[yt-dev] particle filter example

Britton Smith brittonsmith at gmail.com
Mon Dec 2 08:37:17 PST 2013 

Hi Matt,

Moving this to the correct thread (with additions):

The change you suggested solved the problem of
ad['DarkMatter', 'particle_mass']
and
ad['CenOstriker', 'particle_mass']

However, when I do:
ad['all', 'particle_mass']
I get the following:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 189, in __getitem__
    self.get_data(f)
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 535, in get_data
    particles, self, self._current_chunk)
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py",
line 507, in _read_particle_fields
    fields_to_read)
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/utilities/io_handler.py",
line 176, in _read_particle_selection
    rv[field_f][my_ind:my_ind + vals.shape[0],...] = vals
ValueError: could not broadcast input array from shape (4851) into shape
(4361)

Additionally, if I do:
ad['io', 'particle_mass']
I get this (which I got before this change as well):
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 183, in __getitem__
    f = self._determine_fields(key)[0]
  File
"/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 406, in _determine_fields
    raise YTFieldTypeNotFound(ftype)
yt.utilities.exceptions.YTFieldTypeNotFound: Could not find field 'io'.

The 'io' issue seems to come from line 848 in enzo/data_structures.py:
            # If this is the case, then we know we should have a DarkMatter
            # particle type, and we don't need the "io" type.
            self.particle_types = ["DarkMatter"]

Would it be better to switch that to an append and keep the "io" type
around for generality?  I don't know if that would actually be a good idea
since in reality it is just the dark matter for Enzo-3.0 data.

Britton


On Mon, Dec 2, 2013 at 3:41 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> That looks like a failure to convert correctly.  What goes on during
> instantiation is that for each particle type, the function
> _setup_particle_type is called on EnzoStaticOutput.  Then the
> _setup_particle_fields from enzo/fields.py gets called, which should
> set the "particle_mass" function to convert based on Density * cm**3.
> (Note that we now -- in _read_particle_fields -- multiply by the
> grid.dds.prod, so it doesn't need that anywhere else anymore.)
>
> Can you check what pf._get_field_info("DarkMatter", "particle_mass")
> has for its _convert_function ?  It should be a function called
> _convertParticleMass.
>
> I have to go for a few hours, but I can look at an E3 dataset when I get
> back.
>
> -Matt
>
> On Mon, Dec 2, 2013 at 10:33 AM, Britton Smith <brittonsmith at gmail.com>
> wrote:
> > I am getting this with just "DarkMatter" and "CenOstriker", which are not
> > exactly filters (or maybe they are), but the particle types as they are
> > stored on disk by Enzo-3.0.
> >
> >
> > On Mon, Dec 2, 2013 at 3:30 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> On Mon, Dec 2, 2013 at 10:29 AM, Britton Smith <brittonsmith at gmail.com>
> >> wrote:
> >> > Hi Matt,
> >> >
> >> > Thanks, that's very helpful.
> >> >
> >> > I have an additional question.  When I do:
> >> > ad = pf.h.all_data()
> >> > ad['particle_mass'] or
> >> > ad['all', 'particle_mass']
> >> >
> >> > I get numbers that are ~1e44, which sounds about right if it's in
> grams.
> >> > However, when I do:
> >> > ad['DarkMatter', 'particle_mass']
> >> >
> >> > I get numbers that are ~1e-5, which I am guessing is the unconverted
> >> > particle_mass straight out of the file.  How can get the filtered
> >> > particles
> >> > in proper units as well?
> >> >
> >>
> >> Hm, that looks like a bug to me.  What's your filter look like, so I
> >> can reproduce this here?
> >>
> >> > Thanks again,
> >> > Britton
> >> >
> >> >
> >> > On Mon, Dec 2, 2013 at 3:21 PM, Matthew Turk <matthewturk at gmail.com>
> >> > wrote:
> >> >>
> >> >> Hey Britton,
> >> >>
> >> >> On Mon, Dec 2, 2013 at 10:15 AM, Britton Smith <
> brittonsmith at gmail.com>
> >> >> wrote:
> >> >> > Hi all,
> >> >> >
> >> >> > Can someone point me to an example (docs, notebooks, emails,
> >> >> > whatever)
> >> >> > of
> >> >> > defining a custom particle filter for yt-3.0?  I'm trying to do
> this
> >> >> > and
> >> >> > I
> >> >> > know I've seen discussion of this before, but I can't find where.
> >> >> >
> >> >>
> >> >> Yup.  Here's an example:
> >> >>
> >> >>
> >> >>
> >> >>
> http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/534fd19b933e4a3fa002db91f58fb817.ipynb
> >> >>
> >> >> Looks like the nbviewer is down though.
> >> >>
> >> >> Sorry I haven't done much documenting of this.  Particle filters and
> >> >> particle unions are two really cool things that are currently only in
> >> >> example form.  Here's another example of how to define one:
> >> >>
> >> >>
> >> >>
> >> >>
> https://bitbucket.org/mornkr/agora-analysis-script/src/1200830cd1e8d7dc60f66c8f1dc7c09764ca3276/script-Flagship-DM.py?at=default#cl-33
> >> >>
> >> >> and you have to add this by name to each pf you open up:
> >> >>
> >> >>
> >> >>
> >> >>
> https://bitbucket.org/mornkr/agora-analysis-script/src/1200830cd1e8d7dc60f66c8f1dc7c09764ca3276/script-Flagship-DM.py?at=default#cl-57
> >> >>
> >> >> Note that you have to specify *all* the required filtering fields in
> >> >> the constructor for the function.
> >> >>
> >> >> -Matt
> >> >>
> >> >> > Thanks,
> >> >> > Britton
> >> >> >
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