<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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. <div class=""><br class=""></div><div class="">Also, Lukas, is your data vertex-centered or cell-centered?<br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 31, 2016, at 1:43 PM, Stephanie Tonnesen <<a href="mailto:stonnes@gmail.com" class="">stonnes@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Hi Lukas,<br class=""><br class=""></div>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. <br class=""><br class=""></div>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. <br class=""><br class=""></div><div class="">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. <br class=""><br class=""></div><div class="">Best,<br class=""></div><div class="">Stephanie<br class=""></div><div class=""><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div class=""><div class=""><font face="garamond,serif" class="">--<br class="">Dr. Stephanie Tonnesen<br class=""></font></div><font face="garamond,serif" class="">Alvin E. Nashman Postdoctoral Fellow<br class=""></font></div><font face="garamond,serif" class="">Carnegie Observatories, Pasadena, CA<br class=""></font></div><font face="garamond,serif" class=""><a href="mailto:stonnes@gmail.com" target="_blank" class="">stonnes@gmail.com</a><br class=""></font></div></div></div>
<br class=""><div class="gmail_quote">On Sun, May 29, 2016 at 1:36 PM, Lukas Bystricky <span dir="ltr" class=""><<a href="mailto:lukasbystricky@gmail.com" target="_blank" class="">lukasbystricky@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">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. <div class=""><br class=""></div><div class="">I found the Athena source code for how they write their VTK files (<a href="http://www.astro.princeton.edu/~jstone/Athena/doxygen/html.with_source/output__vtk_8c_source.html" target="_blank" class="">http://www.astro.princeton.edu/~jstone/Athena/doxygen/html.with_source/output__vtk_8c_source.html</a>) and it looks similar to mine, except that theirs is in binary and they use a different dataset structure. </div><div class=""><br class=""></div><div class="">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. </div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sun, May 29, 2016 at 4:08 PM, John ZuHone <span dir="ltr" class=""><<a href="mailto:jzuhone@gmail.com" target="_blank" class="">jzuhone@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto" class=""><div class="">Hi Lukas,</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Is this uniformly gridded data, or something else?</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">John</div><div class=""><br class=""><br class=""><div class=""><div style="word-wrap:break-word" class=""><span style="background-color:rgba(255,255,255,0)" class="">================================</span></div><div style="word-wrap:break-word" class=""><span style="background-color:rgba(255,255,255,0)" class="">John ZuHone, Chandra/ACIS Operations<span style="white-space:pre-wrap" class=""> </span></span></div><div style="word-wrap:break-word" class=""><span style="background-color:rgba(255,255,255,0)" class="">Harvard-Smithsonian Center for Astrophysics<br class=""><br class=""></span></div><div style="word-wrap:break-word" class=""><font class=""><span style="background-color:rgba(255,255,255,0)" class=""><a dir="ltr" class="">60 Garden St.</a>, MS-67 (w) <a dir="ltr" href="tel:617-496-1816" target="_blank" class="">617-496-1816</a><br class=""><a dir="ltr" class="">Cambridge, MA 02138</a>. (m) <a dir="ltr" href="tel:781-708-5004" target="_blank" class="">781-708-5004</a></span></font></div><div style="word-wrap:break-word" class=""><span style="background-color:rgba(255,255,255,0)" class=""><br class=""></span></div><div style="word-wrap:break-word" class=""><font class=""><span style="background-color:rgba(255,255,255,0)" class=""><a href="mailto:john.zuhone@cfa.harvard.edu" target="_blank" class="">john.zuhone@cfa.harvard.edu</a><br class=""><a dir="ltr" href="http://hea-www.cfa.harvard.edu/~jzuhone" target="_blank" class="">http://hea-www.cfa.harvard.edu/~jzuhone</a><br class="">================================</span></font><br class=""></div></div></div><div class=""><div class=""><div class=""><br class="">On May 29, 2016, at 3:41 PM, Lukas Bystricky <<a href="mailto:lukasbystricky@gmail.com" target="_blank" class="">lukasbystricky@gmail.com</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class="">Hello all,<div class=""><br class=""></div><div class="">This is a followup to my question here (<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-May/007830.html" target="_blank" class="">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-May/007830.html</a>). 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. </div><div class=""><br class=""></div><div class="">I'm trying to load a legacy VTK file into YT (see format description <a href="http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf" target="_blank" class="">http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf</a>), but I when I try:</div><div class=""><br class=""></div><div class=""><pre style="white-space: pre-wrap;" class="">ds = yt.load("file.vtk")</pre><pre style="white-space: pre-wrap;" class=""><font face="arial, helvetica, sans-serif" class="">I get the error:</font></pre><pre style="white-space: pre-wrap;" class=""><pre style="white-space:pre-wrap" class="">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'</pre><pre style="white-space:pre-wrap" class=""><br class=""></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class="">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? </font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class="">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?</font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class="">Thanks again, and sorry for the double posting. </font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></pre><pre style="white-space:pre-wrap" class=""><font face="arial, helvetica, sans-serif" class="">Lukas</font></pre><pre style="white-space:pre-wrap" class=""><br class=""></pre></pre></div></div>
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