[yt-users] yt.utilities.amr_utils

Michael Kuhlen mqk at astro.berkeley.edu
Tue Jan 22 09:57:43 PST 2013


Hi Matt

First, I got the idea for ValidateGridType from the definition of the field
"particle_density" in yt/data_objects/universal_fields.py, which uses
data.NumerOfParticles and does not result in an error with
AMRSmoothedCoveringGrid. So I guess that field also returns interpolated
particle density?

Secondly, simply commenting out the test for NumberOfParticles == 0 doesn't
work, "DataCubeError: CombineGrids: Three dimensions required for
g_data[0]." Let me know if you want the full traceback.

Btw, here's an example script with which you should be able to reproduce
the error: http://paste.yt-project.org/show/3069/

Mike


On Tue, Jan 22, 2013 at 2:10 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Mike,
>
> I think that the checks for .NumberOfParticles may be unnecessary in
> the dm_density calls.  Removing those, and simply returning an empty
> deposition field if there are no particles, will likely give the same
> results as what it currently does.  Switching between ValidateGridType
> and ValidateSpatial will turn on/off fields in ways I think we may
> want to avoid.  For particle density fields specifically it would
> likely result in estimates for particle density that are generated at
> a coarser level then interpolated to a finer level.
>
> -Matt
>
> On Tue, Jan 22, 2013 at 1:38 AM, Michael Kuhlen <mqk at astro.berkeley.edu>
> wrote:
> > Sorry to revive this old(ish) thread, but I've been experiencing similar
> > troubles to Renyue's. Mine, however, were not completely fixed by
> switching
> > from yt.utilities.amr_utils to yt.utilities.lib. I was still getting this
> > error:
> >
> > AttributeError: 'AMRSmoothedCoveringGrid' object has no attribute
> > 'NumberOfParticles'
> >
> > The solution for me was to switch from validators=[ValidateSpatial(0)] to
> > validators=[ValidateGridType()] in the add_field() call. Since many of
> the
> > fields defined in yt/frontends/*/fields.py still use ValidateSpatial(0),
> I'm
> > getting the same NumberOfParticles AttributeError when I try to do volume
> > renderings of "built-in" fields like dm_density.
> >
> > Cheers,
> > Mike
> >
> >
> >
> >
> >
> >
> > On Sun, Jan 13, 2013 at 1:11 PM, Renyue Cen <cen at astro.princeton.edu>
> wrote:
> >>
> >> HI Matt,
> >>
> >> That worked (after I remove the following things that I added following
> >> the line " from yt.utilities.lib import CICDeposit_3":
> >> #from yt.utilities.cosmology import Cosmology
> >> #from field_info_container import \
> >> #    add_field, \
> >> #    ValidateDataField, \
> >> #    ValidateGridType, \
> >> #    ValidateParameter, \
> >> #    ValidateSpatial, \
> >> #    NeedsGridType, \
> >> #    NeedsOriginalGrid, \
> >> #    NeedsDataField, \
> >> #    NeedsProperty, \
> >> #    NeedsParameter
> >>
> >> which was copied elsewhere earlier and apparent messed up with the
> >> CICDeposit_3 import a line before.
> >>
> >> Thanks very much,
> >> Renyue
> >>
> >>
> >> On Jan 13, 2013, at 3:35 PM, Matthew Turk wrote:
> >>
> >> > Hi Renyue,
> >> >
> >> > No, that should work.  What I'm actually seeing now is that you do in
> >> > fact use amr_utils -- I missed this before -- to get the CICDeposit_3.
> >> > The exception from the NameError is probably killing its
> >> > availability.
> >> >
> >> > So here's what to do:
> >> >
> >> > 1) Replace your previous import, which I suggested you remove, of
> >> > yt.utilities.amr_utils with:
> >> >
> >> > from yt.utilities.lib import CICDeposit_3
> >> >
> >> > 2) Change your call to CICDeposit_3 from amr_utils.CICDeposit_3 to
> >> > CICDeposit_3
> >> >
> >> > And try again?
> >> >
> >> > -Matt
> >> >
> >> > On Sun, Jan 13, 2013 at 3:31 PM, Renyue Cen <cen at astro.princeton.edu>
> >> > wrote:
> >> >> Hi Matt,
> >> >>
> >> >> This field (SFRdensity) was defined before the
> >> >> pf = ...
> >> >> statement, along with some other simpler definitions of gas variables
> >> >> that did not require CIC
> >> >> and seem to work.
> >> >>
> >> >> Was I using the wrong syntax or something?
> >> >>
> >> >> Renyue
> >> >>
> >> >> On Jan 13, 2013, at 3:25 PM, Matthew Turk wrote:
> >> >>
> >> >>> Hi Renyue,
> >> >>>
> >> >>> One important thing to note is that the field has to be added before
> >> >>> you instantiate the parameter file; i.e., you must do:
> >> >>>
> >> >>> add_field( ... )
> >> >>> pf = ...
> >> >>>
> >> >>> because the parameter file, upon creation of the hierarchy, performs
> >> >>> an auto-detection step.  This auto-detection step determines which
> >> >>> fields are available based on their dependencies.
> >> >>>
> >> >>> -Matt
> >> >>>
> >> >>> On Sun, Jan 13, 2013 at 3:22 PM, Renyue Cen <
> cen at astro.princeton.edu>
> >> >>> wrote:
> >> >>>> Hi Matt,
> >> >>>>
> >> >>>> It seems that my attempt to reuse "star_density" for a subset of
> >> >>>> stars does not work:
> >> >>>> "star_density" remains the density of all stars when plotted.
> >> >>>> But I also failed to redefine a new density that is called
> >> >>>> "SFRdensity" and feed it to AMRKDTree which is in turn
> >> >>>> fed to camera to volume render. Here is what I did:
> >> >>>>
> >> >>>> def _convertDensity(data):
> >> >>>>   return data.convert("Density")
> >> >>>> def _SFRdensity(field, data):
> >> >>>>   blank = na.zeros(data.ActiveDimensions, dtype='float32')
> >> >>>>   if data.NumberOfParticles == 0: return blank
> >> >>>> #   filter  = data.pf.time_units['years']*(data.pf.current_time -
> >> >>>> data['creation_time']) < 1.e8
> >> >>>>   filter  = data.pf.time_units['years']*(data.pf.current_time -
> >> >>>> data['creation_time']) < 1.e6
> >> >>>>   if not filter.any(): return blank
> >> >>>>
> >> >>>>
> amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(na.float64),
> >> >>>>
> >> >>>> data["particle_position_y"][filter].astype(na.float64),
> >> >>>>
> >> >>>> data["particle_position_z"][filter].astype(na.float64),
> >> >>>>
> >> >>>> data["particle_mass"][filter].astype(na.float32),
> >> >>>>                          na.int64(na.where(filter)[0].size),
> >> >>>>                          blank,
> >> >>>> na.array(data.LeftEdge).astype(na.float64),
> >> >>>>
> >> >>>> na.array(data.ActiveDimensions).astype(na.int32),
> >> >>>>                          na.float64(data['dx']))
> >> >>>>   return blank
> >> >>>> add_field("SFRdensity", function=_SFRdensity,
> >> >>>>         validators=[ValidateSpatial(0)],
> >> >>>> convert_function=_convertDensity)
> >> >>>>
> >> >>>>   volume3 = AMRKDTree(pf, fields=["SFRdensity"]
> >> >>>>              ,no_ghost=False, tree_type="domain"
> >> >>>>              ,le=c-0.5*WW, re=c+0.5*WW)
> >> >>>>   cam = pf.h.camera(c, L, W, (Nvec,Nvec), tf3, volume=volume3,
> >> >>>> no_ghost=False,log_fields=None
> >> >>>>                 ,north_vector=dir)
> >> >>>>
> >> >>>>
> >> >>>> with the following error message:
> >> >>>>
> >> >>>> Traceback (most recent call last):
> >> >>>> File "SFR.py", line 393, in <module>
> >> >>>>   ,le=c-0.5*WW, re=c+0.5*WW)
> >> >>>> File
> >> >>>>
> "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py",
> >> >>>> line 316, in __init__
> >> >>>>   for field in self.fields]
> >> >>>> File
> >> >>>>
> "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/field_info_container.py",
> >> >>>> line 71, in __missing__
> >> >>>>   return self.fallback[key]
> >> >>>> File
> >> >>>>
> "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/field_info_container.py",
> >> >>>> line 71, in __missing__
> >> >>>>   return self.fallback[key]
> >> >>>> File
> >> >>>>
> "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/data_objects/field_info_container.py",
> >> >>>> line 70, in __missing__
> >> >>>>   raise KeyError("No field named %s" % key)
> >> >>>> KeyError: 'No field named SFRdensity'
> >> >>>>
> >> >>>>
> >> >>>> So I must be doing something wrong with defining the SFRdensity
> >> >>>> field.
> >> >>>>
> >> >>>> Thanks very much,
> >> >>>> Renyue
> >> >>>>
> >> >>>>
> >> >>>> On Jan 13, 2013, at 1:20 PM, Matthew Turk wrote:
> >> >>>>
> >> >>>>> Hi Renyue,
> >> >>>>>
> >> >>>>> The module amr_utils became lib a while back.  But my guess is
> that
> >> >>>>> you probably don't need to import it anyway, unless you are
> >> >>>>> explicitly
> >> >>>>> using one of the routines it provides.
> >> >>>>>
> >> >>>>> -Matt
> >> >>>>>
> >> >>>>> On Sun, Jan 13, 2013 at 12:18 PM, Renyue Cen
> >> >>>>> <cen at astro.princeton.edu> wrote:
> >> >>>>>> Hi,
> >> >>>>>>
> >> >>>>>> I am trying to compute gridded density of some subset of
> particles.
> >> >>>>>> So I tried to import some modules first in the python script as
> >> >>>>>> follows:
> >> >>>>>>
> >> >>>>>> from yt.data_objects.field_info_container import \
> >> >>>>>>  FieldInfoContainer, \
> >> >>>>>>  NullFunc, \
> >> >>>>>>  TranslationFunc, \
> >> >>>>>>  FieldInfo, \
> >> >>>>>>  ValidateParameter, \
> >> >>>>>>  ValidateDataField, \
> >> >>>>>>  ValidateProperty, \
> >> >>>>>>  ValidateSpatial, \
> >> >>>>>>  ValidateGridType
> >> >>>>>> import yt.data_objects.universal_fields
> >> >>>>>> from yt.utilities.physical_constants import mh
> >> >>>>>> from yt.funcs import *
> >> >>>>>> import yt.utilities.amr_utils as amr_utils
> >> >>>>>>
> >> >>>>>>
> >> >>>>>> But I got this error message:
> >> >>>>>>
> >> >>>>>> Traceback (most recent call last):
> >> >>>>>> File "SFR.py", line 28, in <module>
> >> >>>>>>  import yt.utilities.amr_utils as amr_utils
> >> >>>>>> ImportError: No module named amr_utils
> >> >>>>>>
> >> >>>>>>
> >> >>>>>> Am I doing something wrong?
> >> >>>>>>
> >> >>>>>> Thanks,
> >> >>>>>> Renyue
> >> >>>>
> >> >>
> >>
> >> _______________________________________________
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> >
> >
> >
> >
> > --
> > *********************************************************************
> > *                                                                   *
> > *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
> > *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
> > *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
> > *  skype username: mikekuhlen      Berkeley, CA 94720               *
> > *                                                                   *
> > *********************************************************************
> _______________________________________________
> yt-users mailing list
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>



-- 
*********************************************************************
*                                                                   *
*  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
*  email: mqk at astro.berkeley.edu   UC Berkeley                      *
*  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
*  skype username: mikekuhlen      Berkeley, CA 94720               *
*                                                                   *
*********************************************************************
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