[yt-users] yt volume render/AMRKDtree help

Renyue Cen cen at astro.princeton.edu
Mon Jan 14 06:47:54 PST 2013


Hi Sam,

This problem that I mentioned in the attached email sent earlier appears to be
a bit more common that I thought. I mean, it occurs for multiple galaxies at
different redshifts. The data files appear ok in that I could make projection plots
in the same regions just fine without using the AMTKDTree, and a same data file
looks ok for AMRKDTree for a different galaxy at a different location.

This is a bit critical for me because I need to be able to analyze all these galaxies
to gain a full physical understanding.

Your help is appreciated,

Best,
Renyue


On Jan 9, 2013, at 10:57 PM, Renyue Cen wrote:

> Hi Sam,
> 
> I have succeeded in volume rendering regions around some galaxies with the transpose=false fix.
> But, occasionally, for some reason, the exact same piece of yt code on some galaxies
> failed with the following error:
> 
> AttributeError: 'NoneType' object has no attribute 'id'
> Building kd-Tree  0% |                                        | ETA:  --:--:-- ^MTraceback (most recent call last):
>   File "test.py", line 318, in <module>
>     le=c-0.5*WW, re=c+0.5*WW)
>   File "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py", line 376, in __init__
>     self._build(root_grids, None, self.domain_left_edge, self.domain_right_edge)
>   File "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py", line 1059, in _build
>     set_leaf(current_node, current_node.parent_grid, current_node.l_corner, current_node.r_corner)
>   File "/u/jhwise/local/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py", line 154, in set_leaf
>     thisnode.grid = grid_id.id
> AttributeError: 'NoneType' object has no attribute 'id'
> 
> 
> I am not sure what is causing this.
> 
> Thanks very much,
> Renyue
> 
> 
> On Jan 8, 2013, at 12:08 PM, Renyue Cen wrote:
> 
>> Hi Sam,
>> 
>> your transpose fix DOES change things and it indeed may working now. 
>> Here is the first images I got for comparison.
>> I am going to make a few more pictures to see if things are all good.
>> Thanks very much,
>> <test1.png><test2.png>
>> Best,
>> Renyue
>> 
>> On Jan 8, 2013, at 11:25 AM, Sam Skillman wrote:
>> 
>>> Hi Renyue,
>>> 
>>> I have actually seen this on one other system but I could never reproduce it. Could you tell me the version of yt you are using? If you run "yt instinfo" it should tell you. I haven't seen this bug for the last few months so I thought it was gone.  
>>> 
>>> Additionally, can you try the following at the end of your script:
>>> 
>>> im=cam.snapshot('test1.png')
>>> write_bitmap(im, 'test2.png', transpose=False)
>>> 
>>> I think there may have been something wrong with the transposing of the image for a short time period a few months ago.  I have very sporadic and unreliable internet at AAS but I'll try to respond as quickly as possible.
>>> 
>>> Sorry for the trouble,
>>> 
>>> Sam
>>> 
>>> 
>>> 
>>> On Jan 7, 2013 10:11 AM, "Renyue Cen" <cen at astro.princeton.edu> wrote:
>>> Hi,
>>> 
>>> I did some simple volume rendering with the following script:
>>> 
>>>     volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"],
>>>                 no_ghost=False, tree_type="domain",
>>>                 le=c-0.5*WW, re=c+0.5*WW)
>>>     cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False,
>>>                 north_vector=L, steady_north=True)
>>>     cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j))
>>> 
>>> 
>>> I got rather strange results in that the pictures look symmetric, which I am pretty
>>> sure can not be true.
>>> I attach the obtained plot.
>>> Note that I am using KD tree and using 32 cores. 
>>> 
>>> Your help at your earliest convenience is appreciated.
>>> Best,
>>> Renyue
>>> 
>>> 
>>> <C15z1600.0043_iso-DMdensity-000.png>
>> 
> 

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