[yt-dev] [Yt-dev] Field definitions, derived fields, whats-in-a-file and the "deliberate_fields" branch

Matthew Turk matthewturk at gmail.com
Fri Nov 11 11:15:18 PST 2011


Hi all,

It's been a couple days.  Would somebody mind revisiting the pull
request?  I have been running with it here and I haven't seen any
problems.

Thanks,

Matt

On Wed, Nov 9, 2011 at 5:37 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi David,
>
> On Wed, Nov 9, 2011 at 5:34 PM, david collins <antpuncher at gmail.com> wrote:
>>
>> > To be perfectly honest, you were in my list of top one people I thought
>> > would
>> > either love or hate this proposed change.
>>
>> It wouldn't be so much "hate" as much as "gripe because my
>> non-standard code that worked with the 1987 vintage of yt doesn't work
>> with the changes you made in 1995." :D  I'm actually really impressed
>> that it all went so smoothly, that's a pretty major change with many
>> opportunities for bear traps to step in.
>
> Well, in fairness, 1995 was a good year for yt.
>
>>
>> > Ah!  I think this is what TranslateFunc is designed for.  I think the
>> > way I
>> > envision it working is to choose a canonical name, maybe Bx, and then
>> > do:
>> > add_enzo_field("Bx", function=NullFunc)
>> > add_field("Bx", function=TranslateFunction("MagneticField_C_1"))
>>
>> Is this now functioning?   I don't quite get the logic behind the
>> function calls here, why is Bx itself an "add_enzo_field" but the
>> translate is an add_field?
>
> That *should* function.  What it does is say, the canonical name is Bx, and
> that's the one you'll find in a file (even if you find another) and that
> we'll address in yt.  But, just in case, we want it also to return
> MagneticField_C_1, if it can't find Bx itself.  So the first goes to the
> "known" fields, and the second goes to the "derived" fields.  Does that make
> any more sense?
> -Matt
>
>>
>> Thanks a ton,
>> d.
>>
>> > Thank you.  :)  I have updated the pull request with the new changeset
>> > where
>> > con_args is fixed.
>> > Best,
>> > Matt
>> >
>> >>
>> >> Thanks a ton!
>> >> d.
>> >>
>> >> Trace for the first bug:
>> >>  File "go", line 20, in <module>
>> >>    from yt.mods import *
>> >>  File "/Users/dccollins/local/src/yt_turk/yt/mods.py", line 44, in
>> >> <module>
>> >>    from yt.data_objects.api import \
>> >>  File "/Users/dccollins/local/src/yt_turk/yt/data_objects/api.py",
>> >> line 31, in <module>
>> >>    from grid_patch import \
>> >>  File
>> >> "/Users/dccollins/local/src/yt_turk/yt/data_objects/grid_patch.py",
>> >> line 35, in <module>
>> >>    from yt.data_objects.data_containers import YTFieldData
>> >>  File
>> >>
>> >> "/Users/dccollins/local/src/yt_turk/yt/data_objects/data_containers.py",
>> >> line 3407
>> >>    _con_args = {"regions"}
>> >>                          ^
>> >> SyntaxError: invalid syntax
>> >>
>> >>
>> >>
>> >> On Wed, Nov 9, 2011 at 1:25 PM, j s oishi <jsoishi at gmail.com> wrote:
>> >> > Hi Matt,
>> >> >
>> >> > This sounds like a much needed overhaul. However, I'm not quite clear
>> >> > on exactly what this will entail, or how it will work once
>> >> > implemented. Could you or Casey provide an example of a new field or
>> >> > two, demonstrating how these dictionaries, fallbacks, and Null
>> >> > functions work? I think this is likely a very simple thing, but I'm
>> >> > having trouble visualizing it.
>> >> >
>> >> > thanks,
>> >> >
>> >> > j
>> >> >
>> >> > On Wed, Nov 9, 2011 at 9:05 AM, Matthew Turk <matthewturk at gmail.com>
>> >> > wrote:
>> >> >> Hi all,
>> >> >>
>> >> >> Over the last couple months, Casey and I have been working -- on and
>> >> >> off! -- on a new branch of the code called "deliberate_fields."
>> >> >>  This
>> >> >> branch will change, in a substantial but easy-to-update way, how
>> >> >> fields are handled in yt.
>> >> >>
>> >> >> I recognize this email is long.  But if you use non-standard fields,
>> >> >> a
>> >> >> bunch of derived fields, unit modifications, any of that, it may
>> >> >> affect you.  So I *please* ask that you read it and, if you like,
>> >> >> contribute back to the discussion.
>> >> >>
>> >> >> This is one of the items I really want to have done for a
>> >> >> hypothetical
>> >> >> 2.3 release.
>> >> >>
>> >> >> = Background =
>> >> >>
>> >> >> The way fields work currently was designed a bit haphazardly.  They
>> >> >> use FieldInfoContainers, objects which share state and which contain
>> >> >> unions of the known derived fields and the known IO-based fields.
>> >> >>  One
>> >> >> of the problems with this is that the only thing that separates a
>> >> >> derived field from a known field is that function that generates the
>> >> >> field: the IO-based fields all use a lambda which returns None, and
>> >> >> the non-IO based fields return actual fields.  This is pretty
>> >> >> sub-optimal, and it actually lands us in trouble when (for instance)
>> >> >> we have fields wandering around named things like "Thermal_Energy"
>> >> >> and
>> >> >> "ThermalEnergy"; the mechanism by which one is selected and the
>> >> >> other
>> >> >> not is problematic, and to get around infinite recursion, hacks have
>> >> >> had to be applied.
>> >> >>
>> >> >> As it stands, to find a field, the shared-state "field info" on a
>> >> >> parameter file is queried; this then will try to check universal
>> >> >> fields.  But because of how the fields are stored, the field info
>> >> >> cascade can also operate in reverse.  The big problem is that the
>> >> >> field selection mechanism doesn't seem to have a bus factor >= 1.0.
>> >> >> And, it has a number of hacks to make it work with conflicting field
>> >> >> definitiosn and the like.
>> >> >>
>> >> >> Unfortunately, layering these hacks on top of each other makes it
>> >> >> much
>> >> >> harder for other codes to be supported; translations are not
>> >> >> reliable,
>> >> >> and sometimes cause too many levels of recursion to be added.
>> >> >> Something simpler is necessary.
>> >> >>
>> >> >> = What this does =
>> >> >>
>> >> >> Essentially, this creates multi-level, explicit fallbacks.  The
>> >> >> field
>> >> >> info container, which was a bloated, weird shared state object, is
>> >> >> now
>> >> >> simply a dictionary subclass with a "fallback" option.  When you
>> >> >> create them, you can either create it in isolation (with no
>> >> >> fallback)
>> >> >> or with a fallback.  When you query it, if it does not have a field,
>> >> >> it checks its fallback.  There are, additionally, two new functions
>> >> >> for IO: the translation function and the null function.  The first
>> >> >> is
>> >> >> to translate, for instance, "density" to "Density" and the second is
>> >> >> to indicate that a field is expected to be found in an output from
>> >> >> the
>> >> >> simulation code.
>> >> >>
>> >> >> There are now affiliated with each simulation code two field info
>> >> >> objects: the "known" fields, which may appear in files, and the
>> >> >> non-known (i.e., code-specific derived) fields.  These live as the
>> >> >> attributes _fieldinfo_fallback and _fieldinfo_known on the
>> >> >> StaticOutput sublcass corresponding to a simulation code.  When the
>> >> >> Hierarchy (not static output) is instantiated, the first step is to
>> >> >> create a new field_info object.  This has, as a fallback, the
>> >> >> _fieldinfo_fallback, which itself has as a fallback the
>> >> >> universally-known derived fields.  The hierarchy then queries the
>> >> >> output file for which fields are available.  This process then looks
>> >> >> for a corresponding field in fieldinfo_known, and if it finds it, it
>> >> >> adds it to the field_info object, *overriding* any possible derived
>> >> >> fields.  (In this manner, for instance, yt will not recalculate a
>> >> >> "CoolingTime" field if one exists in the output.)
>> >> >>
>> >> >> = What it aims to do in the future =
>> >> >>
>> >> >> This will be utilized in three main ways:
>> >> >>
>> >> >> 1) Making it more clear which fields belong to which code, and which
>> >> >> come from disk and which are derived
>> >> >> 2) Help move IO into fields, to optimize for geometries and data
>> >> >> containers
>> >> >> 3) Make units more clear and specific
>> >> >> 4) This is all designed around better supporting the GDF.
>> >> >>
>> >> >> = Where from here? =
>> >> >>
>> >> >> It would be hugely beneficial if you could test this and report
>> >> >> back.
>> >> >> I have created a pull request:
>> >> >>
>> >> >>
>> >> >>
>> >> >> https://bitbucket.org/yt_analysis/yt/pull-request/27/field-overhaul-to-utilize-explicit
>> >> >>
>> >> >> This is by no means a settled matter; I think we need to have
>> >> >> testing
>> >> >> on this, buy-in from developers and users, and to make sure that old
>> >> >> code doesn't beak.  The test cases all pass for me for Enzo.
>> >> >>
>> >> >> Before this can be merged, I would hope we can get some testing
>> >> >> from:
>> >> >>
>> >> >>  * Enzo
>> >> >>  * Nyx
>> >> >>  * FLASH
>> >> >>  * Orion
>> >> >>
>> >> >> and any other codes that can hear me.
>> >> >>
>> >> >> Thanks very much for your time; please let me know if you have any
>> >> >> questions, concerns, jokes, comments, improvements, CDs of your
>> >> >> band,
>> >> >> suggestions, and so on.  For this major of a change I'd like to keep
>> >> >> discussion on list, so the record of this is a bit more prominent.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Matt
>> >> >> _______________________________________________
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>> >> >>
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>> >>
>> >>
>> >>
>> >> --
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>>
>> --
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