[yt-users] ZeroDivisionError accessing field from ray in spherical 1D FLASH data
Luke Zoltan Kelley
lkelley at cfa.harvard.edu
Mon Jun 23 11:27:59 PDT 2014
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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