[yt-users] clump to field?

[Matthew Turk]

This is a bug; I have no idea why we're putting arguments into
__repr__ like this, but it can be fixed by updating the __repr__
definition in extracted region base.  Can you submit a PR?

On Fri, May 17, 2013 at 4:07 PM, David Collins <dcollins4096 at gmail.com> wrote:
> Ah, Sweet.  I tried this:
>
>>>> pf.h.boolean([pf.h.all_data(), 'NOT', clump.data])
>
> and got this:
>
> Building boolean100%
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Time: 00:00:01
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/data_containers.py",
> line 4104, in __repr__
>     s += region.__repr__(clean = True)
> TypeError: wrapper __repr__ doesn't take keyword arguments
>
> c32.data is of type ExtractedRegion.  It works ok if I use pf.h.sphere.
> What do I need to do to condition the clump.data?
>
> d.
>
>
> On Fri, May 17, 2013 at 1:49 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> I believe that is correct, yes.  One very simple way to test this and
>> verify would be to compare the volume in that object plus the volume
>> in your clump against the volume in the domain.
>>
>> On Fri, May 17, 2013 at 3:48 PM, David Collins <dcollins4096 at gmail.com>
>> wrote:
>> > Oh, right.  I can do
>> >
>> > pf.h.boolean([pf.h.all_data(), "NOT", clump])
>> >
>> > ?
>> >
>> >
>> > On Fri, May 17, 2013 at 1:41 PM, Matthew Turk <matthewturk at gmail.com>
>> > wrote:
>> >>
>> >> On Fri, May 17, 2013 at 3:39 PM, David Collins <dcollins4096 at gmail.com>
>> >> wrote:
>> >> > Is there an easy way to turn
>> >> >   data._get_cut_mask(grid)
>> >> > into an AMR region?
>> >> >
>> >> > Then I could just do a boolean "or" on those regions from each of the
>> >> > regions?
>> >>
>> >> Oh, you want to do it grid-by-grid?  I assumed that you were operating
>> >> on the full clump.  If you have the full clump, you can feed that
>> >> (which should be an AMRExtractedRegion) to the boolean object.
>> >>
>> >> And now that I think about it, AMRExtractedRegion is what should have
>> >> the _flush_to_grids method.
>> >>
>> >> >
>> >> > d.
>> >> >
>> >> >
>> >> > On Fri, May 17, 2013 at 1:34 PM, Matthew Turk <matthewturk at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> On Fri, May 17, 2013 at 3:31 PM, david collins
>> >> >> <dcollins4096 at gmail.com>
>> >> >> wrote:
>> >> >> > Hi, all--
>> >> >> >
>> >> >> > I have a clump that I've gotten with the clump finder.  I'd like
>> >> >> > to
>> >> >> > paint
>> >> >> > those zones of that clump with a flag, so I can exclude that
>> >> >> > region
>> >> >> > from
>> >> >> > other analysis.  I'm a little stuck on how to get this done-- I
>> >> >> > feel
>> >> >> > like it
>> >> >> > needs to involve clump.data._flush_data_to_grids and a cut_mask,
>> >> >> > but
>> >> >> > I'm
>> >> >> > a
>> >> >> > little stuck on how to define the field that I flush_to_grids.
>> >> >> >
>> >> >>
>> >> >> I have to think about specifically how you might do this, but I do
>> >> >> believe that you can probably accomplish what you're looking for by
>> >> >> using a boolean region.
>> >> >>
>> >> >> > Specifically, how to get the cut_mask information to the field,
>> >> >> > and
>> >> >> > how
>> >> >> > to
>> >> >> > avoid clobbering the paint from one clump with another (or, from
>> >> >> > one
>> >> >> > grid
>> >> >> > with another)
>> >> >> >
>> >> >> > I'm trying to do something like:
>> >> >> >
>> >> >> > <code>
>> >> >> > for grid in clump.data._grids:
>> >> >> >     cut_mask = clump.data._get_cut_mask(grid)
>> >> >> >     def masked_region(field,data):
>> >> >> >         cut_mask = data.get_field_parameter('cut_mask', None)
>> >> >> >         try:
>> >> >> >             base = data['masked_region']
>> >> >> >         except:
>> >> >> >             base = na.zeros(data['Density'].shape)
>> >> >> >         if cut_mask is not None:
>> >> >> >             base = na.maximum(base,cut_mask)
>> >> >> >         return base
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > add_field('masked_region',function=masked_region,validators=[ValidateGridType()],
>> >> >> > not_in_all=True)
>> >> >> >     grid.set_field_parameter('cut_mask',cut_mask)
>> >> >> >     print grid, cut_mask.sum(), grid['masked_region'].sum()
>> >> >> > clump.data._flush_to_grids('masked_region',0)
>> >> >> > </code>
>> >> >> >
>> >> >> > but clump['masked_region'].sum() only returns the flagged zones in
>> >> >> > the
>> >> >> > first
>> >> >> > of the grids.
>> >> >> >
>> >> >> > I feel like this is something I've done before, but can't find any
>> >> >> > reference
>> >> >> > to it in my email or old scripts.  Apologies if this has been
>> >> >> > answered
>> >> >> > elsewhere, or it's obvious and I'm being thick.
>> >> >> >
>> >> >> > Thanks!
>> >> >> > d.
>> >> >> >
>> >> >> >
>> >> >> >
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>> >> >> >
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>> >> >
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