[yt-users] xstick label in yt slice plot

Fri May 20 14:03:38 PDT 2016

Thank you. It indeed fixes the issue.

On Fri, May 20, 2016 at 4:45 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> 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
>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>
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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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>>>>>>
>>>>>
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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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>>>
>>>
>>> --
>>> Yan-Fei Jiang
>>>
>>> Einstein Fellow
>>> Harvard-Smithsonian Center for Astrophysics
>>> 60 Garden Street, Cambridge MA USA 02138
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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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-- 
Yan-Fei Jiang

Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
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