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

Matthew Turk matthewturk at gmail.com
Mon Jun 23 12:14:21 PDT 2014


Well, that's weird!  It might be related to it being in 1D.  Can you
try doing a similar operation with a yt-3.0 "bleeding edge" install?
3.0 will have much better support for spherical data.

On Mon, Jun 23, 2014 at 1:38 PM, Luke Zoltan Kelley
<lkelley at cfa.harvard.edu> wrote:
> In [173]: pf.domain_left_edge
> Out[173]: array([ 0.,  0.,  0.])
>
> In [174]: pf.domain_right_edge
> Out[174]: array([  4.00000000e+11,   3.14159265e+00,   1.74532925e-02])
>
>
>
> On Jun 23, 2014, at 2:35 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>
>> 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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