[yt-users] ray objects

Elizabeth Tasker taskere at mcmaster.ca
Wed Aug 17 12:01:48 PDT 2011


Hi Matt,

Thanks! That fixed it. We went from:

--------> print(ray["t"])
[ 0.          0.          0.00434028  0.00651042  0.01302083  0.01302083
  0.01953125  0.02170139  0.03038194  0.03255208  0.0390625   0.0390625
  0.04557292  0.04774306  0.05642361  0.05859375  0.06510417  0.06510417
  0.07161458  0.07378472  0.08246528  0.08463542  0.09114583  0.09114583
  0.09765625  0.09982639  0.10850694  0.11067708  0.1171875   0.1171875
  0.12369792  0.12586806  0.13454861  0.13671875  0.14322917  0.14322917
  0.16059028  0.16276042  0.16927083  0.17795139  0.18880208  0.1953125
  0.21267361  0.21484375  0.22135417  0.23003472  0.24088542  0.24739583
  0.26692708  0.2734375   0.28211806  0.31684028  0.31901042  0.3515625
  0.37109375  0.37760417  0.38628472  0.42100694  0.42317708  0.45572917
  0.47526042  0.48177083  0.49045139  0.52517361  0.52734375  0.55989583
  0.57942708  0.62934028  0.68359375  0.69010417  0.69878472  0.76822917
  0.78776042  0.83767361  0.89192708  0.8984375   0.90711806  0.9765625 ]
 

to

In [1]: print ray["t"]
------> print(ray["t"])
[ 0.          0.00434028  0.00651042  0.01302083  0.01302083  0.01953125
  0.02170139  0.03038194  0.03255208  0.0390625   0.0390625   0.04557292
  0.04774306  0.05642361  0.05859375  0.06510417  0.06510417  0.07161458
  0.07378472  0.08246528  0.08463542  0.09114583  0.09114583  0.09765625
  0.09982639  0.10850694  0.11067708  0.1171875   0.1171875   0.12369792
  0.12586806  0.13454861  0.13671875  0.14322917  0.14322917  0.16059028
  0.16276042  0.16927083  0.17795139  0.18880208  0.1953125   0.21267361
  0.21484375  0.22135417  0.23003472  0.24088542  0.24739583  0.26692708
  0.2734375   0.28211806  0.31684028  0.31901042  0.3515625   0.37109375
  0.37760417  0.38628472  0.42100694  0.42317708  0.45572917  0.47526042
  0.48177083  0.49045139  0.52517361  0.52734375  0.55989583  0.57942708
  0.62934028  0.68359375  0.69010417  0.69878472  0.76822917  0.78776042
  0.83767361  0.89192708  0.8984375   0.90711806  0.9765625   1.        ]


Though

 > yt instinfo -u

hates me and denies the existence of mercurial but

hg pull
hg up
python2.7 setup.py build_ext -i

Was fine.

Thanks again!

Elizabeth





Matthew Turk wrote:
> Elizabeth,
>
> If you check, the sum of dts should be 1.0.  Tracking this down, what
> I saw happening on my machine (after I was able to replicate the bug)
> was that the dts were being set correctly but the t values were not.
> The terminating value would have t = 0.  I used this test script:
>
> http://paste.enzotools.org/show/1749/
>
> I've committed a fix in hash 6c31049e1a99.  Because this touches the
> Cython code, you will have to rebuild.  If you use "yt instinfo -u"
> this should rebuild the code for you.
>
> -Matt
>
> On Tue, Aug 16, 2011 at 4:03 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>   
>> Hi Elizabeth,
>>
>> On Tue, Aug 16, 2011 at 3:52 PM, Elizabeth Tasker <taskere at mcmaster.ca> wrote:
>>     
>>> Hi Sam,
>>>
>>> I'm not sure that explains it. For instance, if I have:
>>>
>>> ray = pf.h.ray((13.20485952,  12.60900681,  15.99610771), (13.00047934,
>>>  12.22629182,  15.98123388))
>>>
>>> I get:
>>>
>>> In [77]: print ray["x"]
>>> -------> print(ray["x"])
>>> yt : [INFO     ] 2011-08-16 15:41:43,802 Getting field t from 28
>>> yt : [INFO     ] 2011-08-16 15:41:44,573 Getting field x from 28
>>> [ 13.00390625  13.20703125  12.99609375  13.19921875  13.19921875
>>>  13.19921875  13.19140625  13.19140625  13.19140625  13.18359375
>>>  13.18359375  13.18359375  13.17578125  13.17578125  13.16796875
>>>  13.16796875  13.16796875  13.16015625  13.16015625  13.16015625
>>>  13.15234375  13.15234375  13.15234375  13.15234375  13.14453125
>>>  13.14453125  13.14453125  13.13671875  13.13671875  13.13671875
>>>  13.12890625  13.12890625  13.12890625  13.12109375  13.12109375
>>>  13.12109375  13.11328125  13.11328125  13.10546875  13.10546875
>>>  13.10546875  13.09765625  13.09765625  13.09765625  13.08984375
>>>  13.08984375  13.08984375  13.08203125  13.08203125  13.08203125
>>>  13.07421875  13.07421875  13.07421875  13.06640625  13.06640625
>>>  13.06640625  13.05859375  13.05859375  13.05859375  13.05078125
>>>  13.05078125  13.04296875  13.04296875  13.04296875  13.04296875
>>>  13.03515625  13.03515625  13.03515625  13.02734375  13.02734375
>>>  13.02734375  13.01953125  13.01953125  13.01953125  13.01171875
>>>  13.01171875  13.01171875  13.00390625  13.00390625]
>>>
>>>
>>> Which ends in the right place, but the first three values look very
>>> confused. And dx in this case is the same throughout:
>>>
>>> In [78]: print ray["dx"]
>>> -------> print(ray["dx"])
>>> yt : [INFO     ] 2011-08-16 15:43:37,576 Getting field dx from 28
>>> [ 0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125  0.0078125
>>>  0.0078125]
>>>
>>> I did check out that page in the docs originally, but I ran into a couple of
>>> problems. Firstly, I wasn't entirely clear whether 't' was a distance or a
>>> time (I thought it might be a time based on a ray tracing scheme assuming
>>> these were light rays... maybe that was dumb!). Secondly, the variable 'dt'
>>> isn't available for me:
>>>       
>> 't' is the parameter, running from 0 .. 1.  The corresponding dts
>> parameter (which shows up in my help(pf.h.ray) call, buyt perhaps is
>> not on the current doc page because of a rebuild lag) should be the
>> width you are looking for.
>>
>> If you are starting at a cell corner it could be causing a confusion.
>> Sam probably knows a bit more than I do about this.  My guess is that
>> somehow 't' is getting set incorrectly during the ray walk, and then
>> during the sort operation it's coming back at the start of the ray
>> value list.
>>
>> My current best guess is that the RayIntegrator.pyx code has multiple
>> hits for "fully enclosed" checks, which should be replaced with "fully
>> enclosed *and* not child masked."
>>
>> -Matt
>>
>>     
>>> In [81]: print ray["dt"]
>>> -------> print(ray["dt"])
>>> yt : [INFO     ] 2011-08-16 15:47:23,212 Getting field dt from 28
>>> ---------------------------------------------------------------------------
>>> KeyError                                  Traceback (most recent call last)
>>>
>>> /1/home/taskere/yt/scripts/iyt in <module>()
>>> ----> 1
>>>     2
>>>     3
>>>     4
>>>     5
>>>
>>> /1/home/taskere/yt/yt/data_objects/data_containers.py in __getitem__(self,
>>> key)
>>>   284             if key not in self.fields:
>>>   285                 self.fields.append(key)
>>> --> 286             self.get_data(key)
>>>   287         return self.data[key]
>>>   288
>>>
>>> /1/home/taskere/yt/yt/data_objects/data_containers.py in get_data(self,
>>> fields, in_grids)
>>>   455             mylog.info("Getting field %s from %s", field,
>>> len(self._grids))
>>>   456             if field not in self.hierarchy.field_list and not
>>> in_grids:
>>> --> 457                 if field not in ("dts", "t") and
>>> self._generate_field(field):
>>>   458                     continue # True means we already assigned it
>>>   459             self[field] = na.concatenate(
>>>
>>> /1/home/taskere/yt/yt/data_objects/data_containers.py in
>>> _generate_field(self, field)
>>>   436                 return True
>>>   437         else: # Can't find the field, try as it might
>>> --> 438             raise KeyError(field)
>>>   439
>>>   440     def get_data(self, fields=None, in_grids=False):
>>>
>>> KeyError: 'dt'
>>>
>>> Although now I look once more, I do see that 't' is zero for the first three
>>> values, so if it is a distance normalised to 1 (which would make a lot more
>>> sense!) it does imply they are not corresponding to distances along the ray:
>>>
>>> In [82]: print ray["t"]
>>> -------> print(ray["t"])
>>> [ 0.          0.          0.          0.00848673  0.01945132  0.03986468
>>>  0.04671206  0.06027804  0.0806914   0.08493739  0.10110477  0.12151813
>>>  0.12316273  0.14193149  0.16138806  0.16234486  0.18275822  0.19961339
>>>  0.20317158  0.22358495  0.23783872  0.24399831  0.26356426  0.26441167
>>>  0.27606405  0.28482503  0.3052384   0.31428938  0.32565176  0.34606512
>>>  0.35251471  0.36647849  0.38689185  0.39074004  0.40730521  0.42771857
>>>  0.42896537  0.44813194  0.4671907   0.4685453   0.48895866  0.50541603
>>>  0.50937203  0.52978539  0.54364136  0.55019875  0.57061212  0.5818667
>>>  0.59102548  0.61143884  0.62009203  0.6318522   0.65226557  0.65831736
>>>  0.67267893  0.69309229  0.69654269  0.71350566  0.73391902  0.73476802
>>>  0.75433238  0.77299335  0.77474574  0.78881566  0.79515911  0.81121868
>>>  0.81557247  0.83598583  0.84944401  0.8563992   0.87681256  0.88766934
>>>  0.89722592  0.91763929  0.92589467  0.93805265  0.95846601  0.96412
>>> 0.97887937]
>>>
>>>
>>> Elizabeth
>>>
>>>
>>>
>>>
>>> Sam Skillman wrote:
>>>       
>>>> Hi Elizabeth,
>>>>
>>>> So the issue here, I think, is that while the rays are sorted, they
>>>> traverse varying sized cells.  When you query the field 'x', you are
>>>> actually querying the 'x' value of the cell that the ray intersects, not the
>>>> position of the ray itself.  This, in combination with the fact that fields
>>>> like 'x' are cell centered, means that you can see weird jumps when you go
>>>> from a highly refined cell to a root grid cell.  You could check this by
>>>> looking at what ray1['dx'] is, and if it is large for the second value, then
>>>> this is the issue.
>>>>
>>>> If you'd like to recover the x,y, position of the ray at that point, I
>>>> would use the field 't', which is the integral of dt (distance) along the
>>>> ray.  You could then use the starting position and the direction to recover
>>>> the position along the ray.
>>>>
>>>> That said, if all you are worried about is the Density, it should in fact
>>>> be giving you the ordered density values.  If you were to
>>>> matplotlib.pylab.plot(ray1['t'], ray1['Density']) it should give you a plot
>>>> of the density along the ray.
>>>>
>>>> For reference, much of this is described here:
>>>> http://yt.enzotools.org/doc/analyzing/generating_processed_data.html#line-queries-and-planar-integrals
>>>>
>>>> Best,
>>>> Sam
>>>>
>>>> On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere at mcmaster.ca
>>>> <mailto:taskere at mcmaster.ca>> wrote:
>>>>
>>>>    Hi,
>>>>
>>>>    When you create a ray object with yt, e.g.
>>>>
>>>>    ray1 = pf.h.ray([10,16,16], [10.3,16.1,16])
>>>>
>>>>    I was expecting to get the values of the cells that lie inbetween
>>>>    those two sets of co-ordinates. Instead, it looks like the first
>>>>    two values back at the start and end points. .e.g.:
>>>>
>>>>    -------> print(ray1["x"])
>>>>    Warning: divide by zero encountered in divide
>>>>    Warning: invalid value encountered in multiply
>>>>    Warning: divide by zero encountered in divide
>>>>    Warning: invalid value encountered in multiply
>>>>    yt : [INFO     ] 2011-08-16 14:47:27,962 Getting field t from 92
>>>>    yt : [INFO     ] 2011-08-16 14:47:28,972 Getting field x from 92
>>>>    [ 10.0078125   10.30078125  10.0234375   10.0390625   10.0390625
>>>>     10.0546875   10.0703125   10.0859375   10.0859375   10.1015625
>>>>     10.1171875   10.1328125   10.1328125   10.1484375   10.1640625
>>>>     10.17578125  10.18359375  10.18359375  10.19140625  10.19921875
>>>>     10.20703125  10.20703125  10.21484375  10.22265625  10.23046875
>>>>     10.23046875  10.23828125  10.24609375  10.25390625  10.25390625
>>>>     10.26171875  10.26953125  10.27734375  10.27734375  10.28515625
>>>>     10.29296875]
>>>>
>>>>    In [53]: print ray1["y"]
>>>>    -------> print(ray1["y"])
>>>>    yt : [INFO     ] 2011-08-16 14:48:23,698 Getting field y from 92
>>>>    [ 16.0078125   16.09765625  16.0078125   16.0078125   16.0234375
>>>>     16.0234375   16.0234375   16.0234375   16.0390625   16.0390625
>>>>     16.0390625   16.0390625   16.0546875   16.0546875   16.0546875
>>>>     16.05859375  16.05859375  16.06640625  16.06640625  16.06640625
>>>>     16.06640625  16.07421875  16.07421875  16.07421875  16.07421875
>>>>     16.08203125  16.08203125  16.08203125  16.08203125  16.08984375
>>>>     16.08984375  16.08984375  16.08984375  16.09765625  16.09765625
>>>>     16.09765625]
>>>>
>>>>
>>>>    Is that right? Should I ignore the first two values of ray1 when
>>>>    I'm examining the data, e.g. ray1["Density"]?
>>>>
>>>>    Thanks!
>>>>
>>>>    Elizabeth
>>>>
>>>>    _______________________________________________
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>>>>    http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
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