[yt-users] xstick label in yt slice plot

[John Zuhone]

Yan-Fei,

Can you send a script that shows this? 

Try pasting the script with paste.yt-project.org <http://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 <mailto: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 <mailto: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 <mailto: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 <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 <mailto: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 <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 <mailto: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 <mailto: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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>> 
>> 
>> -- 
>> 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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