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
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-qu... Best, Sam On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere@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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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: 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-qu...
Best, Sam
On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere@mcmaster.ca <mailto:taskere@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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Hi Elizabeth, On Tue, Aug 16, 2011 at 3:52 PM, Elizabeth Tasker <taskere@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-qu...
Best, Sam
On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere@mcmaster.ca <mailto:taskere@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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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@gmail.com> wrote:
Hi Elizabeth,
On Tue, Aug 16, 2011 at 3:52 PM, Elizabeth Tasker <taskere@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-qu...
Best, Sam
On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere@mcmaster.ca <mailto:taskere@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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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@gmail.com> wrote:
Hi Elizabeth,
On Tue, Aug 16, 2011 at 3:52 PM, Elizabeth Tasker <taskere@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-qu...
Best, Sam
On Tue, Aug 16, 2011 at 12:49 PM, Elizabeth Tasker <taskere@mcmaster.ca <mailto:taskere@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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participants (4)
-
Elizabeth Tasker -
Elizabeth Tasker
-
Matthew Turk -
Sam Skillman