[yt-users] Slice plot error
Ji Suoqing
jisuoqing at gmail.com
Sun Sep 16 16:18:49 PDT 2012
Hi Nathan,
Thanks for your prompt response.
> Can you reply with the output of the 'yt stats' command.
(yt-x86_64)[jisuoqing at hpcmanage object]$ yt stats cellular_hdf5_chk_0000
yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: current_time = 0.0
yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: domain_dimensions = [1280 64 1]
yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2012-09-17 03:22:02,645 Parameters: domain_right_edge = [ 256. 12.8 12.8]
yt : [INFO ] 2012-09-17 03:22:02,645 Parameters: cosmological_simulation = 0.0
yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field enuc to list of fields
yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field ar36 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field c12 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field ca40 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field cr48 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field fe52 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field he4 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field mg24 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field ne20 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field ni56 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field o16 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field s32 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field si28 to list of fields
yt : [INFO ] 2012-09-17 03:22:02,657 Adding unknown field ti44 to list of fields
level # grids # cells
------------------------------
0 64 262144
----------------------------
64 262144
t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years
Smallest Cell:
Width: 1.620e-25 mpc
Width: 1.620e-22 kpc
Width: 1.620e-19 pc
Width: 3.342e-14 au
Width: 7.190e-12 rsun
Width: 3.106e-06 miles
Width: 1.953e-03 unitary
Width: 5.000e-01 1
Width: 5.000e-01 cm
It seems that the only problem is related with slice plot.
Best wishes,
Suoqing
On Sep 16, 2012, at 6:56 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> Hi Suoqing,
>
> This error will show up if yt cannot select any data. Recently we
> changed the way yt handles 2D FLASH data so it's possible that these
> changes have messed up data selection for your setup.
>
> Unfortunately it's difficult to say the exact reason why data
> selection is broken without knowing more about your setup.
>
> Can you reply with the output of the 'yt stats' command. Run this
> from the command line.
>
> It would also help to see the minimum and maximum z values of your
> data. There are a number of ways to do this but a sample script would
> look something like this:
>
> pf = load(your_data)
> dd = pf.h.all_data()
> print dd['z'].min(), dd['z'].max()
>
> Cheers,
>
> Nathan
>
>
> On Sep 16, 2012, at 2:23 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
>
>> Hi all,
>>
>> Yesterday I've updated YT (af06f14fcd9e), but after that I found I got some error in slice plot for 2d FLASH data, in both cartesian and cylindrical cases. In cartesian, the error is:
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> yt : [WARNING ] 2012-09-17 01:19:45,023 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name
>> yt : [WARNING ] 2012-09-17 01:19:45,023 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name
>> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: current_time = 1.01787779719e-09
>> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_dimensions = [1280 64 1]
>> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_left_edge = [ 0. 0. 0.]
>> yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: domain_right_edge = [ 256. 12.8 12.8]
>> yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: cosmological_simulation = 0.0
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field enuc to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ar36 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field c12 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ca40 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field cr48 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field fe52 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field he4 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field mg24 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ne20 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ni56 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field o16 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field s32 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field si28 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ti44 to list of fields
>> yt : [INFO ] 2012-09-17 01:19:45,356 Max Value is 4.25001e+07 at 22.7500000000000000 0.8375000000000000 0.5000000000000000 in grid FLASHGrid_0001 ([64 64 1]) at level 0 (45, 33, 0)
>> yt : [INFO ] 2012-09-17 01:19:45,401 Making a fixed resolution buffer of (dens) 800 by 800
>> Traceback (most recent call last):
>> File "slice.py", line 14, in <module>
>> p1 = SlicePlot(pf, "z", my_var, origin="left-domain")
>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 949, in __init__
>> PWViewerMPL.__init__(self, slc, bounds, origin=origin)
>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 473, in __init__
>> if setup: self._setup_plots()
>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 725, in _setup_plots
>> self.plots[f].image, cax = self.plots[f].cax)
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py", line 1196, in colorbar
>> cb = cbar.Colorbar(cax, mappable, **kw)
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 743, in __init__
>> ColorbarBase.__init__(self, ax, **kw)
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 258, in __init__
>> self.draw_all()
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 272, in draw_all
>> self._process_values()
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 570, in _process_values
>> b = self.norm.inverse(self._uniform_y(self.cmap.N+1))
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colors.py", line 948, in inverse
>> return vmin * ma.power((vmax/vmin), val)
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 3642, in __mul__
>> return multiply(self, other)
>> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 936, in __call__
>> if m:
>> ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> And in cylindrical case, the error is:
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>>> from yt.mods import *
>>>>> pf=load('relax_hdf5_chk_0000')
>> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: current_time = 0.0
>> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_dimensions = [256 128 1]
>> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_left_edge = [ 0.00000000e+00 -6.55360000e+09 0.00000000e+00]
>> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_right_edge = [ 1.31072000e+10 6.55360000e+09 1.74532925e-02]
>> yt : [INFO ] 2012-09-17 01:22:27,083 Parameters: cosmological_simulation = 0.0
>>>>> p1 = SlicePlot(pf, 'z', 'dens', origin="left-domain")
>> 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 948, 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 1045, 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 1079, 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 898, 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.
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> I would very appreciate it if you have any idea on solving these errors.
>>
>> Best wishes,
>> Suoqing
>> _______________________________________________
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>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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