[yt-users] yt volume render/AMRKDtree help

Renyue Cen cen at astro.princeton.edu
Wed Jan 9 19:57:14 PST 2013

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,

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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