[yt-users] error on plotting particle_density

mohammad safarzadeh mtsafarzadeh at gmail.com
Thu Jul 11 18:17:11 PDT 2013


I installed YT all over again,
now the plots that I get are a bit weird. it sounds like it is putting
cubes around haloes:
from this command:
p = ProjectionPlot(pf, "x", "particle_density",[ 0.5808,0.5398, 0.4504
],(4.0,'mpc'))
the image is here:
http://i.imgur.com/z4QA2uz.png

-Mohammad


On Wed, Jul 10, 2013 at 3:58 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Mohammad,
>
> Sorry you're having trouble.  In my version of cde0a641f1bf , the line
> numebrs don't match up with yours.  In particular, my _pdensity
> function starts on line 1010, and looks like this:
>
> def _pdensity(field, data):
>     blank = np.zeros(data.ActiveDimensions, dtype='float64')
>     if data["particle_position_x"].size == 0: return blank
>     CICDeposit_3(data["particle_position_x"].astype(np.float64),
>                  data["particle_position_y"].astype(np.float64),
>                  data["particle_position_z"].astype(np.float64),
>                  data["ParticleMass"],
>                  data["particle_position_x"].size,
>                  blank, np.array(data.LeftEdge).astype(np.float64),
>                  np.array(data.ActiveDimensions).astype(np.int32),
>                  np.float64(data['dx']))
>     np.divide(blank, data["CellVolume"], blank)
>     return blank
> add_field("particle_density", function=_pdensity,
>           validators=[ValidateGridType()],
>           display_name=r"\mathrm{Particle}\/\mathrm{Density}")
>
> The only buffer there that's not cast to float64 is
> data["ParticleMass"].  I don't know why your line numbers and mine do
> not match up, since you don't have a + in your source file, however if
> your function matches mine please try adding the appropriate
> .astype(np.float64).  In 3.0 we have abstracted some of this out to
> use a deposit function that handles types better.
>
> -Matt
>
> On Wed, Jul 10, 2013 at 3:38 PM, mohammad safarzadeh
> <mtsafarzadeh at gmail.com> wrote:
> > Hi,
> > I get this error when trying to do a projection plot:
> > ----> 9 p = ProjectionPlot(pf, "x", "particle_density",[ 0.5808,0.5398,
> > 0.4504 ],(4.0,'mpc'))
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
> > __init__(self, pf, axis, fields, center, width, axes_unit, weight_field,
> > max_level, origin, fontsize, field_parameters, data_source)
> >    1347         if field_parameters is None: field_parameters = {}
> >    1348         proj = pf.h.proj(axis, fields, weight_field=weight_field,
> > max_level=max_level,
> > -> 1349                          center=center, source=data_source,
> > **field_parameters)
> >    1350         PWViewerMPL.__init__(self, proj, bounds, origin=origin,
> > fontsize=fontsize)
> >    1351         self.set_axes_unit(axes_unit)
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > __init__(self, axis, field, weight_field, max_level, center, pf, source,
> > node_name, field_cuts, preload_style, serialize, style, **kwargs)
> >    1758         self.preload_style = preload_style
> >    1759         self._deserialize(node_name)
> > -> 1760         self._refresh_data()
> >    1761         if self._okay_to_serialize and self.serialize:
> > self._serialize(node_name=self._node_name)
> >    1762
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > _refresh_data(self)
> >     318         """
> >     319         self.clear_data()
> > --> 320         self.get_data()
> >     321
> >     322     def keys(self):
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > get_data(self, fields)
> >    1859                                  if g.Level == level],
> >    1860                               self.get_dependencies(fields),
> > self.hierarchy.io)
> > -> 1861             self._add_level_to_tree(tree, level, fields)
> >    1862             mylog.debug("End of projecting level level %s, memory
> > usage %0.3e",
> >    1863                         level, get_memory_usage()/1024.)
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > _add_level_to_tree(self, tree, level, fields)
> >    1981                               % (level, self._max_level),
> > len(grids_to_project))
> >    1982             for pi, grid in enumerate(grids_to_project):
> > -> 1983                 self._add_grid_to_tree(tree, grid, fields,
> zero_out,
> > dls)
> >    1984                 pbar.update(pi)
> >    1985                 grid.clear_data()
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > _add_grid_to_tree(self, tree, grid, fields, zero_out, dls)
> >    1925             if zero_out: weight_data[grid.child_indices] = 0
> >    1926             masked_data = [fd.astype('float64') * weight_data
> > -> 1927                            for fd in
> self._get_data_from_grid(grid,
> > fields)]
> >    1928             wdl = 1.0
> >    1929         else:
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > save_state(self, grid, field, *args, **kwargs)
> >      93         old_keys = grid.field_data.keys()
> >      94         grid.field_parameters = self.field_parameters
> > ---> 95         tr = func(self, grid, field, *args, **kwargs)
> >      96         grid.field_parameters = old_params
> >      97         grid.field_data = YTFieldData( [(k, grid.field_data[k])
> for
> > k in old_keys] )
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
> in
> > _get_data_from_grid(self, grid, fields)
> >    2003         else:
> >    2004             bad_points = 1.0
> > -> 2005         return [grid[field] * bad_points for field in fields]
> >    2006
> >    2007     def _gen_node_name(self):
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> > __getitem__(self, key)
> >     155         """
> >     156         if key not in self.field_data:
> > --> 157             self.get_data(key)
> >     158         return self.field_data[key]
> >     159
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> > get_data(self, field, convert)
> >     198                     else: raise
> >     199             else:
> > --> 200                 self._generate_field(field)
> >     201         return self.field_data[field]
> >     202
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> > _generate_field(self, field)
> >     143                 self[field] = temp_array[sl]
> >     144             else:
> > --> 145                 self[field] = self.pf.field_info[field](self)
> >     146         else: # Can't find the field, try as it might
> >     147             raise exceptions.KeyError(field)
> >
> >
> /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc
> > in __call__(self, data)
> >     393         ii = self.check_available(data)
> >     394         original_fields = data.keys() # Copy
> > --> 395         dd = self._function(self, data)
> >     396         dd *= self._convert_function(data)
> >     397         for field_name in data.keys():
> >
> >
> /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.pyc in
> > _pdensity(field, data)
> >     982                  blank,
> np.array(data.LeftEdge).astype(np.float64),
> >     983
>  np.array(data.ActiveDimensions).astype(np.int32),
> > --> 984                  np.float64(data['dx']))
> >     985     return blank
> >     986 add_field("particle_density", function=_pdensity,
> >
> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/utilities/lib/CICDeposit.so in
> > yt.utilities.lib.CICDeposit.CICDeposit_3
> > (yt/utilities/lib/CICDeposit.c:1485)()
> >
> > ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float'
> >
> > are there alternative ways around it?
> >
> > (yt-x86_64)[safarzadeh at hecate yt-x86_64]$ yt instinfo
> >
> > yt module located at:
> >     /home/safarzadeh/yt-x86_64/src/yt-hg
> > The supplemental repositories are located at:
> >     /home/safarzadeh/yt-x86_64/src/yt-supplemental
> >
> > The current version of the code is:
> >
> > ---
> > cde0a641f1bf
> > ---
> >
> > This installation CAN be automatically updated.
> > Could not determine when yt stack was last updated.
> >
> >
> >
> > Regards,
> > Mohammad
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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