Hi Sam,This problem that I mentioned in the attached email sent earlier appears to bea bit more common that I thought. I mean, it occurs for multiple galaxies atdifferent redshifts. The data files appear ok in that I could make projection plotsin the same regions just fine without using the AMTKDTree, and a same data filelooks 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 galaxiesto gain a full physical understanding.Your help is appreciated,Best,RenyueOn 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 galaxiesfailed 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 _buildset_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_leafthisnode.grid = grid_id.idAttributeError: 'NoneType' object has no attribute 'id'I am not sure what is causing this.Thanks very much,RenyueOn 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,RenyueOn Jan 8, 2013, at 11:25 AM, Sam Skillman wrote:
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:
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,
On Jan 7, 2013 10:11 AM, "Renyue Cen" <email@example.com> 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 prettysure 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>