[yt-users] HDF5 TypeError when writing LightRay

Joseph Tomlinson jmtomlinson95 at gmail.com
Mon Apr 24 13:49:31 PDT 2017


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
>>>>
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