[yt-users] error in light_ray periodic ray creation

Sat Jul 28 13:23:47 PDT 2012

Hi Josh,

I think I was able to find the source of the error.  There was a case in
which rays start on the edge of the domain and are oriented outward that I
hadn't accounted for correctly.  I've just pushed a fix for this to the
development branch of yt.  If you update to the yt branch within the repo,
it should be fine.  However, there was also a minor change in the LightRay
api, so you'll need to adjust your script a little bit.  If you change your
script to resemble something like the following:
http://paste.yt-project.org/show/2579/
everything should be fine.

Let me know if you encounter any more issues.

Britton

On Fri, Jul 27, 2012 at 7:18 PM, Britton Smith <brittonsmith at gmail.com>wrote:

> Hi Josh,
>
> I'm not sure what's causing that as it's never happened to me before. I'm
> away from my computer at the moment but I will take a look at this later.
> Is the script you're using unaltered?  If not, please send me the one
> you're using off-list.
>
> Also, please make sure to send emails to the list from the address that
> you signed up with. Otherwise, it has to be approved by the moderator each
> time.
>
> Britton
> On Jul 27, 2012 7:05 PM, "Joshua Eric Moloney" <
> Joshua.Moloney at colorado.edu> wrote:
>
>> The install I'm running should be the latest stable version of the code:
>>
>> The current version of the code is:
>>
>> ---
>> c23cb264f04c (stable)
>> ---
>>
>> -Josh
>>
>>
>> On Fri, Jul 27, 2012 at 4:54 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>>
>>> Hi Joshua,
>>>
>>> I can't speak to the problem you're having specifically.  However, since
>>> there have been some recent updates to the light ray, it would help us to
>>> figure out what's happening if you could reply with the output of the "yt
>>> instinfo" command, run on the command line.
>>>
>>> Cheers,
>>>
>>> Nathan
>>>
>>> On Jul 27, 2012, at 3:49 PM, Joshua Eric Moloney wrote:
>>>
>>> Hi all,
>>>
>>> I've been trying to get a script (provided to me by Britton) working to
>>> create a bunch of light rays from an Enzo simulation. Depending on the
>>> initial seed value, it makes some of them correctly but eventually fails
>>> with the following error:
>>>
>>> Traceback (most recent call last):
>>>   File "make_light_rays.py", line 32, in <module>
>>>     get_los_velocity=True, get_nearest_galaxy=False)
>>>   File "/home/student/jomo9722/Enzo/
>>> yt-x86_64/src/yt-hg/yt/analysis_modules/light_ray/light_ray.py", line
>>> 275, in make_light_ray
>>>     (sub_ray[field])])
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 319, in __getitem__
>>>     self.get_data(key)
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 508, in get_data
>>>     if field not in ("dts", "t") and self._generate_field(field):
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 349, in _generate_field
>>>     self[field] = self.pf.field_info[field](self)
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
>>> line 316, in __call__
>>>     dd = self._function(self, data)
>>>   File
>>> "/data/moloney/cosmology_test/test_new/ion_balance/SD93IonBalance.py", line
>>> 178, in _ion_number_density
>>>     return solarAbundance[atom] * data[fractionField] *
>>> data['Metallicity'] * \
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 319, in __getitem__
>>>     self.get_data(key)
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 508, in get_data
>>>     if field not in ("dts", "t") and self._generate_field(field):
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 349, in _generate_field
>>>     self[field] = self.pf.field_info[field](self)
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
>>> line 316, in __call__
>>>     dd = self._function(self, data)
>>>   File
>>> "/data/moloney/cosmology_test/test_new/ion_balance/SD93IonBalance.py", line
>>> 193, in _ion_fraction_field
>>>     fraction = na.power(10, interp(data))
>>>   File
>>> "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/utilities/linear_interpolators.py",
>>> line 44, in __call__
>>>     x_i = (na.digitize(x_vals, self.x_bins) - 1).astype('int32')
>>> ValueError: Both x and bins must have non-zero length
>>>
>>> Working through the debugger, I found that for the segment where it
>>> failed the periodic_ray function had produced the following list of
>>> segments.
>>>
>>> [[array([ 0.16103374,  0.78830872,  0.24846128]), array([ 0.14031834,
>>> 0.57367409,  1.        ])], [array([ 0.14031834,  0.57367409,  1.
>>> ]), array([ 0.14031834,  0.57367409,  1.        ])], [array([ 0.14031834,
>>> 0.57367409,  0.        ]), array([ 0.13268221,  0.49455532,  0.2770327 ])]]
>>>
>>> The second segment here has identical start and end points, which is
>>> leading yt to try to interpolate a field with nothing in it (and therefore
>>> throwing the above error). It seems that what's happening is that due to
>>> rounding errors the first segment being produced actually has a value < 1
>>> for the third dimension so that when it checks to see if the segment hit
>>> any of the box walls it thinks that it didn't. It then tries to start a new
>>> segment that's already at the boundary of the box, producing a ray segment
>>> containing 0 grid cells.
>>>
>>> Has anyone run into this problem before, and is there a fix for it
>>> floating around out there somewhere? If not I could probably work something
>>> up that checks to see if the distance from the segment endpoint to the wall
>>> is < SmallNumber and set it equal to the value at the wall if it is.
>>>
>>> Thanks.
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
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>>>
>>>
>>>
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