[yt-users] Visualising spectral cube data in yt

[Kacper Kowalik]

On 02/20/2013 12:24 PM, Kacper Kowalik wrote:
> On 02/20/2013 11:09 AM, Francisco Ocaña González wrote:
>> Dear Eli,
>>
> 
> Hi Paco!
> 
>> I found a post about 3D data in YT ,
>> http://astrobiased.com/3d-data-vis-in-yt.html , very interesting. I am
>> working with spectral cubes from PMAS Spectrograph (at 3.5m CAHA
>> telescope). Thus, I tried to use it. I am newbie with python, but I was
>> able to install everything :-)
> 
> Great to hear that!
> 
>> However I get an error message when loading the data into yt's data
>> structure (script http://paste.yt-project.org/show/3182/ ):
>>
>> ERROR: ValueError: total size of new array must be unchanged
>> [yt.frontends.stream.data_structures]
>> astropy: [ERROR    ] 2013-02-20 10:46:53,395 ValueError: total size of new
>> array must be unchanged
>> Traceback (most recent call last):
>>   File "3d_viewer.py", line 9, in <module>
>>     pf = load_uniform_grid(data, cube.shape, 9e16)
>>   File
>> "/home/fog/YT/yt-x86_64/src/yt-hg/yt/frontends/stream/data_structures.py",
>> line 490, in load_uniform_grid
>>     grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32")
>> ValueError: total size of new array must be unchanged
> 
> That happens due to the fact that load_uniform_grid expects that data
> has 3 dimensions, whereas the data from your fits has only 2. You can
> "fix" that by artificially adding one dimension by e.g. using numpy
> function "expand_dims". I've modified your script slightly:

Maybe I should add that image from that script won't be probably what
you're looking for. You'll need to somehow convert 2D output from PMAS
that you have there, to 3d array that is actual, spatial representation
of your data. Forgive my ignorance, but I have no clue what PMAS
actually gives as an output, so I won't be able to help there.
Cheers,
Kacper

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