[yt-users] Accessing data

[Stuart Mumford]

Hello,

I am starting upon an adventure of actually using yt and I am already
getting the impression I may be using a chainsaw to cut kindling.

My data is uniform grid, not that large (128^3 for now) and I need to
access the fields, both on disk and derived in 3D array format. I have
tried using a covering_grid thus:

```
ts =
yt.load("/archive/io_testing/3D_tube128_Slog_p90_A20r2-3_B005/3D_tube128_Slog_p90_A20r2-3_B005_*.gdf")

ds = ts[10]

cg = ds.h.covering_grid(0, ds.domain_left_edge, ds.domain_dimensions)

cg['density_pert']
```

which soemtimes seems to give me an array full of -999 and sometimes gives
me this lovely traceback:
```

---------------------------------------------------------------------------
DataCubeError                             Traceback (most recent call last)
<ipython-input-55-62e42995fe53> in <module>()
----> 1 cg['density_pert']

/home/stuart/BitBucket/yt/yt/data_objects/data_containers.pyc in
__getitem__(self, key)
    316             if key not in self.fields:
    317                 self.fields.append(key)
--> 318             self.get_data(key)
    319         return self.field_data[key]
    320

/home/stuart/BitBucket/yt/yt/data_objects/data_containers.pyc in
get_data(self, fields)
   3757         for i, grid in enumerate(self._grids):
   3758             if self._use_pbar: pbar.update(i)
-> 3759             count -= self._get_data_from_grid(grid, obtain_fields)
   3760             if count <= 0: break
   3761         if self._use_pbar: pbar.finish()

/home/stuart/BitBucket/yt/yt/data_objects/data_containers.pyc in
save_state(self, grid, field, *args, **kwargs)
     79         old_keys = grid.field_data.keys()
     80         grid.field_parameters = self.field_parameters
---> 81         tr = func(self, grid, field, *args, **kwargs)
     82         grid.field_parameters = old_params
     83         grid.field_data = YTFieldData( [(k, grid.field_data[k]) for
k in old_keys] )

/home/stuart/BitBucket/yt/yt/data_objects/data_containers.pyc in
_get_data_from_grid(self, grid, fields)
   3801             c_fields, g_fields,
   3802             self.ActiveDimensions, grid.ActiveDimensions,
-> 3803             grid.child_mask, self.domain_width, ll, 0)
   3804         return count
   3805

DataCubeError: DataCubeGeneric: Invalid parameters.
```

I only want my arrays :'(

On another, related, note:
I have a bit of code that executes in serial at the top of a otherwise
embarrassingly parallel piece of vtk code, I need the most optimal io
possible for this, as it is all io limited, how well is yt suited to
getting one slice out of my gdf files as fast as humanly possible?

Stuart
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20131106/b81a924f/attachment.htm>