[yt-users] HDF5 TypeError when writing LightRay

Nathan Goldbaum nathan12343 at gmail.com
Mon Apr 24 13:51:51 PDT 2017


Hi Joseph,

I'm unfamiliar with the LightRay interface - can you make a short sample
script that triggers the issue you're seeing? I want to make sure we're on
the same page.

-Nathan

On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson <jmtomlinson95 at gmail.com>
wrote:

> Nathan,
>
> I apologize if I was unclear. I am still having an issue even on the
> latest dev version. I was having a separate issue on the stable branch that
> I believe was the issue you linked me previously.
> The issue I am currently having is that whenever yt tries to load a
> LightRay from my dataset it throws the error
>
> AttributeError: 'str' object has no attribute 'astype'
>
> This occurs from simply loading the hdf5 file generated from a call to
> make_light_ray. It should be easily reproducible by attempting to load the
> file I uploaded at use.yt/upload/9fe32716.
>
> Thanks,
> Joe Tomlinson
> Senior Undergraduate
> Department of Physics, Drexel University
>
>
> On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> You can use the yt curldrop to share the dataset:
>>
>> https://docs.hub.yt/services.html#curldrop
>>
>> But if it's as you said and the issue is fixed already (e.g. you do not
>> have any issues when you build yt from latest version on the "yt" branch in
>> the mercurial repository) then there's no need to go further, since the
>> issue is fixed already. We will hopefully be able to do a yt 3.4 release
>> soon after moving development to github, so that will get this fix out
>> there in a more easily shareable fashion.
>>
>> -Nathan
>>
>> On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson <
>> jmtomlinson95 at gmail.com> wrote:
>>
>>> Nathan,
>>>
>>> That issue is very likely the problem that I was having with the stable
>>> version.
>>>
>>> I tried to recreate the issue I am having with the dev version but the
>>> issue does not occur for any of the public enzo datasets.
>>>
>>> The error occurs after the ray data has been saved and it reloads it .
>>> The saved file is able to be read in h5py and seems correct.
>>> A few layers down the error occurs in _parse_parameter_file() and I
>>> think this may be the difference between the data I was given and the
>>> public sets.
>>> I can't really see the difference between the two myself. I've uploaded
>>> the file here http://paste.yt-project.org/show/7129/ if it becomes
>>> relevant.
>>>
>>> The script to generate the error is extremely basic, I didn't upload it
>>> because its just two lines, making the LightRay then calling make_light_ray.
>>> The error should be reproducible by simply trying to load the resultant
>>> hdf5 file, is there somewhere you would prefer me to upload it? It's not
>>> too large, less than 1MB.
>>> Is there anything else I could provide to help diagnose the issue?
>>>
>>> Thanks,
>>> Joe Tomlinson
>>> Senior Undergraduate
>>> Department of Physics, Drexel University
>>>
>>> On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> Hi Joseph,
>>>>
>>>> I believe you're hitting this issue:
>>>>
>>>> https://bitbucket.org/yt_analysis/yt/issues/1330
>>>>
>>>> Which was fixed here:
>>>>
>>>> https://bitbucket.org/yt_analysis/yt/pull-requests/2541
>>>>
>>>> We haven't had a stable release since that was fixed. If you're running
>>>> yt from a stable release, can you try installing the development version
>>>> from source? If you're using conda you can also use the nightly binary
>>>> builds:
>>>>
>>>> http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
>>>>
>>>> If you are running a recent development version then Britton's fix
>>>> might need to be eloborated upon. If so, can you create a self-contained,
>>>> runnable example script that triggers the issue you're seeing (preferably
>>>> making use of one of the public datasets on yt-project.org/data)?
>>>>
>>>> Best,
>>>>
>>>> Nathan Goldbaum
>>>>
>>>> On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson <
>>>> jmtomlinson95 at gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am trying to use the single dataset LightRay module but I am running
>>>>> into an issue.
>>>>> Whenever I use the data_filename parameter, which I believe is
>>>>> necessary for use with AbsorptionSpectrum, I receive the following error.
>>>>>
>>>>> TypeError: Object dtype dtype('O') has no native HDF5 equivalent
>>>>>
>>>>> This error does not occur when I run the cookbook example so I am a
>>>>> bit lost as to what to do.
>>>>> I am running the latest stable version on anaconda and have tried both
>>>>> h5py 2.7 and 2.6.
>>>>> The simulation is a cosmological Enzo simulation.
>>>>>
>>>>> I have also tried using the nightly dev build which changes the error
>>>>> from being on write to being on load with the following error.
>>>>>
>>>>> AttributeError: 'str' object has no attribute 'astype'
>>>>> from line 326 in _restore_light_ray_solution
>>>>> self.parameters[ksp3] = self.parameters[ksp3].astype(str)
>>>>>
>>>>> When using python 2.7 the error is the same but with 'unicode' instead
>>>>> of 'str'.
>>>>>
>>>>> Any help would be greatly appreciated.
>>>>>
>>>>> Thanks,
>>>>> Joe Tomlinson
>>>>> Senior Undergraduate
>>>>> Department of Physics, Drexel University
>>>>>
>>>>> _______________________________________________
>>>>> 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/20170424/0e3200bd/attachment.html>


More information about the yt-users mailing list