[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
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
More information about the yt-users
mailing list