[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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