[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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