?

Also added the mini gallery to SpecDatabase, plot_cond, and init_database. All getting properly rendered.

[erwanp]

Tiny changes, looks great!!

With the 2 graphs, which one appear in the list of galleries ? It should be the one from plot_cond.
( I don't think we need to plot the spectra anyway. There are already many Gallery examples with spectra)

[erwanp]

I looks like that z_value could be used as an external array. What about :

• if z_value is a str ; and a column name, then use z_value = self.df[z_value]
• else let it as it is (so the user can still use an external array of any kind)

np.array(z_value) ** 0.5
looks like something added for specific (old) purposes, it could be removed.

[erwanp]

Merging to see if it works on the online docs!

[erwanp]

Hello @anandxkumar ; the docs build failed :

generating gallery for auto_examples... [ 90%] plot_SpecDatabase.py
WARNING: /home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/develop/examples/plot_SpecDatabase.py failed to execute correctly: Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/develop/examples/plot_SpecDatabase.py", line 37, in <module>
    db = SpecDatabase(my_folder, lazy_loading=False)
  File "/home/docs/checkouts/readthedocs.org/user_builds/radis/envs/develop/lib/python3.6/site-packages/radis/tools/database.py", line 1867, in __init__
    os.mkdir(path)
FileNotFoundError: [Errno 2] No such file or directory: '/home/pipebomb/Desktop/SpecDatabase_Test/'

generating gallery for auto_examples... [100%] plot_linestrengths.py

Can you use relative links to build the database ?

---

Also; can you use the new PR to build a (wstep, Tgas) matrix of spectra rather than 25 spectra with different Tgas. Will be good-looking with plot_cond.
Like wstep = [0.001 :: 0.1, 4] ; Tgas = [300 :: 3000, 5 ] (20 spectra total)
(warnings={"AccuracyError":"ignore"} may be needed