Re: [yt-users] Make projections for uniform grid FLASH4 data

Hi Matt, Hi John, I've tried slicing, and still got the same error:

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from yt.mods import * pf=load('relax_hdf5_chk_0000') yt : [INFO ] 2012-08-07 23:53:31,172 Parameters: current_time = 0.0 yt : [INFO ] 2012-08-07 23:53:31,172 Parameters: domain_dimensions = [512 256 1] yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: cosmological_simulation = 0.0 p=SlicePlot(pf, 'z', 'Density') yt : [INFO ] 2012-08-07 23:55:10,116 Adding unknown field fspd to list of fields yt : [INFO ] 2012-08-07 23:55:10,116 Adding unknown field spec to list of fields Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 803, in __init__ slc = pf.h.slice(axis, center[axis], fields=fields) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1042, in __init__ self._refresh_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data self.get_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 830, in get_data self._generate_coords() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1076, in _generate_coords for grid in self._get_grids(): File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 900, in _get_grids return ObjectIterator(self, attr='_grids') File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 102, in __init__ raise YTNoDataInObjectError(pobj) yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. It may lie on a grid face. Try offsetting slightly.

And for John, I always use projection to deal with 2D AMR FLASH data and it works fine, because I suspect that projection will add all the data on different refinement level together. But I suspect slicing might not do exactly the same thing. And now for uniform grid data, both projection and slicing failed. All best, Suoqing 在 2012-8-7，下午3:42，John ZuHone 写道：

Suoqing,

Just a quick question... I notice that your dataset is 2D. Have you tried using a SlicePlot instead? If your dataset is 2D, projections and slices should be identical.

I'm not saying that the projection should fail like it does, but I suspect that you probably would not have trouble with a slice and you would get the same result.

Best,

John Z

On Aug 7, 2012, at 3:40 PM, Ji Suoqing wrote:

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Ah, thanks a lot! With your suggestion I have axis ticks now.

And the ug projection is still a problem.

Best wishes, Suoqing

在 2012-8-7，下午3:34，Ji Suoqing 写道：

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Hi Matt,

Thanks for you response. I've tried:

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from yt.mods import * pf=load('relax_hdf5_chk_0000') yt : [INFO ] 2012-08-07 23:39:54,570 Parameters: current_time = 0.0 yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_dimensions = [512 256 1] yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] yt : [INFO ] 2012-08-07 23:39:54,572 Parameters: cosmological_simulation = 0.0 p = ProjectionPlot(pf, "z", "Density") yt : [INFO ] 2012-08-07 23:40:02,771 Adding unknown field fspd to list of fields yt : [INFO ] 2012-08-07 23:40:02,772 Adding unknown field spec to list of fields Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 875, in __init__ proj = pf.h.proj(axis,fields,weight_field=weight_field,max_level=max_level,center=center) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1697, in __init__ self._initialize_source(source) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1724, in _initialize_source source = self.pf.h.all_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 188, in all_data pf.domain_left_edge, pf.domain_right_edge) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3221, in __init__ self._refresh_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data self.get_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2508, in get_data raise YTNoDataInObjectError(self) yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it.

All best, Suoqing

在 2012-8-7，下午3:24，Matthew Turk 写道：

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Hi Suoqing,

Could you try it with the ProjectionPlot call? It should look like this:

p = ProjectionPlot(pf, "z", "Density") p.save()

-Matt

On Tue, Aug 7, 2012 at 3:14 PM, Ji Suoqing wrote:

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Hi all,

I'm trying to make projections for uniform grid FLASH4 data with the most updated YT, but there're errors when adding projections:

yt : [WARNING ] 2012-08-07 23:13:56,239 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2012-08-07 23:13:56,244 Parameters: current_time = 0.0 yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_dimensions = [512 256 1] yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2012-08-07 23:13:56,587 Max Value is 2.46340e+06 at 38378027.3437500000000000 6400000.0000000000000000 0.5000000000000000 in grid FLASHGrid_0033 ([128 128 1]) at level 0 (1, 0, 0) yt : [INFO ] 2012-08-07 23:13:56,587 Created plot collection with default plot-center = [13114700000.0, 0.0, 0.0087266462599716477] Traceback (most recent call last): File "proj.py", line 18, in <module> p1 = pc.add_projection(my_var, 2) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 784, in add_projection **field_parameters) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1697, in __init__ self._initialize_source(source) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1724, in _initialize_source source = self.pf.h.all_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 188, in all_data pf.domain_left_edge, pf.domain_right_edge) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3221, in __init__ self._refresh_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data self.get_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2508, in get_data raise YTNoDataInObjectError(self) yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it.

And another separated question: how can I add axis ticks onto projection or slice plot to show the spacial scale? I suspect there should exist some easy way, but I failed to find it.

Thanks for your care!

All best, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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