[yt-users] Load in ASCII VTK

Tue May 31 10:49:25 PDT 2016

If you're able to read your data into Python outside yt, the oath of least
resistance would most likely be to use load_uniform_grid rather than trying
to emulate Athena VTK files.

If you can load your data using load_uniform_grid, that would also be a
good place to start to figure out what it would take to write a frontend
for this data format.

On Tuesday, May 31, 2016, John ZuHone <jzuhone at gmail.com> wrote:

> This is probably a good first-pass solution—I’m finding at first glance
> that the changes to the Athena frontend to handle ASCII files are not
> trivial. Doable, but not trivial.
>
> Also, Lukas, is your data vertex-centered or cell-centered?
>
> On May 31, 2016, at 1:43 PM, Stephanie Tonnesen <stonnes at gmail.com
> <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>> wrote:
>
> Hi Lukas,
>
> If I were in your shoes, probably the first thing I would do is just use
> python to change your ascii file into a binary file outside yt, then see
> what happens when you try and load the binary version into yt.  If the
> problem is just the file type that might be the easiest fix, and python
> help pages make me think that changing your file from ascii to binary is
> not super difficult.
>
> Looking at my old Athena vtk files, there is a lot more info in the header
> than you seem to have.  You may have to manually put equivalent lines in
> the header, but it seems pretty doable.
>
> It may end up that you should just edit yt, but in the short term it may
> be easier to make the file format changes necessary to use the athena
> reader.  Figuring out what those changes are may also help when trying to
> update a frontend reader.
>
> Best,
> Stephanie
>
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
>
> On Sun, May 29, 2016 at 1:36 PM, Lukas Bystricky <lukasbystricky at gmail.com
> <javascript:_e(%7B%7D,'cvml','lukasbystricky at gmail.com');>> wrote:
>
>> Thanks John for your quick response. I've attached a sample file VTK file
>> that I have. This is from a finite difference simulation, so grids will
>> always be uniform.
>>
>> I found the Athena source code for how they write their VTK files (
>> http://www.astro.princeton.edu/~jstone/Athena/doxygen/html.with_source/output__vtk_8c_source.html)
>> and it looks similar to mine, except that theirs is in binary and they use
>> a different dataset structure.
>>
>> I'm an extremely new YT user (and I've never done any YT development), so
>> I don't know how much help I'd be but if you'd like a hand developing a new
>> frontend let me know.
>>
>> On Sun, May 29, 2016 at 4:08 PM, John ZuHone <jzuhone at gmail.com
>> <javascript:_e(%7B%7D,'cvml','jzuhone at gmail.com');>> wrote:
>>
>>> Hi Lukas,
>>>
>>> I think Nathan's point was that there are other people working on new
>>> frontends currently, and they are smoothing over the instructions for how
>>> to make a new one.
>>>
>>> Probably the best thing to do in the short run is to figure out how to
>>> read your data in using the Athena frontend. If you have a sample dataset
>>> you can post somewhere for us to try that would help.
>>>
>>> I nominally maintain the Athena frontend, but I don't have a ton of time
>>> at the moment, so it sort of depends on how difficult it will be to make
>>> the changes in terms of how long it will take. If you're up for giving it a
>>> shot yourself I'm happy to give you pointers.
>>>
>>> Is this uniformly gridded data, or something else?
>>>
>>> Best,
>>>
>>> John
>>>
>>>
>>> ================================
>>> John ZuHone, Chandra/ACIS Operations
>>> Harvard-Smithsonian Center for Astrophysics
>>>
>>> 60 Garden St., MS-67       (w) 617-496-1816
>>> Cambridge, MA 02138.     (m) 781-708-5004
>>>
>>> john.zuhone at cfa.harvard.edu
>>> <javascript:_e(%7B%7D,'cvml','john.zuhone at cfa.harvard.edu');>
>>> http://hea-www.cfa.harvard.edu/~jzuhone
>>> ================================
>>>
>>> On May 29, 2016, at 3:41 PM, Lukas Bystricky <lukasbystricky at gmail.com
>>> <javascript:_e(%7B%7D,'cvml','lukasbystricky at gmail.com');>> wrote:
>>>
>>> Hello all,
>>>
>>> This is a followup to my question here (
>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-May/007830.html).
>>> Apologies, but I can't seem to figure out how to reply since I was never
>>> sent an e-mail for either my question or Nathan's response.
>>>
>>> I'm trying to load a legacy VTK file into YT (see format description
>>> http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf), but I
>>> when I try:
>>>
>>> ds = yt.load("file.vtk")
>>>
>>> I get the error:
>>>
>>> traceback (most recent call last):
>>> File "visualization.py", line 3, in <module>
>>> ds = yt.load("file.vtk")
>>> File "C:\Users\Dave\Anaconda2\lib\site-packages\yt\convenience.py", line 84, in load
>>> return candidates[0](*args, **kwargs)
>>> File
>>> "C:\Users\Dave\Anaconda2\lib\site-packages\yt\frontends\athena\data_structures.py",
>>> line 470, in __init__
>>> Dataset.__init__(self, filename, dataset_type,
>>> units_override=units_override)
>>> File
>>> "C:\Users\Dave\Anaconda2\lib\site-packages\yt\data_objects\static_output.py",
>>> line 190, in __init__
>>>     self._parse_parameter_file()
>>>   File
>>> "C:\Users\Dave\Anaconda2\lib\site-packages\yt\frontends\athena\data_structures.py",
>>> line 528, in _parse_parameter_file
>>>      self.domain_left_edge = grid['left_edge']
>>> KeyError: 'left_edge'
>>>
>>>
>>> Nathan Goldbaum pointed out is his answer that YT can read in VTK files from Athena. I looked into this and it seems like the difference between my file and Athena's files is that mine are ASCII while Athena's are binary. Is that right?
>>>
>>>
>>> On another note, Nathan also pointed out there are people working on a frontend for the VTK format I'm using. Could I provide any help there?
>>>
>>>
>>> Thanks again, and sorry for the double posting.
>>>
>>>
>>> Lukas
>>>
>>>
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