Re: Setting CellVariable values

[Guyer, Jonathan E. Dr. (Fed) via fipy]

> On Apr 8, 2019, at 4:09 PM, Dario Panada <dario.pan...@gmail.com> wrote:
> 
> DP: That would be diffusion of solubles from blood vessels (endothelial 
> cells). Specifically, glucose or oxygen. It wouldn't change significantly be 
> increasing it to a 40x40x40 grid, you'd just be simulating a larger section 
> of tissue.

Blood vessels aren't 20x20x20 grids and don't have locations like (1,2,3) in 
them. What I'm trying (and failing) to get at is that you have some physical 
locations, in micrometers or furlongs or lightyears, that you actually care 
about. It is better in FiPy to think about the things that you *really* care 
about and not try to second guess what FiPy cares about. Grid locations are an 
implementation detail. If you do grid convergence studies (and you should), 
then your grid locations will all change, but the physical definitions of them 
won't.

> DP: English is my first language but I think that's some tough sarcasm to 
> tell me not to do that. In that case, I'll happily take advice on proper ways 
> of achieving the same result so as not to cumber the dev team with 
> unnecessary refactoring.

I concede the sarcasm. I explained the proper way of achieving the same result 
in my first reply and the discussion kept going on about `_array`. Don't use 
`var._array`. Use `var` or `var.value`.

> So, in essence, I have a 20x20x20 grid of values. I want to somehow input 
> these values into a 20x20x20 structured mesh in the CellVariable object. The 
> fact that the approach might not work in unstructured meshes isn't concerning 
> because I don't require that feature. Setting values in _array appears to 
> work but is not an acceptable solution. From the previous exchange with 
> Martin, using the value property appears possible, although raveling indexes 
> has also been discouraged. So, any advice?

As I said in my first response:

>>> i = np.ravel_multi_index([coordinate[0], coordinate[1], coordinate[2]], 
>>> (20, 20, 20))
>>> sourceGrid[..., i] = sourceRate

Martin's suggestion of 

>>> sourceView = sourceGrid.value.reshape(20, 20, 20)
>>> sourceView[coordinate] = sourceRate

is interesting. It's a little fragile (if the internal storage was strided for 
some reason, then I don't think it would work), but it's worth considering and 
I, at least, find it clearer.

Raveling is not discouraged per se. Martin's `reshape` amounts to the same 
thing.


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