[yt-dev] Coordinate handling pull request

[Matthew Turk]

Hi Anthony,

Thanks for your suggestions!  I've updated the pull request here:

https://bitbucket.org/yt_analysis/yt-3.0/pull-request/5/initial-import-of-coordinate-handler-class

and responded to your suggestions inline.

On Wed, Aug 29, 2012 at 12:00 PM, Anthony Scopatz <scopatz at gmail.com> wrote:
> Hello Matt,
>
> Thanks for putting this together!  After briefly looking this over, it seems
> like some methods which have "cartesian" in the name are slightly mis-named.
> As implemented, cartesian_length() is really just a path_length().

Ah, alright.  I've changed the name to path_length, and cleaned up a
few other methods.

>
> I agree with the sentiment of the convert_to/from_cartesian() methods.
> However, I think half of these could be redundant.  It basically depends on
> whether you are choosing that Cartesian be the canonical form or not.  So I
> see two strategies:
>
> 1) All other systems have to/from cartesian methods.  Only need two methods
> per coord system.  All coord transformations go through this cartesian.
> (What you have, cleaner structure).
>
> 2) All systems have either a to_<othersystem>() method.  One method per
> conversion you wish to support.  Could be faster and have less floating
> point error than #1.  This prevents the situation where to go from Polar ->
> Spherical you actually have to do Polar -> Cartesian -> Spherical.
>
>
> The disadvantage of #2 is that you have to write more methods.  I guess
> nothing is stopping you from implementing #1 and then just tacking on these
> extra methods from #2 for cases where it makes sense.

On thinking about it, I like #2 better as well.  I'm going to start
with just cylindrical and cartesian, and I've gone ahead and
implemented the to/from methods between cartesian and cylindrical.

If everyone likes this, I'll continue on adding fields for it and
looking at how to integrate coordinate handling in a deeper way.  Let
me know if there are any other suggestions.

-Matt

>
> My initial thoughts are that there are only 4 or 5 of these coordinate
> systems so the number of permutations is not so high as to be unmanageable.
> I also doubt that this is the kind of thing that users will be subclassing
> and creating their own versions of.  So this is basically a "write once"
> piece of code (::crosses fingers::).
>
> In any event, I think what you have now is great.  It would just be nice to
> circumvent going through cartesian when that is clearly too much work.
>
> Be Well
> Anthony
>
> PS Sorry if this was rambling.  Must. find. coffee.
>
> On Wed, Aug 29, 2012 at 10:27 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
>>
>> Hi Casey,
>>
>> I've updated the PR:
>>
>>
>> https://bitbucket.org/yt_analysis/yt-3.0/pull-request/5/initial-import-of-coordinate-handler-class
>>
>> I think for now I'm going to leave the ABC in as a bookkeeping
>> exercise while implementing the other handlers, and remove it later.
>>
>> -Matt
>>
>> On Wed, Aug 29, 2012 at 11:18 AM, Casey W. Stark <caseywstark at gmail.com>
>> wrote:
>> > Hey Matt.
>> >
>> > Sounds good. I would guess the dimensionality issue comes down to
>> > implementation, but I think subclasses are fine.
>> >
>> > I am -1 on using abstract classes in general. Completely a style thing,
>> > but
>> > I think it ends up making things harder.
>> >
>> > - Casey
>> >
>> >
>> > On Wed, Aug 29, 2012 at 7:52 AM, Matthew Turk <matthewturk at gmail.com>
>> > wrote:
>> >>
>> >> On Wed, Aug 29, 2012 at 10:43 AM, Casey W. Stark
>> >> <caseywstark at gmail.com>
>> >> wrote:
>> >> > Hey Matt.
>> >> >
>> >> > I think this would be a big improvement, but I was wondering how it
>> >> > interacts with other yt pieces. Does each output have geometry and
>> >> > coordinate_handler objects as attributes?
>> >>
>> >> Yup, that is the plan.  The idea is that we move all of the IO and
>> >> particle/fluid selection into the geometry handler, and the handling
>> >> of spatial layout to the coordinate handler.  This would mean, for
>> >> instance, that we could push periodicity as well as path length into
>> >> the coordinate handler; this would remove some of the need to
>> >> constantly do wraparound checks and the like.
>> >>
>> >> There is still somewhat the issue that *selection* of points to
>> >> understand coordinate systems, which will require a bit more thought
>> >> in the future but I think is still a tractable problem.
>> >>
>> >> >
>> >> > Is it possible to replace axis_name, axis_id, x_axis, and y_axis with
>> >> > only
>> >> > axis_names = ['x', ...]?
>> >>
>> >> It is, but not with abc.abstractproperty.  (Initially I figured the
>> >> cost of creating the dicts was low enough that we could do this to
>> >> avoid worrying about mutable, class-level properties, but I think
>> >> perhaps I like yours better.)  I'll remove some of the fancier
>> >> ABC-stuff and slim it down.
>> >>
>> >> >
>> >> > - Casey
>> >> >
>> >> >
>> >> > On Wed, Aug 29, 2012 at 7:28 AM, Matthew Turk <matthewturk at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> Hi all,
>> >> >>
>> >> >> I've issued a pull request to the 3.0 repository, as I think it
>> >> >> warrants discussion.  It's here:
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt-3.0/pull-request/5/initial-import-of-coordinate-handler-class
>> >> >>
>> >> >> This includes a first pass at a coordinate handling system.  This is
>> >> >> distinct from a geometry handling system; the coordinates here refer
>> >> >> to how we handle coordinates and spatial locations internally,
>> >> >> whereas
>> >> >> geometry refers to how data is distributed throughout a domain and
>> >> >> throughout places on disk.  For instance, coordinate handling would
>> >> >> be
>> >> >> cartesian, polar, spherical.
>> >> >>
>> >> >> The reason I'm bringing it up for discussion is that I believe we
>> >> >> want
>> >> >> to move as much coordinate handling and transformation into a
>> >> >> separate, well-defined class as possible.  Periodicity, distances
>> >> >> and
>> >> >> so on are all currently scattered throughout the code, and I'd like
>> >> >> to
>> >> >> try to consolidate them.  Additionally, as new coordinate systems
>> >> >> (polar, spherical) are added, we'll need clear ways to delegate
>> >> >> responsibility for things like "How do I calculate path length as I
>> >> >> integrate?" or "What's the way to turn this into an image?"  I
>> >> >> believe
>> >> >> the best way to do that is to attach a coordinate system to the
>> >> >> dataset object itself.  (We now have a polar pixelizer
>> >> >> http://i.imgur.com/a4UGg.png !)
>> >> >>
>> >> >> The interface is currently set such that you need to define these
>> >> >> methods and properties in order to implement a coordinate system:
>> >> >>
>> >> >> coordinate_fields (this may go away, but it's for the analogs of
>> >> >> 'x',
>> >> >> 'y', 'z', as well as volume)
>> >> >> pixelize
>> >> >> convert_from_cartesian
>> >> >> convert_to_cartesian
>> >> >> axis_name
>> >> >> axis_id
>> >> >> x_axis
>> >> >> y_axis
>> >> >> period
>> >> >>
>> >> >> Some of these currently live in dictionaries in
>> >> >> yt/utilities/definitions.py, which is pretty sub-optimal.  I'd like
>> >> >> to
>> >> >> ask for feedback:
>> >> >>
>> >> >> 1) Do these methods sufficiently cover everything we need to know in
>> >> >> yt about a coordinate system?  Should any be added?
>> >> >> 2) Do we need to directly address dimensionality as a separate
>> >> >> subclass?
>> >> >> 3) Should any of these be removed?
>> >> >>
>> >> >> This will also help address these issues:
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt/issue/418/use-a-right-handed-coordinate-system
>> >> >>
>> >> >>
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt/issue/422/ray-casting-in-cylindrical-coordinates
>> >> >>
>> >> >>
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt/issue/421/refactor-non-cartesian-geometry
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt/issue/345/non-cartesian-geometry
>> >> >> https://bitbucket.org/yt_analysis/yt/issue/205/periodicity
>> >> >>
>> >> >> -Matt
>> >> >> _______________________________________________
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>> >> >
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