[yt-users] xstick label in yt slice plot

Fri May 20 13:45:09 PDT 2016

I've opened this pull request, which should fix the memory leak:

https://bitbucket.org/yt_analysis/yt/pull-requests/2188

On Fri, May 20, 2016 at 2:46 PM, John ZuHone <jzuhone at gmail.com> wrote:

> All you have to do to get mesh construction to run is access the “index”
> attribute from the dataset:
>
> ds = yt.load(something)
> ds.index
>
> On May 20, 2016, at 3:40 PM, Jiang, Yanfei <yanfei.jiang at cfa.harvard.edu>
> wrote:
>
> Hi John,
>
>    I just paste the script. You can replay the filename with the data  you
> have (I forget which file I sent to you before).
>
>    I should say that at minimum, I should do region selection so that the
> progress bar for mesh construction shows up. Then the memory leaking issue
> also shows up.
>
> On Fri, May 20, 2016 at 3:25 PM, John Zuhone <jzuhone at gmail.com> wrote:
>
>> Yan-Fei,
>>
>> Can you send a script that shows this?
>>
>> Try pasting the script with paste.yt-project.org
>>
>> Best,
>>
>> John
>>
>> On May 20, 2016, at 3:24 PM, Jiang, Yanfei <yanfei.jiang at cfa.harvard.edu>
>> wrote:
>>
>> OK.
>>
>> By the way, the memory leaking issue with the new function for Athena++
>> seems to come from mesh construction. I tried a case with yt just reading
>> the data without any plot, the memory usage still goes up with time.
>>
>> On Fri, May 20, 2016 at 3:13 PM, John Zuhone <jzuhone at gmail.com> wrote:
>>
>>> Hi Yan-Fei,
>>>
>>> And in the athena_pp bookmark I will set this to the default for
>>> cylindrical and spherical coordinates instead of “domain” which is what I
>>> had it set to.
>>>
>>> John
>>>
>>> On May 20, 2016, at 3:12 PM, Jiang, Yanfei <yanfei.jiang at cfa.harvard.edu>
>>> wrote:
>>>
>>> Thank you, Nathan. This indeed is what I need.
>>>
>>> On Fri, May 20, 2016 at 3:09 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> Hi Yanfei,
>>>>
>>>> So I looked a little closer at the code. It looks like the 'domain'
>>>> origin sets the origin of the plot at the lower-left-hand corner of the
>>>> *domain*, which for your dataset is *not* the same thing as setting the
>>>> origin of the plot at the origin of the simulation's coordinate system.
>>>>
>>>> What you want is to set the origin to 'native', which sets the origin
>>>> to be the same as the origin of the simulation coordinate system. Here is
>>>> an example with that choice:
>>>>
>>>> https://gist.github.com/e61ac07b44e5083ea88fcf1bf24a3459
>>>>
>>>> Hope that's helpful,
>>>>
>>>> Nathan
>>>>
>>>> On Thu, May 19, 2016 at 3:29 PM, Jiang, Yanfei <
>>>> yanfei.jiang at cfa.harvard.edu> wrote:
>>>>
>>>>> Hi Nathan,
>>>>>
>>>>>    Here is a much smaller data file that you can try:
>>>>>
>>>>>
>>>>> https://drive.google.com/file/d/0ByTG4wYr-7aOdUxUR0dMWGZVQmM/view?usp=sharing
>>>>>
>>>>> Now the inner boundary is 28 and it is labeled as 0.
>>>>>
>>>>>
>>>>> On Thu, May 19, 2016 at 3:07 PM, Nathan Goldbaum <
>>>>> nathan12343 at gmail.com> wrote:
>>>>>
>>>>>> Hi Yanfei,
>>>>>>
>>>>>> John ZuHone gave me access to your dataset - I think the issue is
>>>>>> that ds.domain_left_edge is [2, 0, 0], and that is confusing the code that
>>>>>> generates the plot coordinates for spherical geometries.
>>>>>>
>>>>>> I don't think this is an issue with the frontend, but a general issue
>>>>>> with plotting data in spherical coordinates with an inner radial boundary.
>>>>>>
>>>>>> I don't have any test datasets besides yours that look like this, and
>>>>>> yours is pretty large, so it would be nice to have a smaller dataset to
>>>>>> play with.
>>>>>>
>>>>>> -Nathan
>>>>>>
>>>>>> On Thu, May 19, 2016 at 10:59 AM, Jiang, Yanfei <
>>>>>> yanfei.jiang at cfa.harvard.edu> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>>    I am trying to make a slice plot with the new capability for
>>>>>>> spherical polar grid in Athena++ data John developed. The attached
>>>>>>> notebook.png shows what I am doing. I take a slice and the origin is set to
>>>>>>> "domain". The image.png is the image from the notebook. In the slice image,
>>>>>>> the empty space near the center corresponds to the inner radial boundary of
>>>>>>> the original spherical coordinate, which is 2 in this case. Therefore, I
>>>>>>> think the x stick where is 0 in the plot should be 2. Do you know any way
>>>>>>> to fix this?
>>>>>>>
>>>>>>> Thanks.
>>>>>>>
>>>>>>> --
>>>>>>> Yan-Fei Jiang
>>>>>>>
>>>>>>> Einstein Fellow
>>>>>>> Harvard-Smithsonian Center for Astrophysics
>>>>>>> 60 Garden Street, Cambridge MA USA 02138
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Yan-Fei Jiang
>>>>>
>>>>> Einstein Fellow
>>>>> Harvard-Smithsonian Center for Astrophysics
>>>>> 60 Garden Street, Cambridge MA USA 02138
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
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>>>
>>>
>>> --
>>> Yan-Fei Jiang
>>>
>>> Einstein Fellow
>>> Harvard-Smithsonian Center for Astrophysics
>>> 60 Garden Street, Cambridge MA USA 02138
>>> _______________________________________________
>>> yt-users mailing list
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>>
>>
>> --
>> Yan-Fei Jiang
>>
>> Einstein Fellow
>> Harvard-Smithsonian Center for Astrophysics
>> 60 Garden Street, Cambridge MA USA 02138
>> _______________________________________________
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>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
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>>
>
>
> --
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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