[yt-users] Error in making light ray for a gadget dataset

[Britton Smith]

Hi Bili,

I have looked into this and it seems there are some problems with
generating rays with particle datasets.  I cannot tell whether yours is a
special case, but what seems to be happening is that certain fields are
being returned with different sizes.  The error happens in the LightRay
code because it first tries to access the "t" field, which comes back with
size 40.  After that, it tries to access one of the coordinate fields ("x",
"y", or "z") and that is being returned with size 81, which doesn't fit
into the arrays made to hold it that already have size 40.

Anyway, you're not seeing this when you make the ray yourself if you first
try to access a field other than the "t" field.  This results in the field
arrays being made with the larger size.  If you do this and then try to
access the "t" array, you will find that the first 40 values have real
numbers but that the rest are just uninitialized values.

Unfortunately, I haven't gotten much past this as I'm having trouble seeing
where the fcoords for this particular object are getting generated.  I have
created an issue, which you can follow here:
https://bitbucket.org/yt_analysis/yt/issues/1175/fcoords-and-tcoords-not-the-same-shape-for

That's about all I can do for now, but if anyone has any thoughts, help
would be appreciated.

Britton

On Wed, Feb 24, 2016 at 7:21 PM, Bili Dong - Gmail <qobilidop at gmail.com>
wrote:

> Hi Britton,
>
> I was using the yt sample dataset 'GadgetDiskGalaxy/snapshot_200.hdf5' to
> test the functionality.
>
> Thanks,
> Bili
>
> On Wed, Feb 24, 2016 at 2:39 AM, Britton Smith <brittonsmith at gmail.com>
> wrote:
>
>> Hi Bili,
>>
>> My apologies for the long delay in replying to this thread.  By now, I
>> think you may be working with Trident.  If things are working, that's
>> great.  However, Trident relies on much of the machinery that you were
>> trying to use, so it's still possible that you see this error.  The problem
>> is likely related to how the LightRay generator is calculating the
>> trajectory for the ray and not with the underlying ray machinery which it
>> relies on.  If it's possible for you to give me access to this dataset, I
>> would be happy to take a look at this.
>>
>> Britton
>>
>> On Mon, Feb 15, 2016 at 9:30 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> I think Cameron, Britton, and Devin have done this for their Trident
>>> project - you might want to contact them.
>>>
>>> On Mon, Feb 15, 2016 at 3:23 PM, Bili Dong - Gmail <qobilidop at gmail.com>
>>> wrote:
>>>
>>>> Hi Matt,
>>>>
>>>> I've tried to construct the ray and ortho_ray objects, neither of which
>>>> can reproduce the error. They work just fine. I haven't succeeded in
>>>> tracing down the error yet, but I'll keep working on that.
>>>>
>>>> Besides, I'm wondering if there are examples of successfully making
>>>> light rays in a particle dataset? That may help figuring out what might go
>>>> wrong.
>>>>
>>>> Thanks,
>>>> Bili
>>>>
>>>> On Fri, Feb 12, 2016 at 12:42 PM, Matthew Turk <matthewturk at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Bili,
>>>>>
>>>>> Hm, I'm honestly not sure.  This looks like an oddity in the way the
>>>>> octree is being constructed in spatial dimensions.  Any chance you can
>>>>> reproduce this with a ray or ortho_ray object, which should simplify the
>>>>> number of moving parts?
>>>>>
>>>>> On Tue, Feb 9, 2016 at 2:04 PM, Bili Dong - Gmail <qobilidop at gmail.com
>>>>> > wrote:
>>>>>
>>>>>> Hi yt users,
>>>>>>
>>>>>> I'm trying to make a light ray for a gadget dataset using this
>>>>>> script: http://paste.yt-project.org/show/6234/
>>>>>>
>>>>>> But I get the following error:
>>>>>>
>>>>>> ```
>>>>>>
>>>>>> /Users/qobilidop/repos/yt/yt/geometry/geometry_handler.py in fcoords(self)    320             c = obj.select_fcoords(self.dobj)    321             if c.shape[0] == 0: continue--> 322             ci[ind:ind+c.shape[0], :] = c    323             ind += c.shape[0]    324         return ci
>>>>>> ValueError: could not broadcast input array from shape (81,3) into shape (40,3)
>>>>>>
>>>>>> ```
>>>>>>
>>>>>>
>>>>>> My yt is on the changeset d47150dfbde6.
>>>>>>
>>>>>>
>>>>>> I'm wondering if I'm doing it the correct way? And how could I solve the problem?
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Bili
>>>>>>
>>>>>>
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