[yt-users] [YT-USERS] Incoherence when ploting a slice - from FLASH simulation

[Nathan Goldbaum]

Sorry to resurrect an old thread but I think I've found the source of the
issue. See this pull request:

https://github.com/yt-project/yt/pull/1493

-Nathan

On Tue, May 2, 2017 at 4:56 PM, Scott Feister <sfeister at gmail.com> wrote:

> Nathan,
>
> Thanks for the lightning-fast response and workaround.
>
> Best,
>
> Scott
>
>
> Scott Feister, Ph.D.
> Postdoctoral Researcher, Flash Center for Computational Science
> University of Chicago, Department of Astronomy and Astrophysics
>
> On Tue, May 2, 2017 at 4:48 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> While we fix this issue (which will hopefully be soon), here is a
>> workaround. I've modified your script to disable antialiasing:
>>
>> import yt
>>
>> ds = yt.load("lasslab_hdf5_plt_cnt_0000.hdf5")
>> plot = yt.SlicePlot(ds, 'z', "dens")
>> plot.frb.antialias = 0
>> plot.save()
>>
>> That will avoid the artifacts until we fix this issue.
>>
>> On Tue, May 2, 2017 at 4:35 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> First, thanks for the report and for sending in the dataset to reproduce
>>> with. I've opened an issue to track this:
>>>
>>> https://github.com/yt-project/yt/issues/1361
>>>
>>> I suspect that we're hitting a corner case bug in the code that
>>> generates pixelized representations of AMR data. I will try to take a
>>> closer look at this in the next few days.
>>>
>>> On Tue, May 2, 2017 at 4:17 PM, Gabriel RIGON <
>>> rigon.g at bureau.luli.polytechnique.fr> wrote:
>>>
>>>> I've uploaded the dataset: http://use.yt/upload/364c7039
>>>>
>>>> Gabriel
>>>>
>>>> ------------------------------
>>>> *De :* yt-users [yt-users-bounces at lists.spacepope.org] de la part de
>>>> Nathan Goldbaum [nathan12343 at gmail.com]
>>>> *Envoyé :* mardi 2 mai 2017 23:09
>>>> *À :* Discussion of the yt analysis package
>>>> *Objet :* Re: [yt-users] [YT-USERS] Incoherence when ploting a slice -
>>>> from FLASH simulation
>>>>
>>>> Could one of you share a dataset that exhibits this behavior?
>>>>
>>>> You can use the yt curldrop to share datasets:
>>>>
>>>> https://docs.hub.yt/services.html#curldrop
>>>>
>>>> -Nathan
>>>>
>>>> On Tue, May 2, 2017 at 4:02 PM, Scott Feister <sfeister at gmail.com>
>>>> wrote:
>>>>
>>>>> Gabriel,
>>>>>
>>>>> I would like to add that I have seen this problem as well in my own
>>>>> usage of FLASH with yt. The streaks appear to be perfectly doubled in value
>>>>> relative to their neighbors. I would love to hear if anyone in the yt
>>>>> community has seen it and/or knows what might be going on! Note: These
>>>>> streaks are not in the FLASH data; VisIt reproduces the data without the
>>>>> streaks. Also, a yt ray output does not show the streaks; the slice plot
>>>>> does.
>>>>>
>>>>> Best,
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> Scott Feister, Ph.D.
>>>>> Postdoctoral Researcher, Flash Center for Computational Science
>>>>> University of Chicago, Department of Astronomy and Astrophysics
>>>>>
>>>>> On Tue, May 2, 2017 at 3:43 PM, Gabriel RIGON <
>>>>> rigon.g at bureau.luli.polytechnique.fr> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> I recently start to work with yt to analyze my FLASH simulation. The
>>>>>> output of those simulation is an hdf5 file.
>>>>>>
>>>>>> When I try to plot a slice of my simulation, some weird lines appear
>>>>>> on it. Here is an example of the python script and the results it leads to.
>>>>>>
>>>>>> """
>>>>>> import yt
>>>>>>
>>>>>> ds = yt.load("lasslab_hdf5_plt_cnt_0000.hdf5")
>>>>>> yt.SlicePlot(ds, 'z', "dens").show()
>>>>>>
>>>>>> """
>>>>>>
>>>>>> Actually they also appear went plotting the results of a frb of a
>>>>>> slice (even when I try to plot the x or y coordinate in 2d).
>>>>>>
>>>>>> Do you have any idea of the reason for such lines, or a solution for
>>>>>> my problem?
>>>>>>
>>>>>> Best regards,
>>>>>> Gabriel Rigon
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20170715/68e9a068/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: flash_slice.png
Type: image/png
Size: 44024 bytes
Desc: not available
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20170715/68e9a068/attachment-0001.png>