[yt-users] yt.utilities.amr_utils
Michael Kuhlen
mqk at astro.berkeley.edu
Mon Jan 21 22:38:24 PST 2013
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 *
* *
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