[yt-users] Reading in arrays from Active Particles

[Nathan Goldbaum]

It looks like you created a new github account to create that issue, so
just in case you don't have your notifications set up, I commented on the
issue here:

https://github.com/yt-project/yt/issues/1565#issuecomment-331484604

On Fri, Sep 22, 2017 at 3:56 AM, John Regan <johnanthonyregan at gmail.com>
wrote:

> Hi Nathan,
>
> Thanks for getting back to me. Yes the array is read is fine and "data"
> stores the array as it should. The problem appears at the masking stage. It
> seems the mask selects just the first element. I'm not sure what the
> workaround is in the case regarding the masking so I'll open an issue on
> github for this. I'll create small dataset that reproduces in the problem.
>
> Cheers,
> John
>
> On Thu, Sep 21, 2017 at 4:03 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi John,
>>
>> The I/O operation is happening here:
>>
>> https://github.com/yt-project/yt/blob/master/yt/frontends/enzo/io.py#L92
>>
>> Here, if you are reading an active particle field, "pds" is a handle to
>> the hdf5 dataset containing the active particle data. The array that we're
>> going to read the particle data into is allocated on line 110. It looks to
>> me like "data" should be multidimensional if the on-disk data are, but
>> perhaps we're doing something further along the line that is causing the
>> issue you're seeing.
>>
>> If you get stuck, feel free to open an issue on github about this. If you
>> do so please include a sample dataset and a script to trigger the issue so
>> one of us can reproduce and debug.
>>
>> -Nathan
>>
>> On Thu, Sep 21, 2017 at 9:41 AM, John Regan <johnanthonyregan at gmail.com>
>> wrote:
>>
>>> Hi All,
>>>
>>> I'm hoping to modify YT to read in arrays from ActiveParticle fields. I
>>> have an array which is part of the AP data structure. At the moment YT sees
>>> the field but only reads the first element which kinda makes sense.
>>>
>>> Just wondering how I can modify the source code so that YT realised that
>>> a field is in fact an array and to read in all the values?
>>>
>>> At the moment YT is also complaining with the message:
>>> yt/yt/frontends/enzo/io.py:140: VisibleDeprecationWarning: boolean
>>> index did not match indexed array along dimension 0; dimension is 20 but
>>> corresponding boolean dimension is 1
>>>
>>> which is because of course the field is an array of length 20 rather
>>> than a scalar.
>>>
>>> Any tips on what is required? I am looking on io.py at the
>>> _read_particle_fields function and I imagine it is this function that needs
>>> modification?
>>>
>>> Cheers,
>>> John
>>>
>>> _______________________________________________
>>> yt-users mailing list
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>>>
>>>
>>
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>
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