Example signal computation with custom emissivity

[flothesof]

As discussed with @Didou09 this is a "new" example (inspired by one of the benchmarks).

[pep8speaks]

Hello @flothesof! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file examples/tutorials/plot_custom_emissivity.py:

Line 5:80: E501 line too long (80 > 79 characters)
Line 34:1: E302 expected 2 blank lines, found 1
Line 37:80: E501 line too long (80 > 79 characters)

• In the file tofu/utils.py:

Line 549:62: E231 missing whitespace after ','

Comment last updated at 2019-11-06 11:04:19 UTC

[codecov-io]

Codecov Report

Merging #207 into devel will decrease coverage by 0.06%.
The diff coverage is 40%.

@@            Coverage Diff             @@
##            devel     #207      +/-   ##
==========================================
- Coverage   43.93%   43.86%   -0.07%     
==========================================
  Files          70       70              
  Lines       21288    21294       +6     
==========================================
- Hits         9352     9340      -12     
- Misses      11936    11954      +18

Impacted Files	Coverage Δ
tofu/data/_plot.py	91.15% <0%> (ø)	⬆️
tofu/version.py	100% <100%> (ø)	⬆️
tofu/utils.py	48.71% <38.88%> (-0.19%)	⬇️
tofu/data/_core_new.py	13.15% <0%> (-0.47%)	⬇️
tofu/geom/_comp.py	59.87% <0%> (-0.22%)	⬇️
tofu/data/_core.py	40.9% <0%> (-0.14%)	⬇️
tofu/geom/_plot.py	65.26% <0%> (-0.11%)	⬇️
tofu/geom/_core.py	63.35% <0%> (-0.11%)	⬇️

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[flothesof]

I've fiddled a bit more with the plots and realized that I have questions about the following items:

• what are the coordinate conventions for tofu ? (X Y Z in most cases, but how is the usual coordinate system defined?) should we make this appear somewhere in the documentation (in a page dedicated to conventions used, or alternatively in the introductory examples?)
• I was unable to get the example working using no time-dependency (setting t=None) gave me this error, while I assumed this would work

  File "tofu\geom\_GG03.pyx", line 3057, in tofu.geom._GG03.LOS_calc_signal
    val_2d = func(pts, t=t, **fkwdargs)
ValueError: Buffer has wrong number of dimensions (expected 2, got 1)

[lasofivec]

I've fiddled a bit more with the plots and realized that I have questions about the following items:

* what are the coordinate conventions for tofu ? (X Y Z in most cases, but how is the usual coordinate system defined?) should we make this appear somewhere in the documentation (in a page dedicated to conventions used, or alternatively in the introductory examples?)

Probably we should do both suggested solutions. For sure a section on "tofu's conventions" is missing in the doc.

* I was unable to get the example working using no time-dependency (setting t=None) gave me this error, while I assumed this would work

  File "tofu\geom\_GG03.pyx", line 3057, in tofu.geom._GG03.LOS_calc_signal
    val_2d = func(pts, t=t, **fkwdargs)
ValueError: Buffer has wrong number of dimensions (expected 2, got 1)

As stated in the doc, the function emissivity should always return a 2D array. I fixed that directly in your example.

tofu/tofu/geom/_GG02.pyx

Lines 2882 to 2888 in 93ae5c5

	func : python function st. func(pts, t=None, vect=None) => data
	with pts : ndarray (3, npts) - points where function is evaluated
	vect : ndarray(3, npts) - if anisotropic signal vector of emiss.
	t: ndarray(m) - times where to compute the function
	returns: data : ndarray(nt,nraf) if nt = 1, the array must be 2D
	values of func at pts, at given time
	func is the function to be integrated along the LOS

However the tutorial is still failing, this time when plotting the signal. I opened an issue regarding this, see Issue #217

[Didou09]

Problem solved, see Issue #217
Tip though : the user needs to click once on the time axis

[lasofivec]

This example is for the online documentation, so the figures will be non interactive.
Could you add a comment in the test with what you mean?

[Didou09]

Plotting issue solved,
But bug found in _GG => opened issue #247 for @lasofivec , top priority
Thanks @flothesof , your example helped us identity a high-priority bug
New release probable when fixed, to be discussed

[lasofivec]

I'm going to merge this pull request since all bugs have been corrected in branch Issue247-bisect and are independent of this branch :)