[yt-users] ZeroDivisionError accessing field from ray in spherical 1D FLASH data

Matthew Turk matthewturk at gmail.com
Mon Jun 23 11:35:01 PDT 2014


Hi Luke,

Not sure if the dimensionality is a problem or not.  But it's saying
it doesn't find any grids intersecting with the ray, which is
confusing.  What's the output of "pf.domain_left_edge" and
"pf.domain_right_edge"?

On Mon, Jun 23, 2014 at 1:27 PM, Luke Zoltan Kelley
<lkelley at cfa.harvard.edu> wrote:
> Thanks for working with me on this Matt, but I got a new one for you:
>
> In [164]: print pf.domain_width
> [  4.00000000e+11   3.14159265e+00   1.74532925e-02]
>
> In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
> yt : [INFO     ] 2014-06-23 14:22:26,386 Getting field x from 0
> ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers]
> astropy: [ERROR    ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
> <ipython-input-165-9633905f901e> in <module>()
> ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
>
> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs)
>     578         self.px, self.py = coords
>     579         self.sort_by = axis_names[self.axis]
> --> 580         self._refresh_data()
>     581
>     582     @property
>
> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self)
>     304         """
>     305         self.clear_data()
> --> 306         self.get_data()
>     307
>     308     def keys(self):
>
> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids)
>     523             self[field] = np.concatenate(
>     524                 [self._get_data_from_grid(grid, field)
> --> 525                  for grid in self._grids])
>     526             if not self.field_data.has_key(field):
>     527                 continue
>
> ValueError: need at least one array to concatenate
>
> could this be something about the data being 1D?
>
> Actually, I have no idea if this means anything, but when I ask for the dimensionality:
>
> In [172]: pf.dimensionality
> Out[172]: 2
>
> In [171]: pf.domain_dimensions
> Out[171]: array([ 8, 16,  1])
>
> But my FLASH log confirms the dimensionality is 1...
>
>
> On Jun 23, 2014, at 2:19 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>
>> Hi Luke,
>>
>> Nah, not a bad influence.  Try putting it at the cell center instead
>> of the cell edge.  :)  (0.0, 0.0) will be the very corner of the
>> domain, so it's skimming along the surface of a cell.
>>
>> On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley
>> <lkelley at cfa.harvard.edu> wrote:
>>> Thanks Matt, but now I'm having new problems with 'ortho_ray', following
>>> (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
>>>
>>>> ray = pf.h.ortho_ray(0, (0.0,0.0))
>>>
>>> which then gave me
>>>
>>> yt : [INFO     ] 2014-06-23 14:15:52,664 Getting field x from 8
>>> ERROR: ValueError: cannot convert float NaN to integer
>>> [yt.data_objects.data_containers]
>>> astropy: [ERROR    ] 2014-06-23 14:15:52,664 ValueError: cannot convert
>>> float NaN to integer
>>> ---------------------------------------------------------------------------
>>> ValueError                                Traceback (most recent call last)
>>> <ipython-input-157-318ebcfbdb94> in <module>()
>>> ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in __init__(self, axis, coords, fields, pf, **kwargs)
>>>    578         self.px, self.py = coords
>>>    579         self.sort_by = axis_names[self.axis]
>>> --> 580         self._refresh_data()
>>>    581
>>>    582     @property
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in _refresh_data(self)
>>>    304         """
>>>    305         self.clear_data()
>>> --> 306         self.get_data()
>>>    307
>>>    308     def keys(self):
>>>
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in get_data(self, fields, in_grids)
>>>    523             self[field] = np.concatenate(
>>>    524                 [self._get_data_from_grid(grid, field)
>>> --> 525                  for grid in self._grids])
>>>    526             if not self.field_data.has_key(field):
>>>    527                 continue
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/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] )
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in _get_data_from_grid(self, grid, field)
>>>    599             gdx = just_one(grid[self.px_dx])
>>>    600             gdy = just_one(grid[self.py_dx])
>>> --> 601             x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx)
>>>    602             y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy)
>>>    603             sl = [None,None,None]
>>>
>>> ValueError: cannot convert float NaN to integer
>>>
>>>
>>> Without doing anything wrong, perhaps I'm just a bad influence.
>>>
>>> Luke
>>>
>>>
>>>
>>>
>>> On Jun 23, 2014, at 2:05 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>>
>>> Hi Luke,
>>>
>>> You didn't do anything wrong.  :)  yt should be able to accept rays
>>> through "ray" that are orthogonal to the axes, but it can't because of
>>> some sloppiness.  You have two options -- either use "ortho_ray"
>>> instead of "ray", which will make it orthogonal (and probably be a bit
>>> faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
>>>
>>> -Matt
>>>
>>> On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley
>>> <lkelley at cfa.harvard.edu> wrote:
>>>
>>> Hello yt-users,
>>>
>>> Just starting using YT, please forgive simple problems.
>>>
>>> I have 1D spherical FLASH data which I'm trying to plot.  I thought I should
>>> use a 'ray', so I created one as such and try to access the data but I'm
>>> getting a ZeroDivision Error:
>>>
>>> from yt.mods import *
>>> pf = load('starwind_hdf5_plt_cnt_0000')
>>> In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"])
>>> In [142]: ray['Density']
>>>
>>> yt : [INFO     ] 2014-06-23 12:40:51,841 Getting field t from 138
>>> ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell]
>>> astropy: [ERROR    ] 2014-06-23 12:40:51,846 ZeroDivisionError: float
>>> division
>>> ---------------------------------------------------------------------------
>>> ZeroDivisionError                         Traceback (most recent call last)
>>> <ipython-input-142-c8a80a171d35> in <module>()
>>> ----> 1 ray['Density']
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/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
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in get_data(self, fields, in_grids)
>>>   523             self[field] = np.concatenate(
>>>   524                 [self._get_data_from_grid(grid, field)
>>> --> 525                  for grid in self._grids])
>>>   526             if not self.field_data.has_key(field):
>>>   527                 continue
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/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] )
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in _get_data_from_grid(self, grid, field)
>>>   689     @restore_grid_state
>>>   690     def _get_data_from_grid(self, grid, field):
>>> --> 691         mask = np.logical_and(self._get_cut_mask(grid),
>>>   692                               grid.child_mask)
>>>   693         if field == 'dts': return self._dts[grid.id][mask]
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in check_cache(self, grid)
>>>   109         elif grid.id not in self._cut_masks or \
>>>   110                 hasattr(self, "_boolean_touched"):
>>> --> 111             cm = func(self, grid)
>>>   112             self._cut_masks[grid.id] = cm
>>>   113         return self._cut_masks[grid.id]
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>>> in _get_cut_mask(self, grid)
>>>   704         ts = np.zeros(grid.ActiveDimensions, dtype='float64')
>>>   705         VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge,
>>> --> 706                        grid.dds, self.center, self.vec)
>>>   707         self._dts[grid.id] = np.abs(dts)
>>>   708         self._ts[grid.id] = np.abs(ts)
>>>
>>> /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so
>>> in yt.utilities.lib.RayIntegrators.VoxelTraversal
>>> (yt/utilities/lib/RayIntegrators.c:3408)()
>>>
>>> ZeroDivisionError: float division
>>>
>>>
>>> yt instinfo
>>> Version = 2.6.1
>>> Changeset = c7bae05dd4ef
>>>
>>>
>>> Any ideas what I'm doing wrong?
>>> Thanks!
>>> Luke
>>>
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