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

Matthew Turk matthewturk at gmail.com
Thu Feb 25 07:43:51 PST 2016 

Hi all,

I will take a look at this, but have limited time today.  I think
Britton's error tracking is right -- it's a difference in the tcoords
and fcoords, which shouldn't happen.  A few things that I will check
are what happens if tcoords is chosen for orthogonal rays, which has a
slightly different selection method, and what the input selector to
the octree tcoords function is.

On Thu, Feb 25, 2016 at 8:39 AM, Britton Smith <brittonsmith at gmail.com> wrote:
> 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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>>>>>>
>>>>>>
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