[FLASH-USERS] Trouble in opening HDF files

[Sonali Khanna]

Thank you so much everyone!

On Fri, 25 Jun 2021, 18:22 Ryan Farber, <rjfarber at umich.edu> wrote:

> You can also use the python package "yt" to open hdf5 files in general:
> https://yt-project.org/
>
> Best,
> --------
> Ryan
>
>
> On Fri, Jun 25, 2021 at 4:47 AM Jiří Löffelmann <loffejir at fjfi.cvut.cz>
> wrote:
>
>> Hi,
>>
>> I found out, that the script extract_rays.py is just outdated. The table
>> lib changed the naming convention of its functions.
>> I attach corrected extract_rays.py, which work for me.
>>
>> Regards
>> Jiří Löffelmann
>>
>> út 22. 6. 2021 v 8:06 odesílatel Ong Jian Fuh <jianfuh.ong at eli-np.ro>
>> napsal:
>>
>>> Hi,
>>>
>>> You can open this file for quick inspection by using visIt. You can
>>> download it here:
>>> https://visit-dav.github.io/visit-website/releases-as-tables/#latest
>>>
>>> The script extract_rays.py is to extract the laser ray only. You still
>>> need visit to find other output like density. You can also use python to
>>> extract the data. Other possibility is to use yt:
>>> https://yt-project.org/doc/visualizing/plots.html
>>>
>>> Regards,
>>>
>>> Dr. Ong Jian Fuh
>>> Extreme Light Infrastructure - Nuclear Physics
>>> "Horia Hulubei" National Institute for Physics and Nuclear Engineering
>>> 30 Reactorului Street, 077125 Magurele (Ilfov), Romaniawww.eli-np.ro
>>>
>>> On 22/06/2021 8:39 am, Sonali Khanna wrote:
>>>
>>> Dear all,
>>>
>>> I am able to run the example problem of the Laser slab.
>>>
>>> ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio
>>> \species=cham,targ +mtmmmt +laser +uhd3t +mgd mgd_meshgroups=6
>>> \-parfile=example.par
>>>
>>> After that, I am trying to open the output "lasslab_hdf5_plt_cnt_0000"
>>> using the code extract_rays.py, but this showing error.
>>>
>>> Traceback (most recent call last):
>>>   File "extract_rays.py", line 156, in <module>
>>>     write_vtk(fn)
>>>   File "extract_rays.py", line 20, in write_vtk
>>>     h5file = tables.openFile(filename, "r")
>>> AttributeError: module 'tables' has no attribute 'openFile'.
>>>
>>> *Is there any way of extracting data from the hdf5 (output) file in
>>> general? Any help in this is much appreciated.  *
>>>
>>> Thanks and regards
>>> Sonali
>>>
>>>
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