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.
On Tue, Jan 22, 2013 at 1:38 AM, Michael Kuhlen email@example.com 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.
On Sun, Jan 13, 2013 at 1:11 PM, Renyue Cen firstname.lastname@example.org wrote:
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:
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:
- Replace your previous import, which I suggested you remove, of
from yt.utilities.lib import CICDeposit_3
- Change your call to CICDeposit_3 from amr_utils.CICDeposit_3 to
And try again?
On Sun, Jan 13, 2013 at 3:31 PM, Renyue Cen email@example.com wrote:
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?
On Jan 13, 2013, at 3:25 PM, Matthew Turk wrote:
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.
On Sun, Jan 13, 2013 at 3:22 PM, Renyue Cen firstname.lastname@example.org wrote:
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
data["particle_mass"][filter].astype(na.float32), na.int64(na.where(filter).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 > email@example.com 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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